Selection of F2 homozygous plants over the QTL9 related to rice panicle structure by using CAPS markers

Abstract

QTL9 is a new potential quantitative trait locus related to rice panicle structure, identified through a GWAS analysis of Vietnamese local rice panel. To validate the QTL9, a biparental population was developed using the low branching (G6) and the high branching (G189) accessions from two haplotypes characterised by a contrasting phenotype for the secondary branch number and spikelet number traits. In parallel, using Gene capture technology combined with new generation sequencing identified 1,002 genetic variants in the QTL9 region between two parents, of which 12 SNPs were found in the cleavage site of 5 restriction enzyme. In this study, 12 primer pairs were tested to amplify the CAPS markers, based on the 12 SNPs, in order to be applied to select homozygous F2 lines over the QTL9 region for both haplotypes. 4 CAPS markers were selected distributing over the QTL9 region and displaying polymorphism between two parents. 275 F2plants were genotyped using 3 CAPS markers leading to the selection of 74 homozygotes plants over the QTL9region for haplotype 1, 66 homozygotes plants over the QTL9 region for haplotype 2, and 153 heterozygous plants. Homozygous lines will be used to develop the F3population, phenotyping of two F3 haplotypes will lead to discovering the role of QTL9 related to rice panicle structure.