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Identification of powdery mildew resistance loci in wheat by integrating genome-wide association study (GWAS) and linkage mapping

Li, Genqiao, Xu, Xiangyang, Tan, Chengcheng, Carver, Brett F., Bai, Guihua, Wang, Xuewen, Bonman, J. Michael, Wu, Yanqi, Hunger, Robert, Cowger, Christina
The crop journal 2019 v.7 no.3 pp. 294-306
Blumeria graminis f. sp. tritici, Triticum, breeding, chromosome mapping, genome-wide association study, high-yielding varieties, landraces, linear models, loci, new variety, population structure, powdery mildew, resistance genes, single nucleotide polymorphism, sustainable agriculture, wheat
Wheat powdery mildew (Blumeria graminis f. sp. tritici, Bgt) is a disease of increasing importance globally due to the adoption of high yielding varieties and modern sustainable farming technologies. Growing resistant cultivars is a preferred approach to managing this disease, and novel powdery mildew resistance genes are urgently needed for new cultivar development. A genome-wide association study was performed on a panel of 1292 wheat landraces and historical cultivars using 5011 single nucleotide polymorphism (SNP) markers. The association panel was evaluated for reactions to three Bgt inoculants, OKS(14)-B-3-1, OKS(14)-C-2-1, and Bgt15. Linkage disequilibrum (LD) analysis indicated that genome-wide LD decayed to 0.1 at 23 Mb, and population structure analysis revealed seven subgroups in the panel. Association analysis using a mixed linear model (MLM) identified three loci for powdery mildew resistance on chromosome 2B, designated QPm.stars-2BL1, QPm.stars-2BL2, and QPm.stars-2BL3. To evaluate the efficacy of GWAS in gene discovery, QPm.stars-2BL2 was validated using F2 and F2:3 populations derived from PI 420646 × OK1059060-126135-3. Linkage analysis delimited the powdery mildew resistance gene in PI 420646 to an interval where QPm.stars-2BL2 was located, lending credence to the GWAS results. QPm.stars-2BL1 and QPm.stars-2BL3, which were associated with four SNPs located at 457.7–461.7 Mb and two SNPs located at 696.6–715.9 Mb in the Chinese Spring reference IWGSC RefSeq v1.0, respectively, are likely novel loci for powdery mildew resistance and can be used in wheat breeding to improve powdery mildew resistance.