TY - CONF TI - A novel method to construct genetic linkage maps in high autopolyploid species using hidden Markov models, with applications in sugarcane AU - Mollinari, M. AU - Marconi, T.G. AU - Mancini, M.C. AU - Costa, E.A. AU - Pinto, L.R. AU - Souza, A.P. AU - Garcia, A.A.F. T2 - International Plant & Animal Genome XX Conference C2 - 2012/// C3 - International Plant & Animal Genome XX Conference CY - San Diego, CA, USA DA - 2012/// PY - 2012/// ER - TY - JOUR TI - Genetic diversity of Metrodorea nigra (Rutaceae) from a small forest remnant in Brazil assessed with microsatellite markers AU - Guidugli, M. C. AU - Ferreira-Ramos, R. AU - Sousa, A. C. B. AU - Cidade, F. W. T2 - Genetics and Molecular Research DA - 2012/// PY - 2012/// VL - 11 IS - 1 SP - 10-16 ER - TY - JOUR TI - Genetic diversity of Metrodorea nigra (Rutaceae) from a small forest remnant in Brazil assessed with microsatellite markers AU - Guidugli, M.C. AU - Ferreira-Ramos, R. AU - Sousa, A.C.B. AU - Cidade, F.W. AU - Marconi, T.G. AU - Mestriner, M.A. AU - Groppo, M. AU - Alzate-Marin, A.L. T2 - Genetics and Molecular Research AB - Metrodorea nigra (Rutaceae) is an endemic Brazilian tree of great ecological importance, frequently found in the submontane regions of ombrophilous dense and semideciduous forests. This tree is useful for reforesting degraded areas and the wood can be employed in construction. We developed 12 microsatellite markers from a genomic library enriched for GA/CA repeats, for this species. Polymorphisms were assessed in 40 trees of a highly fragmented population found in Cravinhos, State of São Paulo, in southeastern Brazil. Among the 12 loci, 8 were polymorphic and only one had fixed alleles in this population. The number of alleles per locus and expected heterozygosity ranged from 2 to 11 and from 0.190 to 0.889, respectively. These results revealed moderate levels of genetic variation in M. nigra population when compared to other tropical species. Additionally, transferability of the 12 primers was tested in seven other Brazilian Rutaceae tree species (endemics: M. stipularis, Galipea jasminiflora, Esenbeckia leiocarpa and non-endemics: E. febrifuga, E. grandiflora, Balfourodendron riedelianum, Zanthoxylum riedelianum). Transferability ranged among species, but at least 8 loci (~67%) amplified in M. stipularis, demonstrating a high potential for transferring microsatellite markers between species of the same genus in the Rutaceae family. DA - 2012/// PY - 2012/// DO - http://dx.doi.org/10.4238/2012.January.9.2 VL - 11 IS - 1 SP - 10-16 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84855692937&partnerID=MN8TOARS ER - TY - JOUR TI - Genetic diversity of Metrodorea nigra (Rutaceae) from a small forest remnant in Brazil assessed with microsatellite markers AU - Guidugli, M.C. AU - Ferreira-Ramos, R. AU - Sousa, A.C.B. AU - Cidade, F.W. AU - Marconi, T.G. AU - Mestriner, M.A. AU - Groppo, M. AU - Alzate-Marin, A.L. T2 - Genetics and Molecular Research AB - Metrodorea nigra (Rutaceae) is an endemic Brazilian tree of great ecological importance, frequently found in the submontane regions of ombrophilous dense and semideciduous forests. This tree is useful for reforesting degraded areas and the wood can be employed in construction. We developed 12 microsatellite markers from a genomic library enriched for GA/CA repeats, for this species. Polymorphisms were assessed in 40 trees of a highly fragmented population found in Cravinhos, State of São Paulo, in southeastern Brazil. Among the 12 loci, 8 were polymorphic and only one had fixed alleles in this population. The number of alleles per locus and expected heterozygosity ranged from 2 to 11 and from 0.190 to 0.889, respectively. These results revealed moderate levels of genetic variation in M. nigra population when compared to other tropical species. Additionally, transferability of the 12 primers was tested in seven other Brazilian Rutaceae tree species (endemics: M. stipularis, Galipea jasminiflora, Esenbeckia leiocarpa and non-endemics: E. febrifuga, E. grandiflora, Balfourodendron riedelianum, Zanthoxylum riedelianum). Transferability ranged among species, but at least 8 loci (~67%) amplified in M. stipularis, demonstrating a high potential for transferring microsatellite markers between species of the same genus in the Rutaceae family. DA - 2012/// PY - 2012/// DO - 10.4238/2012.January.9.2 VL - 11 IS - 1 SP - 10-16 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84930473469&partnerID=MN8TOARS ER - TY - CONF TI - Evaluation of tomato germplasm for flavor and flavor-contributing components AU - Panthee, D.R. AU - Labate, J.L. AU - Robertson, L.D. T2 - Annual Meetings, ASHS C2 - 2012/7/31/ C3 - ASHS Annual Meetings CY - Miami, FL DA - 2012/7/31/ PY - 2012/7/31/ ER - TY - CONF TI - Identification of Potato spindle tuber viroid naturally infecting greenhouse tomatoes in North Carolina and its potential in seed transmission AU - Ling, K.S. AU - Li, R. AU - Panthee, D.R. AU - Gardner, R.G. T2 - 27th Annual Tomato Disease Workshop C2 - 2012/// C3 - 27th Annual Tomato Disease Workshop CY - Wooster, OH DA - 2012/// PY - 2012/10/16/ ER - TY - CHAP TI - Understanding chilling tolerance traits using Arabidopsis chilling-sensitive mutants AU - Zoldan, Dana AU - Band, Reza Shekaste AU - Guy, Charles L AU - Porat, Ron T2 - Environmental Adaptations and Stress Tolerance of Plants in the Era of Climate Change PY - 2012/// SP - 159-173 PB - Springer ER - TY - SOUND TI - Sustainable Turfgrass Systems AU - Seth Carley, D. DA - 2012/7// PY - 2012/7// ER - TY - SOUND TI - Plant Health as a Piece in Sustainable Turfgrass Systems AU - Seth Carley, D. DA - 2012/6// PY - 2012/6// ER - TY - SOUND TI - Increasing Food Security through New Food Initiatives AU - Seth Carley, D. DA - 2012/11// PY - 2012/11// ER - TY - SOUND TI - The Importance of the Green Industry: Hidden Benefits and Future Challenges AU - Seth Carley, D. DA - 2012/12// PY - 2012/12// ER - TY - CONF TI - The Benefits of Turfgrass AU - Seth Carley, D. T2 - Green Industry “Green n’ Growin’” Conference C2 - 2012/1// CY - Greensboro, NC DA - 2012/1// PY - 2012/1// ER - TY - CONF TI - Safe Feedstock Handling For Vermiculture Operations AU - Simmons, O.D., III T2 - North Carolina State University 13th Vermiculture Conference C2 - 2012/11/5/ CY - Chapel Hill, NC DA - 2012/11/5/ PY - 2012/11/5/ ER - TY - SOUND TI - Viruses in Fresh Produce: What Every Producer Should Know! AU - Simmons, O.D., III AU - Jaykus, L.A. DA - 2012/11/27/ PY - 2012/11/27/ ER - TY - CONF TI - Control of Human Virus Contamination in Molluscan Shellfish: Where we are and where we need to be? AU - Simmons, O.D., III AU - Jaykus, L.A. T2 - Intrastate Shellfish Sanitation Conference and South Atlantic Shellfish Conference C2 - 2012/4// CY - Savannah, GA DA - 2012/4// PY - 2012/4// ER - TY - CONF TI - Irrigation Water Concerns and Recommendations for Fruit and Vegetable Growers AU - Gunter, C. AU - Barrier, H. AU - Simmons, O.D., III T2 - Axiall/PPG Industrial Specialists Conference C2 - 2012/// CY - Charlotte, NC DA - 2012/// PY - 2012/// ER - TY - SOUND TI - Farm Commodity Recall Workshop AU - Chapman, B. AU - Gunter, C. AU - Simmons, O.D., III DA - 2012/8/28/ PY - 2012/8/28/ ER - TY - CONF TI - The Role of Water for Maintaining the Microbial Quality of Fresh Produce During Production" AU - Simmons, O.D., III T2 - North Carolina State University Fulbright Scholars Symposium C2 - 2012/// CY - Raleigh, NC DA - 2012/// PY - 2012/// ER - TY - CONF TI - Measurement and Analysis of Temporal and Spatial Variations of Bioaerosol Concentrations in a High-rise Egg Production House AU - Hu, D. AU - Wang-Li, L. AU - O.D. Simmons, O.D., III AU - Osborne, J.A. AU - Classen, J.J. T2 - Air and Waste Management Association Symposium on Air Quality Measurement Methods and Technology C2 - 2012/4/24/ CY - Durham, North Carolina DA - 2012/4/24/ PY - 2012/4/24/ ER - TY - CONF TI - Temporal and Spatial Variations of Bioaerosols Emitted from an Egg Production Facility in Southeast U.S.: Part III – Size Distributions and Viable Versus Non-Viable AU - Hu, D. AU - Wang-Li, L. AU - Simmons, O.D., III AU - Osborne, J.A. AU - Classen, J.J. T2 - American Society of Agricultural and Biological Engineers Annual Meeting C2 - 2012/7/29/ CY - Dallas, Texas DA - 2012/7/29/ PY - 2012/7/29/ ER - TY - CONF TI - Temporal and Spatial Variations of Bioaerosols Emitted from an Egg Production Facility in Southeast U.S Part II - Concentrations in the Vicinity AU - Hu, D. AU - Wang-Li, L. AU - Simmons, O.D., III AU - Osborne, J.A. AU - Classen, J.J. T2 - American Society of Agricultural and Biological Engineers Annual Meeting C2 - 2012/7/29/ CY - Dallas, Texas DA - 2012/7/29/ PY - 2012/7/29/ ER - TY - MGZN TI - Ein Leitfaden zur Identifikation von Wurzelschimmel (Roesleria subterranea (Weinm.) Redhead) in Ertragsanlagen = Guidelines to identify grape root rot (Roesleria subterranea (Weinm.) Redhead) in vineyards AU - Hoffmann, M. AU - Ruehl, E.H. AU - Presser, C. T2 - Deutsches Weinmagazin = German Wine Magazine DA - 2012/9// PY - 2012/9// SP - 16–19 ER - TY - JOUR TI - Molecular mapping of vernalization requirement and fertility restoration genes in carrot AU - Alessandro, María S. AU - Galmarini, Claudio R. AU - Iorizzo, Massimo AU - Simon, Philipp W. T2 - Theoretical and Applied Genetics AB - Carrot (Daucus carota L.) is a cool-season vegetable normally classified as a biennial species, requiring vernalization to induce flowering. Nevertheless, some cultivars adapted to warmer climates require less vernalization and can be classified as annual. Most modern carrot cultivars are hybrids which rely upon cytoplasmic male-sterility for commercial production. One major gene controlling floral initiation and several genes restoring male fertility have been reported but none have been mapped. The objective of the present work was to develop the first linkage map of carrot locating the genomic regions that control vernalization response and fertility restoration. Using an F2 progeny, derived from the intercross between the annual cultivar ‘Criolla INTA’ and a petaloid male sterile biennial carrot evaluated over 2 years, both early flowering habit, which we name Vrn1, and restoration of petaloid cytoplasmic male sterility, which we name Rf1, were found to be dominant traits conditioned by single genes. On a map of 355 markers covering all 9 chromosomes with a total map length of 669 cM and an average marker-to-marker distance of 1.88 cM, Vrn1 mapped to chromosome 2 with flanking markers at 0.70 and 0.46 cM, and Rf1 mapped to chromosome 9 with flanking markers at 4.38 and 1.12 cM. These are the first two reproductive traits mapped in the carrot genome, and their map location and flanking markers provide valuable tools for studying traits important for carrot domestication and reproductive biology, as well as facilitating carrot breeding. DA - 2012/9/27/ PY - 2012/9/27/ DO - 10.1007/S00122-012-1989-1 VL - 126 IS - 2 SP - 415-423 J2 - Theor Appl Genet LA - en OP - SN - 0040-5752 1432-2242 UR - http://dx.doi.org/10.1007/S00122-012-1989-1 DB - Crossref ER - TY - JOUR TI - Interactions of agrochemicals applied to peanut; part 1: Effects on herbicides AU - Chahal, Gurinderbir S. AU - Jordan, David L. AU - Shew, Barbara B. AU - Brandenburg, Rick L. AU - York, Alan C. AU - Burton, James D. AU - Danehower, David T2 - Crop Protection AB - Numerous agrochemicals are applied in peanut production systems. Field and laboratory experiments were conducted in North Carolina to characterize biological and physicochemical interactions when the herbicides clethodim, imazapic, imazethapyr, lactofen, sethoxydim, and 2,4-DB were applied in combination with adjuvants, fungicides, insecticides, and micronutrients. A wide range of interactions was noted when comparing across herbicides, weed species, and agrochemical combinations. There was little consistency across weed species for a herbicide or across herbicides for a weed species when comparing significant main effects and interactions. In most instances, when compared with the standard herbicide treatment and adjuvant applied alone, herbicide efficacy was not affected in the presence of other agrochemicals. Changes in solution pH and formation of precipitates varied according to the herbicide combinations used. Boron, manganese, and 2,4-DB often caused dramatic changes in solution pH. DA - 2012/11// PY - 2012/11// DO - 10.1016/j.cropro.2012.05.014 VL - 41 SP - 134-142 J2 - Crop Protection LA - en OP - SN - 0261-2194 UR - http://dx.doi.org/10.1016/j.cropro.2012.05.014 DB - Crossref KW - Agrochemicals KW - Combinations KW - Herbicide KW - Solution pH KW - Precipitates ER - TY - JOUR TI - Interactions of agrochemicals applied to peanut; part 2: Effects on fungicides AU - Chahal, Gurinderbir S. AU - Jordan, David L. AU - Shew, Barbara B. AU - Brandenburg, Rick L. AU - Burton, James D. AU - Danehower, David AU - York, Alan C. T2 - Crop Protection AB - Field and laboratory experiments were conducted during 2008 and 2009 to study biological and physicochemical compatibility when fungicides were applied in combination with herbicides, insecticides, and micronutrients for the control of leaf spot disease and Sclerotinia blight. In both years, the program with three fungicide sprays was more effective in preventing canopy defoliation caused by early and late leaf spot disease than single fungicide spray irrespective of agrochemical combinations. Although several interactions were noted among agrochemical combinations, most combinations did not affect fungicide efficacy against canopy defoliation or Sclerotinia blight. In some instances, fungicide combinations protected peanut more effectively from canopy defoliation or Sclerotinia blight than standard fungicide treatment. Regardless of the other agrochemicals applied, boscalid was more effective than fluazinam in controlling Sclerotinia blight. Boscalid, boron, clethodim plus crop oil concentrate, chlorothalonil plus tebuconazole, manganese, and 2,4-DB had large effects on solution pH, whereas fluazinam, lambda-cyhalothrin, and pyraclostrobin had little effect on solution pH. Precipitates formed with all fungicide combinations and in most cases permanent precipitates were formed. DA - 2012/11// PY - 2012/11// DO - 10.1016/j.cropro.2012.05.008 VL - 41 SP - 143-149 J2 - Crop Protection LA - en OP - SN - 0261-2194 UR - http://dx.doi.org/10.1016/j.cropro.2012.05.008 DB - Crossref KW - Agrochemicals KW - Combinations KW - Fungicides KW - Interactions KW - Solution pH KW - Disease control KW - Leaf spot KW - Sclerotinia blight ER - TY - JOUR TI - Interactions of agrochemicals applied to peanut; part 3: Effects on insecticides and prohexadione calcium AU - Chahal, Gurinderbir S. AU - Jordan, David L. AU - Brandenburg, Rick L. AU - Shew, Barbara B. AU - Burton, James D. AU - Danehower, David AU - York, Alan C. T2 - Crop Protection AB - A wide range of agrochemicals can be applied in a peanut production system to control various stresses and manage crop growth and development. Field and laboratory experiments were conducted in North Carolina to define biological and physicochemical interactions when insecticides (fenpropathrin and lambda-cyhalothrin) or plant growth regulator (prohexadione calcium) were applied in combination with other agrochemicals including fungicides, herbicides, and micronutrients. Fenpropathrin or lambda-cyhalothrin combinations did not injure peanut in 2008 and 2009. Two sprays of prohexadione calcium improved row visibility and reduced main stem height compared with one prohexadione calcium spray irrespective of agrochemical combinations. In many instances, applying prohexadione calcium with other agrochemicals resulted in lower main stem height compared to prohexadione calcium alone. In one of the experiments, prohexadione calcium with prothioconazole plus tebuconazole lowered fall army worm population compared with prohexadione calcium alone. Addition of boron, manganese, and 2,4-DB to fenpropathrin, lambda-cyhalothrin, and prohexadione calcium combinations changed solution pH dramatically. Prohexadione calcium had the least effect on pH of the carrier. DA - 2012/11// PY - 2012/11// DO - 10.1016/j.cropro.2012.05.006 VL - 41 SP - 150-157 J2 - Crop Protection LA - en OP - SN - 0261-2194 UR - http://dx.doi.org/10.1016/j.cropro.2012.05.006 DB - Crossref KW - Agrochemicals KW - Combinations KW - Precipitates KW - Solution pH ER - TY - MGZN TI - Golf Courses as Good Environmental Stewards AU - Carley, D.S. AU - Hamon, L. T2 - North Carolina Turfgrass Magazine DA - 2012/1// PY - 2012/1// ER - TY - JOUR TI - Fertilization fitness and offspring ploidy in 3x × 2x matings in potato AU - Iorizzo, M. AU - Aversano, R. AU - Bradeen, J. M. AU - Frusciante, L. AU - Carputo, D. T2 - Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology AB - Abstract The main objective of the current research was to study the reproductive behaviour of artificial triploid potato hybrids between wild Solanum commersonii and the cultivated potato Solanum tuberosum. When used in 3x × 2x crosses, triploids gave aneuploid progenies with somatic chromosome number ranging from 29 to 36. Fertilization fitness data suggested that the survival rate of gametes produced by the triploid parents may be related to their chromosome number. In addition, consistent with molecular data, our results indicated that fitness of gametes and chromosome number of progenies are influenced by the genome dosage of interspecific triploids. Since a main route to polyploidy formation is via 2n gametes and triploids, our study may contribute to a better understanding of polyploid plant reproduction, evolution and breeding. DA - 2012/6// PY - 2012/6// DO - 10.1080/11263504.2011.620640 VL - 146 IS - 2 SP - 317-321 J2 - Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology LA - en OP - SN - 1126-3504 1724-5575 UR - http://dx.doi.org/10.1080/11263504.2011.620640 DB - Crossref KW - Endosperm balance number KW - fertilization fitness KW - aneuploid KW - AFLP markers KW - potato ER - TY - JOUR TI - Biological and geochemical markers of the geographical origin and genetic identity of potatoes AU - Adamo, Paola AU - Zampella, Mariavittoria AU - Quétel, Christophe R. AU - Aversano, Riccardo AU - Dal Piaz, Fabrizio AU - De Tommasi, Nunziatina AU - Frusciante, Luigi AU - Iorizzo, Massimo AU - Lepore, Laura AU - Carputo, Domenico T2 - Journal of Geochemical Exploration AB - Abstract There is a growing interest in agriculture productions combining safety and quality attributes with clear regional identity. In the last few years several methods have been employed for food authentication and traceability. In this study we tested geochemical data for elemental concentrations of Mn, Cu, Zn, Rb, Sr and Cd and strontium isotope ratio in combination with biological data of 11 secondary metabolites and DNA as markers for the authentication of the origin of early potatoes at small geographical scale levels in Italy. DNA fingerprints through 12 SSR (simple sequence repeat) primer pairs allowed cultivar identification, confirming the discrimination power of molecular markers. Element concentrations, strontium isotope ratio and secondary metabolite data, through multivariate statistics (partial least squares discriminant analysis, PLS-DA), made it possible to clearly assign all the potato samples to the respective administrative regions of cultivation. The validation of the models was successful. It included external prediction tests on 20% of the data randomly selected from each administrative province and a study on the robustness of these multivariate data treatments to uncertainties on measurement results. DA - 2012/10// PY - 2012/10// DO - 10.1016/j.gexplo.2012.07.006 VL - 121 SP - 62-68 J2 - Journal of Geochemical Exploration LA - en OP - SN - 0375-6742 UR - http://dx.doi.org/10.1016/j.gexplo.2012.07.006 DB - Crossref KW - Traceability KW - DNA analysis KW - Trace elements KW - Strontium isotopic signature KW - Secondary metabolites KW - Discriminant analysis ER - TY - JOUR TI - A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica) AU - Kubisiak, T. L. AU - Nelson, C. D. AU - Staton, M. E. AU - Zhebentyayeva, T. AU - Smith, C. AU - Olukolu, B. A. AU - Fang, G.-C. AU - Hebard, F. V. AU - Anagnostakis, S. AU - Wheeler, N. AU - Sisco, P. H. AU - Abbott, A. G. AU - Sederoff, R. R. T2 - Tree Genetics & Genomes AB - The Chinese chestnut (Castanea mollissima) carries resistance to Cryphonectria parasitica, the fungal pathogen inciting chestnut blight. The pathogen, introduced from Asia, devastated the American chestnut (Castanea dentata) throughout its native range early in the twentieth century. A highly informative genetic map of Chinese chestnut was constructed to extend genomic studies in the Fagaceae and to aid the introgression of Chinese chestnut blight resistance genes into American chestnut. Two mapping populations were established with three Chinese chestnut parents, ‘Mahogany’, ‘Nanking’, and ‘Vanuxem’, totaling 337 progeny. The transcriptome-based genetic map was created with 329 simple sequence repeat and 1,064 single nucleotide polymorphism markers all derived from expressed sequence tag sequences. Genetic maps for each parent were developed and combined to establish 12 consensus linkage groups spanning 742 cM, providing the the most comprehensive genetic map for a Fagaceae species to date. Over 75 % of the mapped markers from the Chinese chestnut consensus genetic map were placed on the physical map using overgo hybridization, providing a fully integrated genetic and physical map resource for Castanea spp. About half (57 %) of the Chinese chestnut genetic map could be assigned to regions of segmental homology with 58 % of the peach (Prunus persica) genome assembly. A three quantitative trait loci (QTL) model for blight resistance was verified using the new genetic markers and an existing interspecies (C. mollissima × C. dentata) F2 mapping population. Two of the blight resistance QTLs in chestnut shared synteny with two QTLs for powdery mildew resistance in peach, indicating the potential conservation of disease resistance genes at these loci. DA - 2012/11/30/ PY - 2012/11/30/ DO - 10.1007/S11295-012-0579-3 VL - 9 IS - 2 SP - 557-571 J2 - Tree Genetics & Genomes LA - en OP - SN - 1614-2942 1614-2950 UR - http://dx.doi.org/10.1007/S11295-012-0579-3 DB - Crossref KW - Fagaceae KW - Castanea spp. KW - Chestnut KW - Genetic map KW - Comparative genomics KW - Disease resistance ER - TY - JOUR TI - Vegetable Seedling Diseases Associated with Earthworm Castings Contaminated with Phytophthora capsici and Pythium Attrantheridium AU - Liu, Bo AU - Roos, Debbie AU - Buttler, Shawn AU - Richter, Brantlee AU - Louws, Frank J. T2 - Plant Health Progress AB - Earthworms and worm castings have been recommended for their beneficial effects in increasing yields and suppressing soilborne diseases. However, in a few cases, earthworm castings have been shown to harbor soilborne pathogens. The research documents that earthworm castings used as an amendment in soilless potting mixes at several organic farms in North Carolina were contaminated with Phytophthora capsici and several Pythium species. Phytophthora capsici and P. attrantheridium were subsequently isolated from rotted roots of vegetable seedlings grown in the potting mix. Commercial producers of earthworm castings should only use clean plant material to maintain earthworms and earthworm castings should be ascertained as pathogen-free before incorporation into plant growth media. Accepted for publication 30 January 2012. Published 21 April 2012. DA - 2012/1// PY - 2012/1// DO - 10.1094/php-2012-0421-01-rs VL - 13 IS - 1 SP - 15 ER - TY - JOUR TI - Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids AU - Serang, Oliver AU - Mollinari, Marcelo AU - Garcia, Antonio Augusto Franco T2 - PLoS ONE AB - The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of the population is unknown. We also introduce an algorithm for finding the exact maximum a posteriori genotype configuration with this model. This algorithm is implemented in a freely available web-based software package SuperMASSA. We demonstrate the utility, efficiency, and flexibility of the model and algorithm by applying them to two different platforms, each of which is applied to a polyploid data set: Illumina GoldenGate data from potato and Sequenom MassARRAY data from sugarcane. Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species. DA - 2012/2/17/ PY - 2012/2/17/ DO - 10.1371/journal.pone.0030906 VL - 7 IS - 2 SP - e30906 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0030906 DB - Crossref ER - TY - JOUR TI - A mixed model QTL analysis for sugarcane multiple-harvest-location trial data AU - Pastina, M.M. AU - Malosetti, M. AU - Gazaffi, R. AU - Mollinari, M. AU - Margarido, G.R.A. AU - Oliveira, K.M. AU - Pinto, L.R. AU - Souza, A.P. AU - Eeuwijk, F.A. AU - Garcia, A.A.F. T2 - Theoretical and Applied Genetics AB - Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane. DA - 2012/3// PY - 2012/3// DO - 10.1007/s00122-011-1748-8 VL - 124 IS - 5 SP - 835-849 UR - http://dx.doi.org/10.1007/s00122-011-1748-8 KW - Polyploids KW - Outcrossing species KW - Integrated linkage map KW - QTL x E ER - TY - JOUR TI - Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences AU - Sabadin, P. K. AU - Malosetti, M. AU - Boer, M. P. AU - Tardin, F. D. AU - Santos, F. G. AU - Guimarães, C. T. AU - Gomide, R. L. AU - Andrade, C. L. T. AU - Albuquerque, P. E. P. AU - Caniato, F. F. AU - Mollinari, M. AU - Margarido, G. R. A. AU - Oliveira, B. F. AU - Schaffert, R. E. AU - Garcia, A. A. F. AU - van Eeuwijk, F. A. AU - Magalhaes, J. V. T2 - Theoretical and Applied Genetics AB - Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum. DA - 2012/2/2/ PY - 2012/2/2/ DO - 10.1007/s00122-012-1795-9 VL - 124 IS - 8 SP - 1389-1402 J2 - Theor Appl Genet LA - en OP - SN - 0040-5752 1432-2242 UR - http://dx.doi.org/10.1007/s00122-012-1795-9 DB - Crossref ER - TY - JOUR TI - A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers AU - Palhares, Alessandra C AU - Rodrigues-Morais, Taislene B AU - Van Sluys, Marie-Anne AU - Domingues, Douglas S AU - Maccheroni, Walter, Jr AU - Jordão, Hamilton, Jr AU - Souza, Anete P AU - Marconi, Thiago G AU - Mollinari, Marcelo AU - Gazaffi, Rodrigo AU - Garcia, Antonio Augusto F AU - Vieira, Maria Lucia Carneiro T2 - BMC Genetics AB - The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily.The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization.Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease. DA - 2012/6/28/ PY - 2012/6/28/ DO - 10.1186/1471-2156-13-51 VL - 13 IS - 1 J2 - BMC Genet LA - en OP - SN - 1471-2156 UR - http://dx.doi.org/10.1186/1471-2156-13-51 DB - Crossref KW - Saccharum spp KW - AFLP KW - EST-SSR KW - Retrotransposon-based markers KW - Single-dose markers KW - Integrated genetic map KW - Marker distribution ER - TY - JOUR TI - Screening Cucumber for Resistance to Downy Mildew Caused by (Berk. and Curt.) Rostov. AU - Call, Adam D. AU - Criswell, Adam D. AU - Wehner, Todd C. AU - Klosinska, Urszula AU - Kozik, Elzbieta U. T2 - Crop Science AB - ABSTRACT Downy mildew, a foliar disease caused by the oomycete Pseudoperonospora cubensis (Berk. and Curt.) Rostov. is one of the most destructive diseases of cucumber ( Cucumis sativus L.). Moderately resistant cultivars are available, but yield losses are high without the use of fungicides. Higher levels of resistance are needed to reduce the need for fungicides. The objective of this study was to identify new sources of resistance to downy mildew among Plant Introduction accessions from the U.S. National Plant Germplasm System, elite cultivars, and breeding lines of cucumber. A total of 1300 cultigens were tested in Clinton, NC, and Skierniewice, Poland, in 2005 to 2007 under natural field epidemics. The most resistant and susceptible cultigens were further evaluated in replicated experiments in North Carolina and India in 2007 to 2009. Fungicide experiments were run in 2008 and 2009 to identify tolerance, involving weekly applications to one of two sets of material at a location. Results from the retest study confirmed the results of the initial screening. The most resistant cultigens over all environments were PI 605996, PI 330628, and PI 197088. Cultigens have been found that significantly outperform checks in all resistance traits. High yielding and tolerant cultigens have also been identified that could be used in developing improved cultivars. DA - 2012/// PY - 2012/// DO - 10.2135/cropsci2011.06.0296 VL - 52 SP - 577-592 SN - 0011-183X UR - http://dx.doi.org/10.2135/cropsci2011.06.0296 ER - TY - JOUR TI - Educator and Institutional Entrepreneur: Cooperative Extension and the Building of Localized Food Systems AU - Dunning, Rebecca AU - Creamer, Nancy AU - Massey Lelekacs, Joanna AU - O'Sullivan, John AU - Thraves, Tes AU - Wymore, Teisha T2 - Journal of Agriculture, Food Systems, and Community Development AB - Cooperative Extension Service educators work within an established network of offices throughout the United States and have the potential to tap both structural and relationship networks to foster collaboration and catalyze institutional change in food systems. The prerequisites and processes to generate systemic change, however, challenge the established logic of information transfer that has dominated Extension Service practice. This paper considers the nature of Extension's engagement in food systems both conceptually and in practice, based on a two-year train-the-trainer professional development project in North Carolina designed to support the emergence of local food systems. Extension initiatives are examined in light of two social change models: diffusion of innovations, based on knowledge transfer and spatial diffusion; and institutional change, based on inter-organizational relationships and mutually held cultural understandings. We suggest that the work of food systems change is more usefully viewed through an institutional lens, with extension educators serving as "institutional entrepreneurs" to address and leverage the concerns of the communities in which they are embedded into lasting food system change. DA - 2012/11/6/ PY - 2012/11/6/ DO - 10.5304/jafscd.2012.031.010 SP - 99-112 J2 - JAFSCD OP - SN - 2152-0801 UR - http://dx.doi.org/10.5304/jafscd.2012.031.010 DB - Crossref KW - community engagement KW - community food systems KW - cooperative extension service KW - diffusion KW - institutional change KW - institutional entrepreneur KW - interviews KW - local food systems KW - networks KW - North Carolina ER - TY - JOUR TI - Tomato seedling growth and morphological responses to supplemental led lighting red: blue ratios under varied daily solar light integrals. AU - Hernández, R. AU - Kubota, C. T2 - Acta Horticulturae DA - 2012/10// PY - 2012/10// DO - 10.17660/actahortic.2012.956.19 VL - 956 SP - 187-194 SN - 0567-7572 2406-6168 UR - http://dx.doi.org/10.17660/actahortic.2012.956.19 ER - TY - RPRT TI - Worms can recycle your garbage AU - Sherman, R. A3 - NC State Cooperative Extension DA - 2012/// PY - 2012/// M1 - AG‐473‐18 PB - NC State Cooperative Extension SN - AG‐473‐18 ER - TY - JOUR TI - Local Food Systems for a Healthy Population AU - Creamer, N.G. AU - Dunning, R.D. T2 - North Carolina Medical Journal DA - 2012/// PY - 2012/// VL - 73 IS - 4 SP - 310–312 ER - TY - JOUR TI - Heat stress and N fertilization affect soil microbial and enzyme activities in the creeping bentgrass (Agrostis Stolonifera L.) rhizosphere AU - Dell, Emily A. AU - Carley, Danesha Seth AU - Rufty, Thomas AU - Shi, Wei T2 - Applied Soil Ecology AB - High summer temperatures often cause damage to bentgrass on putting greens in transition zone regions. One of the most damaging effects is a depression of rooting. Although heat stress effects on plant functions are considered as a main reason for the damage, heat stress also may be related to organic matter (OM) accumulation and poor gas exchange into the rhizosphere. The OM accumulation and the often-observed root dieback suggest that soil microbial processes play a role in summer bentgrass decline. In this study, the impact of high temperature on soil microbial properties and enzyme activities was examined using creeping bentgrass (Agrostis stolonifera) growing in a phytotron controlled environment chamber. The high temperature exposures (34/30 °C versus 22/18 °C for controls) lasted for four weeks and the bentgrass cultures received mineral N at two rates. Our working hypothesis was that not only did high temperatures stimulate overall soil microbial and enzyme activity but also selectively modified microbial catabolic functions. To test this hypothesis, we compared temperature sensitivities and Q10 values of microbial substrate utilization patterns using a Biolog plate approach and soil enzyme activities. The results indicated that soil enzyme activities had similar responses to assay temperatures and their Q10 values averaged ∼2 with changes of laboratory assay temperatures from 12 to 22 °C and from 22 to 34 °C. Such positive responses of microbial activity to high temperatures were supported by parallel increases in rates of microbial substrate utilization. Total substrate availability in Biolog plates also increased with laboratory assay temperatures. This enhancement could not be explained by the overall stimulation of high temperature on microbial activity, but instead by selective modification of microbial community functions. Nitrogen fertilization significantly changed soil biological activities. Phenol oxidase activity was reduced by the high rate of N fertilization, whereas β-glucosidase and β-glucosaminidase activities were increased. Interactions on soil enzyme activities between growth chamber temperatures and N fertilization rates also occurred. Soil peroxidase activity was ∼three-fold greater for bentgrass subjected to heat stress and the low rate of N fertilization. Our results indicated that summer heat stress and the associated increases in root and OM degradation in bentgrass systems are related with overall temperature stimulations on soil microbial and enzyme activities as well as with modifications in functional components of the microbial community. DA - 2012/5// PY - 2012/5// DO - 10.1016/j.apsoil.2012.02.002 VL - 56 SP - 19-26 J2 - Applied Soil Ecology LA - en OP - SN - 0929-1393 UR - http://dx.doi.org/10.1016/j.apsoil.2012.02.002 DB - Crossref KW - Biolog plate KW - Heat stress KW - Microbial substrate utilization pattern KW - Soil enzyme activity KW - Temperature sensitivity KW - Turfgrass ER - TY - CHAP TI - Composite Interval Mapping and Multiple Interval Mapping: Procedures and Guidelines for Using Windows QTL Cartographer AU - Silva, Luciano Da Costa E. AU - Wang, Shengchu AU - Zeng, Zhao-Bang T2 - Methods in Molecular Biology AB - Tremendous progress has been made in recent years on developing statistical methods for mapping quantitative trait loci (QTL) from crosses of inbred lines. In this chapter, we provide an introduction of composite interval mapping and multiple interval mapping methods for mapping QTL from inbred line crosses and also detailed instructions to perform the analyses in Windows QTL Cartographer. For each method, we discuss the meaning of each option in the analysis procedures and how to understand and interpret the mapping results through a work-out example. PY - 2012/// DO - 10.1007/978-1-61779-785-9_6 SP - 75-119 OP - PB - Humana Press SN - 9781617797842 9781617797859 UR - http://dx.doi.org/10.1007/978-1-61779-785-9_6 DB - Crossref ER - TY - JOUR TI - Metabolomics Reveals Amino Acids Contribute to Variation in Response to Simvastatin Treatment AU - Trupp, Miles AU - Zhu, Hongjie AU - Wikoff, William R. AU - Baillie, Rebecca A. AU - Zeng, Zhao-Bang AU - Karp, Peter D. AU - Fiehn, Oliver AU - Krauss, Ronald M. AU - Kaddurah-Daouk, Rima T2 - PLoS ONE AB - Statins are widely prescribed for reducing LDL-cholesterol (C) and risk for cardiovascular disease (CVD), but there is considerable variation in therapeutic response. We used a gas chromatography-time-of-flight mass-spectrometry-based metabolomics platform to evaluate global effects of simvastatin on intermediary metabolism. Analyses were conducted in 148 participants in the Cholesterol and Pharmacogenetics study who were profiled pre and six weeks post treatment with 40 mg/day simvastatin: 100 randomly selected from the full range of the LDL-C response distribution and 24 each from the top and bottom 10% of this distribution (“good” and “poor” responders, respectively). The metabolic signature of drug exposure in the full range of responders included essential amino acids, lauric acid (p<0.0055, q<0.055), and alpha-tocopherol (p<0.0003, q<0.017). Using the HumanCyc database and pathway enrichment analysis, we observed that the metabolites of drug exposure were enriched for the pathway class amino acid degradation (p<0.0032). Metabolites whose change correlated with LDL-C lowering response to simvastatin in the full range responders included cystine, urea cycle intermediates, and the dibasic amino acids ornithine, citrulline and lysine. These dibasic amino acids share plasma membrane transporters with arginine, the rate-limiting substrate for nitric oxide synthase (NOS), a critical mediator of cardiovascular health. Baseline metabolic profiles of the good and poor responders were analyzed by orthogonal partial least square discriminant analysis so as to determine the metabolites that best separated the two response groups and could be predictive of LDL-C response. Among these were xanthine, 2-hydroxyvaleric acid, succinic acid, stearic acid, and fructose. Together, the findings from this study indicate that clusters of metabolites involved in multiple pathways not directly connected with cholesterol metabolism may play a role in modulating the response to simvastatin treatment. Trial Registration ClinicalTrials.gov NCT00451828 DA - 2012/7/9/ PY - 2012/7/9/ DO - 10.1371/journal.pone.0038386 VL - 7 IS - 7 SP - e38386 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0038386 DB - Crossref ER - TY - CHAP TI - Grape root rot (Roesleria subterranea (Weinm.) Redhead – Biology, Distribution and possible causes AU - Hoffmann, M. AU - Huber, L. AU - Ruehl, E.H. T2 - Annuals of German Viticulture PY - 2012/// ER - TY - RPRT TI - How to create a container garden for edibles in the North Carolina Piedmont AU - Richter, K. AU - Bradley, L.K. AU - Sherk, J. AU - Kistler, M. A3 - North Carolina Cooperative Extension DA - 2012/// PY - 2012/// M1 - AG-753 PB - North Carolina Cooperative Extension SN - AG-753 ER - TY - RPRT TI - Minimizing risks of soil contaminants in urban gardens AU - Crozier, C. AU - Polizzotto, M. AU - Bradley, L.K. A3 - NC State Cooperative Extension DA - 2012/// PY - 2012/// M1 - AGW-439-78 PB - NC State Cooperative Extension SN - AGW-439-78 UR - https://content.ces.ncsu.edu/minimizing-risks-of-soil-contaminants-in-urban-gardens ER - TY - RPRT TI - Ornamental sweetpotatoes for the home landscape AU - Carey, D. AU - Whipker, B. AU - Bradley, L. AU - Buhler, W. A3 - North Carolina Cooperative Extension DA - 2012/// PY - 2012/// M1 - AG-755 PB - North Carolina Cooperative Extension SN - AG-755 ER - TY - JOUR TI - An exploratory analysis of student-community interactions in urban agriculture AU - Grossman, J. AU - Sherard, M. AU - Bradley, L.K. AU - Goodell, S. AU - Prohn, S. T2 - Journal of Higher Education Outreach and Engagement DA - 2012/// PY - 2012/// VL - 16 IS - 2 SP - 179–196 UR - http://openjournals.libs.uga.edu/index.php/jheoe/article/view/794/560 ER - TY - JOUR TI - Assessing Extension educator’s needs for the development of homeowner pesticide use and safety information AU - Church, C.S. AU - Buhler, W.G. AU - Bradley, L.K. AU - Stinner, R.E. T2 - Journal of Extension DA - 2012/10// PY - 2012/10// VL - 50 IS - 5 UR - http://www.joe.org/joe/2012october/rb7.php ER - TY - JOUR TI - Diversity Analysis of Tomato Cultivars Based on Coefficient of Parentage and RAPD Molecular Markers AU - Joshi, Bal K. AU - Gardner, Randy G. AU - Panthee, Dilip R. T2 - Journal of Crop Improvement AB - Genetic diversity analysis provides information on the genetic base of the gene pool of released genotypes. The objectives of this study were to assess the diversity of tomato cultivars and breeding lines released from North Carolina State University based on their coefficient of parentage (COP) and RAPD markers, and to estimate the contribution of ancestors to these tomato cultivars and breeding lines. The COP analysis revealed that a single ancestor Walter constituted 25.17% of the North Carolina tomato gene pool followed by Blazer (11.57%) and Fla. 2153 (6.29%). Walter was used in developing 30 lines, whereas Blazer and Fla. 2153 were used in developing 29 lines each. The highest COP value (0.828) was between Summit and Monte Verde, indicating that they were the most similar lines. Similarity coefficients based on the RAPD molecular markers ranged from 0.461 to 0.935, with an average of 0.77. The similarity coefficient of NC3Grape with NCEBR8 was the lowest (0.461), whereas it was the highest (0.935) between NC1CS and NC946. On the basis of molecular data, first and second principal components accounted for 78% and 3.3% of the total variation, respectively. A significant positive correlation (r = 0.19, p = 0.04) existed between two similarity matrices based on the RAPD and the pedigree. This information may be useful for selecting the parents in breeding programs, particularly to widen the genetic base for designing future breeding strategies. DA - 2012/3// PY - 2012/3// DO - 10.1080/15427528.2011.623264 VL - 26 IS - 2 SP - 177-196 J2 - Journal of Crop Improvement LA - en OP - SN - 1542-7528 1542-7536 UR - http://dx.doi.org/10.1080/15427528.2011.623264 DB - Crossref KW - breeding lines KW - cultivars KW - coefficient of parentage KW - tomato KW - Solanum lycopersicum ER - TY - JOUR TI - The Effects of Lawn Plant Diversity on Arthropod Diversity. AU - Marshall, William Samuel DA - 2012/// PY - 2012/// UR - http://www.lib.ncsu.edu/resolver/1840.16/8354 ER - TY - JOUR TI - Improving Professional Skills in Soil Science Outreach Through Experiential Service-Learning Initiatives AU - Smith, Sarah Anne DA - 2012/// PY - 2012/// UR - http://www.lib.ncsu.edu/resolver/1840.16/8083 ER - TY - JOUR TI - Examining the Development and Management of Student Farms Nationwide: A Delphi Study and a Model for Student Farm Design. AU - Ratasky, Stephen Joseph DA - 2012/// PY - 2012/// UR - http://www.lib.ncsu.edu/resolver/1840.16/8455 ER - TY - JOUR TI - Pentanthera webs: Interspecific and interploid hybridization among sympatric azaleas in the southern Appalachian mountains AU - Shearer, K. AU - Ranney, T.G. AU - Miller, R. AU - Towe, C. T2 - Journal of the American Rhododendron Society DA - 2012/// PY - 2012/// VL - 66 IS - 4 SP - 187-197 ER - TY - CONF TI - Micropropagation of Acer platanoides L. ‘Crimson Sentry’ AU - Lattier, J.D. AU - Touchell, D.H. AU - Ranney, T.G. C2 - 2012/// C3 - Proceedings of the Southern Nursery Association Research Conference, 57th Annual Report DA - 2012/// VL - 57 SP - 296–300 ER - TY - CONF TI - Biomass yield and nitrogen response of perennial bioenergy grasses in North Carolina AU - Palmer, I.E. AU - Ranney, T.G. AU - Gehl, R. AU - Touchell, D. AU - George, Nic C2 - 2012/// C3 - Southern Nursery Association Research Conference DA - 2012/// VL - 57 SP - 268–272 ER - TY - JOUR TI - Basal salt composition, cytokinins, and phenolic binding agents influence in vitro growth and ex vitro establishment of Magnolia ‘Ann’ AU - Parris, J.K. AU - Touchell, D.H. AU - Ranney, T.G. AU - Adelberg, J. T2 - HortScience AB - In vitro growth responses of Magnolia ‘Ann’ to basal salt composition, cytokinins, and phenolic binding agents were investigated in a series of experiments to refine micropropagation protocols. Murashige and Skoog (MS), half-strength MS, Woody Plant Medium (WPM), Driver and Kuniyuki (DKW), and Blaydes basal salts in conjunction with 1 g·L −1 activated charcoal (AC) or 1 g·L −1 polyvinylpyrrolidone (PVP) were evaluated as multiplication media. Benzylaminopurine (BAP), meta -topolin ( m T), or 6-(γ,γ-dimethylallylamino) purine (2iP) at 2, 4, or 8 μM was investigated to optimize the cytokinin concentration. Murashige and Skoog medium supplemented with 2 μM BAP with no phenolic binding agent was an optimal multiplication medium that yielded 3.2 ± 0.2 shoots with a mean length of 17.2 ± 1.8 mm over an 8-week period. For rooting, microshoots were cultured on half-strength MS media supplemented with 0, 5, 10, or 20 μM indolebutyric acid (IBA) with or without AC. Media containing AC produced elongated microshoots suitable for rooting and ex vitro establishment. Microshoots cultured on medium supplemented with AC also had higher in vitro rooting (16%) and higher ex vitro rooting (75%) compared with those without AC regardless of in vitro IBA concentration. DA - 2012/// PY - 2012/// DO - 10.21273/hortsci.47.11.1625 VL - 47 IS - 11 SP - 1625-1629 KW - micropropagation KW - polyploidy KW - tissue culture ER - TY - JOUR TI - Overwintering sparrow use of field borders planted as beneficial insect habitat AU - Plush, Charles J. AU - Moorman, Christopher E. AU - Orr, David B. AU - Reberg-Horton, Chris T2 - The Journal of Wildlife Management AB - Abstract Field borders are an effective conservation strategy for providing habitat to overwintering sparrows, and may be a venue through which beneficial insect populations are promoted. However, traditional fallow field borders lack sufficient pollen and nectar sources required to sustain beneficial insect populations; therefore, borders planted to a mix of native prairie flowers and grasses may be needed if increases in beneficial insect populations are desired. Although the value of fallow borders to birds has been established, little is known about bird use of beneficial insect habitats. Using single‐observer transect surveys, we compared overwintering sparrow densities among 4 field border treatments (planted native warm season grasses and prairie flowers, planted prairie flowers only, fallow, and mowed) replicated around 9 organic crop fields from November to March 2009–2010 and 2010–2011. Sparrow densities were 5–10 times lower in mowed borders than in other border treatments in 2009–2010 and 2010–2011, but did not differ among planted and fallow borders in either year. Planted field borders may be a useful conservation practice for providing habitat for both overwintering sparrows and beneficial insects. © 2012 The Wildlife Society. DA - 2012/7// PY - 2012/7// DO - 10.1002/jwmg.436 VL - 77 IS - 1 SP - 200-206 KW - beneficial insects KW - field borders KW - organic farming KW - sparrows KW - winter habitat ER - TY - JOUR TI - Small mammal use of field borders planted as beneficial insect habitat AU - Moorman, Christopher E. AU - Plush, Charles J. AU - Orr, David B. AU - Reberg-Horton, Chris AU - Gardner, Beth T2 - Wildlife Society Bulletin AB - Abstract Field borders established for wildlife conservation have been recognized as a possible venue for also promoting beneficial insect populations, such as parasitic wasps and pollinators, on agricultural lands. However, traditional fallow field borders lack nectar sources required to sustain beneficial insect communities, and their value to small mammals is not well‐understood. In October–November 2009, we trapped small mammals in four field‐border treatments (planted native, warm‐season grasses and prairie flowers, planted prairie flowers only, fallow vegetation, and frequently mowed vegetation) replicated around nine organic crop fields, and developed closed‐population models in Program MARK to estimate abundance in each border. We also measured vegetation cover within each border treatment from June to August 2009. We captured 491 individuals of two species, the hispid cotton rat ( Sigmodon hispidus ) and house mouse ( Mus musculus ). Cotton rat abundance was ≥2 times greater in grass and flower borders and flowers‐only borders than in fallow borders, likely because of greater vegetation density and availability of preferred foods in planted borders. No cotton rats were captured in mowed borders, and house mouse abundance was ≥5 times lower in mowed borders than in other border types. Lower abundance of cotton rats and house mice in mowed borders emphasizes the importance of structurally complex non‐crop vegetation for supporting small‐mammal communities in agricultural landscapes. Field borders planted to promote beneficial insects may be a useful tool for maximizing the ecological services provided by non‐crop vegetation. © 2012 The Wildlife Society. DA - 2012/11// PY - 2012/11// DO - 10.1002/wsb.226 VL - 37 IS - 1 SP - 209-215 KW - agriculture KW - beneficial insects KW - field borders KW - Mus musculus KW - Sigmodon hispidus KW - small mammals ER - TY - MGZN TI - Farmland field borders – the relationships between beneficial insects and wildlife AU - Plush, C. AU - Moorman, C. AU - Orr, D. AU - Reberg-Horton, C. T2 - The Upland Gazette DA - 2012/// PY - 2012/// VL - 17 SP - 11–13 ER - TY - JOUR TI - Utilizing cover crop mulches to reduce tillage in organic systems in the Southeast AU - Reberg-Horton, S.C. AU - Grossman, J.M. AU - Kornecki, T.S. AU - Meijer, A.D. AU - Price, A.J. AU - Place, G.T. AU - Webster, T.M. T2 - Renewable Agriculture and Food Systems DA - 2012/// PY - 2012/// VL - 27 SP - 41–48 ER - TY - JOUR TI - Influence of Virginia market type genotype on peanut response to weed interference AU - Place, G.T. AU - Reberg-Horton, S.C. AU - Jordan, D.L. AU - Isleib, T.G. AU - Wilkerson, G.G. T2 - Peanut Science AB - Abstract Differences in the ability of cultivars to compete with weeds are not well-defined for peanut. Research was conducted in 2007 and 2008 to compare the growth and competitiveness of the virginia market type cultivars NC 10C, NC-V 11, NC 12C, Phillips, VA 98R, and breeding lines N99027L, N01013T, and N02020J under weedy and weed-free conditions. Weed-free peanut was established by applying preemergence and postemergence herbicides throughout the growing season supplemented by weekly hand removal of weeds. Clethodim was applied to weedy peanut to eliminate annual grass interference but not interference from broadleaf weeds and sedges. Weed-free peanut biomass, weedy peanut biomass, and weed biomass were not affected by genotype 10 weeks after peanut emergence. Although substantial yield loss was noted in presence of weeds, the percent yield loss did not vary by genotype when comparing weedy and weed-free yield. These data suggest that cultivar selection within virginia market type peanut will have limited utility in a comprehensive weed management strategy. DA - 2012/// PY - 2012/// DO - 10.3146/ps10-12.1 VL - 39 IS - 1 SP - 22–29 ER - TY - JOUR TI - Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres AU - Paterson, Andrew H. AU - Wendel, Jonathan F. AU - Gundlach, Heidrun AU - Guo, Hui AU - Jenkins, Jerry AU - Jin, Dianchuan AU - Llewellyn, Danny AU - Showmaker, Kurtis C. AU - Shu, Shengqiang AU - Udall, Joshua AU - Yoo, Mi-jeong AU - Byers, Robert AU - Chen, Wei AU - Doron-Faigenboim, Adi AU - Duke, Mary V. AU - Gong, Lei AU - Grimwood, Jane AU - Grover, Corrinne AU - Grupp, Kara AU - Hu, Guanjing AU - Lee, Tae-ho AU - Li, Jingping AU - Lin, Lifeng AU - Liu, Tao AU - Marler, Barry S. AU - Page, Justin T. AU - Roberts, Alison W. AU - Romanel, Elisson AU - Sanders, William S. AU - Szadkowski, Emmanuel AU - Tan, Xu AU - Tang, Haibao AU - Xu, Chunming AU - Wang, Jinpeng AU - Wang, Zining AU - Zhang, Dong AU - Zhang, Lan AU - Ashrafi, Hamid AU - Bedon, Frank AU - Bowers, John E. AU - Brubaker, Curt L. AU - Chee, Peng W. AU - Das, Sayan AU - Gingle, Alan R. AU - Haigler, Candace H. AU - Harker, David AU - Hoffmann, Lucia V. AU - Hovav, Ran AU - Jones, Donald C. AU - Lemke, Cornelia AU - Mansoor, Shahid AU - Rahman, Mehboob AU - Rainville, Lisa N. AU - Rambani, Aditi AU - Reddy, Umesh K. AU - Rong, Jun-kang AU - Saranga, Yehoshua AU - Scheffler, Brian E. AU - Scheffler, Jodi A. AU - Stelly, David M. AU - Triplett, Barbara A. AU - Deynze, Allen Van AU - Vaslin, Maite F. S. AU - Waghmare, Vijay N. AU - Walford, Sally A. AU - Wright, Robert J. AU - Zaki, Essam A. AU - Zhang, Tianzhen AU - Dennis, Elizabeth S. AU - Mayer, Klaus F. X. AU - Peterson, Daniel G. AU - Rokhsar, Daniel S. AU - Wang, Xiyin AU - Schmutz, Jeremy T2 - Nature AB - The Gossypium genus is used to investigate emergent consequences of polyploidy in cotton species; comparative genomic analyses reveal a complex evolutionary history including interactions among subgenomes that result in genetic novelty in elite cottons and provide insight into the evolution of spinnable fibres. A phylogenetic and genomic study of plants of the cotton genus Gossypium provides insights into the role of polyploidy in the angiosperm evolution, and specifically, in the emergence of spinnable fibres in domesticated cottons. The authors show that an abrupt five- to sixfold ploidy increase about 60 million years ago, and allopolyploidy reuniting divergent genomes approximately 1–2 million years ago, conferred a roughly 30-fold duplication of ancestral flowering plant genes in the 'elite' cottons G. hirsutum and G. barbadense compared to their presumed progenitor G. raimondii. Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments1. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1–2 Myr ago2, conferred about 30–36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica3 among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum AtDt (in which ‘t’ indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups. DA - 2012/// PY - 2012/// DO - 10.1038/nature11798 VL - 492 IS - 7429 SP - 423-427 ER - TY - JOUR TI - Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.) AU - Stoffel, Kevin AU - Leeuwen, Hans AU - Kozik, Alexander AU - Caldwell, David AU - Ashrafi, Hamid AU - Cui, Xinping AU - Tan, Xiaoping AU - Hill, Theresa AU - Reyes-Chin-Wo, Sebastian AU - Truco, Maria-Jose AU - Michelmore, Richard W AU - Deynze, Allen Van T2 - BMC Genomics AB - Abstract Background High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce ( Lactuca sativa ). Results We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species ( L. serriola , L. saligna , L. virosa and L. perennis ). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. Conclusion By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously. DA - 2012/// PY - 2012/// DO - 10.1186/1471-2164-13-185 VL - 13 IS - 1 SP - 185 ER - TY - JOUR TI - Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development AU - Powell, A. L. T. AU - Nguyen, C. V. AU - Hill, T. AU - Cheng, K. L. AU - Figueroa-Balderas, R. AU - Aktas, H. AU - Ashrafi, H. AU - Pons, C. AU - Fernandez-Munoz, R. AU - Vicente, A. AU - Lopez-Baltazar, J. AU - Barry, C. S. AU - Liu, Y. AU - Chetelat, R. AU - Granell, A. AU - Deynze, A. Van AU - Giovannoni, J. J. AU - Bennett, A. B. T2 - Science AB - Modern tomato (Solanum lycopersicum) varieties are bred for uniform ripening (u) light green fruit phenotypes to facilitate harvests of evenly ripened fruit. U encodes a Golden 2-like (GLK) transcription factor, SlGLK2, which determines chlorophyll accumulation and distribution in developing fruit. In tomato, two GLKs--SlGLK1 and SlGLK2--are expressed in leaves, but only SlGLK2 is expressed in fruit. Expressing GLKs increased the chlorophyll content of fruit, whereas SlGLK2 suppression recapitulated the u mutant phenotype. GLK overexpression enhanced fruit photosynthesis gene expression and chloroplast development, leading to elevated carbohydrates and carotenoids in ripe fruit. SlGLK2 influences photosynthesis in developing fruit, contributing to mature fruit characteristics and suggesting that selection of u inadvertently compromised ripe fruit quality in exchange for desirable production traits. DA - 2012/6// PY - 2012/6// DO - 10.1126/science.1222218 VL - 336 IS - 6089 SP - 1711-1715 ER - TY - JOUR TI - Selective genotyping to identify late blight resistance genes in an accession of the tomato wild species Solanum pimpinellifolium AU - Merk, Heather L. AU - Ashrafi, Hamid AU - Foolad, Majid R. T2 - Euphytica DA - 2012/6// PY - 2012/6// DO - 10.1007/s10681-012-0729-6 VL - 187 IS - 1 SP - 63-75 KW - Disease resistance KW - Phytophthora infestans KW - Qualitative resistance KW - Solanum pimpinellifolium KW - Trait-based analysis KW - Tomato KW - Resistance breeding KW - Vertical resistance ER - TY - JOUR TI - De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes AU - Ashrafi, Hamid AU - Hill, Theresa AU - Stoffel, Kevin AU - Kozik, Alexander AU - Yao, JiQiang AU - Chin-Wo, Sebastian AU - Deynze, Allen Van T2 - BMC Genomics AB - Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, the majority of sequencing data were generated by the Sanger sequencing method. By leveraging Sanger EST data, we have generated a wealth of genetic information for pepper including thousands of SNPs and Single Position Polymorphic (SPP) markers. To complement and enhance these resources, we applied NGS to three pepper genotypes: Maor, Early Jalapeño and Criollo de Morelos-334 (CM334) to identify SNPs and SSRs in the assembly of these three genotypes.Two pepper transcriptome assemblies were developed with different purposes. The first reference sequence, assembled by CAP3 software, comprises 31,196 contigs from >125,000 Sanger-EST sequences that were mainly derived from a Korean F1-hybrid line, Bukang. Overlapping probes were designed for 30,815 unigenes to construct a pepper Affymetrix GeneChip® microarray for whole genome analyses. In addition, custom Python scripts were used to identify 4,236 SNPs in contigs of the assembly. A total of 2,489 simple sequence repeats (SSRs) were identified from the assembly, and primers were designed for the SSRs. Annotation of contigs using Blast2GO software resulted in information for 60% of the unigenes in the assembly. The second transcriptome assembly was constructed from more than 200 million Illumina Genome Analyzer II reads (80-120 nt) using a combination of Velvet, CLC workbench and CAP3 software packages. BWA, SAMtools and in-house Perl scripts were used to identify SNPs among three pepper genotypes. The SNPs were filtered to be at least 50 bp from any intron-exon junctions as well as flanking SNPs. More than 22,000 high-quality putative SNPs were identified. Using the MISA software, 10,398 SSR markers were also identified within the Illumina transcriptome assembly and primers were designed for the identified markers. The assembly was annotated by Blast2GO and 14,740 (12%) of annotated contigs were associated with functional proteins.Before availability of pepper genome sequence, assembling transcriptomes of this economically important crop was required to generate thousands of high-quality molecular markers that could be used in breeding programs. In order to have a better understanding of the assembled sequences and to identify candidate genes underlying QTLs, we annotated the contigs of Sanger-EST and Illumina transcriptome assemblies. These and other information have been curated in a database that we have dedicated for pepper project. DA - 2012/// PY - 2012/// DO - 10.1186/1471-2164-13-571 VL - 13 IS - 1 SP - 571 KW - Pepper KW - Capsicum spp KW - Molecular Markers KW - EST KW - Transcriptome KW - RNAseq KW - Annotation KW - SNP KW - SSR KW - SPP ER - TY - SOUND TI - Genome-Wide Gossypium SNP Development and Validation AU - Wang, Fei AU - Hulse, Amanda M. AU - Hoegenauer, Kevin AU - Stelly, David M. AU - Ashrafi, Hamid AU - Deynze, Allen Van AU - Yu, John DA - 2012/1/3/ PY - 2012/1/3/ UR - http://www.cotton.org/beltwide/index.cfm?page=beltwide_overview ER - TY - SOUND TI - Genome-wide SNP discovery from de novo assemblies of pepper (Capsicum annuum) transcriptomes AU - Ashrafi, Hamid AU - Yao, Jiqiang AU - Stoffel, Kevin AU - Reyes-Chin-Wo, Sebastian AU - Hill, Theresa AU - Kozik, Alexander AU - Van Deynze, Allen DA - 2012/1/14/ PY - 2012/1/14/ M3 - poster N1 - Poster P0480 RN - Poster P0480 ER - TY - SOUND TI - Genome-wide SNP development and validation for allotetraploid Gossypium AU - Hulse, Amanda M. AU - Wang, Fei AU - Hoegenauer, Kevin AU - Stelly, David M. AU - Ashrafi, Hamid AU - Deynze, Allen Van AU - Yu, John Z. AU - Chen, Jeffrey Z. AU - Udall, Joshua A. AU - Jones, Dan C. DA - 2012/1/14/ PY - 2012/1/14/ M3 - poster N1 - Poster P0199 RN - Poster P0199 ER - TY - SOUND TI - Comparisons of high-density EST-based maps in pepper species AU - Hill, Theresa AU - Ashrafi, Hamid AU - Reyes-Chin-Wo, Sebastian AU - Romero, Marcelo Solano AU - Kozik, Alexander AU - Deynze, Allen Van DA - 2012/1/14/ PY - 2012/1/14/ M3 - poster N1 - Poster P0479 RN - Poster P0479 ER - TY - SOUND TI - Comparison and evaluation of cotton SNPs developed by transcriptome, genome reduction on restriction site conservation and RAD-based sequencing AU - Ashrafi, H. DA - 2012/10/9/ PY - 2012/10/9/ ER - TY - SOUND TI - Collaborative Development of SNPs for Cotton Research, Introgression, MAS and Breeding. Genome-Wide Gossypium SNP Development and Validation AU - Wang, Fei AU - Hulse, Amanda M. AU - Hoegenauer, Kevin AU - Stelly, David M. AU - Ashrafi, Hamid AU - Deynze, Allen Van AU - Yu, John Z. DA - 2012/1/3/ PY - 2012/1/3/ UR - http://www.cotton.org/beltwide/index.cfm?page=beltwide_overview ER - TY - JOUR TI - Removing the tension from extension AU - Bradley, L. AU - Driscoll, E AU - Bardon, R. E. T2 - Journal of Extension DA - 2012/// PY - 2012/// VL - 50 IS - 2 ER - TY - JOUR TI - Values, objectivity and credibility of scientists in a contentious natural resource debate AU - Yamamoto, Yuri T. T2 - PUBLIC UNDERSTANDING OF SCIENCE AB - In contentious natural resource debates, the credibility of scientists is at risk. In this case study, citizens in contending communities and scientists in a forest management controversy constructed the scientists’ credibility differently. Shared values and views of the nature of science and objectivity were primary factors for constructing scientists’ credibility. Citizens who expected value-free, objective scientists to authenticate their knowledge were concerned about how the values of scientists on the opposite side affected research framing. Citizens who emphasized limited objectivity were less skeptical of scientists. Scientists acknowledged their values but defended their credibility in terms of professional standards, balance and resource constraints. In short, scientists’ credibility is relative because each individual has unique values and views of the nature of science and objectivity. Through a collaborative policymaking process, citizens and scientists should develop shared values and visions to reconstruct a temporary, intersubjective sense of credibility. DA - 2012/1// PY - 2012/1// DO - 10.1177/0963662510371435 VL - 21 IS - 1 SP - 101-125 SN - 1361-6609 KW - interaction experts/publics KW - public participation KW - public understanding of science KW - science attitudes and perceptions KW - science experts KW - scientists' attitudes ER - TY - CONF TI - Postharvest response of peach and nectarine cultivars to 1-methylcyclopropene treatment AU - Parker, M. L. AU - Blankenship, S. M. AB - With the registration of 1-methylcyclopropene (1-MCP) in the USA and large scale use on apples, the question was posed of how effective the product would be in maintaining the flesh firmness of tree ripened peaches. In NC where peaches are sold primarily through retail outlets immediately after harvest, high quality tree-ripened peaches are expected. However, to meet this expectation peaches are picked at a more advanced stage of maturity and they are softer with a reduced shelf life. Six peach (Prunus persica L. Batsch) cultivars and one nectarine cultivar were harvested at tree-ripe maturity. The cultivars were selected to represent a range of maturity from early to late season. The cultivars included in this study were: 'Candor', 'Goldprince', 'Carolina Red', 'Redhaven', 'Contender', 'China Pearl', and 'Big Red'. After harvest the fruit were cooled overnight to remove field heat and then treated with 1-MCP for 24 h at 5°C. After treatment with one µL/L 1-MCP the fruit were held at 21°C for up to 8 days to simulate retail and consumer conditions after purchase. Treatment with 1-MCP resulted in fruit with higher flesh firmness, particularly during the first 5 days at 21°C, compared to untreated fruit. Treated fruit were significantly firmer than the untreated fruit after approximately seven days, but this was somewhat dependent on harvest maturity. On fruit harvested at a later stage of maturity that had significantly softened, 1-MCP had little effect. One µl/L reduced the respiration rate of the fruit. Effect on soluble solid concentration was not consistent. It was concluded that use of 1-MCP would allow a tree-ripened peach to maintain slightly greater flesh firmness for a longer period of time when held under room temperature conditions. However, the commercial economics of this treatment need to be determined. C2 - 2012/// C3 - Vii international peach symposium DA - 2012/// DO - 10.17660/actahortic.2012.962.74 VL - 962 SP - 549-555 ER - TY - JOUR TI - Abscisic Acid Applications in Peach AU - Parker, M. L. AU - Clark, M. B. AU - Campbell, C. T2 - VII INTERNATIONAL PEACH SYMPOSIUM DA - 2012/// PY - 2012/// DO - 10.17660/actahortic.2012.962.55 VL - 962 SP - 403-409 SN - 0567-7572 KW - Prunus persica KW - ABA KW - soil drench KW - tree growth KW - root growth ER - TY - JOUR TI - Soil organic amendment impacts on corn resistance to Helicoverpa zea: Constitutive or induced? AU - Cardoza, Yasmin J. AU - Buhler, Wayne G. T2 - PEDOBIOLOGIA AB - Earthworm produced compost or vermicompost has been shown to improve plant growth and productivity. Vermicompost amendment to the soil also results in plant resistance to arthropod pests. In the present study we used corn, Zea mays L., and the corn earworm, Helicoverpa zea Boddie (Lepidoptera: Noctuidae) to investigate the effects of two vermicompost sources Oregon (OSC) and Raleigh (Ral) and previous feeding by H. zea larvae on the response and preference of immature and adult stages of the insect to corn plants. Results from our study show that Ral and OSC vermicompost were both effective in inducing corn antixenosis (non preference) and antibiosis (lower performance) resistance to H. zea that is effective against adult (decreased oviposition) and immature insect stages (lower immature weight gain and survival), respectively. We also found that previous conspecific induction appears to have a phagostimulatory effect on larval vermicompost leaf tissue consumption, especially for the Ral treatment. Conspecific induction also buffered the resistance effects of the vermicompost resulting in a stimulatory effect on oviposition by adults. The potential factors leading to the insect responses observed are discussed within the context of previous studies evaluating vermicompost-mediated resistance to pests. DA - 2012/// PY - 2012/// DO - 10.1016/j.pedobi.2012.08.002 VL - 55 IS - 6 SP - 343-347 SN - 0031-4056 KW - Corn KW - Corn earworm KW - Vermicompost KW - Induced-resistance KW - Feeding preference KW - Oviposition ER - TY - JOUR TI - Watermelon: From dessert to functional food AU - Perkins-Veazie, P. AU - Davis, A. AU - Collins, J. K. T2 - Israel Journal of Plant Sciences DA - 2012/// PY - 2012/// VL - 60 IS - 4 SP - 395-402 ER - TY - JOUR TI - Multiple trait multiple interval mapping of quantitative trait loci from inbred line crosses AU - Silva, L. D. E. AU - Wang, S. C. AU - Zeng, Z. B. T2 - BMC Genetics DA - 2012/// PY - 2012/// VL - 13 ER - TY - JOUR TI - Pressurized liquid extraction and quantification of anthocyanins in purple-fleshed sweet potato genotypes AU - Truong, V. D. AU - Hu, Z. AU - Thompson, R. L. AU - Yencho, G. C. AU - Pecota, K. V. T2 - JOURNAL OF FOOD COMPOSITION AND ANALYSIS AB - Analysis of anthocyanins responsible for the purple flesh color is important for breeding programs and development of value-added products. This study aimed to optimize the conditions for anthocyanin extraction from purple-fleshed sweet potatoes (PFSP) using pressurized-liquid extraction (PLE) method and quantify anthocyanins in various genotypes. Freeze-dried powders of PFSP genotypes were extracted with acidified methanol using an accelerated solvent extractor. Anthocyanin content of the extract was characterized by (a) pH-differential method and (b) color value protocol measuring absorbance at 530 nm, which is commonly used in Japan as a commercial indicator of total anthocyanin quantity. Highest anthocyanin yields by PLE were with an acetic acid:methanol:water mixture of 7:75:18% (v/v), sample weight of <0.5 g and 80–120 °C. Among 335 genotypes, the anthocyanin content varied widely from 0 to 663 mg cyanidine-3-glucoside equivalent/100 g powder or 0–210 mg/100 g fresh weight. The total monomeric anthocyanin (TMA) contents determined by the pH-differential method were highly correlated with the Japan color value (JCV) protocol, TMA = (0.145) JCV, R2 = 0.943. These results can be useful for sweet potato breeding programs and processing industry in development of PFSP cultivars and processed products with high anthocyanin levels. DA - 2012/// PY - 2012/// DO - 10.1016/j.jfca.2012.03.006 VL - 26 IS - 1-2 SP - 96-103 SN - 1096-0481 KW - Ipomoea batatas L. KW - Purple-fleshed sweetpotatoes KW - Anthocyanins KW - Extraction KW - pH-differential method KW - Color values KW - Food analysis KW - Food composition ER - TY - JOUR TI - Nitrogen application rate, leaf position and age affect leaf nutrient status of five specialty cut flowers AU - Ahmad, Iftikhar AU - Dole, John M. AU - Nelson, Paul T2 - SCIENTIA HORTICULTURAE AB - This study was conducted to determine the effect of nitrogen fertilizer levels on growth and yield of specialty cut flowers, ‘Chief’ celosia, ‘Sensation’ cosmos, ‘Sunbright’ and ‘Sunrich Orange’ sunflowers and ‘Benary Giant Mix’ zinnia, as well as record influence of leaf position and age on leaf nutrient concentrations. Plants grown in open field were supplied with five different N levels beginning five days after transplanting: no added N (control); one, two or three applications of N at 112 kg ha−1 at 40 day intervals; and a single application of 336 kg ha−1. Plants fertilized with two or three applications of 112 kg ha−1 produced the most flowers in celosia and all fertilizer applications increased yield equally in zinnia, but had no effect on cosmos and both cultivars of sunflower. Nitrogen fertilization produced the longest flower stems for cosmos and both sunflower cultivars, but had no effect on celosia and zinnia stem length. Nitrogen fertilization rate did not significantly affect days to harvest of all species tested. For leaf nutrient analysis, the upper one-third of the plant proved to be a reliable tissue source in all species. Generally, young leaf samples collected early in the season had higher nutrient concentrations as compared with the same leaf position at mid or late season. Increasing N fertilization increased N content of foliage for all species. Our recommended tissue nutrient levels were generally lower than those previously recommended for greenhouse-grown bedding plant cultivars of the same species. DA - 2012/7/13/ PY - 2012/7/13/ DO - 10.1016/j.scienta.2012.04.009 VL - 142 SP - 14-22 SN - 1879-1018 KW - Plant nutrition KW - Leaf analysis KW - Celosia KW - Cosmos KW - Leaf position KW - Sunflower KW - Zinnia ER - TY - JOUR TI - Assessing the integrated pest management practices of southeastern US ornamental nursery operations AU - LeBude, Anthony V AU - White, Sarah A AU - Fulcher, Amy F AU - Frank, Steve AU - Klingeman III, William E AU - Chong, Juang-Horng AU - Chappell, Matthew R AU - Windham, Alan AU - Braman, Kris AU - Hale, Frank AU - Dunwell, Winston AU - Williams-Woodward, Jean AU - Ivors, Kelly AU - Adkins, Craig AU - Neal, Joe T2 - Pest Management Science AB - Abstract BACKGROUND: The Southern Nursery Integrated Pest Management (SNIPM) working group surveyed ornamental nursery crop growers in the southeastern United States to determine their pest management practices. Respondents answered questions about monitoring practices for insects, diseases and weeds, prevention techniques, intervention decisions, concerns about IPM and educational opportunities. Survey respondents were categorized into three groups based on IPM knowledge and pest management practices adopted. RESULTS: The three groups differed in the use of standardized sampling plans for scouting pests, in monitoring techniques, e.g. sticky cards, phenology and growing degree days, in record‐keeping, in the use of spot‐spraying and in the number of samples sent to a diagnostic clinic for identification and management recommendation. CONCLUSIONS: Stronger emphasis is needed on deliberate scouting techniques and tools to monitor pest populations to provide earlier pest detection and greater flexibility of management options. Most respondents thought that IPM was effective and beneficial for both the environment and employees, but had concerns about the ability of natural enemies to control insect pests, and about the availability and effectiveness of alternatives to chemical controls. Research and field demonstration is needed for selecting appropriate natural enemies for augmentative biological control. Two groups utilized cooperative extension almost exclusively, which would be an avenue for educating those respondents. Copyright © 2012 Society of Chemical Industry DA - 2012/4/19/ PY - 2012/4/19/ DO - 10.1002/ps.3295 VL - 68 IS - 9 SP - 1278-1288 J2 - Pest. Manag. Sci. LA - en OP - SN - 1526-498X UR - http://dx.doi.org/10.1002/ps.3295 DB - Crossref KW - cooperative extension KW - IPM KW - ornamental nursery crops KW - survey ER - TY - JOUR TI - Tolerance of Tomato to Herbicides Applied through Drip Irrigation AU - Dittmar, Peter J. AU - Monks, David W. AU - Jennings, Katherine M. AU - Booker, Fitzgerald L. T2 - WEED TECHNOLOGY AB - Greenhouse and field studies were conducted to determine tolerance of tomato to halosulfuron, imazosulfuron, and trifloxysulfuron herbicides applied through drip irrigation. In greenhouse studies, PRE- and POST-applied trifloxysulfuron caused greater tomato injury (14 and 54% injury, respectively) than PRE- and POST-applied halosulfuron (5 and 26% injury, respectively) or imazosulfuron (5 and 23% injury, respectively). All herbicide treatments in the greenhouse studies caused greater injury to tomato than the nontreated. Greater tomato injury was observed in the greenhouse from herbicides applied POST than when soil applied. Tomato injury from POST-applied halosulfuron, imazosulfuron, or trifloxysulfuron followed a linear relationship, with tomato injury increasing with increasing herbicide rate. Tomato photosynthetic rate did not differ among the herbicide treatments (32.7 to 55.0 μmol m −2 s −1 ) and the nontreated (38.0 to 55.0 μmol m −2 s −1 ). At 5 to 16 days after treatment (DAT), tomato treated with imazosulfuron POST (0.26 to 0.46 cm s −1 ) or trifloxysulfuron POST (0.27 to 0.51 cm s −1 ) had lower stomatal conductance compared to the stomatal conductance of the nontreated tomato (0.65 to 0.76 cm s −1 ). Chlorophyll content did not differ among treatments at 0 to 6 DAT. At 7 to 12 DAT, tomato treated with imazosulfuron POST (34.0 to 40.1 SPAD) and trifloxysulfuron POST (35.0 to 41.6 SPAD) had lower chlorophyll content compared to the nontreated (39.1 to 48.1 SPAD). In 2008 and 2009 field studies, no tomato injury was observed. Herbicide, herbicide application method, and herbicide rate had no effect on tomato height (73 to 77 cm 14 DAT, 79 to 84 cm 21 DAT) and total fruit yield (62,722 to 80,328 kg ha −1 ). DA - 2012/// PY - 2012/// DO - 10.1614/wt-d-11-00181.1 VL - 26 IS - 4 SP - 684-690 SN - 1550-2740 KW - Application method KW - drip applied KW - methyl bromide alternatives KW - sulfonylurea ER - TY - JOUR TI - Nutrient disorders of 'Evolution' Mealy-cup Sage AU - Barnes, J. AU - Whipker, B. AU - McCall, I. AU - Frantz, J. T2 - HortTechnology DA - 2012/// PY - 2012/// VL - 22 IS - 4 SP - 502-508 ER - TY - JOUR TI - Influence of Induced Polyploidy on Fertility and Morphology of Rudbeckia Species and Hybrids AU - Oates, Kelly M. AU - Ranney, Thomas G. AU - Touchell, Darren H. T2 - HORTSCIENCE AB - Rudbeckia spp. are adaptable and valuable ornamental wildflowers. Development of new varieties of Rudbeckia spp., with improved commercial characteristics, would be highly desirable. Interspecific hybridization and induced polyploidy may be avenues for improvement within the genus. The objective of this study was to evaluate fertility, morphology, phenology of flowering, and perennialness (overwintering survival) for lines of diploid and induced allotetraploids of R. subtomentosa × hirta and diploid and autotetraploids of R. subtomentosa ‘Henry Eilers’. Polyploid lines were developed and propagated in vitro and then grown ex vitro in a randomized complete block design with 12 replications. Compared with their diploid counterparts, autotetraploid lines of R. subtomentosa ‘Henry Eilers’ had similar internode lengths, plant heights, number of stems, flowering times (date at first anthesis), and fall and spring survival (100%); reduced number of inflorescences and male and female fertility; and increased inflorescence diameters. Compared with their diploid counterparts, allotetraploids of R. subtomentosa × hirta had similar internode lengths, reduced number of inflorescences, delayed flowering times, and increased pollen staining. Allotetraploids had limited male and female fertility compared with no detectable fertility in their diploid counterparts. Plant height and number of stems either decreased or showed no change with induced allotetraploidy. Spring survival of diploid hybrid genotypes ranged from 0% to 82% and was not improved in the allotetraploid hybrids. For a given genotype, some polyploidy lines varied significantly in certain morphological traits (e.g., plant height) indicating somaclonal variation may have developed in vitro or there were variable genomic or epigenetic changes associated with induced polyploidy. DA - 2012/9// PY - 2012/9// DO - 10.21273/hortsci.47.9.1217 VL - 47 IS - 9 SP - 1217-1221 SN - 2327-9834 KW - Asteraceae KW - autotetraploid KW - allotetraploid KW - blackeyed Susan KW - chromosome doubling KW - coneflower KW - whole genome duplication KW - plant breeding ER - TY - JOUR TI - High Tunnel and Field Production of Organic Heirloom Tomatoes: Yield, Fruit Quality, Disease, and Microclimate AU - O'Connell, Suzanne AU - Rivard, Cary AU - Peet, Mary M. AU - Harlow, Chris AU - Louws, Frank T2 - HORTSCIENCE AB - Organic and heirloom tomatoes are high-value products with growing demand but there are many challenges to successful cultivation. A systems comparison study was carried out to evaluate the production of the popular heirloom tomato ‘Cherokee Purple’ ( Solanum lycopersicum L.) under high tunnel and open field systems in North Carolina from 2007 to 2008. Management of the high tunnel (i.e., temperature and irrigation), weather events as well as pest and disease pressure influenced crop quality and yield. The high tunnel and field systems achieved similar total yields (100 t·ha −1 ) the first season but yields were 33% greater in the high tunnel system than the field system in the second year (100 t·ha −1 and 67 t·ha −1 , respectively). Both years, the tomatoes were planted in high tunnels 1 month earlier and harvested 3 weeks earlier than the field. The accumulation of ≈1100 growing degree-days (GDD) was required in both systems before 50% of the fruit was harvested. Fruit cracking, cat-facing, blossom-end rot, and insect damage were the major categories of defects in both systems. Incidence of both Tomato Spotted Wilt Virus (TSWV) and Gray Leaf Spot (GLS) were lower in the high tunnel compared with the field in 2007 and 2008, respectively. Results of this study suggest that with proper management techniques, high tunnels can optimize yields, increase fruit quality, and provide season extension opportunities for high-value horticultural crops. DA - 2012/9// PY - 2012/9// DO - 10.21273/hortsci.47.9.1283 VL - 47 IS - 9 SP - 1283-1290 SN - 2327-9834 KW - Solanum lycopersicum KW - greenhouse KW - season extension KW - plasticulture KW - hoop house KW - local markets KW - IPM ER - TY - JOUR TI - Height control of 'Hot Lips' Hybrid sage to flurprimidol substrate drench AU - Fair, B. A. AU - Whipker, B. AU - McCall, I. AU - Buhler, W. T2 - HortTechnology DA - 2012/// PY - 2012/// VL - 22 IS - 4 SP - 539-541 ER - TY - JOUR TI - Dry Storage Effects on Postharvest Performance of Selected Cut Flowers AU - Ahmad, Iftikhar AU - Dole, John M. AU - Amjad, Atyab AU - Ahmad, Sagheer T2 - HORTTECHNOLOGY AB - Effects of wet and dry storage methods were compared to improve postharvest performance of specialty cut flower species. While increasing duration of storage reduced vase life, vase life declined less with dry storage for marigold ( Tagetes erecta ) and rose ( Rosa hybrida ), but not for zinnia ( Zinnia elegans ) or lisianthus ( Eustoma grandiflorum ) over wet storage. Marigold stems had 1.9, 4.6, and 1.5 days longer vase life after 1, 2, or 3 weeks in dry storage, respectively, as compared with storage in water. Zinnia stems did not tolerate either wet or dry storage, while lisianthus stems had a longer vase life when stored in water as compared with dry storage. For rose, dry storage for 2 weeks increased vase life compared with wet storage. Dry stored marigold and lisianthus stems had higher water uptake after being placed in the vase as compared with the stems stored in water, while zinnia and rose had less uptake. Storage method had no effect on leaf relative water content (LRWC) in lisianthus, marigold, and zinnia; however, LRWC decreased with increased storage duration. This necessitates evaluation of storage method and duration effects for each species and cultivar to ensure extended storage life and improve postharvest quality. DA - 2012/8// PY - 2012/8// DO - 10.21273/horttech.22.4.463 VL - 22 IS - 4 SP - 463-469 SN - 1943-7714 KW - Eustoma grandiflorum KW - Rosa hybrida KW - specialty cut species KW - Tagetes erecta KW - vase life KW - Zinnia elegans ER - TY - JOUR TI - Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm AU - Verde, Ignazio AU - Bassil, Nahla AU - Scalabrin, Simone AU - Gilmore, Barbara AU - Lawley, Cynthia T. AU - Gasic, Ksenija AU - Micheletti, Diego AU - Rosyara, Umesh R. AU - Cattonaro, Federica AU - Vendramin, Elisa AU - Main, Dorrie AU - Aramini, Valeria AU - Blas, Andrea L. AU - Mockler, Todd C. AU - Bryant, Douglas W. AU - Wilhelm, Larry AU - Troggio, Michela AU - Sosinski, Bryon AU - Jose Aranzana, Maria AU - Arus, Pere AU - Iezzoni, Amy AU - Morgante, Michele AU - Peace, Cameron T2 - PLOS ONE AB - Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs.The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species. DA - 2012/4/20/ PY - 2012/4/20/ DO - 10.1371/journal.pone.0035668 VL - 7 IS - 4 SP - SN - 1932-6203 ER - TY - JOUR TI - A standard reaction condition and a single HPLC separation system are sufficient for estimation of monolignol biosynthetic pathway enzyme activities AU - Liu, Jie AU - Shi, Rui AU - Li, Quanzi AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - PLANTA DA - 2012/9// PY - 2012/9// DO - 10.1007/s00425-012-1688-9 VL - 236 IS - 3 SP - 879-885 SN - 0032-0935 KW - Monolignols KW - Enzyme activity KW - Populus trichocarpa KW - Pinus taeda KW - Angiosperm KW - Gymnosperm ER - TY - JOUR TI - eApples: A case study in using eXtension to increase access to research-based information AU - Hoover, E. E. AU - Marini, R. P. AU - Tepe, E. AU - Autio, W. R. AU - Biggs, A. R. AU - Clements, J. M. AU - Crassweller, R. M. AU - Foster, D. D. AU - Foster, M. J. AU - Hirst, P. M. AU - Miller, D. D. AU - Parker, M. L. AU - Peck, G. M. AU - Racsko, J. AU - Robinson, T. L. AU - Warmund, M. R. T2 - HortTechnology DA - 2012/// PY - 2012/// VL - 22 IS - 5 SP - 576-579 ER - TY - JOUR TI - Staminate Flower Production and Fusarium Wilt Reaction of Diploid Cultivars Used as Pollenizers for Triploid Watermelon AU - Gunter, Chris AU - Egel, Daniel S. T2 - HORTTECHNOLOGY AB - Several cultivars of nonharvested watermelon ( Citrullus lanatus ) pollenizers were compared for staminate flower production in field tests and disease reaction to fusarium wilt [ Fusarium oxysporum f. sp. Niveum (FON)] in both greenhouse and field tests. Differences were observed in staminate flower counts and fusarium wilt reactions in both years of field evaluations and to fusarium wilt among cultivars evaluated in the greenhouse. ‘SP-1’, ‘Sidekick’, and ‘5WDL 6146’ were the cultivars with high staminate flower counts in the field both years. These cultivars also were among the most resistant to fusarium wilt in both years of field tests. Significant correlations occurred between the rankings of the cultivar’s fusarium wilt reactions in both the two field and three greenhouse experiments, indicating a high degree of correlation between field and greenhouse tests. DA - 2012/10// PY - 2012/10// DO - 10.21273/horttech.22.5.694 VL - 22 IS - 5 SP - 694-699 SN - 1943-7714 KW - Citrullus lanatus KW - Fusarium oxysporum f. sp niveum KW - nonharvested KW - pollination KW - host resistance ER - TY - JOUR TI - Growth regulators improve the intercrossing rate of cucumber families for recurrent selection AU - Kumar, R. AU - Wehner, T. C. T2 - Crop Science DA - 2012/// PY - 2012/// VL - 52 IS - 5 SP - 2115-2120 ER - TY - JOUR TI - Assisting Farmers to Produce High-quality Medicinal Herbs AU - Davis, Jeanine M. T2 - HORTSCIENCE AB - Farmers are looking for new crops to grow to diversify their farms and increase profitability. Medicinal herbs are often of interest because they are generally perceived as being easy to grow, in high demand, return good prices, and serve as useful rotational crops. In reality, most farmers who have not previously grown medicinal herbs do not understand the global herb market. They do not know how to find a buyer or which herbs to grow. To help growers produce and market medicinal herbs, we initiated the Medicinal Herbs for Commerce Project. We also conducted studies on production problems for a variety of herbs. An issue that should be addressed is that there are hundreds of medicinal herbs in commerce and it is impossible for a small number of research programs to independently answer all the questions that are being asked by the industry. Developing a consortium of researchers around the world to coordinate efforts on how best to grow and process medicinal herbs and to create a database of information for farmers and agricultural advisors would be a great service for this industry. DA - 2012/8// PY - 2012/8// DO - 10.21273/hortsci.47.8.976 VL - 47 IS - 8 SP - 976-978 SN - 2327-9834 KW - Actaea racemosa KW - Allium tricoccum KW - botanical KW - Echinacea purpurea KW - Hydrastis canadensis KW - Sanguinaria canadensis ER - TY - JOUR TI - Cerebrospinal Fluid Metabolome in Mood Disorders-Remission State has a Unique Metabolic Profile AU - Kaddurah-Daouk, Rima AU - Yuan, Peixiong AU - Boyle, Stephen H. AU - Matson, Wayne AU - Wang, Zhi AU - Zeng, Zhao Bang AU - Zhu, Hongjie AU - Dougherty, George G. AU - Yao, Jeffrey K. AU - Chen, Guang AU - Guitart, Xavier AU - Carlson, Paul J. AU - Neumeister, Alexander AU - Zarate, Carlos AU - Krishnan, Ranga R. AU - Manji, Husseini K. AU - Drevets, Wayne T2 - Scientific Reports AB - Targeted metabolomics provides an approach to quantify metabolites involved in specific molecular pathways. We applied an electrochemistry-based, targeted metabolomics platform to define changes in tryptophan, tyrosine, purine and related pathways in the depressed and remitted phases of major depressive disorder (MDD). Biochemical profiles in the cerebrospinal fluid of unmedicated depressed (n = 14; dMDD) or remitted MDD subjects (n = 14; rMDD) were compared against those in healthy controls (n = 18; HC). The rMDD group showed differences in tryptophan and tyrosine metabolism relative to the other groups. The rMDD group also had higher methionine levels and larger methionine-to-glutathione ratios than the other groups, implicating methylation and oxidative stress pathways. The dMDD sample showed nonsignificant differences in the same direction in several of the metabolic branches assessed. The reductions in metabolites associated with tryptophan and tyrosine pathways in rMDD may relate to the vulnerability this population shows for developing depressive symptoms under tryptophan or catecholamine depletion. DA - 2012/9/19/ PY - 2012/9/19/ DO - 10.1038/srep00667 VL - 2 IS - 1 J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/srep00667 DB - Crossref ER - TY - JOUR TI - Simultaneous extraction and quantitation of carotenoids, chlorophylls, and tocopherols in brassica vegetables AU - Guzman, I. AU - Yousef, G. G. AU - Brown, A. F. T2 - Journal of Agricultural and Food Chemistry DA - 2012/// PY - 2012/// VL - 60 IS - 29 SP - 7238-7244 ER - TY - JOUR TI - Michael W. Neff, 25 years of service to ASHS AU - Davies, F. T. AU - Albrecht, M. L. AU - Bosland, P. AU - Clark, J. R. AU - De Vos, N. E. AU - Ingram, D. AU - Janick, J. AU - Lamont, W. J. AU - Lineberger, D. AU - Maynard, D. N. AU - Mitchell, C. A. AU - Ray, D. T. AU - Reed, D. AU - Sams, C. AU - Wilson, L. G. AU - Cantliffe, D. T2 - HortScience DA - 2012/// PY - 2012/// DO - 10.21273/hortsci.47.7.813 VL - 47 IS - 7 SP - 813-818 ER - TY - JOUR TI - High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding AU - Sim, Sung-Chur AU - Van Deynze, Allen AU - Stoffel, Kevin AU - Douches, David S. AU - Zarka, Daniel AU - Ganal, Martin W. AU - Chetelat, Roger T. AU - Hutton, Samuel F. AU - Scott, John W. AU - Gardner, Randolph G. AU - Panthee, Dilip R. AU - Mutschler, Martha AU - Myers, James R. AU - Francis, David M. T2 - PLOS ONE AB - The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F(st) supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage), particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F(st) outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD) was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization. DA - 2012/9/20/ PY - 2012/9/20/ DO - 10.1371/journal.pone.0045520 VL - 7 IS - 9 SP - SN - 1932-6203 ER - TY - JOUR TI - The peach genome AU - Arus, P. AU - Verde, I. AU - Sosinski, B. AU - Zhebentyayeva, T. AU - Abbott, A. G. T2 - Tree Genetics & Genomes DA - 2012/// PY - 2012/// VL - 8 IS - 3 SP - 531-547 ER - TY - JOUR TI - Magnitude of Genotype x Environment Interactions Affecting Tomato Fruit Quality AU - Panthee, Dilip R. AU - Cao, Chunxue AU - Debenport, Spencer J. AU - Rodriguez, Gustavo R. AU - Labate, Joanne A. AU - Robertson, Larry D. AU - Breksa, Andrew P., III AU - Knaap, Esther AU - Gardener, Brian B. McSpadden T2 - HORTSCIENCE AB - There is a growing interest by consumers to purchase fresh tomatoes with improved quality traits including lycopene, total soluble solids (TSS), vitamin C, and total titratable acid (TTA) content. As a result, there are considerable efforts by tomato breeders to improve tomato for these traits. However, suitable varieties developed for one location may not perform the same in different locations. This causes a problem for plant breeders because it is too labor-intensive to develop varieties for each specific location. The objective of this study was to determine the extent of genotype × environment (G×E) interaction that influences tomato fruit quality. To achieve this objective, we grew a set of 42 diverse tomato genotypes with different fruit shapes in replicated trials in three locations: North Carolina, New York, and Ohio. Fruits were harvested at the red ripe stage and analyzed for lycopene, TSS, vitamin C, and TTA. Analysis of variance (ANOVA) revealed that there were significant differences ( P < 0.05) among tomato genotypes, locations, and their interaction. Further analysis of quality traits from individual locations revealed that there was as much as 211% change in performance of some genotypes in a certain location compared with the average performance of a genotype. Lycopene was found to be most influenced by the environment, whereas TTA was the least influenced. This was in agreement with heritability estimates observed in the study for these quality traits, because heritability estimate for lycopene was 16%, whereas that for TTA was 87%. The extent of G×E interaction found for the fruit quality traits in the tomato varieties included in this study may be useful in identifying optimal locations for future field trials by tomato breeders aiming to improve tomato fruit quality. DA - 2012/6// PY - 2012/6// DO - 10.21273/hortsci.47.6.721 VL - 47 IS - 6 SP - 721-726 SN - 2327-9834 KW - heritability KW - lycopene KW - Solanum lycopersieum KW - total soluble solids KW - vitamin C ER - TY - JOUR TI - Grafting Tomato to Manage Bacterial Wilt Caused by Ralstonia solanacearum in the Southeastern United States AU - Rivard, C. L. AU - S. O'Connell, AU - Peet, M. M. AU - Welker, R. M. AU - Louws, F. J. T2 - PLANT DISEASE AB - Bacterial wilt, caused by Ralstonia solanacearum, can result in severe losses to tomato (Solanum lycopersicum) growers in the southeastern United States, and grafting with resistant rootstocks may be an effective strategy for managing this disease. However, R. solanacearum populations maintain considerable diversity, and little information is known regarding the efficacy of commercially available rootstocks to reduce bacterial wilt incidence and subsequent crop loss in the United States. In this study, tomato plants grafted onto 'Dai Honmei' and 'RST-04-105-T' rootstocks had significantly lower area under the disease progress curve (AUDPC) values compared with nongrafted plants (P < 0.05). Across three locations in North Carolina, final bacterial wilt incidence for non- and self-grafted plants was 82 ± 14 to 100%. In contrast, bacterial wilt incidence for the grafted plants was 0 to 65 ± 21%. Final bacterial wilt incidence of plants grafted with Dai Honmei rootstock was 0 and 13 ± 3% at two locations in western North Carolina but 50 ± 3% at a third site in eastern North Carolina. Similarly, grafting onto RST-04-105-T rootstock significantly reduced AUDPC values at two of the three locations (P < 0.05) compared with that of the nongrafted plants, but performed poorly at the third site. Total fruit yields were significantly increased by grafting onto resistant rootstocks at all three sites (P < 0.05). Regression analyses indicated that yield was significantly negatively correlated with bacterial wilt AUDPC values (R2 was 0.4048 to 0.8034), and the use of resistant rootstocks enabled economically viable tomato production in soils naturally infested with R. solanacearum. DA - 2012/7// PY - 2012/7// DO - 10.1094/pdis-12-10-0877 VL - 96 IS - 7 SP - 973-978 SN - 1943-7692 ER - TY - JOUR TI - Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies AU - Jung, S. AU - Cestaro, A. AU - Troggio, M. AU - Main, D. AU - Zheng, P. AU - Cho, I. AU - Folta, K. M. AU - Sosinski, B. AU - Abbott, A. AU - Celton, J. M. AU - Arus, P. AU - Shulaev, V. AU - Verde, I. AU - Morgante, M. AU - Rokhsar, D. AU - Velasco, R. AU - Sargent, D. J. T2 - BMC Genomics AB - Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes.Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes.Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae. DA - 2012/// PY - 2012/// DO - 10.1186/1471-2164-13-129 VL - 13 ER - TY - JOUR TI - Survey of Nutrient Status in Vitis vinifera Grapes in North Carolina AU - Havlin, J. L. AU - Hardy, D. H. AU - Gehl, R. J. AU - Spayd, S. E. T2 - COMMUNICATIONS IN SOIL SCIENCE AND PLANT ANALYSIS AB - Grape (Vitis vinifera L.) production is a rapidly growing industry in North Carolina; however, no local-research-based information is available to support nutrient-management decisions. Field studies were initiated to survey soil and plant nutrient status over a wide range in geography and management conditions in the dominant V. vinifera regions in North Carolina. While the survey data are still being analyzed, significant information was initially obtained to identify aluminum toxicity and phosphorus and potassium deficiency as potential limiting factors to vine health and productivity. Field studies were initiated to quantify soil test and plant nutrient responses to lime, phosphorus, and potassium rates. Responses to phosphorus and potassium application were observed at most sites predicted by soil tests. However, lime responses were not observed in either petiole or blade samples collected at full bloom or veraison. These studies will be continued until sufficient response data are collected to establish soil test and plant nutrient diagnostic criteria for efficient nutrient management of V. vinifera in North Carolina. DA - 2012/// PY - 2012/// DO - 10.1080/00103624.2011.638600 VL - 43 IS - 1-2 SP - 299-314 SN - 0010-3624 KW - Nutrient management KW - soil fertility KW - wine grapes ER - TY - JOUR TI - Merging pharmacometabolomics with pharmacogenomics using ‘1000 Genomes’ single-nucleotide polymorphism imputation AU - Abo, Ryan AU - Hebbring, Scott AU - Ji, Yuan AU - Zhu, Hongjie AU - Zeng, Zhao-Bang AU - Batzler, Anthony AU - Jenkins, Gregory D. AU - Biernacka, Joanna AU - Snyder, Karen AU - Drews, Maureen AU - Fiehn, Oliver AU - Fridley, Brooke AU - Schaid, Daniel AU - Kamatani, Naoyuki AU - Nakamura, Yusuke AU - Kubo, Michiaki AU - Mushiroda, Taisei AU - Kaddurah-Daouk, Rima AU - Mrazek, David A. AU - Weinshilboum, Richard M. T2 - Pharmacogenetics and Genomics AB - Objective We set out to test the hypothesis that pharmacometabolomic data could be efficiently merged with pharmacogenomic data by single-nucleotide polymorphism (SNP) imputation of metabolomic-derived pathway data on a ‘scaffolding’ of genome-wide association (GWAS) SNP data to broaden and accelerate ‘pharmacometabolomics-informed pharmacogenomic’ studies by eliminating the need for initial genotyping and by making broader SNP association testing possible. Methods We previously genotyped 131 tag SNPs for six genes encoding enzymes in the glycine synthesis and degradation pathway using DNA from 529 depressed patients treated with citalopram/escitalopram to pursue a glycine metabolomics ‘signal’ associated with selective serotonine reuptake inhibitor response. We identified a significant SNP in the glycine dehydrogenase gene. Subsequently, GWAS SNP data were generated for the same patients. In this study, we compared SNP imputation within 200 kb of these same six genes with the results of the previous tag SNP strategy as a rapid strategy for merging pharmacometabolomic and pharmacogenomic data. Results Imputed genotype data provided greater coverage and higher resolution than did tag SNP genotyping, with a higher average genotype concordance between genotyped and imputed SNP data for ‘1000 Genomes’ (96.4%) than HapMap 2 (93.2%) imputation. Many low P-value SNPs with novel locations within genes were observed for imputed compared with tag SNPs, thus altering the focus for subsequent functional genomic studies. Conclusion These results indicate that the use of GWAS data to impute SNPs for genes in pathways identified by other ‘omics’ approaches makes it possible to rapidly and cost efficiently identify SNP markers to ‘broaden’ and accelerate pharmacogenomic studies. DA - 2012/4// PY - 2012/4// DO - 10.1097/fpc.0b013e32835001c9 VL - 22 IS - 4 SP - 247-253 J2 - Pharmacogenetics and Genomics LA - en OP - SN - 1744-6872 UR - http://dx.doi.org/10.1097/FPC.0b013e32835001c9 DB - Crossref KW - 1000 Genomes KW - HapMap KW - imputation KW - major depressive disorder KW - pharmacometabolomics KW - pharmacogenomics KW - selective serotonin reuptake inhibitors KW - tag single-nucleotide polymorphisms ER - TY - JOUR TI - Comparison of Flavonoid Composition of Red Raspberries (Rubus idaeus L.) Grown in the Southern United States AU - Bradish, Christine M. AU - Perkins-Veazie, Penelope AU - Fernandez, Gina E. AU - Xie, Guoxiang AU - Jia, Wei T2 - JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY AB - Raspberry flavonoid compounds have significant antioxidant activities, and regular consumption may help prevent and/or moderate chronic diseases. Targeted metabolite profiling is useful to identify compounds contributing to these antioxidant properties and health benefits and for tailored breeding for functional foods. In this study, metabolomic variation was determined among three fall-fruiting red raspberry cultivars ('Autumn Britten', 'Caroline', 'Nantahala') grown at three North Carolina locations differing in elevation and average day/night temperatures. 'Nantahala' was specifically bred for the mountainous regions of the southern United States. Ten flavonoid compounds were detected by liquid chromatography-time-of-flight-mass spectrometry (LC-TOF-MS). Of those, cyanidin-3-glucoside, cyanidin-3-sophoroside, cyanidin-3-rutinoside, cyanidin-3-sambubioside, and quercetin-3-glucoside were quantified against external standards. Variation in flavonoid composition was primarily attributed to genotype and associated with night temperature and hours exposed to temperatures over 29 °C. 'Nantahala' had particularly high levels of cyanidin-3-sambubioside, indicative of its purple raspberry lineage. Quercetin-3-glucoside levels increased the most with elevated temperatures. DA - 2012/6/13/ PY - 2012/6/13/ DO - 10.1021/jf203474e VL - 60 IS - 23 SP - 5779-5786 SN - 1520-5118 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84862185617&partnerID=MN8TOARS KW - raspberries KW - Rubus idaeus KW - anthocyanins KW - antioxidant capacity KW - FRAP KW - LC-MS KW - LC-TOF-MS KW - phenolics KW - flavonoids KW - PCA KW - targeted metabolite profiling ER - TY - JOUR TI - A reexamination of molecular markers for use in marker-assisted breeding in tomato (Retracted article. See vol. 194, pg. 149, 2013) AU - Panthee, Dilip R. AU - Foolad, Majid R. T2 - EUPHYTICA DA - 2012/3// PY - 2012/3// DO - 10.1007/s10681-011-0544-5 VL - 184 IS - 2 SP - 165-179 SN - 1573-5060 KW - Disease resistance KW - Marker validation KW - Molecular breeding KW - Molecular markers KW - Solanum lycopersicum ER - TY - JOUR TI - A rapid qualitative molecular method for the identification of Colletotrichum acutatum and C. gloeosporioides AU - Liu, Bo AU - Louws, Frank J. AU - Sutton, Turner B. AU - Correll, James C. T2 - EUROPEAN JOURNAL OF PLANT PATHOLOGY DA - 2012/4// PY - 2012/4// DO - 10.1007/s10658-011-9904-1 VL - 132 IS - 4 SP - 593-607 SN - 1573-8469 KW - Rapid identification KW - Diagnosis KW - C. acutatum KW - C. gloeosporioides KW - Glutamine synthetase (GS) gene KW - Restriction enzyme digestion ER - TY - JOUR TI - A Novel Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) Promoter for Expressing Transgenes in the Halotolerant Alga Dunaliella salina AU - Jia, Yanlong AU - Li, Shenke AU - Allen, George AU - Feng, Shuying AU - Xue, Lexun T2 - CURRENT MICROBIOLOGY DA - 2012/5// PY - 2012/5// DO - 10.1007/s00284-012-0102-y VL - 64 IS - 5 SP - 506-513 SN - 0343-8651 ER - TY - JOUR TI - Vaccinium species of section Hemimyrtillus: their value to cultivated blueberry and approaches to utilization AU - Ehlenfeldt, M. K. AU - Ballington, J. R. T2 - Botany = Botanique DA - 2012/// PY - 2012/// VL - 90 IS - 5 SP - 347-353 ER - TY - JOUR TI - Genetic Variation for Potato Tuber Micronutrient Content and Implications for Biofortification of Potatoes to Reduce Micronutrient Malnutrition AU - Haynes, K. G. AU - Yencho, G. C. AU - Clough, M. E. AU - Henninger, M. R. AU - Sterrett, S. B. T2 - AMERICAN JOURNAL OF POTATO RESEARCH DA - 2012/6// PY - 2012/6// DO - 10.1007/s12230-012-9242-7 VL - 89 IS - 3 SP - 192-198 SN - 1874-9380 KW - Copper KW - Iron KW - Manganese KW - Zinc KW - Nutrition ER - TY - JOUR TI - Estimation of heritability of benzoxazinoid production in rye (Secale cereale) using gas chromatographic analysis AU - Brooks, Ashley M. AU - Danehower, David A. AU - Murphy, J. Paul AU - Reberg-Horton, S. Chris AU - Burton, James D. T2 - PLANT BREEDING AB - With 4 tables Abstract The 2,4‐dihydroxy‐1,4‐benzoxazin‐3‐one (DIBOA) content of Secale cereale is strongly associated with allelopathy. This has led to interest in developing allelopathic cultivars with increased DIBOA to improve weed control in this important cover crop. Objectives of this study were to determine heritability estimates for DIBOA in rye and determine the utility of gas chromatography (GC) as a screening tool in a rye allelopathy breeding programme. A synthetic population of half‐sib families varying in production of DIBOA was analysed. DIBOA concentrations ranged from 0.52 to 1.15 mg/g dwt tissue (mean = 0.70 mg/g dwt). Analysis of variance indicated significant variability for DIBOA content in rye harvested at the flag leaf stage. Year × location × genotype and block (year × location) interactions were also significant. Several genotypes were consistently ‘high’ or ‘low’ DIBOA producers across all locations and years. Narrow sense heritability estimates were 0.18 ± 0.04 SE on a per plot basis and 0.57 ± 0.07 SE on an entry mean basis. GC analysis was determined to be a good system for moderate throughput screening of lines. DA - 2012/2// PY - 2012/2// DO - 10.1111/j.1439-0523.2011.01885.x VL - 131 IS - 1 SP - 104-109 SN - 1439-0523 KW - Secale cereale KW - allelopathy KW - DIBOA KW - benzoxazinoid KW - heritability ER - TY - JOUR TI - Early generation selection at multiple locations may identify potato parents that produce more widely adapted progeny AU - Haynes, K. G. AU - Gergela, D. M. AU - Hutchinson, C. M. AU - Yencho, G. C. AU - Clough, M. E. AU - Henninger, M. R. AU - Halseth, D. E. AU - Sandsted, E. AU - Porter, G. A. AU - Ocaya, P. C. AU - al. T2 - EUPHYTICA DA - 2012/7// PY - 2012/7// DO - 10.1007/s10681-012-0685-1 VL - 186 IS - 2 SP - 573-583 SN - 0014-2336 KW - Potato KW - Solanum tuberosum KW - Genotype x environment interaction KW - Broad adaptation KW - Superior parents ER - TY - JOUR TI - Winter Grain-Short Season Corn Double Crop Forage Production for New England AU - Jemison, John M. AU - Darby, Heather M. AU - Reberg-Horton, S. Chris T2 - Agronomy Journal; Madison AB - Alternative organic forage systems that provide high quality feed and low weed pressure are required to improve farm viability. Five site‐year locations of research were conducted in Stillwater, ME and Alburgh, VT to evaluate winter grain–short season corn (WGSSC) double crops compared to full season corn (FSC) ( Zea mays L.) for dry matter yield (DMY), weed biomass, and forage quality. Small grains evaluated in the study included winter barley (WB) ( Hordeum vulgare L.), triticale (TC) (X Triticosecale ), and winter wheat (WW) ( Triticum aestivum L.). Low degree‐day open‐pollinated and hybrid corns were planted following cereal boot or soft dough stage harvest and were evaluated relative to FSC. A moderately winterkilled WB stand reduced DMY by 33 to 50% relative to TC and WW, and WB was weakly competitive against weeds. In most measures, WB forage quality was significantly higher than TC or WW. Delaying harvest to soft dough stage nearly doubled small grain DMY and forage quality yield for most measures. Corn planted after boot stage grain harvest produced 1700 kg ha −1 greater DMY than later planted corn, but weed biomass was not significantly affected by planting date. Forage quality and forage quality yield were approximately 15% greater for corn planted after boot stage harvest. Dense TC and WW stands reduced weed biomass by 300% relative to WB‐corn double crop. Highest forage quality/yield was found with soft‐dough stage WB–corn double crop. Double crop forage systems can reduce environmental risk and lower organic dairy production costs, and provide high yielding, high quality feed. DA - 2012/3// PY - 2012/3// DO - 10.2134/agronj2011.0275 VL - 104 IS - 2 SP - 256-264 LA - English SN - 00021962 UR - https://search.proquest.com/docview/1001213755/citation/F53DED1B14C945D0PQ/1 DB - ProQuest Y2 - 2019/2/7/ ER - TY - JOUR TI - Simple Sequence Repeat Markers from Cercis canadensis Show Wide Cross-species Transfer and Use in Genetic Studies AU - Wadl, Phillip A. AU - Trigiano, Robert N. AU - Werner, Dennis J. AU - Pooler, Margaret R. AU - Rinehart, Timothy A. T2 - JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE AB - There are 11 recognized Cercis L. species, but identification is problematic using morphological characters, which are largely quantitative and continuous. Previous studies have combined morphological and molecular data to resolve taxonomic questions about geographic distribution of Cercis species, identifying botanical varieties, and associations between morphological variation and the environment. Three species have been used in ornamental plant breeding in the United States, including three botanical varieties of C. canadensis L. from North America and two Asian species, C. chingii Chun and C. chinensis Bunge. In this article, 51 taxa were sampled comprising eight species of Cercis and a closely related species, Bauhinia faberi Oliv. Sixty-eight polymorphic simple sequence repeat markers were used to assess genetic relationships between species and cultivars. For all samples the number of alleles detected ranged from two to 20 and 10 or more alleles were detected at 22 loci. Average polymorphic information content was 0.57 and values ranged from 0.06 to 0.91 with 44 loci 0.50 or greater. Cross-species transfer within Cercis was extremely high with 55 loci that amplified at 100%. Results support previously reported phylogenetic relationships of the North American and western Eurasian species and indicate suitability of these markers for mapping studies involving C. canadensis and C. chinensis . Results also support known pedigrees from ornamental tree breeding programs for the widely cultivated C. canadensis and C. chinensis species, which comprised the majority of the samples analyzed. DA - 2012/5// PY - 2012/5// DO - 10.21273/jashs.137.3.189 VL - 137 IS - 3 SP - 189-201 SN - 0003-1062 KW - microsatellites KW - redbud KW - SSR KW - woody ornamental tree ER - TY - JOUR TI - Marker-Assisted Selection in Tomato Breeding AU - Foolad, Majid R. AU - Panthee, Dilip R. T2 - CRITICAL REVIEWS IN PLANT SCIENCES AB - The cultivated tomato, Solanum lycopersicum L., is the second most consumed vegetable crop after potato and unquestionably the most popular garden crop in the world. There are more varieties of tomato sold worldwide than any other vegetable crop. Most of the commercial cultivars of tomato have been developed through phenotypic selection and traditional breeding. However, with the advent of molecular markers and marker-assisted selection (MAS) technology, tomato genetics and breeding research has entered into a new and exciting era. Molecular markers have been used extensively for genetic mapping as well as identification and characterization of genes and QTLs for many agriculturally important traits in tomato, including disease and insect resistance, abiotic stress tolerance, and flower- and fruit-related characteristics. The technology also has been utilized for marker-assisted breeding for several economically important traits, in particular disease resistance. However, the extent to which MAS has been employed in public and private tomato breeding programs has not been clearly determined. The objectives of this study were to review the publically-available molecular markers for major disease resistance traits in tomato and assess their current and potential use in public and private tomato breeding programs. A review of the literature indicated that although markers have been identified for most disease resistance traits in tomato, not all of them have been verified or are readily applicable in breeding programs. For example, many markers are not validated across tomato genotypes or are not polymorphic within tomato breeding populations, thus greatly reducing their utility in crop improvement programs. However, there seems to be a considerable use of markers, particularly in the private sector, for various purposes, including testing hybrid purity, screening breeding populations for disease resistance, and marker assisted backcross breeding. Here we provide a summary of molecular markers available for major disease resistance traits in tomato and discuss their actual use in tomato breeding programs. It appears that many of the available markers may need to be further refined or examined for trait association and presence of polymorphism in breeding populations. However, with the recent advances in tomato genome and transcriptome sequencing, it is becoming increasingly possible to develop new and more informative PCR-based markers, including single nucleotide polymorphisms (SNPs), to further facilitate the use of markers in tomato breeding. It is also expected that more markers will become available via the emerging technology of genotyping by sequencing (GBS). DA - 2012/// PY - 2012/// DO - 10.1080/07352689.2011.616057 VL - 31 IS - 2 SP - 93-123 SN - 1549-7836 KW - disease resistance KW - molecular breeding KW - molecular markers KW - QTL KW - Solanum lycopersicum KW - stress tolerance KW - tomato breeding ER - TY - JOUR TI - Tomato spotted wilt virus-resistant fresh-market tomato breeding lines: NC 58S, NC 123S, NC 127S, and NC 132S AU - Gardner, R. G. AU - Panthee, D. R. T2 - HortScience DA - 2012/// PY - 2012/// VL - 47 IS - 4 SP - 531-532 ER - TY - JOUR TI - Substrate drenches containing flurprimidol suppress height of 'Nellie White' Easter lilies AU - Currey, C. J. AU - Lopez, R. G. AU - Krug, B. A. AU - McCall, I. AU - Whipker, B. E. T2 - HortTechnology DA - 2012/// PY - 2012/// VL - 22 IS - 2 SP - 164-168 ER - TY - JOUR TI - Requirement for pollenizer in new monoecious hybrid cucumber 'NC-Sunshine' AU - Wehner, T. C. AU - Kumar, R. T2 - HortTechnology DA - 2012/// PY - 2012/// VL - 22 IS - 2 SP - 191-195 ER - TY - JOUR TI - Quantitative determination of the representative triterpenoids in the extracts of Ganoderma lucidum with different growth stages using high-performance liquid chromatography for evaluation of their 5 alpha-reductase inhibitory properties AU - Liu, Jie AU - Kurashiki, Kenji AU - Fukuta, Atsuko AU - Kaneko, Shuhei AU - Suimi, Yoshitaro AU - Shimizu, Kuniyoshi AU - Kondo, Ryuichiro T2 - FOOD CHEMISTRY AB - For quantitative determination of 5 triterpenoid constituents, including one ganoderma alcohol (ganodermatriol) and four ganoderma acids (ganoderic acid TR, DM, A, and D), in the products of Ganoderma lucidum, an analytical system was developed using high-performance liquid chromatography. The mobile phase was a linear gradient of 2% AcOH/H2O–CH3CN, and the elution profile was monitored at 243 and 252 nm for ganoderma alcohols and acids, respectively. This system was applied to a quantitative determination of the constituents in the different stage of G. lucidum (BMC9049 strain). The analytical results indicated that the quantity and composition of these triterpenoids differed appreciably among various stages. The stage that showed the highest concentration of ganoderic acid DM and TR also showed the strongest 5α-reductase inhibitory activity. This stage (stage 5 of 6) is thus the prime stage for harvesting this strain. Further, the contents of 5α-reductase inhibitors such as ganoderic acid TR and DM in G. lucidum extracts could be a very useful indicator to assess their 5α-reductase inhibitory activity and verify their potency. DA - 2012/8/1/ PY - 2012/8/1/ DO - 10.1016/j.foodchem.2012.01.034 VL - 133 IS - 3 SP - 1034-1038 SN - 1873-7072 KW - Triterpenoids KW - Ganoderma lucidum KW - 5 alpha-Reductase inhibition KW - Growth stage KW - HPLC analysis ER - TY - JOUR TI - Comparison of the effects of metamitron on chlorophyll fluorescence and fruit set in apple and peach AU - McArtney, S. J. AU - Obermiller, J. D. AU - Arellano, C. T2 - HortScience DA - 2012/// PY - 2012/// VL - 47 IS - 4 SP - 509-514 ER - TY - JOUR TI - Genetic Evidence for an Indispensable Role of Somatic Embryogenesis Receptor Kinases in Brassinosteroid Signaling AU - Gou, Xiaoping AU - Yin, Hongju AU - He, Kai AU - Du, Junbo AU - Yi, Jing AU - Xu, Shengbao AU - Lin, Honghui AU - Clouse, Steven D. AU - Li, Jia T2 - PLOS GENETICS AB - The Arabidopsis thaliana somatic embryogenesis receptor kinases (SERKs) consist of five members, SERK1 to SERK5, of the leucine-rich repeat receptor-like kinase subfamily II (LRR-RLK II). SERK3 was named BRI1-Associated Receptor Kinase 1 (BAK1) due to its direct interaction with the brassinosteroid (BR) receptor BRI1 in vivo, while SERK4 has also been designated as BAK1-Like 1 (BKK1) for its functionally redundant role with BAK1. Here we provide genetic and biochemical evidence to demonstrate that SERKs are absolutely required for early steps in BR signaling. Overexpression of four of the five SERKs-SERK1, SERK2, SERK3/BAK1, and SERK4/BKK1-suppressed the phenotypes of an intermediate BRI1 mutant, bri1-5. Overexpression of the kinase-dead versions of these four genes in the bri1-5 background, on the other hand, resulted in typical dominant negative phenotypes, resembling those of null BRI1 mutants. We isolated and generated single, double, triple, and quadruple mutants and analyzed their phenotypes in detail. While the quadruple mutant is embryo-lethal, the serk1 bak1 bkk1 triple null mutant exhibits an extreme de-etiolated phenotype similar to a null bri1 mutant. While overexpression of BRI1 can drastically increase hypocotyl growth of wild-type plants, overexpression of BRI1 does not alter hypocotyl growth of the serk1 bak1 bkk1 triple mutant. Biochemical analysis indicated that the phosphorylation level of BRI1 in serk1 bak1 bkk1 is incapable of sensing exogenously applied BR. As a result, the unphosphorylated level of BES1 has lost its sensitivity to the BR treatment in the triple mutant, indicating that the BR signaling pathway has been completely abolished in the triple mutant. These data clearly demonstrate that SERKs are essential to the early events of BR signaling. DA - 2012/1// PY - 2012/1// DO - 10.1371/journal.pgen.1002452 VL - 8 IS - 1 SP - SN - 1553-7390 ER - TY - JOUR TI - Utilizing cover crop mulches to reduce tillage in organic systems in the southeastern USA AU - Reberg-Horton, S. Chris AU - Grossman, Julie M. AU - Kornecki, Ted S. AU - Meijer, Alan D. AU - Price, Andrew J. AU - Place, George T. AU - Webster, Theodore M. T2 - RENEWABLE AGRICULTURE AND FOOD SYSTEMS AB - Abstract Organic systems in the southeastern USA offer unique challenges and solutions to crop production due to regional soil and climate characterized by highly weathered soil types, high precipitation and the capacity to grow cover crops in the winter. Recently, the interest of producers and researchers in high-residue cover crops and conservation tillage systems has increased. Various designs of the roller–crimper to manage cover crops have been invented and demonstrated to growers in the southeastern region of the USA over the past 17 years. The impacts of high-residue cover crop mulches on the agronomic systems in the region are diverse. Legume cover crops assist with meeting N demand from cash crops though they decompose rapidly and are seldom sufficient for N demanding crops such as corn. Cereal cover crop mulches can have the opposite effect by immobilizing N and have a longer impact on soil moisture and weed dynamics. While undesirable for many crops, N immobilization is one possible mechanism for weed suppression in legume cash crops planted into cereal residues. Other cover crop weed suppression mechanisms include physical impedance, light availability, allelopathy and microclimate effects. Regardless of the cause, successful weed control by mulches is highly dependent on having substantial biomass. The southeastern region is capable of producing cover crop biomass in excess of 9000 kg ha −1 , which is sufficient for weed control in many cash crops, although supplementary weed control is sometimes necessary. Long-term data are needed to predict when farmers should add supplementary weed control. More work is also needed on how much additional N is required for the cash crops and how best to deliver that N in a high-residue environment using organic sources. DA - 2012/3// PY - 2012/3// DO - 10.1017/s1742170511000469 VL - 27 IS - 1 SP - 41-48 SN - 1742-1713 KW - roller-crimper KW - organic KW - no-till ER - TY - JOUR TI - Overview and comparison of conservation tillage practices and organic farming in Europe and North America AU - Carr, P. M. AU - Mader, P. AU - Creamer, N. G. AU - Beeby, J. S. T2 - Renewable Agriculture and Food Systems DA - 2012/// PY - 2012/// VL - 27 IS - 1 SP - 2-6 ER - TY - JOUR TI - Deactivation of the Arabidopsis BRASSINOSTEROID INSENSITIVE 1 (BRI1) receptor kinase by autophosphorylation within the glycine-rich loop AU - Oh, Man-Ho AU - Wang, Xiaofeng AU - Clouse, Steven D. AU - Huber, Steven C. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - The activity of the dual-specificity receptor kinase, brassinosteroid insensitive 1 (BRI1), reflects the balance between phosphorylation-dependent activation and several potential mechanisms for deactivation of the receptor. In the present report, we elucidate a unique mechanism for deactivation that involves autophosphorylation of serine-891 in the ATP-binding domain. Serine-891 was identified previously as a potential site of autophosphorylation by mass spectrometry, and sequence-specific antibodies and mutagenesis studies now unambiguously establish phosphorylation of this residue. In vivo, phosphorylation of serine-891 increased slowly with time following application of brassinolide (BL) to Arabidopsis seedlings, whereas phosphorylation of threonine residues increased rapidly and then remained constant. Transgenic plants expressing the BRI1(S891A)-Flag-directed mutant have increased hypocotyl and petiole lengths, relative to wild-type BRI1-Flag (both in the bri1-5 background), and accumulate higher levels of the unphosphorylated form of the BES1 transcription factor in response to exogenous BL. In contrast, plants expressing the phosphomimetic S891D-directed mutant are severely dwarfed and do not accumulate unphosphorylated BES1 in response to BL. Collectively, these results suggest that autophosphorylation of serine-891 is one of the deactivation mechanisms that inhibit BRI1 activity and BR signaling in vivo. Many arginine-aspartate (RD)-type leucine-rich repeat receptor-like kinases have a phosphorylatable residue within the ATP-binding domain, suggesting that this mechanism may play a broad role in receptor kinase deactivation. DA - 2012/1/3/ PY - 2012/1/3/ DO - 10.1073/pnas.1108321109 VL - 109 IS - 1 SP - 327-332 SN - 0027-8424 KW - phosphotyrosine KW - signal transduction KW - phosphoserine KW - modification-specific antibodies ER - TY - JOUR TI - Screening cucumber for resistance to downy mildew caused by Pseudoperonospora cubensis (Berk. And Curt.) Rostov. AU - Call, A. D. AU - Criswell, A. D. AU - Weimer, T. C. AU - Klosinska, U. AU - Kozik, E. U. T2 - Crop Science DA - 2012/// PY - 2012/// VL - 52 IS - 2 SP - 577-592 ER - TY - JOUR TI - Resistance of Cucumber Cultivars to a New Strain of Cucurbit Downy Mildew AU - Call, Adam D. AU - Criswell, Adam D. AU - Wehner, Todd C. AU - Ando, Kaori AU - Grumet, Rebecca T2 - HORTSCIENCE AB - Downy mildew, a foliar disease caused by the oomycete Pseudoperonospora cubensis (Berk. and Curt.) Rostow, is one of the most destructive pathogens of cucurbits. From 1961 to 2003, resistant cucumber cultivars in the United States had sufficient resistance to grow a successful crop without the use of fungicides. The pathogen resurged as a major problem in 2004. Since then, the dm-1 gene has not been effective against the new strain of downy mildew, and yield losses are high without the use of fungicides. The objective of this experiment was to identify cultivars having high yield and resistance to the new downy mildew. The experiment had 86 cultivars and breeding lines (hereafter collectively referred to as cultigens) and was conducted in Clinton, NC, in 2007 and 2009, in Castle Hayne, NC, in 2008 and 2009, and in Bath, MI, in 2007 to 2009. Plots were rated weekly on a 0 to 9 scale (0 = none, 1–2 = trace, 3–4 = slight, 5–6 = moderate, 7–8 = severe, and 9 = dead). Mean ratings for downy mildew leaf damage ranged from 2.9 to 5.7 in Michigan in 2008 and 2009 and from 3.8 to 6.8 in North Carolina in 2007 to 2009. None of the cultigens tested in this study showed a high level of resistance, although differences in resistance were detected. Lines WI 2757 and M 21 and cultivar Picklet were consistently among the top resistant lines in North Carolina and Michigan. The cultivars Coolgreen, Wis. SMR 18, and Straight 8 were identified as moderately to highly susceptible. An unreleased hybrid, ‘Nun 5053 F1’, and the cultivar Cates were the top yielding lines overall. The highest yield in a single year and location was from the cultivar Cates in Clinton, NC, in 2009, with 25.6 Mg·ha −1 . The best cultivars in this study were only moderately resistant and would likely require fungicide applications to achieve high yield and quality in the presence of downy mildew. Until high resistance becomes available, growers would benefit by using fungicides in combination with tolerant and moderately resistant cultigens. DA - 2012/2// PY - 2012/2// DO - 10.21273/hortsci.47.2.171 VL - 47 IS - 2 SP - 171-178 SN - 0018-5345 KW - Cucumis satvus KW - disease KW - Pseudoperonospora cubensis ER - TY - BOOK TI - Greenhouse operation and management AU - Nelson, P. V. DA - 2012/// PY - 2012/// PB - Boston: Prentice Hall ER - TY - JOUR TI - 'Mountain Magic': An early blight and late blight-resistant specialty type F-1 hybrid tomato AU - Gardner, R. G. AU - Panthee, D. R. T2 - HortScience DA - 2012/// PY - 2012/// VL - 47 IS - 2 SP - 299-300 ER -