Genome-wide association study identifies loci for the general combining ability of Pythium root and stalk rot caused by Pythium arrhenomanes in maize (Zea mays L.)

Abstract

Pythium arrhenomanes Drechsler is a destructive soil-borne pathogen threatening forage maize (Zea mays L.) production worldwide, leading to substantial economic losses due to root and stalk rot (RSR). Developing resistant varieties is the most sustainable and effective management strategy. However, studies analyzing general combining ability (GCA) for disease resistance using genome-wide association study (GWAS) are lacking. This study investigated the genetic architecture of resistance to Pythium RSR using 107 maize inbred lines using GCA for disease resistance as a phenotypic trait, addressing instability of disease expression in inbred lines and targeting additive genetic variance crucial for F₁ hybrid breeding. A GWAS was conducted using 49,187 high-quality single-nucleotide polymorphism (SNP) markers. Five SNPs were significantly associated with resistance GCA that did not form linkage disequilibrium blocks in their vicinity. One SNP on chromosome 9 conferred a beneficial reduction in GCA, indicating an increase in resistance. Four of the five SNPs exhibited an apparent effect and were polymorphic between the resistant ‘Na71’ and susceptible ‘Ho112’ inbred lines, indicating their direct applicability in applied breeding. Overall, these loci are strong candidates for marker-assisted selection, providing a direct route to accelerate the development of forage maize hybrids with enhanced disease resistance and agronomic performance.