@article{ward_merrill_bulli_pumphrey_mason_mergoum_johnson_sapkota_lopez_marshall_et al._2021, title={Analysis of the primary sources of quantitative adult plant resistance to stripe rust in US soft red winter wheat germplasm}, volume={14}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20082}, abstractNote={AbstractStripe rust, or yellow rust (Puccinia striiformis Westend. f. sp. tritic), is a disease of wheat (Triticum aestivum L.) historically causing significant economic losses in cooler growing regions. Novel isolates of stripe rust with increased tolerance for high temperatures were detected in the United States circa 2000. This increased heat tolerance puts geographic regions, such as the soft red winter wheat (SRWW) growing region of the southeastern United States, at greater risk of stripe rust induced losses. In order to identify sources of stripe rust resistance in contemporary germplasm, we conducted genome‐wide association (GWA) studies on stripe rust severity measured in two panels. The first consisted of 273 older varieties, landraces, and some modern elite breeding lines and was evaluated in environments in the U.S. Pacific Northwest and the southeastern United States. The second panel consisted of 588 modern, elite SRWW breeding lines and was evaluated in four environments in Arkansas and Georgia. The analyses identified three major resistance loci on chromosomes: 2AS (presumably the 2NS:2AS alien introgression from Aegilops ventricosa Tausch; syn. Ae. caudata L.), 3BS, and 4BL. The 4BL locus explained a greater portion of variance in resistance than either the 2AS or 3BS loci in southeastern environments. However, its effects were unstable across different environments and sets of germplasm, possibly a result of its involvement in epistatic interactions. Relatively few lines carry resistance alleles at all three loci, suggesting that there is a pre‐existing reservoir of enhanced stripe rust resistance that may be further exploited by regional breeding programs.}, number={1}, journal={PLANT GENOME}, author={Ward, Brian P. and Merrill, Keith and Bulli, Peter and Pumphrey, Mike and Mason, Richard Esten and Mergoum, Mohamed and Johnson, Jerry and Sapkota, Suraj and Lopez, Benjamin and Marshall, David and et al.}, year={2021}, month={Mar} }
 @article{winn_acharya_merrill_lyerly_brown-guedira_cambron_harrison_reisig_murphy_2021, title={Mapping of a novel major effect Hessian fly field partial-resistance locus in southern soft red winter wheat line LA03136E71}, volume={8}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-021-03936-6}, abstractNote={Hessian fly resistance has centralized around resistance loci that are biotype specific. We show that field resistance is evident and controlled by a single locus on chromosome 7D. Hessian flies (Mayetiola destructor Say) infest and feed upon wheat (Triticum aestivum L) resulting in significant yield loss. Genetically resistant cultivars are the most effective method of Hessian fly management. Wheat breeders in the southern USA have observed cultivars exhibiting a "field resistance" to Hessian fly that is not detectable by greenhouse assay. The resistant breeding line "LA03136E71" and susceptible cultivar "Shirley" were crossed to develop a population of 200 random F 4:5  lines using single seed descent. The population was evaluated in a total of five locations in North Carolina during the 2019, 2020, and 2021 seasons. A subsample of each plot was evaluated for the total number of tillers, number of infested tillers, and total number of larvae/pupae. From these data, the percent infested tillers, number of larvae/pupae per tiller, and the number of larvae/pupae per infested tiller were estimated. In all within and across environment combinations for all traits recorded, the genotype effect was significant (p < 0.05). Interval mapping identified a single large effect QTL distally on the short arm of chromosome 7D for all environment-trait combinations. This locus was identified on a chromosome where no other Hessian fly resistance/tolerance QTL has been previously identified. This novel Hessian fly partial-resistance QTL is termed QHft.nc-7D. Fine mapping must be conducted in this region to narrow down the causal agents responsible for this trait, and investigation into the mode of action is highly suggested.}, journal={THEORETICAL AND APPLIED GENETICS}, author={Winn, Z. J. and Acharya, R. and Merrill, K. and Lyerly, J. and Brown-Guedira, G. and Cambron, S. and Harrison, S. H. and Reisig, D. and Murphy, J. P.}, year={2021}, month={Aug} }
 @article{lozada_mason_babar_carver_guedira_merrill_arguello_acuna_vieira_holder_et al._2017, title={Association mapping reveals loci associated with multiple traits that affect grain yield and adaptation in soft winter wheat}, volume={213}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-017-2005-2}, number={9}, journal={EUPHYTICA}, author={Lozada, Dennis N. and Mason, R. Esten and Babar, Md Ali and Carver, Brett F. and Guedira, Gina-Brown and Merrill, Keith and Arguello, Maria Nelly and Acuna, Andrea and Vieira, Lucas and Holder, Amanda and et al.}, year={2017}, month={Sep} }
 @article{arruda_brown_brown-guedira_krill_thurber_merrill_foresman_kolb_2016, title={Genome-Wide Association Mapping of Fusarium Head Blight Resistance in Wheat using Genotyping-by-Sequencing}, volume={9}, ISSN={["1940-3372"]}, DOI={10.3835/plantgenome2015.04.0028}, abstractNote={Fusarium head blight (FHB) is one of the most important wheat (Triticum aestivum L.) diseases worldwide, and host resistance displays complex genetic control. A genome‐wide association study (GWAS) was performed on 273 winter wheat breeding lines from the midwestern and eastern regions of the United States to identify chromosomal regions associated with FHB resistance. Genotyping‐by‐sequencing (GBS) was used to identify 19,992 single‐nucleotide polymorphisms (SNPs) covering all 21 wheat chromosomes. Marker–trait associations were performed with different statistical models, the most appropriate being a compressed mixed linear model (cMLM) controlling for relatedness and population structure. Ten significant SNP–trait associations were detected on chromosomes 4A, 6A, 7A, 1D, 4D, and 7D, and multiple SNPs were associated with Fhb1 on chromosome 3B. Although combination of favorable alleles of these SNPs resulted in lower levels of severity (SEV), incidence (INC), and deoxynivalenol concentration (DON), lines carrying multiple beneficial alleles were in very low frequency for most traits. These SNPs can now be used for creating new breeding lines with different combinations of favorable alleles. This is one of the first GWAS using genomic resources from the International Wheat Genome Sequencing Consortium (IWGSC).}, number={1}, journal={PLANT GENOME}, author={Arruda, Marcio P. and Brown, Patrick and Brown-Guedira, Gina and Krill, Allison M. and Thurber, Carrie and Merrill, Keith R. and Foresman, Bradley J. and Kolb, Frederic L.}, year={2016}, month={Mar} }
 @article{meyer_ghimire_decker_merrill_coleman_2013, title={The Ghost of Outcrossing Past in Downy Brome, an Inbreeding Annual Grass}, volume={104}, ISSN={["0022-1503"]}, DOI={10.1093/jhered/est019}, abstractNote={We investigated the frequency of outcrossing in downy brome (Bromus tectorum L.), a cleistogamous weedy annual grass, in both common garden and wild populations, using microsatellite and single nucleotide polymorphic (SNP) markers. In the common garden study, 25 lines with strongly contrasting genotypes were planted in close proximity. We fingerprinted 10 seed progeny from 8 individuals of each line and detected 15 first-generation heterozygotes for a t-value (corrected for cryptic crosses) of 0.0082. Different genotypes were significantly overrepresented as maternal versus paternal parents of heterozygotes, suggesting gender-function-dependent genetic control of outcrossing rates. In 4 wild populations (>300 individuals each), expected heterozygosity ranged from 0.149 to 0.336, whereas t-values ranged from 0.0027 to 0.0133, indicating high levels of both genetic diversity and inbreeding. Up to a third of the individuals in each population belonged to groups with identical or nearly identical SNP genotypes, whereas many of the remaining individuals were members of loose clusters of apparently related plants that probably represent descendants from past outcrossing events. Strict inbreeding in some lineages within a population with occasional outcrossing in others may be related to positive selection on adaptive syndromes associated with specific inbreeding lineages, or possibly to among-lineage differences in genetic regulation of outcrossing.}, number={4}, journal={JOURNAL OF HEREDITY}, author={Meyer, Susan E. and Ghimire, Sudeep and Decker, Samuel and Merrill, Keith R. and Coleman, Craig E.}, year={2013}, pages={476–490} }