Genome-wide association study reveals genetic basis and candidate genes for chlorophyll content of leaves in maize (Z<i>ea mays</i> L.)

The chlorophyll content (CC) directly affects photosynthesis, growth, and yield. However, the genetic basis of CC is still unclear in maize (<i>Zea mays</i> L.). Here, we conducted a genome-wide association study using mixed linear model for CC of the fifth leaves at seedling stage (CCFSS) and the ear leaves at filling stage (CCEFS) for 334 maize inbred lines. The heritability estimates for CCFSS and CCEFS, obtained <i>via</i> variance components analysis using the lme4 package in R, were 70.84% and 78.99%, respectively, indicating that the CC of leaves is primarily controlled by genetic factors. A total of 15 CC-related SNPs and 177 candidate genes were identified with a <i>p-value</i> < 4.49 × 10^-5, which explained 4.98-7.59% of the phenotypic variation. Lines with more favorable gene variants showed higher CC. Meanwhile, Gene Ontology (GO) analysis implied that these candidate genes were probably related to chlorophyll biosynthesis. In addition, gene-based association analyses revealed that six variants in <i>GRMZM2G037152</i>, <i>GRMZM5G816561</i>, <i>GRMZM2G324462</i>, and <i>GRMZM2G064657</i> genes were significantly (<i>p-value</i> < 0.01) correlated with CC, of which <i>GRMZM2G064657</i> (encodes a phosphate transporter protein) and <i>GRMZM5G816561</i> (encodes a cytochrome P450 protein) were specifically highly expressed in leaves tissues. Interestingly, these candidate genes were previously reported to involve in the regulation of the contents of chlorophyll in plants or Chlamydomonas. These results may contribute to the understanding of genetic basis and molecular mechanisms of maize CC and the selection of maize varieties with improved CC.