Detection and fine mapping of two quantitative trait loci for partial resistance to stripe virus in rice (Oryza sativa L.)

Rice stripe virus (RSV) is one of the most destructive pathogens of rice (Oryza sativa L.) in East Asia. Development of resistant varieties offers a more economical and efficient way to control this disease. In the present study, tests using four inoculation methods were used on 85 backcross inbred lines of Sasanishiki (japonica)/Habataki (indica) to map quantitative trait loci (QTL) conferring resistance to RSV. One QTL on chromosome 3 and two on chromosome 11 were detected, jointly explaining 18–47 % of the trait variance. The QTL (qSTV11HAB-1 and qSTV11HAB-2) on chromosome 11 were closely linked, and mapped in the intervals G257-RM457 and RM457-RM187, respectively. The stabilities of qSTV11HAB-1 and qSTV11HAB-2 were validated using a set of 38 established chromosome segmental substitution lines. The two QTL, when combined, showed higher resistance than either of them alone in both field and mass inoculation tests, indicating additivity. Fine mapping of the two genes was carried out using 147 recombined F2:3 lines selected from 2,750 secondary F2 plants of the cross Sasanishiki/SL437. Four SSR (simple sequence repeat) and eight InDel (insertion–deletion) markers newly developed to fine-map the two loci. According to the Nipponbare genomic sequence, qSTV11HAB-1 was localized to a 333.2-kb interval which was about 230 kb from the well-known Stvb-i. The other locus, qSTV11HAB-2, which appears to be a new QTL for RSV resistance, was delimited to a 203.9-kb region. Four flanking markers (R15, RM209, R69 and R73) can be used in marker-assisted selection. These results provide an opportunity for map-based cloning of qSTV11HAB-1 and qSTV11HAB-2, thereby promoting the breeding program of RSV resistance.