Genome-wide association study and metabolic pathway prediction of barrenness in maize as a response to high planting density
2021
ZHANG, Xu-huan | Liu, Hao | MA, Xu-hui | ZHOU, Gu-yi | RUAN, Hong-qiang | CUI, Hong-wei | PANG, Jun-ling | SIFFAT Ullah, Khan | ZONG, Na | WANG, Ren-zhong | LENG, Peng-fei | Zhao, Jun
Increasing planting density is one way to enhance grain production in maize. However, higher planting density brings about growth and developmental defects, of which barrenness is the major factor limiting grain yield. In this study, the barrenness was characterized in an association panel comprising 280 inbred lines under normal (67500 plants ha⁻1, ND) and high (120000 plants ha⁻¹, HD) planting density in 2017 and 2018. The population was genotyped using 776254 single nucleotide polymorphism (SNP) markers with minor allele frequency >5% and with <20% missing data. Genome-wide association study (GWAS) was conducted for barrenness under ND and HD, and barrenness ratio (HD/ND), applying Mix Linear Model that controls both population structure and relative kinship (Q+K). Totally, 20 SNPs located in nine genes were significantly (P<6.44×10⁻⁸) associated with barrenness under different planting densities. Among them, seven SNPs for barrenness at ND and HD were located in two genes, of which four SNPs were common under both ND and HD; in addition, 13 SNPs for barrenness ratio were located in seven genes. A complementary pathway analysis indicated that metabolic pathways of amino acids, such as glutamate and arginine, and the MAPK signaling pathway might play important roles in tolerance to high planting density tolerance. These results provide insights into the genetic basis of high planting density tolerance and will facilitate high yield maize breeding.
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