Evaluating genetic variations on brown plant hopper (Nilaparvata lugens stal) resistance gene Os06g0125132 of rice for molecular marker development

Abstract

Brown plant hopper (BPH) is the most devastating insect pest of rice (Oryza sativa L.).Hence, cultivation of rice varieties carrying genetic resistance to BPH is the mostpromising approach for mitigating its damage. BPH resistance is controlled by manygenes. The expression of Os06g0125132 was found to be significantly upregulated underBPH infection and hence, a KASP marker for marker-assisted selection (MAS) wasdeveloped targeting a SNP in the intron region. Non-synonymous sequence variations inthe exons that could alter the protein structure and/or its domains could be potentialtarget sites for the development of alternative molecular markers compatible withtechnology-limited setups. In the current study, to identify such genetic variations, ahaplotype analysis was conducted using the coding sequence of Os06g0125132 (177bp),retrieved from 2,804 accessions sequenced in the 3K Rice Genomes Project. Theextracted sequences were aligned using UGENE and four SNPs with ≥5% occurrencefrequency in the rice panel were identified (three SNPs at exon 1 and one SNP at exon 2)and three confirmed haplotypes (with ≥1% occurrence frequency) were defined usingDnaSP. Given all three haplotype-defining SNPs were non-synonymous, the respectiveputative amino acid sequences were modeled using the ab-initio algorithmTrRefineRosetta in Robetta. The modeled output suggested that all three putativeproteins would fold into alpha helical structures (confidence of ≥0.8) and with nodetectable 3-D structural difference. InterPro scan of the amino acid sequences detecteda TMhelix, Transmembrane, Cytoplasmic and Non cytoplasmic domain each for all threeputative proteins, indicating that the three identified non-synonymous SNPs had noimpact on the domains. However, given the significance of Os06g0125132 for BPHresistance, and its potential involvement in carbohydrate metabolism via thetricarboxylic acid cycle, further investigation is warranted to identify alternative sites formarker development targeting users in technology limited setups.