High‐density SNP‐based genetic diversity and heterotic patterns of tropical maize breeding lines

Abstract

AbstractUnderstanding the crop diversity is critical for a successful breeding program, helping to dissect the genetic relationship among lines, and to identify superior parents. This study aimed to investigate the genetic diversity of maize (Zea mays L.) inbred lines and to verify the relationship between genetic diversity and heterotic patterns based on hybrid yield performance. A total of 1,041 maize inbred lines were genotyped‐by‐sequencing, generating 32,840 quality‐filtered single nucleotide polymorphisms (SNPs). Diversity analyses were performed using the neighbor‐joining clustering method, which generated diversity groups. The clustering of lines based on the diversity groups was compared with the predefined heterotic groups using the additive genomic relationship matrix and unweighted pair group method with arithmetic mean. Additionally, the genetic diversity of lines was correlated with yield performance of their corresponding 591 single‐cross hybrids. The SNP‐based genetic diversity analysis was efficient and reliable to assign lines within predefined heterotic groups. However, these genetic distances among inbred lines were not good predictors of the hybrid performance for grain yield, once a low but significant Pearson's correlation (.22, p‐value ≤ .01) was obtained between parental genetic distances and adjusted means of hybrids. Thus, SNP‐based genetic distances provided important insights for effective parental selection, avoiding crosses between genetically similar tropical maize lines.