Genetic diversity, linkage disequilibrium and population structure among CIMMYT maize inbred lines, selected for heat tolerance study

Abstract

Rising temperatures has led to reduced maize yields in tropical and sub tropical countries. This provides he necessity for identifying the diverse inbred lines that can produce high yielding hybrids under high temperature regimes. With this view, the present study was conducted to analyse the extent of genetic diversity and population structure among 64 CIMMYT maize inbred lines using SNP markers derived from GBS (Genotyping by sequencing) along with characterization of haplotype blocks and linkage disequilibrium. The average polymorphic information content (0.37) and gene diversity was very high (0.5) with mean kinship coefficients of 0.28 and genetic distance more than 0.4 between pair of two inbred lines. Clustering analysis based on ward’s method and euclidian distance showed presence of three sub groups. The population structure analysis using principle components showed three sub population. The average physical distance between pairs of markers was 27.7 kb with linkage disequilibrium (LD) estimation (r\ ) of 0.36 across all chromosomes., with rapid LD decay of 6.34 kb at r2 = 0.2. Haplotype analysis with 75,664 SNPs under confidence interval model revealed 616 halpotype blocks across all chromosomes with highest number of blocks on chromosome 5. The results clearly indicate the uniqueness of the majority of the inbred lines, which can contribute to new alleles in breeding programme for heat tolerance.