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

Abstract

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.

Rice black‐streaked dwarf virus: From multiparty interactions among plant–virus–vector to intermittent epidemics

“…Although commercial varieties lack resistance to RBSDV, several resistance sources have been identified in the germplasm of diverse cultivars of rice and maize and related species (Luan et al, 2012;Hajano et al, 2016;Feng et al, 2019). These studies revealed a low percentage of resistant lines and no immune or highly resistant materials among the temperate sources of japonica germplasm, but several aus-type, indica, and tropical japonica subspecies have high levels of resistance, which have been reported to be controlled by quantitative trait loci (QTLs) or multiple genes (Wang et al, 2010;Zheng et al, 2012).…”

“…These studies revealed a low percentage of resistant lines and no immune or highly resistant materials among the temperate sources of japonica germplasm, but several aus-type, indica, and tropical japonica subspecies have high levels of resistance, which have been reported to be controlled by quantitative trait loci (QTLs) or multiple genes (Wang et al, 2010;Zheng et al, 2012). To facilitate the use and transfer of host resistance in breeding programmes, recent QTL mapping or genome-wide association studies have identified genomic regions associated with RBSDV resistance and linked DNA markers (Feng et al, 2019;Xiao et al, 2019). Several QTLs on different chromosomes have been identified in japonica cultivar Koshihikari, and indica cultivars Minghui 63, WR24, Tetep, IR36, and 9194 (Wang et al, 2010;Li et al, 2013;Zhou et al, 2015a;Zhang et al, 2016;Sun et al, 2017;Xu et al, 2018).…”

“…Some QTLs such as qRBSDVD5, qRBSDVD6, and qRBSDV-6.3 that confer stable resistance have been introgressed into susceptible rice cultivars by marker-assisted selection (Feng et al, 2019;Xiao et al, 2019). In addition, five QTLs, qMRD2, qMRD6, qMRD7, qMRD8, and qMRD10, were identified in elite maize line 90110.…”

Development of marker‐free rice with stable and high resistance to rice black‐streaked dwarf virus disease through RNA interference

“…Breeding resistant cultivars are one of the most economical and effective strategies to control the disease. In the past two decades, there were several studies on the identification of cultivars and the detection of QTLs for RBSDV resistance (Feng et al ., 2019). However, few highly resistant germplasms or genes have been found (Sun et al ., 2017), severely hindering the development of elite varieties with high RBSDV resistance through either conventional breeding or marker‐assisted selection (MAS) breeding.…”

Nitric Oxide Enhances Rice Resistance to Rice Black-Streaked Dwarf Virus Infection

“…Rice black-streaked dwarf virus (RBSDV) is a member in the Genus Fijivirus, family Reoviridae. RBSDV is known to be transmitted by small brown planthopper (SBPH, Laodelphax striatellus) in a persistent manner (Shikata and Kitagawa 1977;Hibino 1996;Feng et al 2019), and can cause severe damages to rice (Oryza sativa), maize (Zea mays), and several other cereal crops in the eastern region of Asia. RBSDV symptoms in rice plants include plant stunting, leaf dark greening, pale green enation formation, and dark color leaf vein swellings (Bai et al 2002;Chen and Zhang 2005;Lee et al 2005).…”