Genetic Variation in ZmPAT7 Contributes to Tassel Branch Number in Maize

Tassel branch number (TBN) is one of the important agronomic traits that contribute to the efficiency of seed production and has been selected strongly during the modern maize breeding process. However, the genetic mechanisms of TBN in maize are not entirely clear. In this study, we used a B73 x CML247 recombination inbred lines (RILs) population to detect quantitative trait loci (QTLs) for TBN. A total of four QTLs (qTBN2a, qTBN2b, qTBN4, and qTBN6) and six candidate genes were identified through expression analysis. Further, one of the candidates (GRMZM2G010011, ZmPAT7) encoding an S-acyltransferase was selected to validate its function by CRISPR-Cas9 technology, and its loss-of-function lines showed a significant increase in TBN. A key SNP(-101) variation in the promoter of ZmPAT7 was significantly associated with TBN. A total of 17 distant eQTLs associated with the expression of ZmPAT7 were identified in expression quantitative trait loci (eQTL) analysis, and ZmNAC3 may be a major factor involved in regulating ZmPAT7. These findings of the present study promote our understanding of the genetic basis of tassel architecture and provide new gene resources for maize breeding improvement.

Automated summary

In this study, using a B73 x CML247 RILs population, four QTLs for tassel branch number (TBN) in maize were identified, and six candidate genes were found to be associated with TBN through expression analysis. The function of one candidate gene, ZmPAT7, was validated using CRISPR-Cas9 technology, and its loss-of-function lines showed a significant increase in TBN. Additionally, key SNP variation in the promoter region of ZmPAT7 and distant eQTLs associated with its expression were identified. These findings enhance our understanding of the genetic basis of tassel architecture and provide new gene resources for maize breeding improvement.