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Title: Genomic, transcriptomic and phenomic variation reveals the complex adaptation to stress response of modern maize breeding

item LIU, HAIJUN - Huazhong Agricultural University
item WANG, XIAQING - Huazhong Agricultural University
item Warburton, Marilyn
item WEN, WEIWEI - Huazhong Agricultural University
item JIN, MINLIANG - Huazhong Agricultural University
item LIU, JIE - Huazhong Agricultural University
item TONG, HAO - Huazhong Agricultural University
item PAN, QINGCHUN - China Agricultural University
item YANG, XIAOHONG - China Agricultural University
item DONG, XIAOFEI - Huazhong Agricultural University
item YAN, JIANBING - Huazhong Agricultural University

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/21/2015
Publication Date: 6/20/2015
Citation: Liu, H., Wang, X., Warburton, M.L., Wen, W., Jin, M., Liu, J., Tong, H., Pan, Q., Yang, X., Dong, X., Yan, J. 2015. Genomic, transcriptomic and phenomic variation reveals the complex adaptation to stress response of modern maize breeding. Molecular Plant. 8:871-884.

Interpretive Summary: Maize (corn), one of the most important crop species on earth both economically and for food security, was domesticated in central Mexico about 9000 years ago from its wild ancestor, teosinte. The genomic changes at the DNA level in the domestication process have been well studied. From central Mexico, maize spread north and south, reaching extreme latitudes in Canada and Southern Chile and Brazil. The genomic changes that allowed maize to adapt to the very different environmental conditions found in the temperate north and south, compared to the tropical conditions found in the middle latitudes, are not as well studied. These changes, however, would be in traits of particular interest to plant breeders, because they deal with adaptation to new biotic and abiotic stresses. Data on DNA sequence polymorphisms, expression level differences of all expressed genes from different tissues, and traits measured on plants grown in the field were collected from 368 diverse maize inbred lines. Analysis of these data revealed that the movement of maize into temperate environments happened very early after domestication, perhaps as early as 6,700 years ago. Changes in DNA sequence and gene expression were found between temperate and tropical maize, especially in regulatory gene sequences. These findings suggest that maize has developed a flexible and fast method to adapt to environment changes over dramatically shorter periods of time.

Technical Abstract: Early maize adaptation to different agricultural environments was an important process associated with the creation of a stable food supply that allowed the evolution of human civilization in the Americas. To explore the mechanisms of maize adaptation, genomic, transcriptomic and phenomic data were collected from 368 diverse maize inbred lines. Results indicate that divergence between tropical and temperate lines occurred 3,400-6,700 years ago. A number of selection signals in the genome, differentially expressed genes, and genes with altered expression conservation were identified. Adaptation to widely varying environmental conditions faced by temperate maize as it was migrated far north and south of its domestication center could have been the key cause of the genomic and transcriptomic differences identified. Stress adaptation can be detected in maize during the entire life cycle, involving protein-coding sequence evolutionary as well as transcriptome-level regulatory changes. These generally occurred via regulatory gene sequence changes that altered the transcriptome. However, in contrast to the selection of rare variants and genomic processes that affect adaptation over an evolutionary time frame, transcriptome regulation is more flexible and dynamic and may allow maize to adapt to environment changes over dramatically shorter periods of time.