Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT's maize inbred lines.

Popcorn is the most ancient type of cultivated maize. However, little research has examined the genetic basis of popping-related traits based on genotyping-by-sequencing (GBS) technology. Here, we characterized the phenotypic variation for seven popping-related traits in the kernel among 526 CIMMYT inbred lines (CMLs). In total, 155,083 high-quality SNP markers were identified by a GBS approach. One hundred and sixty-two trait-associated loci were detected by GWAS (26, 58, 15, 22, 16, 13, 12 for color, PEV, shape, pericarp, IF, Floury/Vitreous, protein, respectively) , explained a majority of the observed phenotypic variance, and were validated by a diversity panel comprising 764 tropical landrace accessions. Of the 162 loci, 62 have undergone selection, as revealed by an EigenGWAS analysis. On average, the frequencies in CMLs of alleles for popping related SNPs that promote popping was 55.27%. Our work not only pinpoints previously unknown QTLs for popping-related traits and reveals that many of these loci have undergone selection; also helps to decipher the complex genetic interactions underlying the observed phenotypic diversity. Beyond establishing a new benchmark for the genetics of popcorn, our study provides a foundation for gene discovery and breeding, and provides more evidence to puzzle out the role of gradual loss of popping ability as a by-product of diversification of culinary uses throughout the evolution of teosinte-to-modern maize.