Identification of QTLs and Candidate Genes Associated with Leaf Angle and Leaf Orientation Value in Maize (Zea mays L.) Based on GBS

Leaf angle (LA) and leaf orientation value (LOV) are two crucial traits constituting the plant architecture (PA) of maize. Screening of quantitative trait loci (QTLs) and candidate genes (CGs) related to leaf angle and leaf orientation value provides the molecular basis for the improvement of maize plant architecture. In this study, we utilized genotyping by sequencing (GBS) on 179 maize recombined inbred lines (RILs) obtained by crossing two inbred lines with significant variation in leaf angle and leaf orientation value. A total of 4235 markers were used for the construction of the genetic linkage map. The total length of the genetic map was 1514.57 cM with the average genetic distance between each marker of 0.36 cM. On association of this map with phenotypic data from four environments, nine QTLs associated with leaf angle and nine QTLs associated with leaf orientation value were identified, explaining 78.89% and 59.71% of the phenotypic variation of leaf angle and leaf orientation value, respectively. Two QTLs explained greater than 10% of the phenotypic variation and three QTLs controlling both leaf angle and leaf orientation value were screened. Three candidate genes were identified as the most possible genes associated with leaf angle and leaf orientation value by screening the annotations of genes underlying these crucial QTLs. These were Zm00001d019053 might be associated with leaf angle, Zm00001d028164 and Zm00001d025352 might be associated with leaf angle and leaf orientation value, respectively. Expression analysis of candidate genes from parents and subsets also confirmed the significant variation in expression. Differences in DNA of the inbred lines with different phenotype were identified based on analysis of allelic variations in the candidate genes. These results not only enrich QTLs and candidate genes associated with leaf angle and leaf orientation value of maize, but also provide references for the improvement of plant architecture and molecular marker-assisted breeding.