Mapping and progress toward map-based cloning of brown planthopper biotype-4 resistance gene introgressed from Oryza officinalis into cultivated rice, O. sativa

Brown plant hopper (BPH), Nilaparvata lugens (Stal.), is a serious insect pest of rice in Asia, causing direct losses and vectoring Rice grassy stunt virus (RGSV) and Rice ragged stunt virus (RRSV). Recombinant inbred lines (RILs) developed from a cross between 'IR50' and 'IR54745-2-21-12-17-6' were used to identify random amplified polymorphic DNA (RAPD) markers closely linked to a BPH Biotype-4 resistance gene [Bphl3 (t)] derived from Oryza officinalis Wall. Bulked segregant analysis (BSA) using RAPD primers identified 11 polymorphic fragments. Six fragments, AJ09 260 a, AL05 220 a, AK10 690 a, AK10 430 c, AK10 380 d, and AJ01 200 a, were linked in coupling phase to the Bphl3 (t) locus. The remaining five fragments, AJ09 230 b, AJ09 180 c, AJ09 100 d, AL05 400 b, and AK10 340 e, were linked in repulsion. The most closely linked RAPD marker, AJ09 230 b, was converted to a codominant linked sequence tagged sites (STS) marker. This marker mapped 1.3 centimorgans (cM) from the resistance gene and was placed on rice chromosome 3 by means of 'IR64' × 'Azucena' doubled haploid (DH) population. The tightly linked STS marker could be used for marker-assisted selection (MAS). In addition, these markers will be useful for a positional cloning strategy to isolate the resistance gene.