@article{pascuzzi_flores-vergara_lee_sosinski_vaughn_hanley-bowdoin_thompson_allen_2014, title={In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts}, volume={26}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.113.121194}, abstractNote={This work uses tiling microarrays to map S/MARs on Arabidopsis chromosome 4. S/MARs were found to be spaced more closely than in the large plant and animal genomes studied to date and preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation. Most S/MARs occur near gene transcription start sites, and these genes show an increased probability of expression. Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function.}, number={1}, journal={PLANT CELL}, author={Pascuzzi, Pete E. and Flores-Vergara, Miguel A. and Lee, Tae-Jin and Sosinski, Bryon and Vaughn, Matthew W. and Hanley-Bowdoin, Linda and Thompson, William F. and Allen, George C.}, year={2014}, month={Jan}, pages={102–120} }
 @article{molina-bravo_fernandez_sosinski_2014, title={Quantitative trait locus analysis of tolerance to temperature fluctuations in winter, fruit characteristics, flower color, and prickle-free canes in raspberry}, volume={33}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-013-9947-4}, number={2}, journal={MOLECULAR BREEDING}, author={Molina-Bravo, Ramon and Fernandez, Gina E. and Sosinski, Bryon R.}, year={2014}, month={Feb}, pages={267–280} }
 @article{verde_abbott_scalabrin_jung_shu_marroni_zhebentyayeva_dettori_grimwood_cattonaro_et al._2013, title={The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution}, volume={45}, ISSN={["1061-4036"]}, DOI={10.1038/ng.2586}, abstractNote={Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.}, number={5}, journal={NATURE GENETICS}, author={Verde, Ignazio and Abbott, Albert G. and Scalabrin, Simone and Jung, Sook and Shu, Shengqiang and Marroni, Fabio and Zhebentyayeva, Tatyana and Dettori, Maria Teresa and Grimwood, Jane and Cattonaro, Federica and et al.}, year={2013}, month={May}, pages={487–U47} }
 @article{verde_bassil_scalabrin_gilmore_lawley_gasic_micheletti_rosyara_cattonaro_vendramin_et al._2012, title={Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0035668}, abstractNote={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.}, number={4}, journal={PLOS ONE}, author={Verde, Ignazio and Bassil, Nahla and Scalabrin, Simone and Gilmore, Barbara and Lawley, Cynthia T. and Gasic, Ksenija and Micheletti, Diego and Rosyara, Umesh R. and Cattonaro, Federica and Vendramin, Elisa and et al.}, year={2012}, month={Apr} }
 @misc{arus_verde_sosinski_zhebentyayeva_abbott_2012, title={The peach genome}, volume={8}, number={3}, journal={Tree Genetics & Genomes}, author={Arus, P. and Verde, I. and Sosinski, B. and Zhebentyayeva, T. and Abbott, A. G.}, year={2012}, pages={531–547} }
 @article{jung_cestaro_troggio_main_zheng_cho_folta_sosinski_abbott_celton_et al._2012, title={Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies}, volume={13}, DOI={10.1186/1471-2164-13-129}, abstractNote={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.}, journal={BMC Genomics}, author={Jung, S. and Cestaro, A. and Troggio, M. and Main, D. and Zheng, P. and Cho, I. and Folta, K. M. and Sosinski, B. and Abbott, A. and Celton, J. M. and et al.}, year={2012} }
 @article{molina-bravo_arellano_sosinski_fernandez_2011, title={A protocol to assess heat tolerance in a segregating population of raspberry using chlorophyll fluorescence}, volume={130}, ISSN={["1879-1018"]}, DOI={10.1016/j.scienta.2011.07.022}, abstractNote={A detached leaf protocol was developed to assess heat tolerance in raspberry (Rubus L. subgenus Idaeobatus) by measuring chlorophyll fluorescence. In order to establish the heat screen protocol for field measurements in a segregating population, several baseline experiments were performed on genotypes with known heat tolerance based on visual observations in multiple climates. ‘Mandarin’ and ‘Qualicum’ were used as heat tolerant and heat susceptible controls, respectively. We determined that: optimum collection time was in the morning before ambient temperatures reached 28 °C, critical temperature (Tc) was 45 °C, minimum duration of dark adaptation was 15 min, and optimum heat shock duration was 30 min. Parameters established in baseline experiments were subsequently used for screening a large population (196 genotypes) planted in the field, where warm conditions commonly occur (maximum temperatures ranging between 30 and 35 °C). A significant difference in chlorophyll fluorescence was found between the two controls; ‘Qualicum’, the heat sensitive cultivar, had the lowest Fv/Fm (variable fluorescence/maximum fluorescence) value, while 18.8% of the segregating population had a higher Fv/Fm value than ‘Mandarin’, the heat tolerant cultivar. We have identified 106 individuals with an Fv/Fm above 0.600 (representing 52% of the population), and 7 individuals above 0.680 (4% of the population). The distribution of heat tolerance within the population was essentially normal, and thus quantitative trait analysis is a plausible approach for studying heat tolerance. This protocol has potential application to other Rosaceae species, and is not dependent on visual assessment.}, number={3}, journal={SCIENTIA HORTICULTURAE}, author={Molina-Bravo, Ramon and Arellano, Consuelo and Sosinski, Bryon R. and Fernandez, Gina E.}, year={2011}, month={Sep}, pages={524–530} }
 @article{cervantes-flores_sosinski_pecota_mwanga_catignani_truong_watkins_ulmer_yencho_2011, title={Identification of quantitative trait loci for dry-matter, starch, and beta-carotene content in sweetpotato}, volume={28}, ISSN={["1380-3743"]}, DOI={10.1007/s11032-010-9474-5}, number={2}, journal={MOLECULAR BREEDING}, publisher={Springer Nature}, author={Cervantes-Flores, J. C. and Sosinski, B. and Pecota, K. V. and Mwanga, R. O. M. and Catignani, G. L. and Truong, V. D. and Watkins, R. H. and Ulmer, M. R. and Yencho, G. C.}, year={2011}, month={Aug}, pages={201–216} }
 @article{mccord_sosinski_haynes_clough_yencho_2011, title={Linkage Mapping and QTL Analysis of Agronomic Traits in Tetraploid Potato (Solanum tuberosum subsp tuberosum)}, volume={51}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2010.02.0108}, abstractNote={ABSTRACTPotato (Solanum tuberosum L.) is one of the world's most important crops. Using a tetraploid population, we developed a linkage map using amplified fragment length polymorphism and simple sequence repeat (SSR) markers, and searched for quantitative trait loci (QTL) via interval mapping and single‐marker analysis of variance. Quantitative trait loci were detected for flower color, foliage maturity, tuber skin texture, dry matter content, specific gravity, and yield. Most linkage groups were anchored to Solanum chromosomes using SSRs. The most significant QTL detected was for flower color. It was located on chromosome II and explained over 40% of the variation for this trait. This QTL most likely corresponds to the R locus for red anthocyanin production. We also confirmed the presence of QTL for foliage maturity on chromosomes III and V. For skin texture, a trait that has not been previously mapped in potato, we detected multiple QTL. One of these, found on chromosome III, explained 20% of the variation. By measuring specific gravity and dry matter independently we were able to detect QTL for these traits that did not co‐locate, even though the traits are strongly correlated. Yield QTL were detected on multiple chromosomes, including a novel one on chromosome III. Many QTL could be modeled as simplex or duplex with dominant effects, but a large number displayed additive or interallelic interactive effects. The mapping and modeling of traits in this tetraploid population could be improved by the use of more codominant markers, such as single nucleotide polymorphisms.}, number={2}, journal={CROP SCIENCE}, publisher={Crop Science Society of America}, author={McCord, Per H. and Sosinski, Bryon R. and Haynes, Kathleen G. and Clough, Mark E. and Yencho, G. Craig}, year={2011}, month={Mar}, pages={771–785} }
 @article{post_ali_krings_xiang_sosinski_neal_2011, title={On the Identity of the Weedy Bittercresses (Cardamine: Brassicaceae) in United States Nurseries: Evidence from Molecules and Morphology}, volume={59}, ISSN={["1550-2759"]}, DOI={10.1614/ws-d-10-00063.1}, abstractNote={Bittercress (Brassicaceae) is one of the most prolific and costly weeds of the container nursery industry. Bittercress accessions from container nurseries throughout the major production zones in the United States were examined and compared with herbarium specimens. The identity of these weedy bittercress species were further explored using sequences of the nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) region and the nrDNA region for the COP1-interacting protein 7 (CIP7). Four species of bittercress were detected in the nursery industry of the United States, including New Zealand bittercress, hairy bittercress, flexuous bittercress, and little bittercress. The taxon referred to here as Cardamine flexuosa With. (flexuous bittercress) likely contains two genotypes previously reported as European C. flexuosa and Asian C. flexuosa. Phylogenetic relationships between the four species we examined, particularly in relationship to flexuous bittercress, were not fully resolved by the molecular evidence generated for this study. New Zealand bittercress is nonnative and does not appear in current keys to the species for the United States. Flexuous bittercress is also an alien species, which appears in some U.S. keys but not in all. To aid nurserymen and botanists in identification of these four closely related bittercress species, a key was developed and is accompanied by detailed descriptions and illustrations.}, number={1}, journal={WEED SCIENCE}, author={Post, Angela R. and Ali, Regina and Krings, Alexander and Xiang, Jenny and Sosinski, Brian R. and Neal, Joseph C.}, year={2011}, pages={123–135} }
 @article{mccord_sosinski_haynes_clough_yencho_2011, title={QTL mapping of internal heat necrosis in tetraploid potato}, volume={122}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-010-1429-z}, abstractNote={Internal heat necrosis (IHN) is a physiological disorder of potato tubers. We developed a linkage map of tetraploid potato using AFLP and SSR markers, and mapped QTL for mean severity and percent incidence of IHN. Phenotypic data indicated that the distribution of IHN is skewed toward resistance. Late foliage maturity was slightly but significantly correlated with increased IHN symptoms. The linkage map for 'Atlantic', the IHN-susceptible parent, covered 1034.4 cM and included 13 linkage groups, and the map for B1829-5, the IHN-resistant parent, covered 940.2 cM and contained 14 linkage groups. QTL for increased resistance to IHN were located on chromosomes IV, V, and groups VII and X of 'Atlantic', and on group VII of B1829-5 in at least 2 of 3 years. The QTL explained between 4.5 and 29.4% of the variation for mean severity, and from 3.7 to 14.5% of the variation for percent incidence. Most QTL detected were dominant, and associated with decreased IHN symptoms. One SSR and 13 AFLP markers that were linked to IHN were tested in a second population. One AFLP marker was associated with decreased symptoms in both populations. The SSR marker was not associated with IHN in the second population, but was closely linked in repulsion to another marker that was associated with IHN, and had the same (negative) effect on the trait as the SSR marker did in the first population. The correlation between maturity and IHN may be partially explained by the presence of markers on chromosome V that are linked to both traits. This research represents the first molecular genetic research of IHN in potato.}, number={1}, journal={THEORETICAL AND APPLIED GENETICS}, publisher={Springer Nature}, author={McCord, P. H. and Sosinski, B. R. and Haynes, K. G. and Clough, M. E. and Yencho, G. C.}, year={2011}, month={Jan}, pages={129–142} }
 @article{santa-maria_yencho_haigler_thompson_kelly_sosinski_2011, title={Starch Self-Processing in Transgenic Sweet Potato Roots Expressing a Hyperthermophilic alpha-Amylase}, volume={27}, ISSN={["1520-6033"]}, url={http://europepmc.org/abstract/med/21365786}, DOI={10.1002/btpr.573}, abstractNote={Abstract}, number={2}, journal={BIOTECHNOLOGY PROGRESS}, author={Santa-Maria, Monica C. and Yencho, Craig G. and Haigler, Candace H. and Thompson, William F. and Kelly, Robert M. and Sosinski, Bryon}, year={2011}, pages={351–359} }
 @article{lee_pascuzzi_settlage_shultz_tanurdzic_rabinowicz_menges_zheng_main_murray_et al._2010, title={Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State}, volume={6}, ISSN={1553-7404}, url={http://dx.doi.org/10.1371/journal.pgen.1000982}, DOI={10.1371/journal.pgen.1000982}, abstractNote={DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We used flow cytometry and tiling microarrays to profile DNA replication of Arabidopsis thaliana chromosome 4 (chr4) during early, mid, and late S phase. Replication profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes the remaining euchromatin and essentially all of the heterochromatin. Termination zones were consistent between experiments, allowing us to define 163 putative replicons on chr4 that clustered into larger domains of predominately early or late replication. Early-replicating sequences, especially the initiation zones of early replicons, displayed a pattern of epigenetic modifications specifying an open chromatin conformation. Late replicons, and the termination zones of early replicons, showed an opposite pattern. Histone H3 acetylated on lysine 56 (H3K56ac) was enriched in early replicons, as well as the initiation zones of both early and late replicons. H3K56ac was also associated with expressed genes, but this effect was local whereas replication time correlated with H3K56ac over broad regions. The similarity of the replication profiles for early and mid S phase cells indicates that replication origin activation in euchromatin is stochastic. Replicon organization in Arabidopsis is strongly influenced by epigenetic modifications to histones and DNA. The domain organization of Arabidopsis is more similar to that in Drosophila than that in mammals, which may reflect genome size and complexity. The distinct patterns of association of H3K56ac with gene expression and early replication provide evidence that H3K56ac may be associated with initiation zones and replication origins.}, number={6}, journal={PLoS Genetics}, publisher={Public Library of Science (PLoS)}, author={Lee, Tae-Jin and Pascuzzi, Pete E. and Settlage, Sharon B. and Shultz, Randall W. and Tanurdzic, Milos and Rabinowicz, Pablo D. and Menges, Margit and Zheng, Ping and Main, Dorrie and Murray, James A. H. and et al.}, editor={Copenhaver, Gregory P.Editor}, year={2010}, month={Jun}, pages={e1000982} }
 @article{post_neal_krings_sosinski_xiang_2009, title={New Zealand Bittercress (Cardamine corymbosa; Brassicaceae): New to the United States}, volume={23}, ISSN={["1550-2740"]}, DOI={10.1614/WT-09-017.1}, abstractNote={New Zealand bittercress is reported as new to the United States. While collecting specimens to determine what Cardamine species occur in the nursery trade, New Zealand bittercress was discovered in a container nursery in Wilkes County, North Carolina. The nursery tracked the shipment of contaminated plants to a wholesale nursery in Washington County, Oregon. It was subsequently confirmed that New Zealand bittercress also occurs in a nursery in Clackamas County, Oregon, and has likely been distributed throughout the United States as a contaminant in container grown ornamental plants. Thus far there have been no reports of naturalized populations outside of container nursery crop production facilities.}, number={4}, journal={WEED TECHNOLOGY}, author={Post, A. R. and Neal, J. C. and Krings, A. and Sosinski, B. R. and Xiang, Q.}, year={2009}, pages={604–607} }
 @article{santa-maria_chou_yencho_haigler_thompson_kelly_sosinski_2009, title={Plant cell calcium-rich environment enhances thermostability of recombinantly produced α-amylase from the hyperthermophilic bacterium Thermotoga maritime}, volume={104}, ISSN={0006-3592 1097-0290}, url={http://dx.doi.org/10.1002/bit.22468}, DOI={10.1002/bit.22468}, abstractNote={Abstract}, number={5}, journal={Biotechnology and Bioengineering}, publisher={Wiley}, author={Santa-Maria, Monica C. and Chou, Chung-Jung and Yencho, G. Craig and Haigler, Candace H. and Thompson, William F. and Kelly, Robert M. and Sosinski, Bryon}, year={2009}, month={Dec}, pages={947–956} }
 @article{santa-maria_pecota_yencho_allen_sosinski_2009, title={Rapid shoot regeneration in industrial 'high starch' sweetpotato (Ipomoea batatas L.) genotypes}, volume={97}, ISSN={["1573-5044"]}, DOI={10.1007/s11240-009-9504-3}, number={1}, journal={PLANT CELL TISSUE AND ORGAN CULTURE}, author={Santa-Maria, Monica and Pecota, Kenneth V. and Yencho, Craig G. and Allen, George and Sosinski, Bryon}, year={2009}, month={Apr}, pages={109–117} }
 @article{jung_jiwan_cho_lee_abbott_sosinski_main_2009, title={Synteny of Prunus and other model plant species}, volume={10}, ISSN={["1471-2164"]}, DOI={10.1186/1471-2164-10-76}, abstractNote={Fragmentary conservation of synteny has been reported between map-anchored Prunus sequences and Arabidopsis. With the availability of genome sequence for fellow rosid I members Populus and Medicago, we analyzed the synteny between Prunus and the three model genomes. Eight Prunus BAC sequences and map-anchored Prunus sequences were used in the comparison.We found a well conserved synteny across the Prunus species -- peach, plum, and apricot -- and Populus using a set of homologous Prunus BACs. Conversely, we could not detect any synteny with Arabidopsis in this region. Other peach BACs also showed extensive synteny with Populus. The syntenic regions detected were up to 477 kb in Populus. Two syntenic regions between Arabidopsis and these BACs were much shorter, around 10 kb. We also found syntenic regions that are conserved between the Prunus BACs and Medicago. The array of synteny corresponded with the proposed whole genome duplication events in Populus and Medicago. Using map-anchored Prunus sequences, we detected many syntenic blocks with several gene pairs between Prunus and Populus or Arabidopsis. We observed a more complex network of synteny between Prunus-Arabidopsis, indicative of multiple genome duplication and subsequence gene loss in Arabidopsis.Our result shows the striking microsynteny between the Prunus BACs and the genome of Populus and Medicago. In macrosynteny analysis, more distinct Prunus regions were syntenic to Populus than to Arabidopsis.}, journal={BMC GENOMICS}, author={Jung, Sook and Jiwan, Derick and Cho, Ilhyung and Lee, Taein and Abbott, Albert and Sosinski, Bryon and Main, Dorrie}, year={2009}, month={Feb} }
 @article{zhebentyayeva_swire-clark_georgi_garay_jung_forrest_blenda_blackmon_mook_horn_et al._2008, title={A framework physical map for peach, a model Rosaceae species}, volume={4}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-008-0147-z}, number={4}, journal={TREE GENETICS & GENOMES}, author={Zhebentyayeva, T. N. and Swire-Clark, G. and Georgi, L. L. and Garay, L. and Jung, S. and Forrest, S. and Blenda, A. V. and Blackmon, B. and Mook, J. and Horn, R. and et al.}, year={2008}, month={Oct}, pages={745–756} }
 @article{cervantes-flores_yencho_pecota_sosinski_mwanga_2008, title={Detection of quantitative trait loci and inheritance of root-knot nematode resistance in sweetpotato}, volume={133}, number={6}, journal={Journal of the American Society for Horticultural Science}, author={Cervantes-Flores, J. C. and Yencho, G. C. and Pecota, K. V. and Sosinski, B. and Mwanga, R. O. M.}, year={2008}, pages={844–851} }
 @article{cervantes-flores_yencho_kriegner_pecota_faulk_mwanga_sosinski_2008, title={Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers}, volume={21}, ISSN={["1380-3743"]}, DOI={10.1007/s11032-007-9150-6}, number={4}, journal={MOLECULAR BREEDING}, publisher={Springer Nature}, author={Cervantes-Flores, Jim C. and Yencho, G. Craig and Kriegner, Albert and Pecota, Kenneth V. and Faulk, Maria A. and Mwanga, Robert O. M. and Sosinski, Bryon R.}, year={2008}, month={May}, pages={511–532} }
 @misc{tanurdzic_vaughn_jiang_lee_slotkin_sosinski_thompson_doerge_martienssen_2008, title={Epigenomic consequences of immortalized plant cell suspension culture}, volume={6}, number={12}, journal={PLoS Biology}, author={Tanurdzic, M. and Vaughn, M. W. and Jiang, H. and Lee, T. J. and Slotkin, R. K. and Sosinski, B. and Thompson, W. F. and Doerge, R. W. and Martienssen, R. A.}, year={2008}, pages={2880–2895} }
 @misc{shulaev_korban_sosinski_abbott_2008, title={Multiple models for Rosaceae genomics}, volume={147}, number={3}, journal={Plant Physiology}, author={Shulaev, V. and Korban, S. S. and Sosinski, B. and Abbott, A. G.}, year={2008}, pages={985–1003} }
 @article{opperman_bird_williamson_rokhsar_burke_cohn_cromer_diener_gajan_graham_et al._2008, title={Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism}, volume={105}, ISSN={["1091-6490"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-54149092490&partnerID=MN8TOARS}, DOI={10.1073/pnas.0805946105}, abstractNote={
            We have established
            Meloidogyne hapla
            as a tractable model plant-parasitic nematode amenable to forward and reverse genetics, and we present a complete genome sequence. At 54 Mbp,
            M. hapla
            represents not only the smallest nematode genome yet completed, but also the smallest metazoan, and defines a platform to elucidate mechanisms of parasitism by what is the largest uncontrolled group of plant pathogens worldwide. The
            M. hapla
            genome encodes significantly fewer genes than does the free-living nematode
            Caenorhabditis elegans
            (most notably through a reduction of odorant receptors and other gene families), yet it has acquired horizontally from other kingdoms numerous genes suspected to be involved in adaptations to parasitism. In some cases, amplification and tandem duplication have occurred with genes suspected of being acquired horizontally and involved in parasitism of plants. Although
            M. hapla
            and
            C. elegans
            diverged >500 million years ago, many developmental and biochemical pathways, including those for dauer formation and RNAi, are conserved. Although overall genome organization is not conserved, there are areas of microsynteny that may suggest a primary biological function in nematodes for those genes in these areas. This sequence and map represent a wealth of biological information on both the nature of nematode parasitism of plants and its evolution.
          }, number={39}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Opperman, Charles H. and Bird, David M. and Williamson, Valerie M. and Rokhsar, Dan S. and Burke, Mark and Cohn, Jonathan and Cromer, John and Diener, Steve and Gajan, Jim and Graham, Steve and et al.}, year={2008}, month={Sep}, pages={14802–14807} }
 @article{horn_lecouls_callahan_dandekar_garay_mccord_howad_chan_verde_main_et al._2005, title={Candidate gene database and transcript map for peach, a model species for fruit trees}, volume={110}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-005-1968-x}, abstractNote={Peach (Prunus persica) is a model species for the Rosaceae, which includes a number of economically important fruit tree species. To develop an extensive Prunus expressed sequence tag (EST) database for identifying and cloning the genes important to fruit and tree development, we generated 9,984 high-quality ESTs from a peach cDNA library of developing fruit mesocarp. After assembly and annotation, a putative peach unigene set consisting of 3,842 ESTs was defined. Gene ontology (GO) classification was assigned based on the annotation of the single "best hit" match against the Swiss-Prot database. No significant homology could be found in the GenBank nr databases for 24.3% of the sequences. Using core markers from the general Prunus genetic map, we anchored bacterial artificial chromosome (BAC) clones on the genetic map, thereby providing a framework for the construction of a physical and transcript map. A transcript map was developed by hybridizing 1,236 ESTs from the putative peach unigene set and an additional 68 peach cDNA clones against the peach BAC library. Hybridizing ESTs to genetically anchored BACs immediately localized 11.2% of the ESTs on the genetic map. ESTs showed a clustering of expressed genes in defined regions of the linkage groups. [The data were built into a regularly updated Genome Database for Rosaceae (GDR), available at (http://www.genome.clemson.edu/gdr/).].}, number={8}, journal={THEORETICAL AND APPLIED GENETICS}, author={Horn, R and Lecouls, AC and Callahan, A and Dandekar, A and Garay, L and McCord, P and Howad, W and Chan, H and Verde, I and Main, D and et al.}, year={2005}, month={May}, pages={1419–1428} }
 @article{mcgregor_he_ali_sosinski_jankowicz_burg_labonte_2005, title={The  effect of replicate number and image analysis method on sweetpotato [Ipomoea batatas (L.) Lam.] cDNA microarray results}, volume={23}, number={4}, journal={Plant Molecular Biology Reporter}, author={McGregor, C. E. and He, L. and Ali, R. M. and Sosinski, B. and Jankowicz, J. and Burg, K. and Labonte, D. R.}, year={2005}, pages={367–381} }
 @inproceedings{yencho_pecota_schultheis_sosinski_2002, title={Grower-participatory sweetpotato breeding efforts in North Carolina}, volume={583}, DOI={10.17660/actahortic.2002.583.6}, abstractNote={Sweetpotato, based on area and value, is the most important vegetable crop produced in North Carolina, and NC is the leading supplier of sweetpotatoes in the US producing ca. 218 thousand metric tons per year (ca. 35-40% of the national supply) worth an estimated $55.7 million. In 1997, we initiated a grower-participatory breeding effort to develop improved sweetpotato varieties for NC growers. This highly collaborative project involves researchers and extension specialists from NC State University, county extension agents, growers and industry representatives. Our variety development efforts are supported by the NC Sweetpotato Commission. To date, the project has been highly successful. This manuscript will describe our overall breeding efforts and it will focus on how this project has resulted in: 1) improved two-way learning between the breeding program and our clientele - growers; and 2) increased support and awareness of our conventional and genomics-based sweetpotato breeding and research efforts.}, number={583}, booktitle={Proceedings of the first international conference on sweetpotato food and health: Lima, Peru 26-29 July, 2001}, publisher={Leuven, Belgium: International Society for Horticultural Science}, author={Yencho, G. C. and Pecota, K. V. and Schultheis, J. R. and Sosinski, B. R.}, year={2002}, pages={69–76} }
 @article{sosinski_he_cervantes-flores_pokrzywa_bruckner_yencho_2002, title={Sweetpotato Genomics at North Carolina State University}, volume={8}, ISBN={["90-6605-985-0"]}, ISSN={["2406-6168"]}, DOI={10.17660/actahortic.2002.583.4}, number={583}, journal={PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON SWEETPOTATO: FOOD AND HEALTH FOR THE FUTURE}, publisher={International Society for Horticultural Science (ISHS)}, author={Sosinski, B and He, L and Cervantes-Flores, J and Pokrzywa, RM and Bruckner, A and Yencho, GC}, year={2002}, pages={51–60} }