Linkage disequilibrium in salt tolerant genotypes of rice (Oryza sativa L)

Genome wide linkage disequilibrium (LD) was investigated in a set of 32 genotypes representing salt tolerant improved varieties and landraces and six salt sensitive genotypes of rice with 64 microsatellite markers to identify the genomic regions that are associated with salt tolerance in rice. Out of 64 markers analyzed, 36% SSR pairs exhibited significant LD at 0.05. A few regions were identified as targets of selection in 10 chromosomes with high r² values. The model-based groups from Bayesian clustering analysis are largely consistent with known pedigrees of the lines. The increased percentage of association of SSR loci in the improved varieties indicated the role of selection in linkage disequilibrium especially for salt tolerance. LD was extended as far as 100 cM in the present study. Most of the markers (43.8%) with significant LD values were observed in the genomic regions of reported QTL for salt tolerance in rice.