@article{kloppe_whetten_kim_powell_lück_douchkov_whetten_hulse‐kemp_balint‐kurti_cowger_2023, title={Two pathogen loci determine <i>Blumeria graminis}, volume={238}, ISSN={0028-646X 1469-8137}, url={http://dx.doi.org/10.1111/nph.18809}, DOI={10.1111/nph.18809}, abstractNote={Summary}, number={4}, journal={New Phytologist}, publisher={Wiley}, author={Kloppe, Tim and Whetten, Rebecca B. and Kim, Saet‐Byul and Powell, Oliver R. and Lück, Stefanie and Douchkov, Dimitar and Whetten, Ross W. and Hulse‐Kemp, Amanda M. and Balint‐Kurti, Peter and Cowger, Christina}, year={2023}, month={Mar}, pages={1546–1561} }
 @article{cowger_meyers_whetten_2022, title={Sensitivity of the US Wheat Powdery Mildew Population to Quinone Outside Inhibitor Fungicides and Determination of the Complete Blumeria graminis f. sp. tritici Cytochrome b Gene}, volume={112}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-04-21-0132-R}, DOI={10.1094/PHYTO-04-21-0132-R}, abstractNote={ Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, is managed primarily with cultivar resistance and foliar fungicides. Quinone outside inhibitors (QoIs), which target the mitochondrial cytochrome b (cytb) gene, are one of the two main fungicide classes used on wheat. While European populations of B. graminis f. sp. tritici are widely insensitive to QoIs, largely because of the cytb mutation G143A, the QoI sensitivity of the U.S. B. graminis f. sp. tritici population had never been evaluated despite years of QoI use on U.S. wheat. A total of 381 B. graminis f. sp. tritici isolates from 15 central and eastern U.S. states were screened for sensitivity to QoI fungicides pyraclostrobin and picoxystrobin. A modest range of sensitivities was observed, with maximum resistance factors of 11.2 for pyraclostrobin and 5.3 for picoxystrobin. The F129L, G137R, and G143A cytb mutations were not detected in the U.S. B. graminis f. sp. tritici population, nor were mutations identified in the PEWY loop, a key part of the Qo site. Thus, no genetic basis for the observed quantitative variation in QoI sensitivity of U.S. B. graminis f. sp. tritici was identified. Isolate sporulation was weakly negatively associated with reduced QoI sensitivity, suggesting a fitness cost. In the course of the study, the complete B. graminis f. sp. tritici cytb gene sequence was determined for the first time in the isolate 96224 v. 3.16 reference genome. Contrary to previous reports, the gene has an intron that appears to belong to intron group II, which is unusual in fungi. The study was the first QoI sensitivity screening of a large, geographically diverse set of U.S. B. graminis f. sp. tritici isolates, and while the population as a whole remains relatively sensitive, some quantitative loss of efficacy was observed. }, number={2}, journal={PHYTOPATHOLOGY}, author={Cowger, Christina and Meyers, Emily and Whetten, Rebecca}, year={2022}, month={Feb}, pages={249–260} }
 @article{lee_sung_locke_taliercio_whetten_zhang_carter_burton_mian_2019, title={Registration of USDA‐N6003LP Soybean Germplasm with Low Seed Phytate}, volume={13}, ISSN={1936-5209 1940-3496}, url={http://dx.doi.org/10.3198/jpr2018.09.0064crg}, DOI={10.3198/jpr2018.09.0064crg}, abstractNote={Soybean [Glycine max (L.) Merr.] meal is the main source of protein in poultry and swine rations worldwide. Phytate, the main storage form of phosphorous in soybean meal, is largely indigestible by monogastric animals and, thus, a major concern both for nutrition and for environmental pollution. USDA‐N6003LP (Reg. no. GP‐435, PI 689999) is a low‐phytate (LP) determinate, lodging‐resistant early maturity group (MG) VI soybean germplasm developed and released jointly by the USDA‐ARS and the North Carolina Agricultural Research Service. USDA‐N6003LP is derived from a backcross (BC1) between recurrent parent ‘NC‐Roy’ and LP donor line USDA CX1834. NC‐Roy is a high‐yielding MG VI cultivar adapted to the southern United States. USDA‐N6003LP has 60% lower phytate and 4.8 times higher inorganic phosphorus (Pi) contents in its seed than the seed of NC‐Roy. It matures approximately 5 d earlier and has larger seed size and better lodging resistance (P < 0.05) compared with NC‐Roy. Across 17 environments in the USDA Uniform Soybean Tests, Southern States and over four local yield trials in North Carolina, USDA‐N6003LP yielded 91 and 97% of NC‐Roy, respectively. Field emergences of this line in four tests in NC were 79 to 80% compared with 89 to 90% for NC‐Roy. USDA‐N6003LP is the first early MG VI LP germplasm release with good agronomic performance and relatively normal field emergence. It will be useful as parental stock for soybean breeders interested in developing LP soybean cultivars.}, number={3}, journal={Journal of Plant Registrations}, publisher={Wiley}, author={Lee, Sungwoo and Sung, Mikyung and Locke, Anna and Taliercio, Earl and Whetten, Rebecca and Zhang, Bo and Carter, Thomas E., Jr. and Burton, Joseph W. and Mian, M. A. Rouf}, year={2019}, month={Sep}, pages={427–432} }
 @article{wiersma_whetten_zhang_sehgal_kolb_poland_mason_carter_cowger_olson_2018, title={Registration of Two Wheat Germplasm Lines Fixed for Pm58}, volume={12}, ISSN={["1940-3496"]}, DOI={10.3198/jpr2017.06.0036crg}, abstractNote={Powdery mildew is a persistent threat to global wheat (Triticum aestivum L.) production. To broaden the genetic base for resistance to powdery mildew in wheat, germplasm lines U6714‐A‐011 (Reg. No. GP‐1023, PI 682090) and U6714‐B‐056 (Reg. No. GP‐1022, PI 682089) were developed at Michigan State University and are fixed for the novel powdery mildew resistance gene Pm58. This gene was identified in Aegilops tauschii Coss. accession TA1662, introgressed, and mapped to wheat chromosome 2DS. The two germplasm lines described are BC2F4–derived inbred backcrossed lines from a direct cross between TA1662 and the recurrent wheat parent KS05HW14, a hard white winter wheat line adapted to western Kansas. In addition to exhibiting resistant reactions to multiple Bgt isolates with broad virulence profiles, both lines have moderate yield potential and good agronomic characteristics, making them suitable as breeding germplasm. The availability of these lines will enable the incorporation of Pm58 into wheat breeding programs, providing additional genetic variation for resistance to powdery mildew.}, number={2}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Wiersma, Andrew T. and Whetten, Rebecca B. and Zhang, Guorong and Sehgal, Sunish K. and Kolb, Frederic L. and Poland, Jesse A. and Mason, R. Esten and Carter, Arron H. and Cowger, Christina and Olson, Eric L.}, year={2018}, month={May}, pages={270–273} }
 @article{kohlway_whetten_benson_frampton_2017, title={Response of Turkish and Trojan fir to Phytophthora cinnamomi and P. cryptogea}, volume={32}, ISSN={0282-7581 1651-1891}, url={http://dx.doi.org/10.1080/02827581.2017.1280076}, DOI={10.1080/02827581.2017.1280076}, abstractNote={ABSTRACT Phytophthora root rot, primarily caused by the oomycete Phytophthora cinnamomi, is a large problem for the Christmas tree industry in North Carolina. Fraser fir (Abies fraseri) has no known innate resistance to this pathogen while some exotic fir species, such as Trojan (Abies equi-trojani) and Turkish (Abies bornmuelleriana) fir display varying amounts of resistance. A Phytophthora-resistance screening trial was completed with 1600 seedlings from 12 Turkish and Trojan fir families and Fraser and momi fir (A. firma). Seedlings from each family or species were inoculated with each of eight Phytophthora isolates, six P. cinnamomi and two Phytophthora cryptogea, in an effort to describe variability in isolate aggressiveness. Mortality was assessed as percent shoot necrosis bi-weekly for 16 weeks. Overall, rankings of resistance in fir species confirmed previous single-isolate-based results; momi fir was the most resistant, followed by Turkish, Trojan, and Fraser fir. P. cinnamomi isolates were generally more aggressive than P. cryptogea isolates. The two P. cryptogea isolates resulted in 5.6% and 0.8% mortality on Turkish fir, and 10.9% and 6.7% mortality on Trojan fir, the first reported resistance screen of these host-pathogen combinations. Pearson’s correlation testing identified a high degree of correlation between most isolates and overall mean mortality. Turkish and Trojan fir families appear to possess resistance to Phytophthora species common in North Carolina.}, number={5}, journal={Scandinavian Journal of Forest Research}, publisher={Informa UK Limited}, author={Kohlway, W. H. and Whetten, R. W. and Benson, D. M. and Frampton, J.}, year={2017}, month={Feb}, pages={406–411} }
 @article{qi_yu_liu_pais_ranney_whetten_xiang_2015, title={Phylogenomics of polyploidy Fothergilla (Hamamelidaceae) by RAD-tag based GBS—Insights into species origin and effects of software pipelines}, volume={53}, ISSN={16744918}, url={http://doi.wiley.com/10.1111/jse.12176}, DOI={10.1111/jse.12176}, abstractNote={Abstract}, number={5}, journal={Journal of Systematics and Evolution}, publisher={Wiley}, author={Qi, Zhe-Chen and Yu, Yi and Liu, Xiang and Pais, Andrew and Ranney, Thomas and Whetten, Ross and Xiang, Qiu-Yun Jenny}, year={2015}, month={Sep}, pages={432–447} }
 @article{moraga-suazo_orellana_quiroga_balocchi_sanfuentes_whetten_hasbún_valenzuela_2014, title={Development of a genetic linkage map for Pinus radiata and detection of pitch canker disease resistance associated QTLs}, volume={28}, ISSN={0931-1890 1432-2285}, url={http://dx.doi.org/10.1007/s00468-014-1090-2}, DOI={10.1007/s00468-014-1090-2}, number={6}, journal={Trees}, publisher={Springer Science and Business Media LLC}, author={Moraga-Suazo, P. and Orellana, L. and Quiroga, P. and Balocchi, C. and Sanfuentes, E. and Whetten, R. W. and Hasbún, R. and Valenzuela, S.}, year={2014}, month={Sep}, pages={1823–1835} }
 @article{cardinal_whetten_wang_auclair_hyten_cregan_bachlava_gillman_ramirez_dewey_et al._2014, title={Mapping the low palmitate fap1 mutation and validation of its effects in soybean oil and agronomic traits in three soybean populations}, volume={127}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-013-2204-8}, abstractNote={fap 1 mutation is caused by a G174A change in GmKASIIIA that disrupts a donor splice site recognition and creates a GATCTG motif that enhanced its expression. Soybean oil with reduced palmitic acid content is desirable to reduce the health risks associated with consumption of this fatty acid. The objectives of this study were: to identify the genomic location of the reduced palmitate fap1 mutation, determine its molecular basis, estimate the amount of phenotypic variation in fatty acid composition explained by this locus, determine if there are epistatic interactions between the fap1 and fap nc loci and, determine if the fap1 mutation has pleiotropic effects on seed yield, oil and protein content in three soybean populations. This study detected two major QTL for 16:0 content located in chromosome 5 (GmFATB1a, fap nc) and chromosome 9 near BARCSOYSSR_09_1707 that explained, with their interaction, 66–94 % of the variation in 16:0 content in the three populations. Sequencing results of a putative candidate gene, GmKASIIIA, revealed a single unique polymorphism in the germplasm line C1726, which was predicted to disrupt the donor splice site recognition between exon one and intron one and produce a truncated KASIIIA protein. This G to A change also created the GATCTG motif that enhanced gene expression of the mutated GmKASIIIA gene. Lines homozygous for the GmKASIIIA mutation (fap1) had a significant reduction in 16:0, 18:0, and oil content; and an increase in unsaturated fatty acids content. There were significant epistatic interactions between GmKASIIIA (fap1) and fap nc for 16:0 and oil contents, and seed yield in two populations. In conclusion, the fap1 phenotype is caused by a single unique SNP in the GmKASIIIA gene.}, number={1}, journal={THEORETICAL AND APPLIED GENETICS}, author={Cardinal, Andrea J. and Whetten, Rebecca and Wang, Sanbao and Auclair, Jerome and Hyten, David and Cregan, Perry and Bachlava, Eleni and Gillman, Jason and Ramirez, Martha and Dewey, Ralph and et al.}, year={2014}, month={Jan}, pages={97–111} }
 @article{zapata-valenzuela_whetten_neale_mckeand_isik_2013, title={Genomic Estimated Breeding Values Using Genomic Relationship Matrices in a Cloned Population of Loblolly Pine}, volume={3}, ISSN={2160-1836}, url={http://dx.doi.org/10.1534/g3.113.005975}, DOI={10.1534/g3.113.005975}, abstractNote={Abstract}, number={5}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Zapata-Valenzuela, Jaime and Whetten, Ross W. and Neale, David and McKeand, Steve and Isik, Fikret}, year={2013}, month={Apr}, pages={909–916} }
 @article{cumbie_eckert_wegrzyn_whetten_neale_goldfarb_2011, title={Association genetics of carbon isotope discrimination, height and foliar nitrogen in a natural population of Pinus taeda L}, volume={107}, ISSN={0018-067X 1365-2540}, url={http://dx.doi.org/10.1038/hdy.2010.168}, DOI={10.1038/hdy.2010.168}, abstractNote={Loblolly pine, Pinus taeda L., is one of the most widely planted, commercially and ecologically important tree species in North America. We took an association genetics approach, using an unimproved population of 380 clonally replicated unrelated trees, to test 3,938 single nucleotide polymorphisms (SNPs) in as many genes for association with phenotypic variation in carbon isotope discrimination, foliar nitrogen concentration and total tree height after two growing seasons. Best linear unbiased prediction (BLUP) was used with a spatial adjustment to remove environmental variation from phenotypic data derived from a common garden experiment. After correction for multiple testing, a total of 14 SNPs were associated with the traits of carbon isotope discrimination (n = 7), height (n = 1) and foliar nitrogen concentration (n = 6) using 380 clones. Tails of the population phenotypic distribution were compared for allele frequency differences, revealing 10 SNPs with allele frequency in at least one tail significantly different from the overall population. Eight associated SNPs were in sequences similar to known genes, such as an AP2 transcription factor related to carbon isotope discrimination and glutamate decarboxylase associated with foliar nitrogen concentration, and others were from unknown genes without homologs in Arabidopsis.}, number={2}, journal={Heredity}, publisher={Springer Science and Business Media LLC}, author={Cumbie, W P and Eckert, A and Wegrzyn, J and Whetten, R and Neale, D and Goldfarb, B}, year={2011}, month={Jan}, pages={105–114} }
 @article{cardinal_burton_camacho-roger_whetten_chappell_bilyeu_auclair_dewey_2011, title={Molecular Analysis of GmFAD3A in Two Soybean Populations Segregating for the fan, fap1, and fap(nc) Loci}, volume={51}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2010.08.0500}, abstractNote={Soybeans [Glycine max (L.) Merr.] have undesirable levels of polyunsaturated fatty acids in their oil that result in oxidative instability and poor flavor. The process of hydrogenation improves the stability but creates undesirable trans fats. Lines carrying fan genes have decreased linolenic acid (18:3) content. Changes in transcription or activity of the desaturase encoded by the GmFAD3 gene cause a reduction in 18:3 content in certain lines. The objectives of this study were to determine the molecular basis of the fan allele in PI 123440, develop molecular markers to assay for the GmFAD3 gene in lines carrying fan(PI 123440), and estimate the variation in the 18:3 explained by the GmFAD3A locus. Sequence analysis of the GmFAD3A from ‘Soyola’, the fan(PI 123440) allele, and ‘Dare’ showed no sequence polymorphisms that would alter the amino acid sequence of the enzyme. RNA blot analysis of a low‐18:3 line carrying a fan(PI 123440) allele, a line with normal 18:3 content, and three of their progenies showed a decrease in steady‐state FAD3A RNA levels in low‐18:3 lines. A marker for GmFAD3A was tested in two populations segregating for fan(PI 123440). Lines homozygous the GmFAD3A allele inherited from PI 123440 had a significant reduction in 18:3 when compared to lines homozygous for the GmFAD3A allele from the normal 18:3 parent. The differences between the two groups explained more than 77.5% of the genetic variation in 18:3 seed‐oil content in the populations. In summary, a reduction in the steady‐state mRNA levels of the GmFAD3A leads to a reduction in 18:3 synthesis within the developing seed in plants containing the fan(PI 123440) allele.}, number={5}, journal={CROP SCIENCE}, author={Cardinal, Andrea J. and Burton, Joseph W. and Camacho-Roger, Ana Maria and Whetten, Rebecca and Chappell, Andrew S. and Bilyeu, Kristin D. and Auclair, Jerome and Dewey, Ralph E.}, year={2011}, month={Sep}, pages={2104–2112} }
 @inproceedings{isik_whetten_garcia_cumbie_mckeand_grissom_batista_2007, title={Using markers in breeding, testing and selection
in loblolly pine ? current and future research.}, booktitle={Conference Proceedings}, author={Isik, F. and Whetten, R. and Garcia, S. and Cumbie, P. and McKeand, S. and Grissom, J. and Batista, T.}, year={2007} }
 @article{isik_whetten_garcia_cumbie_mckeand_grissom_batista_2007, title={Using markers in breeding, testing and selection in loblolly pine: Current and future research}, journal={GENECAR Meeting: Application of DNA based tools for genetic research, molecular breeding, management and monitoring of genetic resources}, author={Isik, F. and Whetten, R. and Garcia, S. and Cumbie, P. and McKeand, S. and Grissom, J. and Batista, T.}, year={2007} }
 @article{busov_johannes_whetten_sederoff_spiker_lanz-garcia_goldfarb_2004, title={An auxin-inducible gene from loblolly pine ( Pinus taeda L.) is differentially expressed in mature and juvenile-phase shoots and encodes a putative transmembrane protein}, volume={218}, ISSN={0032-0935 1432-2048}, url={http://dx.doi.org/10.1007/s00425-003-1175-4}, DOI={10.1007/s00425-003-1175-4}, abstractNote={We have isolated a gene from loblolly pine, 5NG4, that is highly and specifically induced by auxin in juvenile loblolly pine shoots prior to adventitious root formation, but substantially down-regulated in physiologically mature shoots that are adventitious rooting incompetent. 5NG4 was highly auxin-induced in roots, stems and hypocotyls, organs that can form either lateral or adventitious roots following an auxin treatment, but was not induced to the same level in needles and cotyledons, organs that do not form roots. The deduced amino acid sequence shows homology to the MtN21 nodulin gene from Medicago truncatula. The expression pattern of 5NG4 and its homology to a protein from Medicago involved in a root-related process suggest a possible role for this gene in adventitious root formation. Homology searches also identified similar proteins in Arabidopsis thaliana and Oryza sativa. High conservation across these evolutionarily distant species suggests essential functions in plant growth and development. A 38-member family of genes homologous to 5NG4 was identified in the A. thaliana genome. The physiological significance of this redundancy is most likely associated with functional divergence and/or expression specificity of the different family members. The exact biochemical function of the gene is still unknown, but sequence and structure predictions and 5NG4::GFP fusion protein localizations indicate it is a transmembrane protein with a possible transport function.}, number={6}, journal={Planta}, publisher={Springer Science and Business Media LLC}, author={Busov, Victor B. and Johannes, Eva and Whetten, Ross W. and Sederoff, Ronald R. and Spiker, Steven L. and Lanz-Garcia, Carmen and Goldfarb, Barry}, year={2004}, month={Apr}, pages={916–927} }
 @article{egertsdotter_zyl_mackay_peter_kirst_clark_whetten_sederoff_2004, title={Gene Expression during Formation of Earlywood and Latewood in Loblolly Pine: Expression Profiles of 350 Genes}, volume={6}, ISSN={1435-8603 1438-8677}, url={http://dx.doi.org/10.1055/s-2004-830383}, DOI={10.1055/s-2004-830383}, abstractNote={Abstract:  The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http:web.ahc.umn.edubiodatansfpine). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy‐one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process.}, number={6}, journal={Plant Biology}, publisher={Wiley}, author={Egertsdotter, U. and Zyl, L. M. and MacKay, J. and Peter, G. and Kirst, M. and Clark, C. and Whetten, R. and Sederoff, R.}, year={2004}, month={Nov}, pages={654–663} }
 @article{myburg_vogl_griffin_sederoff_whetten_2004, title={Genetics of Postzygotic Isolation in Eucalyptus: Whole-Genome Analysis of Barriers to Introgression in a Wide Interspecific Cross of Eucalyptus grandis and E. globulus}, volume={166}, ISSN={0016-6731 1943-2631}, url={http://dx.doi.org/10.1534/genetics.166.3.1405}, DOI={10.1534/genetics.166.3.1405}, abstractNote={Abstract}, number={3}, journal={Genetics}, publisher={Genetics Society of America}, author={Myburg, Alexander A. and Vogl, Claus and Griffin, A. Rod and Sederoff, Ronald R. and Whetten, Ross W.}, year={2004}, month={Mar}, pages={1405–1418} }
 @inproceedings{whetten_li_mckeand_2004, title={Microarray analysis of gene expression in OP pine families in field plantings}, booktitle={Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future,  IUFRO Joint Conference of Division 2, Conference Proceedings}, author={Whetten, R. W. and Li, Z. and McKeand, S. E.}, editor={Li, B. and McKeand, S.Editors}, year={2004}, pages={257–269} }
 @article{zhang_brown_whetten_loopstra_neale_kieliszewski_sederoff_2003, title={An arabinogalactan protein associated with secondary cell wall formation in differentiating xylem of loblolly pine}, volume={52}, ISSN={["0167-4412"]}, url={http://dx.doi.org/10.1023/a:1023978210001}, DOI={10.1023/A:1023978210001}, abstractNote={Arabinogalactan proteins (AGPs) are abundant plant proteoglycans implicated in plant growth and development. Here, we report the genetic characterization, partial purification and immunolocalization of a classical AGP (PtaAGP6, accession number AF101785) in loblolly pine (Pinus taeda L.). A PtaAGP6 full-length cDNA clone was expressed in bacteria. PtaAGP6 resembles tomato LeAGP-1 and Arabidopsis AtAGP17-19 in that they all possess a subdomain composed of basic amino acids. The accessibility of this domain in the glycoprotein makes it possible to label the PtaAGP6 epitopes on the cell surface or in the cell wall with polyclonal antibodies raised against this subdomain. The antibodies recognize the peptide of the basic subdomain and bind to the intact protein molecule. A soluble protein-containing fraction was purified from the differentiating xylem of pine trees by using beta-glucosyl Yariv reagent (beta-glcY) and was recognized by antibodies against the basic subdomain. Immunolocalization studies showed that the PtaAGP6 epitopes are restricted to a file of cells that just precede secondary cell wall thickening, suggesting roles in xylem differentiation and wood formation. The location of apparent labeling of the PtaAGP6 epitopes is separated from the location of lignin deposition. Multiple single nucleotide polymorphisms (SNPs) were detected in EST variants. Denaturing HPLC analysis of PCR products suggests that PtaAGP6 is encoded by a single gene. Mobility variation in denaturing gel electrophoresis was used to map PtaAGP6 SNPs to a site on linkage group 5.}, number={1}, journal={Plant Molecular Biology}, author={Zhang, Y. and Brown, G. and Whetten, R. and Loopstra, C.A. and Neale, D. and Kieliszewski, M.J. and Sederoff, R.R.}, year={2003}, pages={91–102} }
 @article{kirst_johnson_baucom_ulrich_hubbard_staggs_paule_retzel_whetten_sederoff_2003, title={Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana}, volume={100}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1132171100}, DOI={10.1073/pnas.1132171100}, abstractNote={
            Pinus taeda
            L. (loblolly pine) and
            Arabidopsis thaliana
            differ greatly in form, ecological niche, evolutionary history, and genome  size.
            Arabidopsis
            is a small, herbaceous, annual dicotyledon, whereas  pines are large, long-lived, coniferous forest trees. Such diverse plants  might be expected to differ in a large number of functional genes. We have  obtained and analyzed 59,797 expressed sequence tags (ESTs) from wood-forming  tissues of loblolly pine and compared them to the gene sequences inferred from  the complete sequence of the
            Arabidopsis
            genome. Approximately 50% of  pine ESTs have no apparent homologs in
            Arabidopsis
            or any other  angiosperm in public databases. When evaluated by using contigs containing  long, high-quality sequences, we find a higher level of apparent homology  between the inferred genes of these two species. For those contigs 1,100 bp or  longer, ≈90% have an apparent
            Arabidopsis
            homolog (
            E
            value < 10
            -
            10
            ). Pines and
            Arabidopsis
            last  shared a common ancestor ≈300 million years ago. Few genes would be  expected to retain high sequence similarity for this time if they did not have  essential functions. These observations suggest substantial conservation of  gene sequence in seed plants.
          }, number={12}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Kirst, M. and Johnson, A. F. and Baucom, C. and Ulrich, E. and Hubbard, K. and Staggs, R. and Paule, C. and Retzel, E. and Whetten, R. and Sederoff, R.}, year={2003}, month={May}, pages={7383–7388} }
 @article{goldfarb_lanz-garcia_lian_whetten_2003, title={Aux/IAA gene family is conserved in the gymnosperm, loblolly pine (Pinus taeda)}, volume={23}, ISSN={0829-318X 1758-4469}, url={http://dx.doi.org/10.1093/treephys/23.17.1181}, DOI={10.1093/treephys/23.17.1181}, abstractNote={We isolated five members of the Aux/IAA gene family in loblolly pine (Pinus taeda L.). Degenerate primers complementary to conserved regions of angiosperm Aux/IAA genes were used to amplify fragments that were, in turn, used as probes to screen a cDNA library constructed from auxin-treated hypocotyls. The five unique clones, named PTIAA1-5, contain the four highly conserved domains that are characteristic of the Aux/IAA proteins. All clones contain the bipartite nuclear localization signal (NLS) between Domains I and II that is predicted in most angiosperm Aux/IAA genes, but only one, PTIAA2, contains the conserved NLS in Domain IV. The five invariant residues in Domain II that have been found to constitute part of a protein destabilization element in Arabidopsis thaliana (L.) Heynh. are conserved in all the PTIAAs. A postulated phosphorylation site located between Domains I and II and proximal to the conserved bipartite NLS was conserved in 20 out of 36 genes in this analysis, including the pine genes. Transcripts of all five PTIAAs accumulated specifically in the hypocotyls in response to exogenous auxin treatment and were induced by all auxins tested. Transcript abundance above basal levels in response to 1-naphthaleneacetic acid treatment was first detected after 10 min (PTIAA3) to 3 h (PTIAA2) in the different genes and remained above basal levels throughout 7 days. Induction of PTIAA2 was inhibited by the protein synthesis inhibitor cycloheximide, indicating that PTIAA2 is a secondary response gene. Phylogenetic analysis showed that all five pine genes clustered within a single class (Class I) of the dendrogram. Clone PTIAA2 has a sequence that is relatively distinct from the other four and is the most closely related to the angiosperm genes of Class I. Class I contains both primary and secondary auxin response genes, suggesting that it is the original lineage and that other gene classes have evolved subsequent to the angiosperm/gymnosperm divergence.}, number={17}, journal={Tree Physiology}, publisher={Oxford University Press (OUP)}, author={Goldfarb, B. and Lanz-Garcia, C. and Lian, Z. and Whetten, R.}, year={2003}, month={Dec}, pages={1181–1192} }
 @article{patzlaff_newman_dubos_whetten_smith_mcinnis_bevan_sederoff_campbell_2003, title={Characterisation of PtMYB1, an R2R3-MYB from pine xylem}, volume={53}, ISSN={0167-4412}, url={http://dx.doi.org/10.1023/b:plan.0000019066.07933.d6}, DOI={10.1023/B:PLAN.0000019066.07933.d6}, abstractNote={A cDNA encoding a member of the R2R3-MYB family of transcription factors was cloned from a library constructed from differentiating Pinus taeda (loblolly pine) xylem RNA. This MYB family member, Pinus taeda MYB1 (PtMYB1), was most abundantly expressed in differentiating xylem, as assessed by both ribonuclease protection assays, and by northern blot analysis with poly(A)-enriched RNA. Similar to other plant R2R3-MYB family members, recombinant Pt MYB1 protein was able to bind to AC elements in electrophoretic mobility shift assays (EMSAs). AC elements are DNA motifs rich in adenosine and cytosine that have been implicated in the xylem-localised regulation of genes encoding lignin biosynthetic enzymes. Pt MYB1 not only bound to AC elements, but was also able to induce AC-element-dependent shifts in the electrophoretic mobility of a plant promoter that contains three AC elements, the minimal PHENYLALANINE AMMONIA-LYASE 2 (PAL2) promoter from Phaseolus vulgaris. Transcriptional activation assays conducted using yeast showed that Pt MYB1 also activated transcription, and that it did so in an AC-element-dependent fashion. Pt MYB1 also activated transcription from the minimal PAL2 promoter in plant cells in an AC-element-dependent fashion, as revealed by transient transcriptional activation assays with microprojectile-bombarded tobacco NT-1 cells. Taken together, these finding are consistent with the hypothesis that Pt MYB1 may regulate transcription from cis -acting AC elements in pine xylem.}, number={4}, journal={Plant Molecular Biology}, publisher={Springer Nature}, author={Patzlaff, Astrid and Newman, Lisa J. and Dubos, Christian and Whetten, Ross W. and Smith, Caroline and McInnis, Stephanie and Bevan, Michael W. and Sederoff, Ronald R. and Campbell, Malcolm M.}, year={2003}, month={Nov}, pages={597–608} }
 @article{patzlaff_mcinnis_courtenay_surman_newman_smith_bevan_mansfield_whetten_sederoff_et al._2003, title={Characterisation of a pine MYB that regulates lignification}, volume={36}, ISSN={0960-7412 1365-313X}, url={http://dx.doi.org/10.1046/j.1365-313x.2003.01916.x}, DOI={10.1046/j.1365-313X.2003.01916.x}, abstractNote={Summary}, number={6}, journal={The Plant Journal}, publisher={Wiley}, author={Patzlaff, Astrid and McInnis, Stephanie and Courtenay, Adrian and Surman, Christine and Newman, Lisa J. and Smith, Caroline and Bevan, Michael W. and Mansfield, Shawn and Whetten, Ross W. and Sederoff, Ronald R. and et al.}, year={2003}, month={Dec}, pages={743–754} }
 @inbook{hessler_whetten_loopstra_penner_shriver_zeigler_fletcher_torrie_comstock_2002, title={Golden rice}, ISBN={081382835X}, booktitle={Life science ethics}, publisher={Ames, IA: Iowa State University Press}, author={Hessler, K. and Whetten, R. and Loopstra, C. and Penner, K. P. and Shriver, S. and Zeigler, R. and Fletcher, J. and Torrie, M. and Comstock, G. L.}, year={2002}, pages={307–368} }
 @article{whetten_sun_zhang_sederoff_2001, title={Functional genomics and cell wall biosynthesis in loblolly pine}, volume={47}, ISSN={0167-4412}, url={http://dx.doi.org/10.1023/a:1010652003395}, DOI={10.1023/A:1010652003395}, number={1/2}, journal={Plant Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Whetten, Ross and Sun, Ying-Hsuan and Zhang, Yi and Sederoff, Ron}, year={2001}, month={Sep}, pages={275–291} }
 @article{tang_whetten_sederoff_2001, title={Genotypic control of high-frequency adventitious shoot regeneration via somatic organogenesis in loblolly pine}, volume={161}, ISSN={0168-9452}, url={http://dx.doi.org/10.1016/s0168-9452(01)00394-6}, DOI={10.1016/S0168-9452(01)00394-6}, abstractNote={Mature zygotic embryos of 24 genotypes of loblolly pine (Pinus taeda L.) were used as explants to establish an adventitious shoot regeneration system through somatic organogenesis. Callus formation frequencies of 18.2 (genotype 11-1103) -77.7% (genotype 7-100) have been induced from mature zygotic embryos of all genotypes tested on callus induction medium (basal salts) containing 2,4-dichlorophenoxyacetic acid (2,4-D) or alpha-naphthaleneacetic acid (NAA), 6-benzyladenine (BA), and kinetin. Adventitious shoot regeneration via organogenesis with the frequency of 5.4 (genotype 11-1103 and 7-2) -77.2% (genotype 8-1082) was obtained from callus and tissue cultures derived from mature zygotic embryos of 24 genotypes of loblolly pine. The highest mean number of 18 adventitious buds per piece of callus 0.5x0.5 cm(2) in size was obtained from genotype 8-1082. Elongation of adventitious buds was achieved on TE medium supplemented with 0.5 mg/l indole-3-butyric acid (IBA) and 1 mg/l BA. After rooting, regenerated plantlets were established in soil. These results suggested that adventitious shoot regeneration via somatic organogenesis was influenced by the genotypes. The in vitro regeneration procedure established in this investigation could be used for clonal micropropagation of some genotypes of loblolly pine, as well as for establishing a transformation system in coniferous species.}, number={2}, journal={Plant Science}, publisher={Elsevier BV}, author={Tang, Wei and Whetten, Ross and Sederoff, Ron}, year={2001}, month={Jul}, pages={267–272} }
 @article{sato_wuli_sederoff_whetten_2001, title={Molecular Cloning and Expression of Eight Laccase cDNAs in Loblolly Pine (Pinus taeda)*}, volume={114}, ISSN={0918-9440}, url={http://dx.doi.org/10.1007/pl00013978}, DOI={10.1007/PL00013978}, number={2}, journal={Journal of Plant Research}, publisher={Springer Science and Business Media LLC}, author={Sato, Yasushi and Wuli, Bao and Sederoff, Ronald and Whetten, Ross}, year={2001}, month={Jun}, pages={147–155} }
 @article{bergmann_lin_whetten_1999, title={Susceptibility of Paulownia elongata to Agrobacterium and production of transgenic calli and hairy roots by in vitro inoculation}, volume={55}, DOI={10.1023/A:1026481926560}, number={1}, journal={Plant Cell, Tissue and Organ Culture}, author={Bergmann, Ben and Lin, X. and Whetten, R.}, year={1999}, pages={45–51} }
 @article{bergmann_whetten_1998, title={In vitro rooting and early greenhouse growth of micropropagated Paulownia elongata shoots}, volume={15}, ISSN={["0169-4286"]}, DOI={10.1023/A:1006591704075}, number={2}, journal={NEW FORESTS}, author={Bergmann, BA and Whetten, R}, year={1998}, month={Mar}, pages={127–138} }
 @inbook{goldfarb_lian_lanz-garcia_whetten_1997, title={Auxin-induced gene expression during rooting of loblolly pine stem cuttings}, ISBN={0306457067}, DOI={10.1007/978-1-4615-5403-5_31}, booktitle={Biology of Root Formation and Development}, publisher={New York: Plenum Press}, author={Goldfarb, B. and Lian, Z. and Lanz-Garcia, C. and Whetten, R. K.}, editor={A. Altman and Waisel, Y.Editors}, year={1997}, pages={163–167} }
 @inproceedings{o'malley_grattapaglia_chaparro_wilcox_amerson_liu_whetten_mckeand_kuhlman_mccord_et al._1996, title={Molecular markers,  forest genetics, and tree breeding}, DOI={10.1007/978-1-4899-0280-1_7}, abstractNote={Several years ago, Strauss et al. (1992) thoughtfully evaluated the application of molecular markers in forest tree breeding for marker aided selection. The purpose of their paper was to emphasize the limitations and shortcomings of marker-aided selection particularly in conifers. They argued that studies of quantitative trait loci identified in agronomic crops, which have significant utility (e.g. Stuber, 1992; Stuber et al., 1992), are of little relevance to assessing the potential for marker aided selection in populations of forest trees, and that the near term usefulness of molecular markers for forest tree breeding will be limited. The major barriers to application included cost, the lack of association of markers with traits across breeding populations due to linkage equilibrium, variation in expression of loci affecting quantitative traits due to differences in genetic background, genotype environment interactions, and stability of marker-trait associations over multiple generations. In addition, Strauss et al. (1992) noted that marker-aided selection would be most useful for within family selection, where the economic values of the traits are high, the trait heritabilities are low, and where markers are able to explain much of the genetic variance. However, they argued that important traits in forest trees such as wood volume, are likely to be controlled by large numbers of genes with small effects, and therefore, are unlikely to have useful marker trait associations.}, booktitle={Genomes of Plants and Animals: 21 Stadler Genetics Symposium}, publisher={Plenum Press,  NY}, author={O'Malley, D. M. and Grattapaglia, D. and Chaparro, J. X. and Wilcox, P. L. and Amerson, H. V. and Liu, B-H and Whetten, R. and McKeand, Steven and Kuhlman, E. G. and McCord, S. and et al.}, editor={Gustafson, J. P. and Flavell, R. B.Editors}, year={1996}, pages={87–102} }
 @inproceedings{grattapaglia_chaparro_wilcox_mccord_crane_amerson_werner_liu_o'malley_whetten_et al._1993, title={Application of genetic markers to tree breeding}, booktitle={Proceedings of the 22nd Southern Forest Tree Improvement Conference}, author={Grattapaglia, D. and Chaparro, J. and Wilcox, P. and McCord, S. and Crane, B. and Amerson, H. and Werner, D. and Liu, B. H. and O'Malley, D. and Whetten, R. and et al.}, year={1993}, pages={452–463} }
 @inproceedings{grattapaglia_chaparro_wilcox_mccord_werner_amerson_mckeand_bridgwater_whetten_o'malley_et al._1992, title={Mapping in woody plants with RAPD markers: application to breeding in forestry and horticulture}, booktitle={Proceedings of the Symposium on the Applications of RAPD Technology to Plant Breeding}, publisher={Joint Plant Breeding Symposium Series,  Crop Science Society of America, American Society for Horticultural Science, and American Genetics Association}, author={Grattapaglia, D. and Chaparro, J. and Wilcox, P. and McCord, S. and Werner, D. and Amerson, H. and McKeand, S. and Bridgwater, F. and Whetten, R. and O'Malley, D. and et al.}, year={1992}, pages={37–40} }
 @article{whetten_sederoff_1991, title={Genetic engineering of wood}, volume={43}, ISSN={0378-1127}, url={http://dx.doi.org/10.1016/0378-1127(91)90133-g}, DOI={10.1016/0378-1127(91)90133-G}, abstractNote={The technology of genetic engineering provides an opportunity to accelerate tree improvement and to make directed modifications in the physical and chemical properties of wood. Modifications that lead to more efficient pulping of wood for paper may be among the earliest applications because of the information available on the pathway for lignin bisosynthesis. Other potential areas of application include fiber morphology, wood density, extractive content, biomass-utilization efficiency and dimensional stability. Widespread application of this technology awaits two developments: better methods of gene transfer, and a fundamental understanding of the development process of wood formation. If it can be successfully applied, genetic engineering will help to meet the projected demand for wood and paper products in the next century.}, number={3-4}, journal={Forest Ecology and Management}, publisher={Elsevier BV}, author={Whetten, Ross and Sederoff, Ronald}, year={1991}, month={Oct}, pages={301–316} }