Genetic Diversity, Population Structure and Linkage Disequilibrium Analyses in Tropical Maize Using Genotyping by Sequencing

Several maize breeding programs in India have developed numerous inbred lines but the lines have not been characterized using high-density molecular markers. Here, we studied the molecular diversity, population structure, and linkage disequilibrium (LD) patterns in a panel of 314 tropical normal corn, two sweet corn, and six popcorn inbred lines developed by 17 research centers in India, and 62 normal corn from the International Maize and Wheat Improvement Center (CIMMYT). The 384 inbred lines were genotyped with 60,227 polymorphic single nucleotide polymorphisms (SNPs). Most of the pair-wise relative kinship coefficients (58.5%) were equal or close to 0, which suggests the lack of redundancy in the genomic composition in the majority of inbred lines. Genetic distance among most pairs of lines (98.3%) varied from 0.20 to 0.34 as compared with just 1.7% of the pairs of lines that differed by <0.20, which suggests greater genetic variation even among sister lines. The overall average of 17% heterogeneity was observed in the panel indicated the need for further inbreeding in the high heterogeneous genotypes. The mean nucleotide diversity and frequency of polymorphic sites observed in the panel were 0.28 and 0.02, respectively. The model-based population structure, principal component analysis, and phylogenetic analysis revealed three to six groups with no clear patterns of clustering by centers-wise breeding lines, types of corn, kernel characteristics, maturity, plant height, and ear placement. However, genotypes were grouped partially based on their source germplasm from where they derived.