Abstract
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.
Highlights
The characteristics of maize plant types, including the leaf angle, leaf orientation value, leaf length, and leaf width, are associated with the spatial distribution of maize [1,2]
All 3 single nucleotide polymorphism (SNP) were significantly associated with the leaf orientation value, and the phenotype contribution rate was higher than 8%, which was consistent with published QTLs. sLOV150000363, which was significantly correlated with leaf angle and leaf orientation value, was 0.12 Mb; this finding was consistent with Ku [32], who identified an important region controlling the leaf orientation value; in addition, bnlg619-IDP8193.sLOV-6165883 was 0.8 Mb, which was consistent with Liu et al [34], who identified region bnlg1014.sLOV-182906583, which was 2.5 Mb, consistent with Ku et al [31], who identified region umc1086-umc2289
A total of 22 SNPs were significantly associated with the leaf angle, and 5 SNPs showed phenotype contribution rates greater than 8%
Summary
The characteristics of maize plant types, including the leaf angle, leaf orientation value, leaf length, and leaf width, are associated with the spatial distribution of maize [1,2]. Leaf orientation value, GWAS and candidate genes verification utilization rate, which is an important factor in increasing population yield in maize [3,4]. Mickelson et al [7] identified 9 leaf angle QTLs that were distributed on chromosomes 1, 2, 4, 5, 6 and 7 in two environments using an RFLP technique in the B73 × Mo17 population with 180 recombinant inbred lines (RILs). Pelleschi et al [8] identified 2 leaf length QTLs and 3 leaf width QTLs using an RFLP technique to analyze the F-2 × MBS847 population. Reflecting the limitations of low density and a large confidence interval, these published QTLs were primarily confined to the positioning level, and it is difficult to further screen and verify candidate genes
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