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

Popcorn 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 362 popcorn accessions was evaluated using 417,218 single nucleotide polymorphisms generated using a genotyping-by-sequencing approach. Using this genomic data, a model-based clustering analysis identified two populations. The first comprised North American Yellow Pearl Popcorns and several accessions of the Chilean Curagua landrace. The second, the Pointed and Latin American Popcorns, included all remaining North American (pointed and early popcorns), Latin American, and global accessions. The two populations exhibited large differences in population structure and genetic diversity. The North American Yellow Pearl Popcorns constitute a highly inbred population with limited genetic diversity compared to the Pointed and Latin American Popcorns. Additionally, phenotypic differences between the two populations 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. Core IdeasO_LINorth American Popcorn is composed of two distinct populations that differ genetically and phenotypically. C_LIO_LINorth American Yellow Pearl Popcorns contain limited genetic diversity and are highly inbred. C_LIO_LIPointed and Latin American Popcorns exhibit considerable genetic diversity and rapid linkage disequilibrium decay. C_LIO_LIKernel color does not affect nicosulfuron sensitivity and instead reflects differences between the populations. C_LIO_LIPopcorn-specific candidate genes for nicosulfuron tolerance are distinct from dent corn. C_LI