Insilico Screening Of Genome Wide Dna Polymorphisms For Hopper Resistance In Rice

Abstract

Brown plant hopper, white backed plant hopper and green leaf hoppers are devastating rice pests with yield loss up to 60% and are vectors for major viral diseases. Host plant resistance is the most practical and economical approach to control insect pests. It is a complex quantitative trait which can be dissected effectively by genome-wide mutation analyses between contrasting phenotypes. In this report we have analyzed unique SNPs and indels present in Para Nellu, a hopper resistant land race and TN1 and IR22, hopper susceptible varieties against the reference genome Nipponbare. The coding and noncoding SNPs were further categorized using the available expression data on hopper resistance to identify the genes and their associated functional pathways. The land race Para Nellu exhibited more than 1000 fold variation with 8,76,862 SNPs and Indels as compared against IR 22 with only 635 SNPs.  Chromosome 11 showed the highest SNP density in both Para Nellu and TN1. Hopper resistance being a quantitative trait, the SNPs were predominantly present in the noncoding region implying a multilevel regulation of several genes. Mutations were present in the coding region of the gene NDS-LRR, which is known to be involved in plant hopper resistance.