Potentiality of evenly distributed hypervariable microsatellite markers in marker-assisted breeding of rice

Abstract

With 4 figures and 1 table Abstract To provide ready-to-use markers for background selection in marker-assisted breeding of rice, we have extracted 840 hypervariable microsatellite markers (hvRMs) evenly distributed in the genome from 18 828 Class I simple sequence repeats. These hvRMs were grouped into bins of 5-Mb intervals with 5–8 bins depending on the chromosome length. In each bin, 10 hvRMs were selected based on their microsatellite repeat number and type. Of 840, a representative of 36 hvRMs were selected and its polymorphic information content (PIC) was estimated by amplifying 24 diverse rice cultivars. The findings revealed that hvRMs show high PIC values and more alleles when compared to the 25 randomly chosen microsatellite markers. The informative hvRMs developed for background selection across cultivars in this study along with the already established molecular markers tightly linked to the genes of agronomic value could be of value for the development of a ‘MAS kit’ for speeding up the efforts of plant breeders for targeted crop improvement.