Characterization of Proteome Variation During Modern Maize Breeding.
Lu-Guang Jiang, Bo Li, Sheng-Xue Liu, Hong-Wei Wang, Cui-Ping Li, Shu-Hui Song, Mary Beatty, Gina Zastrow-Hayes, Xiao-Hong Yang, Feng Qin, Yan He
Author Information
Lu-Guang Jiang: MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China.
Bo Li: MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China.
Sheng-Xue Liu: College of Biological Sciences, China Agricultural University, Beijing 100094, China.
Hong-Wei Wang: Agricultural College, Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Hubei 434000, China.
Cui-Ping Li: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
Shu-Hui Song: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
Mary Beatty: DuPont Pioneer, Johnston, IA 50131.
Gina Zastrow-Hayes: DuPont Pioneer, Johnston, IA 50131.
Xiao-Hong Yang: MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China.
Feng Qin: College of Biological Sciences, China Agricultural University, Beijing 100094, China;. Electronic address: qinfeng@cau.edu.cn.
Yan He: MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China;. Electronic address: yh352@cau.edu.cn.
The success of modern maize breeding has been demonstrated by remarkable increases in productivity with tremendous modification of agricultural phenotypes over the last century. Although the underlying genetic changes of the maize adaptation from tropical to temperate regions have been extensively studied, our knowledge is limited regarding the accordance of protein and mRNA expression levels accompanying such adaptation. Here we conducted an integrative analysis of proteomic and transcriptomic changes in a maize association panel. The minimum extent of correlation between protein and RNA levels suggests that variation in mRNA expression is often not indicative of protein expression at a population scale. This is corroborated by the observation that mRNA- and protein-based coexpression networks are relatively independent of each other, and many pQTLs arise without the presence of corresponding eQTLs. Importantly, compared with transcriptome, the subtypes categorized by the proteome show a markedly high accuracy to resemble the genomic subpopulation. These findings suggest that proteome evolved under a greater evolutionary constraint than transcriptome during maize adaptation from tropical to temperate regions. Overall, the integrated multi-omics analysis provides a functional context to interpret gene expression variation during modern maize breeding.
