Study of QTL By Environment Interactions for Stripe Rust Resistance in TAM 111 Using Saturated Genetic Maps with 90K and GBS SNPs.

Study of QTL by Environment Interactions for Stripe Rust Resistance in TAM 111 Using Saturated Genetic Maps With 90K And GBS SNPs Yan Yang1, Bhoja Basnet1,3 Amir M.H. Ibrahim1, Jackie C. Rudd2, Qingwu Xue2, Charlie Johnson4, Shuyu Liu2 1Dept. of Soil and Crop Sciences, Texas A&M University (TAMU), College Station, TX 77843; 2Texas A&M AgriLife Research and Extension Center, TAMU, Amarillo, TX 79106; 3International Maize and Wheat Improvement Center (CIMMYT), Apdo Postal 6-641, C.P. 06600, D.F., Mexico; 4Genomics and Bioinformatic Center, Texas A&M AgriLife Research, College Station, TX 77843. Corresponding to: SLiu@ag.tamu.edu Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), is an important disease of wheat (Triticum aestivum L.) in the United States and other parts of the world. With the purpose of identifying the genetic basis of resistance conferred by the winter wheat cultivar ‘TAM 111’, a mapping population of 124 F6 recombinant inbred lines (RILs) developed from the cross of TAM 112/TAM 111 was evaluated against Pst populations in eight environments in the United States. A high-density genetic map was constructed by genotyping with the wheat 90K iSelect array and genotype-by-sequence (GBS). A set of 9928 markers forming 80 chromosome fragments and covering all 21 chromosomes, including 19 SSR and STS, 5094 GBS, 4815 SNPs from 90K were used for QTL analyses. The largest and most consistent stripe rust resistance QTL was identified on the long arm of chromosome 2B, explained for 9% to 49.2% of the phenotypic variance in Infection type (IT) and 3.1% to 28.5% of the variance in disease severity (DS) across the eight environments. Six tightly linked SNP markers were converted to Kompetitive allele specific PCR (KASP) marker for high throughput screening and used to estimate the effects of this 2BL QTL. QYr.tamu-2A was involved in three out of six A × A epistatic interactions for DS, one of which with the major QTL QYr.tamu-2BL. This pair of QTL was also shown in the significant interaction for IT. Significant epistasis by environment interactions for DS, existed between QYr.tamu-2A and QYr.tamu-2BL, was showed in seven out of twelve environments, and they have the largest epistasis effects. These QTLs should be taken into account with effective major genes when enhancing the stripe rust resistance and diagnostic markers should be applied through marker-assisted breeding.