TY - JOUR T1 - Genomic, transcriptomic and phenomic variation reveals the complex adaptation of modern maize breeding JF - bioRxiv DO - 10.1101/005751 SP - 005751 AU - Haijun Liu AU - Xiaqing Wang AU - Marilyn L. Warburton AU - Weiwei Wen AU - Minliang Jin AU - Min Deng AU - Jie Liu AU - Hao Tong AU - Qingchun Pan AU - Xiaohong Yang AU - Jianbing Yan Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/06/03/005751.abstract N2 - The temperate-tropical division of early maize germplasm to different agricultural environments was arguably the greatest adaptation process associated with the success and near ubiquitous importance of global maize production. Deciphering this history is challenging, but new insight has been gained from the genomic, transcriptomic and phenotypic variation collected from 368 diverse temperate and tropical maize inbred lines in this study. This is the first attempt to systematically explore the mechanisms of the adaptation process. Our results indicated that divergence between tropical and temperate lines seem occur 3,400-6,700 years ago. A number of genomic selection signals and transcriptomic variants including differentially expressed individual genes and rewired co-expression networks of genes were identified. These candidate signals were found to be functionally related to stress response and most were associated with directionally selected traits, which may have been an advantage under widely varying environmental conditions faced by maize as it was migrated away from its domestication center. It’s also clear in our study that such stress adaptation could involve evolution of protein-coding sequences as well as transcriptome-level regulatory changes. This latter process may be a more flexible and dynamic way for maize to adapt to environmental changes over this dramatically short evolutionary time frame. ER -