Genetic diversity of North American popcorn germplasm and the effect of population structure on nicosulfuron response

Abstract

Popcorn (Zea mays) is an important crop in the United States; however, genetic analyses of popcorn are limited and tend to utilize relatively few markers that cannot capture the total genomic variation. To improve the genomic resources in popcorn, a panel of 320 popcorn accessions was evaluated using 308,811 single nucleotide polymorphisms (SNPs) generated using a genotyping-by-sequencing approach. Using this genomic data, several model-based clustering analyses identified two major groups. The first comprised North American Yellow Pearl Popcorns and accessions of the Chilean Curagua landrace, separated into three subgroups. The second, the Pointed and Latin American Popcorns, included all remaining North American, Latin American, and global accessions. These groups exhibited differences in population structure and genetic diversity. The North American Yellow Pearl Popcorns contain limited genetic diversity compared to the Pointed and Latin American Popcorns. Additionally, phenotypic differences between the two groups were observed in kernel color and nicosulfuron sensitivity. A filtered set of SNPs was curated and used for genome-wide association studies and popcorn-specific candidate genes for nicosulfuron tolerance were identified. The genomic characterization described here can be used by breeding programs to accelerate the rate of genetic gain and incorporate genetic diversity into elite popcorn germplasm.