Genome-wide association study and metabolic pathway prediction of barrenness in maize as a response to high planting density

Increasing the planting density is one way to enhance grain production in maize. However, high planting density brings about growth and developmental defects such as barrenness, which is the major factor limiting grain yield. In this study, the barrenness was characterized in an association panel comprising 280 inbred lines under normal (67 500 plants ha–1, ND) and high (120 000 plants ha–1, HD) planting densities in 2017 and 2018. The population was genotyped using 776 254 single nucleotide polymorphism (SNP) markers with criteria of minor allele frequency >5% and <20% missing data. A genome-wide association study (GWAS) was conducted for barrenness under ND and HD, as well as the barrenness ratio (HD/ND), by applying a Mixed Linear Model that controls both population structure and relative kinship (Q+K). In total, 20 SNPs located in nine genes were significantly (P<6.44×10–8) associated with barrenness under the different planting densities. Among them, seven SNPs for barrenness at ND and HD were located in two genes, four of which were common under both ND and HD. In addition, 13 SNPs for the barrenness ratio were located in seven genes. A complementary pathway analysis indicated that the metabolic pathways of amino acids, such as glutamate and arginine, and the mitogen-activated protein kinase (MAPK) signaling pathway might play important roles in tolerance to high planting density. These results provide insights into the genetic basis of high planting density tolerance and will facilitate high yield maize breeding.