Development of InDel markers of Bph3 and pyramiding of four brown planthopper resistance genes into an elite rice variety

Brown planthopper (BPH) is one of the most destructive pests in rice. Breeding resistant cultivars is the most effective strategy to control BPH.Bph3is a broad-spectrum and durable BPH resistance locus spanning similar to 50 kb on the short arm of rice chromosome 4. Using the genomic variation data of 4726 rice varieties from public database, we developed 8 InDel markers within the Bph3locus. By analyzing 563 rice varieties, we demonstrated that these markers could effectively identify Bph3-carriers, with an accuracy rate near to 90%. Through marker-assisted backcross breeding (MABC), we introduced four BPH resistance genes (Bph3/14/18/32) into an elite rice variety, Guang 8B. The results showed thatBph3had the biggest effect, followed by Bph14 and Bph32, and Bph18 had the smallest effect. In addition, the level of BPH resistance increased with the number of genes pyramided. However, in the case of only two genes being pyramided, the resistance increase was not significant in comparison with the larger effect of the two genes. This suggests that the resistance effects are not simply additive, but epistasis may be involved. The InDel markers and pyramiding lines developed in this study will facilitateBph3-carrier identification and BPH resistance breeding in rice.