Genetic Variation in ZmPAT7 Contributes to Tassel Branch Number in Maize

Abstract

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 × 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.

QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize

“…Following the isolation of relevant mutants, dozens of genes affecting TBN have been cloned and functionally dissected, which uncovered several genetic pathways such as meristem maintenance and determinacy 22,24,47,48 , phytohormones [49][50][51][52] , or sugar and nutrition 53 . However, only a few quantitative TBN genes have been verified, which limits our understanding of TBN genetic architecture and how to harness this trait in crop breeding 30,31 .…”

“…Cloning of conventional TBN genes based on isolation of their corresponding mutants has enabled the identification of a series of TBN genes and uncovered several molecular pathways behind TBN [20][21][22][23][24][25][26][27][28][29] . However, only a few of the causal genes underlying QTLs have been cloned, even though several hundred QTLs have been identified 30,31 , which limits the pace of modern maize improvement.…”

Harnessing Knowledge from Plant Functional Genomics and Multi-Omics for Genetic Improvement

“…In maize, Guan et al mapped four QTLs (qTBN2a, qTBN2b, qTBN4, qTBN6) of the tassel branch number (TBN) trait and identified six candidate genes within the QTL regions. Importantly, one of the candidate genes ( GRMZM2G010011 , ZmPAT7) , encoding an S-acyltransferase, was functionally validated by using the CRISPR-Cas9-edited lines [ 34 ]. Another maize study also employed QTL mapping to reveal the genetic loci involved in Zn deficiency tolerance with potential candidate genes identified [ 35 ].…”