Screening and verification of genes associated with leaf angle and leaf orientation value in inbred maize lines.

Leaf angle and leaf orientation value are important traits affecting planting density and photosynthetic efficiency. To identify the genes involved in controlling leaf angle and leaf orientation value, we utilized 1.49×106 single nucleotide polymorphism (SNP) markers obtained after sequencing 80 backbone inbred maize lines in Jilin Province, based on phenotype data from two years, and analyzed these two traits in a genome-wide association study (GWAS). A total of 33 SNPs were significantly associated (P<0.000001) with the two target traits. Twenty-two SNPs were significantly associated with leaf angle and distributed on chromosomes 1, 3, 4, 5, 6, 7, 8, and 9, explaining 21.62% of the phenotypic variation. Eleven SNPs were significantly associated with leaf orientation value and distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9, explaining 29.63% of the phenotypic variation. Within the mean linkage disequilibrium (LD) distance of 9.7 kb for the significant SNP locus, 22 leaf angle candidate genes were detected, and 3 of these candidate genes harbored significant SNPs, with phenotype contribution rates greater than 10%. Two candidate genes at distances less than 100 bp from significant SNPs showed phenotype contribution rates greater than 8%. Seven leaf orientation value candidate genes were detected: 3 of these candidate genes harbored significant SNPs, with phenotype contribution rates greater than 10%. Eight inbred maize lines with significant differences in leaf angle and leaf orientation value were selected to test candidate gene expression levels from 182 recombinant inbred lines (RILs). The 5 leaf angle candidate genes and 3 leaf orientation value candidate genes were verified using quantitative real-time PCR (qRT-PCR). The results showed significant differences in the expression levels of the above eight genes between inbred maize lines with significant differences in leaf angle and leaf orientation value.