Molecular characterization of popcorn inbreds using 25k SNP array

Abstract

Popcorn is a type of specialty maize and plays important role in the history and the spread of this species. This type of maize historicaly received little atention in genetic diversity studies while the fact is that information on genetic variability and population structure is of crucial importance for improvement of breeding programs. The genetic variation of popcorn maize was mainly analysed using SSR markers, but there are not many studies applying high-density SNP markers with lower genotyping errors. The aim of this study was the assesment of genetic diversity and population structure of popcorn germplasm which represents the genetic resources currently used in breeding programs in Maize Research Institute „Zemun Polje“. Molecular characterization of 44 popcorn genotypes was done using 25k SNP Illumina Infinum Array for maize. After quality control filtering, 12335 SNPs were selected for downstream analyses. Genetic distance detected ranged from 0.001 to 0.51 with an average of 0.33. The majority of genetic distances (70.6%) fell between 0.30 and 0.51 revealing significant genetic variability in a set of maize genotypes under study. SNP markes were moderatly informative with an average PIC value of 0.26. Also, for more than 50% of SNPs, PIC value was greater than 0.30. The average observed heterozygosity was 0.04 ranging from 0 to 0.11. The clustering, principal component and model-based STRUCTURE analyses showed similar grouping of popcorn lines, generally in accordance with their genetic background. The results of this research gave valuable information for initiation of future breeding strategies.