Genome-wide association study and linkage analysis on resistance to rice black-streaked dwarf virus disease

Rice black-streaked dwarf virus disease (RBSDVD) transmitted by small brown planthopper (SBPH, Laodelphax striatellus) is one of the most destructive viral diseases in rice (Oryza sativa L.). It is urgent to explore resistance resources and genes to breed resistant cultivars for controlling this disease. In the present study, linkage analysis was performed using an RIL (recombinant inbred line) population including 181 lines and two quantitative trait loci (QTLs) underlying resistance to RBSDVD, qRBSDVD5 and qRBSDVD6 were detected on chromosomes 5 and 6. Furthermore, 1070 sequenced diverse rice accessions collected from 72 countries or regions were evaluated for resistance to RBSDVD. Moreover, a significantly associated locus was also detected in the same interval of qRBSDVD6 by genome-wide association study (GWAS). Candidate genes were predicted in the significantly association interval with RBSDVD resistance. Among the five haplotypes of LOC_Os06g03120, encoding an aspartyl protease precursor, haplotype 1 showed higher resistance than the other four. The study provides a powerful resource for elucidating the mechanism underlying RBSDVD resistance and breeding resistance rice cultivars by molecular-assisted selection (MAS).