Assessment of the Sequence-Based Haplotype-Variants in Selected DNA Marker Loci for the Molecular Breeding of Resistant Rice Varieties to Brown Plant Hopper

Abstract

Brown plant hopper (BPH) is the most devastating insect pest of rice. The BPH damage is trivial that farmers may end up with zero or below average yields. The application of insecticide would only lead to the emergence of virulent biotypes, thus marker assisted breeding of BPH resistant rice varieties is the only feasible solution. Although, the molecular genetics of BPH resistance and the linked DNA makers are known; the breeders struggle to use them in marker assisted breeding due to the limited ability to identify length-based allele polymorphisms in gel electrophoresis. Therefore, the present study was conducted to assess the employability of haplotype variants of the DNA markers linked to BPH resistant genes using a set of resistant and moderately resistant rice cultivars. The BPH resistant landraces Murungakayan302, PtB33, Sulai and moderately resistant Bg300, and Bw367 cultivars in Sri Lanka were assessed using six DNA makers linked to Bph resistant genes. The band length polymorphism using 2.5% agarose gel electrophoresis and haplotype variants using 3× sequence-reads of the PCR products of DNA markers were assessed. The DNA markers RM246 and C3-14 provide Murungakayan302 and Sulai specific haplotypes respectively. The DNA markers assessed yielded polymorphic bands that are closely positioned in agarose gels making the band scoring cumbersome and ambiguous. The sequences of PCR products provided distinct haplotypes for the rice cultivars. Thus, the introgression of BPH resistance or moderate resistance into rice cultivars can be undertaken using the sequence based haplotypes in place of the band polymorphisms