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Title: Genome-wide association mapping reveals novel QTL for seedling leaf rust resistance in a worldwide collection of winter wheat

Author
item LI, GENQIAO - Oklahoma State University
item Xu, Xiangyang
item Bai, Guihua
item CARVER, BRETT - Oklahoma State University
item HUNGER, ROBERT - Oklahoma State University
item Bonman, John
item Kolmer, James
item DONG, HONGXU - University Of Illinois

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/29/2016
Publication Date: 8/9/2016
Citation: Li, G., Xu, X., Bai, G., Carver, B.F., Hunger, R., Bonman, J.M., Kolmer, J.A., Dong, H. 2016. Genome-wide association mapping reveals novel QTL for seedling leaf rust resistance in a worldwide collection of winter wheat. The Plant Genome. 9(3):1-12. doi:10.3835/plantgenome2016.06.0051.

Interpretive Summary: Leaf rust, caused by P. recondita, is a major disease that regularly reduces 5-15% yield of susceptible wheat cultivars. Most of leaf rust resistance genes conditioned effective levels of resistance when first released, and lost resistance within a few years in the Great Plains. The short-lived nature of leaf rust resistance genes necessitate continuously discovering novel genes. We performed a genome-wide association study (GWAS) on a panel of 1596 germplasm lines collected from 85 countries, and identified 14 quantitative trait loci (QTL) for leaf rust resistance at a false discovery rate (FDR) of 0.01. Of these QTL, nine QTLs reside in the vicinity of known genes or QTLs in bread wheat. Another QTL is new in bread wheat, but is close to a locus previously identified in durum wheat. The other four QTLs are likely novel loci for leaf rust resistance. In addition, another 31 QTLs were significantly associated with leaf rust resistance at a less stringent FDR of 0.05. The novel QTL identified in this study represent a valuable addition to the leaf rust resistance gene pool available for wheat breeding programs to fight this devastating pathogen.

Technical Abstract: Leaf rust is a major disease that causes significant wheat yield losses worldwide. Growing resistant cultivars is an effective approach to reduce disease losses. The short-lived nature of leaf rust resistance (Lr) genes necessitates a continuous search for novel sources of resistance. We performed a genome-wide association study (GWAS) on a panel of 1596 wheat accessions. The panel was evaluated for leaf rust resistance in a greenhouse by testing against a bulk of Puccinia triticina isolates collected from multiple fields of Oklahoma in 2013, and two predominant races in the fields of Oklahoma in 2015. A set of 5011 single nucleotide polymorphism (SNP) markers were used to genotype the panel for GWAS, and structure analysis divided the panel into six subgroups. A total of 14 quantitative trait loci (QTLs) for leaf rust resistance were identified at a false discovery rate (FDR) of 0.01 using the general linear model. Of these, nine QTLs reside in the vicinity of known genes or QTLs in bread wheat. QLr.stars-7AL1 is a new QTL to bread wheat, but is close to a locus previously identified in durum wheat. The other four QTLs, including QLr.stars-1BL3, QLr.stars-1DC1, QLr.stars-2BL1, and QLr.stars-5BL1, are likely novel loci for leaf rust resistance. The uneven distribution of the 14 QTLs in the six subpopulations of the panel suggests that wheat breeders can enhance leaf rust resistance by selectively introgressing some of the QTLs into their breeding materials. In addition, another 31 QTLs were significantly associated with leaf rust resistance at a less stringent FDR of 0.05, and some of them may also be useful sources of resistance for breeding.