Jie Zhang, Riliang Gu, Xinxin Miao, Renate H Schmidt, Zhenxiang Xu, Jiawen Lu, Yuting Ma, Tao Yang, Pingxi Wang, Yangyang Liu, Xiaoli Wang, Xuemei Du, Nannan Zheng, Sihan Zhen, Chengyong Liang, Yuxin Xie, Yongrui Wu, Lin Li, Jochen C Reif, Yong Jiang, Jianhua Wang,  Junjie Fu, and Hongwei Zhang

Plant Communications; 2025; IF: 9.4

DOI:10.1016/j.xplc.2025.101289

Abstract

Understanding the role of heterotic genes in contributing to heterosis is essential for advancing hybrid breeding. We analyzed plant height (PH), ear height (EH), and transcriptomic data from a maize hybrid population. GWAS identified that dominance effects of QTL play a significant role in hybrid traits and mid-parent heterosis. By integrating GWAS, expression GWAS (eGWAS) analysis, and module eGWAS, six candidate heterotic genes underlying six QTL were prioritized, including one QTL spanned the bZIP29 gene. In the hybrid population, bZIP29 exhibited additive expression and dominance effects for both traits and mid-parent heterosis, with its favorable allele correlating positively with PH and EH. bZIP29 demonstrated dominance or over-dominance patterns in the hybrids derived from crosses between transgenic and wildtype lines, contingent upon its expression. tsCUT&Tag assay revealed that bZIP29 bound directly to a gene regulated by its associated eQTL and six genes within expression modules governed by their meQTL. Regulatory networks involving bZIP29 were more extensive in hybrid sub-populations compared to the parental population. This study offers insights into key heterotic genes and networks underpinning the robust growth of hybrid maize.