Linqian Han, Wanshun Zhong, Jia Qian, Minliang Jin, Peng Tian, Wanchao Zhu, Hongwei Zhang, Yonghao Sun, Jia-Wu Feng, Xiangguo Liu, Guo Chen, Babar Farid, Ruonan Li, Zimo Xiong, Zhihui Tian, Juan Li, Zi Luo, Dengxiang Du, Sijia Chen, Qixiao Jin, Jiaxin Li, Zhao Li, Yan Liang, Xiaomeng Jin, Yong Peng, Chang Zheng, Xinnan Ye, Yuejia Yin, Hong Chen, Weifu Li, Ling-Ling Chen, Qing Li, Jianbing Yan, Fang Yang, Lin Li
Nature Genetics(2022), Published: 29 December 2022
Networks are powerful tools to uncover functional roles of genes in phenotypic variation at a system-wide scale. Here, we constructed a maize network map that contains the genomic, transcriptomic, translatomic and proteomic networks across maize development. This map comprises over 2.8 million edges in more than 1,400 functional subnetworks, demonstrating an extensive network divergence of duplicated genes. We applied this map to identify factors regulating flowering time and identified 2,651 genes enriched in eight subnetworks. We validated the functions of 20 genes, including 18 with previously unknown connections to flowering time in maize. Furthermore, we uncovered a flowering pathway involving histone modification. The multi-omics integrative network map illustrates the principles of how molecular networks connect different types of genes and potential pathways to map a genome-wide functional landscape in maize, which should be applicable in a wide range of species.