Study of allelic variation at genome wide ssr loci in parents of mapping population for high grain zinc in rice (Oryza sativa l.)

Abstract

Rice (Oryza sativa L.) is the source of energy and nutrition for more than half of the world’s population hence it is a crop of global significance. Breeding of mineral dense rice varieties is the main target of biofortification strategy to address micronutrient malnutrition globally. Landraces and local genotypes are proven sources of novel alleles and are a promising donor for high grain mineral. A parental polymorphism survey is a prerequisite of any QTL mapping experiment. Present study consisting of SSR markers based parental polymorphism survey at IRRI South Asia Hub ICRISAT, Hyderabad. Parents of mapping population viz Rajendrakasturi (short grain aromatic rice variety with low grain content) and URG-30 (a local genotype from Eastern Uttar Pradesh with high grain zinc content) were screened with 1013 microsatellite markers covering the entire length of all 12 chromosomes to study allelic variation at genome-wide SSR loci. The geographical diverse origin of parents is reflected in genotypic variations in terms of polymorphism. Out of 1013 whole genome wide SSR markers screened, 294 were found to be polymorphic which resulted in 29.02% polymorphism between the two parents. The highest polymorphism was observed with chromosome 4 (40.96%) whereas the lowest polymorphism was observed in chromosome 9 (16%). Based on the outcomes of the present study, a set of genome-wide polymorphic SSRs will be selected for genotyping of mapping population, preparation of linkage map and QTL analysis for high grain zinc content, iron content, grain quality and yield traits. © 2020, Editorial board of Journal of Experimental Biology and Agricultural Sciences. All rights reserved.