| Diseases are the main factors that cause yield loss in barley and are best controlled through the development of resistant cultivars. To identify and map loci conferring resistance to three important diseases (spot blotch, stem rust and Septoria Speckled Leaf Blotch (SSLB)) in ten US barley breeding programs, an association mapping (AM) approach was used. Population structure and linkage disequilibrium (LD) decay are two critical aspects in AM and were examined in 3,840 breeding lines and also cultivars genotyped with 3,072 single nucleotide polymorphism (SNP) markers. Nine subpopulations (sp1-9), mostly comprised of lines from individual breeding programs, were identified. LD decayed across a range between 4.0 to 19.8 cM as determined by the pair-wise r2 (squared value of the correlation coefficient between two loci) method and between 6.3 to 7.5 cM as determined by the mixed linear model (MLM) method. AM using the MLM method was then conducted to reveal the genetic architecture of disease resistance in US breeding germplasm. For spot blotch, three Quantitative Trait Loci (QTL) (Rcs-qtl-1H-11_10764, Rcs-qtl-3H-11_10565, and Rcs-qtl-7H-11_20162 ) governing both seedling and adult plant resistance were identified and comprise the genetic basis of durable spot blotch resistance in Midwest six-rowed lines. These three QTL together can reduce spot blotch disease level 47% and 83% at the seedling and adult plant stages, respectively. To stem rust race TTKSK, one novel adult plant resistance locus was identified on chromosome 5H and reduced disease severity by3.7 to 55.0%. Four QTL ( Rsp-qtl-1H_12_31144, Rsp-qtl-3H_12_31448, Rsp-qtl-6H_11_10064, and Rsp-qtl-6H_11_21032) for SSLB resistance were identified on chromosomes 1H, 3H, and 6H. These four QTL individually showed a small to moderate allelic effect (9-38%) in reducing disease, but the combination of all four reduced disease by 84%. The QTL identified in this study through AM will be useful in the marker-assisted development of cultivars with multiple disease resistance. |
