Genome-Wide Comparative Analysis of Genetic Diversity of Regular and Specialty Maize Inbred Lines Through Genotyping by Target Sequencing (GBTS)

Specialty maize is widely used for human and animal consumption. It is therefore important to conduct a genome-wide comparison of regular and specialty maize. In the present study, a total of 20,000 SNP markers were generated using genotyping by target sequencing (GBTS) approach, of which 18,497 high-quality SNPs were used to explore the population structure and genetic diversity of both regular (163) and specialty (124) maize resources. Neighbor-joining clustering analysis classified the 287 tested maize inbred lines into three major groups, in which popcorn and other types of maize clustered into separate groups. The regular temperate maize was further divided into five heterotic subgroups, while the waxy maize and regular tropical maize were divided into two separate subgroups. However, the quality protein maize (QPM) could not be distinguished from regular tropical maize. The highest difference in allele frequency (P < 0.05) was observed between popcorn and waxy maize (28.2%), while 26.0% SNPs between popcorn and regular tropical maize, and 25.4% SNPs between popcorn and regular temperate maize. The information generated in this study is helpful for incorporating identified genetic variation into hybrid breeding programs for specialty maize improvement and also for genome-wide association mapping in specialty maize.