Genetic variation in YIGE1 contributes to ear length and grain yield in maize.

Ear length (EL), controlled by quantitative trait loci (QTL), is an important component of grain yield and as such a key target trait in maize breeding. However, very few EL QTL have been cloned and their molecular mechanisms are largely unknown. Here, using genome wide association study (GWAS), we identified a QTL-YIGE1, which encodes an unknown protein that regulates EL by affecting pistillate floret number. Overexpression of YIGE1 enlarged female inflorescence meristem (IM) size, increased EL and kernel number per row (KNPR) thus enhanced grain yield. By contrast, CRISPR/Cas9 knock out or Mutator insertion mutant lines of YIGE1 displayed decreased IM size and EL. The SNP located in the regulatory region of YIGE1 had strong effect on its promoter strength which positively affected EL by increasing gene expression. Further analysis shows that YIGE1 may be involved in sugar and auxin signal pathways to regulate maize ear development, thus, affecting IM activity and floret production in maize inflorescence morphogenesis. These findings provide new insights of ear development and will ultimately facilitate maize molecular breeding.