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

Authors: SULLIVAN, MADSEN - University Of Illinois; Williams, Martin; STUDER, ANTHONY - University Of Illinois

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2023
Publication Date: 7/3/2023
Citation: Sullivan, M., Williams II, M.M., Studer, A. 2023. Genetic diversity of North American popcorn germplasm and the effect of population structure on nicosulfuron response. Crop Science. 63(5):2894-2912. https://doi.org/10.1002/csc2.21039.
DOI: https://doi.org/10.1002/csc2.21039

Interpretive Summary: The United States grows and consumes more popcorn than any other nation. Herbicides registered on popcorn often are available for use on yellow kernel hybrids but not white kernel hybrids. An evaluation of a diversity panel of 362 popcorn accessions identified two groups of popcorn within the panel. The first group, dominated by yellow kernel accessions, had limited genetic diversity and tolerance to nicosulfuron herbicide compared to the second group, dominated by white kernel accessions and sensitivity to nicosulfuron. Candidate genes conditioning response to nicosulfuron appear to differ from previous research findings in field corn and sweet corn. The research showed that popcorn population, not kernel color, accounts for differential response to nicosulfuron.

Technical Abstract: Popcorn is an important crop in the United States, with more popcorn grown and consumed than in any other nation. However, genetic analyses of popcorn are limited and tend to utilize relatively few markers that cannot capture the total genetic variation of genomes. A panel of 362 popcorn accessions of North American, Latin American, and global origins was evaluated using 417,218 single nucleotide polymorphisms generated using a genotyping-by-sequencing approach. Using this genomic data, a model-based clustering analysis performed using the ADMIXTURE software identified two groups of popcorn within the panel. The first group was composed of North American Yellow Pearl Popcorns and several accessions of the Chilean Curagua landrace. The second group was designated as Pointed and Latin American Popcorns, as it included all remaining North American accessions (pointed and early popcorns), Latin American accessions, and all accessions of global origin. These two populations exhibited large differences in linkage disequilibrium decay, frequency of monomorphic sites, and minor allele frequencies. Specifically, the North American Popcorns showed characteristics of a highly inbred population with limited genetic diversity compared to the Pointed and Latin American Popcorns. Additionally, phenotypic differences were observed, as North American Yellow Pearl Popcorns generally had yellow kernels and tolerance to nicosulfuron, while approximately half of the Pointed and Latin American Popcorns had white kernels and a higher incidence of sensitivity to nicosulfuron. A filtered set of SNPs was curated and used for genome-wide association studies to look at the genetic architecture of these traits in popcorn. Interestingly, these analyses identified popcorn-specific candidate genes for nicosulfuron tolerance. The genomic characterization described here can be used by popcorn breeding programs to accelerate the rate of genetic gain and identify sources of genetic diversity to incorporate into elite popcorn germplasm.