Construction of microsatellite linkage map and detection of segregation distortion in indica rice (oryza sativa l.)

Abstract

High density molecular linkage map is a prerequisite to identify the quantitative traits loci. Construction of linkage maps, using mapping populations derived from two major subspecies: indica and japonica in rice, have been reported. However, limited work was conducted in indica subspecies. Present studies focused to construct a molecular map based on indica × indica (Shaheen Basmati × Pokkali) derived F2 mapping population. The detected microsatellite polymorphism was only 50.64% between parental cultivars. A total of 107 microsatellite markers were employed to amplify 108 loci, distributed throughout the genome. The marker data of 190 individuals was recorded for map construction. Most of the markers were found co-dominant, where as eight markers exhibited dominance in favor of Shaheen Basmati alleles and four in favor of Pokkali alleles. Detected segregation distortion was 7.47%, which was significantly low than previous studies. MapMaker was used to construct the linkage groups. The map spanned 1753.9 cM (Kosambi function) with microsatellite markers on 12 rice chromosomes and an average distance of 16.2 cM between markers. This map contained a greater and least percentage of markers on linkage group 3 and 12, respectively. Maximum common interval size (MCIS) analysis revealed that present map (indica × indica) covered the rice genome 98% of previous investigation (japonica × indica). Because of diverse background of parental cultivars, low segregation distortion and high genome coverage, revealed that molecular linkage map would be used as marker framework to investigate the genetics of important agronomic traits in indica rice