Mining favorable alleles for rice sheath blight resistance by association mapping

Abstract

Sheath blight is a serious rice disease that causes great yield losses worldwide. Sheath blight resistance is controlled by genes with minor effect. It is an urgent need to identify the resistance genes in rice germplasm and utilize them in breeding. The purpose of this study is to identify the sheath blight-resistant alleles in different rice germplasm by association mapping and explore the potential of the resistance alleles in utilization. A total of 273 rice genotypes were inoculated and evaluated for sheath blight resistance in the field for 5 years, and 158 genotypes with relatively stable disease resistance phenotype were chosen for association mapping. A wide range of phenotypic variation for sheath blight resistance was observed in the 158-genotype population. Structure analyses divided the 158 genotypes into 4 subgroups, which was consistent with principal component analysis and cluster analysis. Association mapping performed using mixed linear model with 213 markers identified 14 resistance loci, locating on all chromosomes except chromosome 6, 10 and 12. Three novel resistance loci (D704, D855, and D905) which were different from the previously reported were detected. Thirty-eight alleles were detected at the 14 loci, among which favorable alleles at 11 loci showed consistent resistance across 5 years. It was found that the favorable resistance alleles can be pyramided to improve sheath blight resistance. These results enhance the understanding of how different resistance alleles at multiple loci in regulating sheath blight resistance, and provide markers for sheath blight resistance breeding in rice.