Genome‐Wide Association Mapping Reveals Novel QTL for Seedling Leaf Rust Resistance in a Worldwide Collection of Winter Wheat

Abstract

Leaf rust of wheat (Triticum aestivum L.) is a major disease that causes significant yield losses worldwide. 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 reaction by testing with a bulk of Puccinia triticina Eriks. (Pt) isolates collected from multiple fields of Oklahoma in 2013 and two predominant races in the fields of Oklahoma in 2015. The panel was genotyped with a set of 5011 single-nucleotide polymorphism (SNP) markers. A total of 14 quantitative trait loci (QTL) for leaf rust resistance were identified at a false discovery rate (FDR) of 0.01 using the mixed linear model (MLM). Of these, eight QTL reside in the vicinity of known genes or QTL, and more studies are needed to determine their relationship with known loci. QLr.stars-7AL1 is a new QTL to bread wheat but is close to a locus previously identified in durum wheat [Triticum turgidum L. subsp. durum (Desf.) Husn.]. The other five QTL, including QLr. , are likely novel loci for leaf rust resistance. The uneven distribution of the 14 QTL in the six subpopulations of the panel suggests that wheat breeders can enhance leaf rust resistance by selectively introgressing some of these QTL into their breeding materials. In addition, another 31 QTL were significantly associated with leaf rust resistance at a FDR of 0.05. L eaf rust, caused by Puccinia, is a major foliar disease that has afflicted wheat for thousands of years (Bolton et al., 2008). Leaf rust occurs nearly everywhere wheat is grown and typically reduces yield by 5 to 15% or more depending on crop developmental stage when the initial rust infection occurs (Samborski, 1995 Abbreviations: FDR, false discovery rate; GWAS, genome-wide association study; HR, highly resistant; HS, highly susceptible; iCore, informative core; IT, infection type; LD, linkage disequilibrium; LnP(D), log probability of data; MLM, mixed linear model; MR, moderately resistant; MS, moderately susceptible; NSGC, National Small Grains Collection; PCR, polymerase chain reaction; Pt, Puccinia triticina Eriks.; QTL, quantitative trait loci; SNP, single-nucleotide polymorphism. Core Ideas• The association panel used in this study may represent the largest in wheat GWAS• Three pathotypes, including a bulked races collected in the field, were used• A total of 14 QTL for leaf rust resistance were identified at a FDR of 0.01.• Six QTL identified in this study are novel loci in bread wheat• Thirty-one additional QTL were significant at a FDR of 0.05.

The potential of hybrid breeding to enhance leaf rust and stripe rust resistance in wheat

“…Chromosome 4A appears to be an important genome region with a high potential for leaf rust resistance in wheat. Correspondingly, promising loci were previously detected in association studies observing adult plant resistance in a set of American spring wheat (Gao et al 2016) and in a diverse core set including winter and spring wheat (Li et al 2016) or considering seedling resistance in a wheat collection of CIMMYT (Juliana et al 2018). The detected single nucleotide polymorphism (SNP) BobWhite_c47168_289 (SNP332) was also found as significantly associated with leaf rust resistance on wheat chromosome 4A by Gao et al (2016).…”

Genetic architecture of adult plant resistance to leaf rust in a wheat association mapping panel

“…Genome‐wide association studies have been reported as being a useful approach to identify linked markers with genes controlling important agronomic traits (Zhu et al ., ). In recent GWAS, using DArT and SNP (single nucleotide polymorphism) markers, several genetic regions associated with resistance to leaf rust in wheat have been identified (Crossa et al ., ; Kertho et al ., ; Gao et al ., ; Jighly et al ., ; Li et al ., ). In the present study, 13 QTLs associated with resistance to leaf rust were found linked to 14 DArT markers on the chromosomes 1BL, 1DS, 2AS, 2BL, 2DS, 3BS, 3BL, 4AL, 6BS (two), 7DS, 5BL/7BS and 6AL/6BS.…”

“…Resistance to fungal diseases, and particularly to P. triticina , constitutes a valuable target trait for conducting genome‐wide association studies (GWAS). Recent studies using this methodology have identified several quantitative trait loci (QTLs) for resistance to leaf rust (Crossa et al ., ; Kertho et al ., ; Gao et al ., ; Jighly et al ., ; Li et al ., ). As the variation of complex traits usually shows QTL × environment interaction (QEI) (Mathews et al ., ), this should be considered to determine whether the genetic factors are reasonably stable across environments, determining their potential value in breeding programmes.…”

Population structure and association analyses of the core collection of hexaploid accessions conserved <i>ex situ</i> in the Japanese gene bank NBRP-Wheat

“…In addition to QTL analysis, which is based on phenotypic and genotypic polymorphisms within a bi-parental mapping population, association mapping is also applicable to a much larger gene pool and a more diverse genetic structure (Remington et al, 2001). Whole-genome association mapping has been applied to common wheat for several agronomic traits (Breseghello and Sorrells, 2006;Crossa et al, 2007;Neumann et al, 2011;Le Gouis et al, 2012;Edae et al, 2014;Wang et al, 2014;Zanke et al, 2014Zanke et al, , 2015Zanke et al, , 2017Li et al, 2016). However, these studies focused on a common wheat (T. aestivum) population but not on other hexaploid Triticum species.…”