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Background  The rice black-streaked dwarf virus (RBSDV) disease causes severe rice yield losses in Eastern China and other East Asian countries. Breeding resistant cultivars is the most economical and effective strategy to control the disease. However, few varieties and QTLs for RBSDV resistance have been identified to date.    Results  In this study, we conducted a genome-wide association study (GWAS) on RBSDV resistance using the rice diversity panel 1 (RDP1) cultivars that were genotyped by a 44,000 high-density single nucleotide polymorphism (SNP) markers array. We found that less than 15% of these cultivars displayed resistance to RBSDV when tested under natural infection conditions at two locations with serious RBSDV occurrence. The  aus ,  indica  and  tropical japonica  sub-populations displayed higher RBSDV resistance than the  aromatic  and  temperate japonica  sub-populations. In particular, we identified four varieties that displayed stable levels of RBSDV resistance at all testing locations. GWAS identified 84 non-redundant SNP loci significantly associated with RBSDV resistance at two locations, leading to the identification of 13 QTLs for RBSDV resistance. Among them,  qRBSDV-4.2  and  qRBSDV-6.3  were detected at both locations, suggesting their resistance stability against environmental influence. Field disease evaluations showed that  qRBSDV-6.3  significantly reduces RBSDV disease severity by 20%. Furthermore, introgression of  qRBSDV-6.3  into two susceptible rice cultivars by marker-assisted selection demonstrated the effectiveness of  qRBSDV-6.3  in enhancing RBSDV resistance.    Conclusions  The new resistant cultivars and QTLs against RBSDV disease identified in this study provide important information and genetic materials for the cloning of RBSDV resistance genes as well as developing RBSDV resistant varieties through marker-assisted selection.    Electronic supplementary material  The online version of this article (10.1186/s12284-019-0310-1) contains supplementary material, which is available to authorized users.

Identification of new rice cultivars and resistance loci against rice black-streaked dwarf virus disease through genome-wide association study