An Integration of Linkage Mapping and GWAS Reveals the Key Genes for Ear Shank Length in Maize.

Ear shank length (ESL) has significant effects on grain yield and kernel dehydration rate in maize. Herein, linkage mapping and genome-wide association study were combined to reveal the genetic architecture of maize ESL. Sixteen quantitative trait loci (QTL) were identified in the segregation population, among which five were repeatedly detected across multiple environments. Meanwhile, 23 single nucleotide polymorphisms were associated with the ESL in the association panel, of which four were located in the QTL identified by linkage mapping and were designated as the population-common loci. A total of 42 genes residing in the linkage disequilibrium regions of these common variants and 12 of them were responsive to ear shank elongation. Of the 12 genes, five encode leucine-rich repeat receptor-like protein kinases, proline-rich proteins, and cyclin11, respectively, which were previously shown to regulate cell division, expansion, and elongation. Gene-based association analyses revealed that the variant located in Cyclin11 promoter affected the ESL among different lines. Cyclin11 showed the highest expression in the ear shank 15 days after silking among diverse tissues of maize, suggesting its role in modulating ESL. Our study contributes to the understanding of the genetic mechanism underlying maize ESL and genetic modification of maize dehydration rate and kernel yield.

Genome-wide association study reveals genetic basis and candidate genes for chlorophyll content of leaves in maize (Zea mays L.).

The chlorophyll content (CC) directly affects photosynthesis, growth, and yield. However, the genetic basis of CC is still unclear in maize (Zea mays 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 via 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 p-value < 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 GRMZM2G037152, GRMZM5G816561, GRMZM2G324462, and GRMZM2G064657 genes were significantly (p-value < 0.01) correlated with CC, of which GRMZM2G064657 (encodes a phosphate transporter protein) and GRMZM5G816561 (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.