Identification of SSR marker linked to the stigma exsertion in maintainer lines of hybrid rice

Abstract

Among 454 SSR markers, 118 markers exhibited polymorphism. Among these, three best polymorphic markers on each chromosome covering all 12 chromosomes were employed for selective genotyping of 188 F2 mapping population derived from APMS-6B, a low stigma exsertion parent and BF-16B, a high stigma exsertion parent and one marker on each chromosome and two reported markers used for single marker analysis. For phenotypic study parents, F1 and F2 population were evaluated for stigma exsertion trait in order to understand the inheritance as well as linkage with SSR markers. A co-segregation analysis with respect to marker (based on the amplification pattern of the marker) and trait phenotype revealed that three markers RM20060 on chromosome 6, RM5647on chromosome 8 and RM4771 on chromosome 10 showed least recombination frequency and these three markers found to be linked to the stigma exsertion trait. These markers could be used in marker assisted selection programs to develop a male sterile line with a high stigma exsertion.