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Genome wide association study of seedling and adult plant leaf rust resistance in elite spring wheat breeding lines

Gao, Liangliang, Turner, M. Kathryn, Chao, Shiaoman, Kolmer, James, Anderson, James A.
Plos One 2016 v.11 no.2 pp. e0148671
Triticum aestivum, breeding lines, computer software, crop production, disease resistance, field experimentation, genes, genome-wide association study, leaf rust, mature plants, phenotype, plant breeding, population structure, quantitative trait loci, races, seedlings, single nucleotide polymorphism, spring wheat
Leaf rust is an important disease, threatening wheat production annually. Identification of resistance genes or QTLs for effective field resistance could greatly enhance our ability to breed durably resistant varieties. We applied a genome wide association study (GWAS) approach to identify resistance genes or QTLs in 338 spring wheat breeding lines from public and private sectors that were predominately developed in the Americas. A total of 46 QTLs were identified for field and seedling traits and approximately 20-30 confer field resistance in varying degrees. The 10 QTLs accounting for the most variation in field resistance explained 26-30% of the total variation (depending on traits: percent severity, coefficient of infection or response type), similarly the 10 QTLs accounting for most of the variation in seedling resistance to different races explained 24-34% of the variation, after correcting for population structure. Two potentially novel QTLs (QLr.umn-1AL, QLr.umn-4AS) were identified. Identification of novel genes or QTLs and validation of previously identified genes or QTLs for seedling and especially adult plant resistance will enhance understanding of leaf rust resistance and assist breeding for resistant wheat varieties. We also developed computer programs to automate field and seedling rust phenotype data conversions. This is the first GWAS study of leaf rust resistance in elite wheat breeding lines genotyped with high density 90K SNP arrays.