Genetic diversity and population structure of popcorn germplasm resources using genome-wide SNPs through genotyping-by-sequencing

Abstract

Popcorn is a kind of snack food and has a breeding history of nearly 40 years in China, however, there are relatively few studies on its genetic diversity. Therefore, we present a genetic diversity and population structure analysis of 103 popcorn accessions, including 10 landraces from Latin America, 8 landraces from Southwest China and 76 and 9 popcorn breeding lines from China and the US, respectively, using polymorphic single-nucleotide polymorphisms (SNPs) developed by genotyping-by-sequencing. A total of 40,120 high-quality SNPs (19.21 SNPs per 1 Mb) were identified across the genome. Relative kinship analysis showed that the kinship coefficients for 0.3% of the pairs of lines were above 0.300, which agrees with the pedigree. The 103 accessions could be classified into three major groups based on model-based population structure, Neighbor-joining clustering, and principal component analysis based on the genetic background of the parents used for breeding. Group I consisted of landraces from both China and the Latin American countries, with some improved lines from landraces, while Group II and Group III consisted of lines primarily developed from popcorn commercial varieties, but with different levels of popping expansion ability. The average linkage disequilibrium decay distance in the entire panel under r2 < 0.1 was 0.28 Mb and varied among different groups, indicating a narrow genetic resource. The information provided in this study will be helpful for breeders to incorporate identified genetic variation into hybrid breeding programs.