@article{rivera-burgos_vangessel_guedira_smith_marshall_jin_rouse_brown-guedira_2024, title={Fine mapping of stem rust resistance derived from soft red winter wheat cultivar AGS2000 to an NLR gene cluster on chromosome 6D}, volume={137}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-024-04702-0}, abstractNote={Abstract The Puccinia graminis f. sp. tritici ( Pgt ) Ug99-emerging virulent races present a major challenge to global wheat production. To meet present and future needs, new sources of resistance must be found. Identification of markers that allow tracking of resistance genes is needed for deployment strategies to combat highly virulent pathogen races. Field evaluation of a DH population located a QTL for stem rust (Sr) resistance, QSr.nc-6D from the breeding line MD01W28-08-11 to the distal region of chromosome arm 6DS where Sr resistance genes Sr42 , SrCad , and SrTmp have been identified. A locus for seedling resistance to Pgt race TTKSK was identified in a DH population and an RIL population derived from the cross AGS2000 × LA95135. The resistant cultivar AGS2000 is in the pedigree of MD01W28-08-11 and our results suggest that it is the source of Sr resistance in this breeding line. We exploited published markers and exome capture data to enrich marker density in a 10 Mb region flanking QSr.nc-6D . Our fine mapping in heterozygous inbred families identified three markers co-segregating with resistance and delimited QSr.nc-6D to a 1.3 Mb region. We further exploited information from other genome assemblies and identified collinear regions of 6DS harboring clusters of NLR genes. Evaluation of KASP assays corresponding to our co-segregating SNP suggests that they can be used to track this Sr resistance in breeding programs. However, our results also underscore the challenges posed in identifying genes underlying resistance in such complex regions in the absence of genome sequence from the resistant genotypes.}, number={9}, journal={THEORETICAL AND APPLIED GENETICS}, author={Rivera-Burgos, L. and VanGessel, C. and Guedira, M. and Smith, J. and Marshall, D. and Jin, Y. and Rouse, M. and Brown-Guedira, G.}, year={2024}, month={Sep} } @article{dewitt_lyerly_guedira_holland_murphy_ward_boyles_mergoum_babar_shakiba_et al._2023, title={Bearded or smooth? Awns improve yield when wheat experiences heat stress during grain fill in the southeastern United States}, volume={74}, ISSN={["1460-2431"]}, url={https://doi.org/10.1093/jxb/erad318}, DOI={10.1093/jxb/erad318}, abstractNote={Abstract The presence or absence of awns—whether wheat heads are ‘bearded’ or ‘smooth’ – is the most visible phenotype distinguishing wheat cultivars. Previous studies suggest that awns may improve yields in heat or water-stressed environments, but the exact contribution of awns to yield differences remains unclear. Here we leverage historical phenotypic, genotypic, and climate data for wheat (Triticum aestivum) to estimate the yield effects of awns under different environmental conditions over a 12-year period in the southeastern USA. Lines were classified as awned or awnless based on sequence data, and observed heading dates were used to associate grain fill periods of each line in each environment with climatic data and grain yield. In most environments, awn suppression was associated with higher yields, but awns were associated with better performance in heat-stressed environments more common at southern locations. Wheat breeders in environments where awns are only beneficial in some years may consider selection for awned lines to reduce year-to-year yield variability, and with an eye towards future climates.}, number={21}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={DeWitt, Noah and Lyerly, Jeanette and Guedira, Mohammed and Holland, James B. and Murphy, J. Paul and Ward, Brian P. and Boyles, Richard E. and Mergoum, Mohamed and Babar, Md Ali and Shakiba, Ehsan and et al.}, editor={Dreisigacker, SusanneEditor}, year={2023}, month={Nov}, pages={6749–6759} } @article{dewitt_guedira_murphy_marshall_mergoum_maltecca_brown-guedira_2022, title={A network modeling approach provides insights into the environment-specific yield architecture of wheat}, volume={5}, ISSN={["1943-2631"]}, url={https://doi.org/10.1093/genetics/iyac076}, DOI={10.1093/genetics/iyac076}, abstractNote={Abstract Wheat (Triticum aestivum) yield is impacted by a diversity of developmental processes which interact with the environment during plant growth. This complex genetic architecture complicates identifying quantitative trait loci that can be used to improve yield. Trait data collected on individual processes or components of yield have simpler genetic bases and can be used to model how quantitative trait loci generate yield variation. The objectives of this experiment were to identify quantitative trait loci affecting spike yield, evaluate how their effects on spike yield proceed from effects on component phenotypes, and to understand how the genetic basis of spike yield variation changes between environments. A 358 F5:6 recombinant inbred line population developed from the cross of LA-95135 and SS-MPV-57 was evaluated in 2 replications at 5 locations over the 2018 and 2019 seasons. The parents were 2 soft red winter wheat cultivars differing in flowering, plant height, and yield component characters. Data on yield components and plant growth were used to assemble a structural equation model to characterize the relationships between quantitative trait loci, yield components, and overall spike yield. The effects of major quantitative trait loci on spike yield varied by environment, and their effects on total spike yield were proportionally smaller than their effects on component traits. This typically resulted from contrasting effects on component traits, where an increase in traits associated with kernel number was generally associated with a decrease in traits related to kernel size. In all, the complete set of identified quantitative trait loci was sufficient to explain most of the spike yield variation observed within each environment. Still, the relative importance of individual quantitative trait loci varied dramatically. Path analysis based on coefficients estimated through structural equation model demonstrated that these variations in effects resulted from both different effects of quantitative trait loci on phenotypes and environment-by-environment differences in the effects of phenotypes on one another, providing a conceptual model for yield genotype-by-environment interactions in wheat.}, number={3}, journal={GENETICS}, author={DeWitt, Noah and Guedira, Mohammed and Murphy, Joseph Paul and Marshall, David and Mergoum, Mohamed and Maltecca, Christian and Brown-Guedira, Gina}, editor={Juenger, TEditor}, year={2022}, month={May} } @article{dewitt_guedira_lauer_murphy_marshall_mergoum_johnson_holland_brown-guedira_2021, title={Characterizing the oligogenic architecture of plant growth phenotypes informs genomic selection approaches in a common wheat population}, volume={22}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-021-07574-6}, abstractNote={Abstract Background Genetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characterized in wheat genetics. While the major variants for these traits have been cloned, the importance of these variants in contributing to genetic variation for plant growth over time is not fully understood. Here we develop a biparental population segregating for major variants for both plant height and flowering time to characterize the genetic architecture of the traits and identify additional novel QTL. Results We find that additive genetic variation for both traits is almost entirely associated with major and moderate-effect QTL, including four novel heading date QTL and four novel plant height QTL. FT2 and Vrn-A3 are proposed as candidate genes underlying QTL on chromosomes 3A and 7A, while Rht8 is mapped to chromosome 2D. These mapped QTL also underlie genetic variation in a longitudinal analysis of plant growth over time. The oligogenic architecture of these traits is further demonstrated by the superior trait prediction accuracy of QTL-based prediction models compared to polygenic genomic selection models. Conclusions In a population constructed from two modern wheat cultivars adapted to the southeast U.S., almost all additive genetic variation in plant growth traits is associated with known major variants or novel moderate-effect QTL. Major transgressive segregation was observed in this population despite the similar plant height and heading date characters of the parental lines. This segregation is being driven primarily by a small number of mapped QTL, instead of by many small-effect, undetected QTL. As most breeding populations in the southeast U.S. segregate for known QTL for these traits, genetic variation in plant height and heading date in these populations likely emerges from similar combinations of major and moderate effect QTL. We can make more accurate and cost-effective prediction models by targeted genotyping of key SNPs. }, number={1}, journal={BMC GENOMICS}, author={DeWitt, Noah and Guedira, Mohammed and Lauer, Edwin and Murphy, J. Paul and Marshall, David and Mergoum, Mohamed and Johnson, Jerry and Holland, James B. and Brown-Guedira, Gina}, year={2021}, month={May} } @article{dewitt_guedira_lauer_sarinelli_tyagi_fu_hao_murphy_marshall_akhunova_et al._2020, title={Sequence-based mapping identifies a candidate transcription repressor underlying awn suppression at the B1 locus in wheat}, volume={225}, ISSN={["1469-8137"]}, DOI={10.1111/nph.16152}, abstractNote={Summary Awns are stiff, hair‐like structures which grow from the lemmas of wheat (Triticum aestivum) and other grasses that contribute to photosynthesis and play a role in seed dispersal. Variation in awn length in domesticated wheat is controlled primarily by three major genes, most commonly the dominant awn suppressor Tipped1 (B1). This study identifies a transcription repressor responsible for awn inhibition at the B1 locus. Association mapping was combined with analysis in biparental populations to delimit B1 to a distal region of 5AL colocalized with QTL for number of spikelets per spike, kernel weight, kernel length, and test weight. Fine‐mapping located B1 to a region containing only two predicted genes, including C2H2 zinc finger transcriptional repressor TraesCS5A02G542800 upregulated in developing spikes of awnless individuals. Deletions encompassing this candidate gene were present in awned mutants of an awnless wheat. Sequence polymorphisms in the B1 coding region were not observed in diverse wheat germplasm whereas a nearby polymorphism was highly predictive of awn suppression. Transcriptional repression by B1 is the major determinant of awn suppression in global wheat germplasm. It is associated with increased number of spikelets per spike and decreased kernel size. }, number={1}, journal={NEW PHYTOLOGIST}, author={DeWitt, Noah and Guedira, Mohammed and Lauer, Edwin and Sarinelli, Martin and Tyagi, Priyanka and Fu, Daolin and Hao, QunQun and Murphy, J. Paul and Marshall, David and Akhunova, Alina and et al.}, year={2020}, month={Jan}, pages={326–339} } @article{kippes_guedira_lin_alvarez_brown-guedira_dubcovsky_2018, title={Single nucleotide polymorphisms in a regulatory site of VRN-A1 first intron are associated with differences in vernalization requirement in winter wheat}, volume={293}, ISSN={["1617-4623"]}, DOI={10.1007/s00438-018-1455-0}, abstractNote={Winter wheats require a long exposure to cold temperatures (vernalization) to accelerate flowering. However, varieties differ in the length of the period of cold required to saturate the vernalization response. Here we show that single nucleotide polymorphisms (SNP) at the binding site of the GRP2 protein in the VRN-A1 first intron (henceforth, RIP3) are associated with significant differences in heading time after a partial vernalization treatment. The ancestral winter VRN-A1 allele in 'Triple Dirk C' has one SNP in the RIP3 region (1_SNP) relative to the canonical RIP3 sequence, whereas the derived 'Jagger' allele has three SNPs (3_SNPs). Both varieties have a single VRN-A1 copy encoding identical proteins. In an F2 population generated from a cross between these two varieties, plants with the 3_SNPs haplotype headed significantly earlier (P < 0.001) than those with the 1_SNP haplotype, both in the absence of vernalization (17 days difference) and after 3-weeks of vernalization (11 days difference). Plants with the 3_SNPs haplotype showed higher VRN-A1 transcript levels than those with the 1_SNP haplotype. The 3_SNPs haplotype was also associated with early heading in a panel of 127 winter wheat varieties grown in three separate controlled-environment experiments under partial vernalization (36 to 54 days, P < 0.001) and one experiment under field conditions (21 d, P < 0.0001). The RIP3 polymorphisms can be used by wheat breeders to develop winter wheat varieties adapted to regions with different duration or intensity of the cold season.}, number={5}, journal={MOLECULAR GENETICS AND GENOMICS}, author={Kippes, Nestor and Guedira, Mohammed and Lin, Lijuan and Alvarez, Maria A. and Brown-Guedira, Gina L. and Dubcovsky, Jorge}, year={2018}, month={Oct}, pages={1231–1243} } @article{mason_addison_babar_acuna_lozada_subramanian_arguello_miller_brown-guedira_guedira_et al._2018, title={Diagnostic Markers for Vernalization and Photoperiod Loci Improve Genomic Selection for Grain Yield and Spectral Reflectance in Wheat}, volume={58}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2017.06.0348}, abstractNote={ABSTRACTThe objective of this study was to identify quantitative trait loci (QTL) associated with normalized difference vegetation index (NDVI) measured across different growth stages in a wheat (Triticum aestivum L.) recombinant inbred line (RIL) population and to determine the predictability of NDVI and grain yield (GY) using a genomic selection (GS) approach. The RILs were grown over three seasons in 12 total site‐years and NDVI was measured in seven site‐years. Measurements of NDVI from tillering to physiological maturity showed low to moderate heritability (h2 = 0.06–0.68). Positive correlations were observed among NDVI, GY, and biomass, particularly in low‐yielding site‐years. Quantitative trait loci analysis found 18 genomic regions associated with NDVI, with most pleiotropic across multiple growth stages. The QTL were detected near markers for Ppd‐B1, Ppd‐D1, vrn‐A1, and vrn‐B1, with Ppd‐D1 having the largest effect. Multiple QTL models showed that epistatic interactions between Ppd and Vrn loci also significantly influenced NDVI. Genomic selection accuracy ranged from r = −0.10 to 0.54 for NDVI across growth stages. However, the inclusion of Vrn and Ppd loci as fixed effect covariates increased GS accuracy for NDVI and GY in site‐year groupings with the lowest heritability. The highest accuracy for GY (r = 0.58–0.59) was observed in the site‐year grouping with the highest heritability (h2 = 0.85). Overall, these results will aid in future selection of optimal plant growth for target environments using both phenotypic and GS approaches.}, number={1}, journal={CROP SCIENCE}, author={Mason, R. Esten and Addison, Christopher K. and Babar, Ali and Acuna, Andrea and Lozada, Dennis and Subramanian, Nithya and Arguello, Maria Nelly and Miller, Randall G. and Brown-Guedira, Gina and Guedira, Mohammed and et al.}, year={2018}, pages={242–252} } @article{guedira_xiong_hao_johnson_harrison_marshall_brown-guedira_2016, title={Heading Date QTL in Winter Wheat (Triticum aestivum L.) Coincide with Major Developmental Genes VERNALIZATION1 and PHOTOPERIOD1}, volume={11}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0154242}, abstractNote={In wheat (Triticum aestivum L.), time from planting to spike emergence is influenced by genes controlling vernalization requirement and photoperiod response. Characterizing the available genetic diversity of known and novel alleles of VERNALIZATION1 (VRN1) and PHOTOPERIOD1 (PPD1) in winter wheat can inform approaches for breeding climate resilient cultivars. This study identified QTL for heading date (HD) associated with multiple VRN1 and PPD1 loci in a population developed from a cross between two early flowering winter wheat cultivars. When the population was grown in the greenhouse after partial vernalization treatment, major heading date QTLs co-located with the VRN-A1 and VRN-B1 loci. Copy number variation at the VRN-A1 locus influenced HD such that RIL having three copies required longer cold exposure to transition to flowering than RIL having two VRN-A1 copies. Sequencing vrn-B1 winter alleles of the parents revealed multiple polymorphisms in the first intron that were the basis of mapping a major HD QTL coinciding with VRN-B1. A 36 bp deletion in the first intron of VRN-B1 was associated with earlier HD after partial vernalization in lines having either two or three haploid copies of VRN-A1. The VRN1 loci interacted significantly and influenced time to heading in field experiments in Louisiana, Georgia and North Carolina. The PPD1 loci were significant determinants of heading date in the fully vernalized treatment in the greenhouse and in all field environments. Heading date QTL were associated with alleles having large deletions in the upstream regions of PPD-A1 and PPD-D1 and with copy number variants at the PPD-B1 locus. The PPD-D1 locus was determined to have the largest genetic effect, followed by PPD-A1 and PPD-B1. Our results demonstrate that VRN1 and PPD1 alleles of varying strength allow fine tuning of flowering time in diverse winter wheat growing environments.}, number={5}, journal={PLOS ONE}, author={Guedira, Mohammed and Xiong, Mai and Hao, Yuan Feng and Johnson, Jerry and Harrison, Steve and Marshall, David and Brown-Guedira, Gina}, year={2016}, month={May} } @article{addison_mason_brown-guedira_guedira_hao_miller_subramanian_lozada_acuna_arguello_et al._2016, title={QTL and major genes influencing grain yield potential in soft red winter wheat adapted to the southern United States}, volume={209}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-016-1650-1}, number={3}, journal={EUPHYTICA}, author={Addison, Christopher K. and Mason, R. Esten and Brown-Guedira, Gina and Guedira, Mohammed and Hao, Yuanfeng and Miller, Randall G. and Subramanian, Nithya and Lozada, Dennis N. and Acuna, Andrea and Arguello, Maria N. and et al.}, year={2016}, month={Jun}, pages={665–677} } @article{hao_parks_cowger_chen_wang_bland_murphy_guedira_brown-guedira_johnson_et al._2015, title={Molecular characterization of a new powdery mildew resistance gene Pm54 in soft red winter wheat}, volume={128}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-014-2445-1}, abstractNote={A new powdery mildew resistance gene Pm54 was identified on chromosome 6BL in soft red winter wheat. Powdery mildew is causing increasing damage to wheat production in the southeastern USA. To combat the disease, a continuing need exists to discover new genes for powdery mildew resistance and to incorporate those genes into breeding programs. Pioneer(®) variety 26R61 (shortened as 26R61) and AGS 2000 have been used as checks in the Uniform Southern Soft Red Winter Wheat Nursery for a decade, and both have provided good resistance across regions during that time. In the present study, a genetic analysis of mildew resistance was conducted on a RIL population developed from a cross of 26R61 and AGS 2000. Phenotypic evaluation was conducted in the field at Plains, GA, and Raleigh, NC, in 2012 and 2013, a total of four environments. Three quantitative trait loci (QTL) with major effect were consistently detected on wheat chromosomes 2BL, 4A and 6BL. The 2BL QTL contributed by 26R61 was different from Pm6, a widely used gene in the southeastern USA. The other two QTL were identified from AGS 2000. The 6BL QTL was subsequently characterized as a simple Mendelian factor when the population was inoculated with a single Blumeria graminis f. sp. tritici (Bgt) isolate in controlled environments. Since there is no known powdery mildew resistance gene (Pm) on this particular location of common wheat, the gene was designated Pm54. The closely linked marker Xbarc134 was highly polymorphic in a set of mildew differentials, indicating that the marker should be useful for pyramiding Pm54 with other Pm genes by marker-assisted selection.}, number={3}, journal={THEORETICAL AND APPLIED GENETICS}, author={Hao, Y. F. and Parks, R. and Cowger, C. and Chen, Z. B. and Wang, Y. Y. and Bland, D. and Murphy, J. P. and Guedira, M. and Brown-Guedira, Gina and Johnson, J. and et al.}, year={2015}, month={Mar}, pages={465–476} } @article{guedira_maloney_xiong_petersen_murphy_marshall_johnson_harrison_brown-guedira_2014, title={Vernalization Duration Requirement in Soft Winter Wheat is Associated with Variation at the VRN-B1 Locus}, volume={54}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2013.12.0833}, abstractNote={ABSTRACTGenetic variation in the factors controlling flowering in wheat (Triticum aestivum L.) allow it to be grown in a wide range of environments. The aim of this study was to identify genetic determinants of flowering time in winter wheat cultivars adapted to regions of the United States differing in latitude and the duration of cold temperatures during winter. Quantitative trait locus (QTL) analysis was performed in a recombinant inbred line (RIL) population from the cross between cultivars NC‐Neuse and AGS 2000 that are adapted to the Mid‐Atlantic and Southeastern regions, respectively. We identified a QTL for heading date (HD) in the greenhouse after 4 wk of vernalization, designated Qvdr.nc‐5BL, which also had a large effect on winter dormancy release and HD when the population was evaluated in the field at locations in North Carolina, Georgia, and Louisiana during 2012 and North Carolina during 2013. However, Qvdr.nc‐5BL did not have a significant effect on HD in greenhouse grown plants vernalized for 8 wk or in plants grown in the field at Raleigh, NC during 2011. In those environments where Qvdr.nc‐5BL was not significant, a region on chromosome 2B, probably associated with the Ppd‐B1 locus, was determined to have a HD effect. Interrogation of the population with gene‐based markers for Vrn‐B1 and Ppd‐B1 suggests that these loci are major determinants of HD in winter wheat and are important for adaptation to diverse growing environments.}, number={5}, journal={CROP SCIENCE}, author={Guedira, Mohammed and Maloney, Peter and Xiong, Mai and Petersen, Stine and Murphy, J. Paul and Marshall, David and Johnson, Jerry and Harrison, Steve and Brown-Guedira, Gina}, year={2014}, pages={1960–1971} } @article{guedira_brown-guedira_van sanford_sneller_souza_marshall_2010, title={Distribution of Rht Genes in Modern and Historic Winter Wheat Cultivars from the Eastern and Central USA}, volume={50}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2009.10.0626}, abstractNote={ABSTRACTOver 70% of wheat (Triticum aestivum L.) cultivars grown worldwide have a semidwarf phenotype controlled by the major genes Rht‐B1, Rht‐D1, and Rht8c The objective of this study was to determine their frequency in a set of historic and modern soft and hard winter wheat cultivars grown in the central and eastern USA. Three hundred sixty‐two cultivars that were developed from 1808 to 2008 were evaluated with molecular markers for Rht‐B1, Rht‐D1, and Rht8c All cultivars released before 1964 (41 soft winter wheat and 6 hard winter wheat) had wild‐type (tall) alleles at all three loci. After introduction of the dwarfing genes, the percentage of tested lines carrying either Rht‐B1b or Rht‐D1b increased rapidly to greater than 90% of modern varieties. Among soft winter wheat cultivars, the Rht‐D1b dwarfing gene was the most frequent being present in 45% of all lines tested and Rht‐B1b was present in 28%, while in the hard winter wheat cultivars the Rht‐B1b allele is the most prevalent in 77% of lines. Only 8% of the hard cultivars tested had the Rht‐D1b allele. The presence of the 192‐base pair (bp) allele of the microsatellite marker Xgwm261 indicated that Rht8c was less frequently used as a source of dwarfing in U.S. winter wheat germplasm, being present in 8 and 3% of the soft winter wheat and the hard winter wheats, respectively. A number of modern cultivars were identified that did not carry any of the dwarfing genes assayed and may possess alternative reduced height genes.}, number={5}, journal={CROP SCIENCE}, author={Guedira, M. and Brown-Guedira, G. and Van Sanford, D. and Sneller, C. and Souza, E. and Marshall, D.}, year={2010}, pages={1811–1822} }