title: Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding.
abstract: The temperate-tropical division of early maize germplasms 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 examining 558 529 single nucleotide polymorphisms, expression data of 28 769 genes, and 662 traits collected from 368 diverse temperate and tropical maize inbred lines in this study. This is a new attempt to systematically exploit the mechanisms of the adaptation process in maize. Our results indicate that divergence between tropical and temperate lines apparently occurred 3400-6700 years ago. Seven hundred and one genomic selection signals and transcriptomic variants including 2700 differentially expressed individual genes and 389 rewired co-expression network genes were identified. These candidate signals were found to be functionally related to stress responses, 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. Our study also clearly indicates that such stress adaptation could involve evolution of protein-coding sequences as well as transcriptome-level regulatory changes. The latter process may be a more flexible and dynamic way for maize to adapt to environmental changes along its short evolutionary history.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Haijun
authors.initials: H
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xiaqing
authors.initials: X
authors.lastname: Wang
authors.affiliation: Corn Host Plant Resistance Research Unit, United States Department of Agriculture-Agricultural Research Service, Box 9555, Mississippi State, MS 39762, USA.
authors.forename: Marilyn L
authors.initials: ML
authors.lastname: Warburton
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Wen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Minliang
authors.initials: M
authors.lastname: Jin
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Min
authors.initials: M
authors.lastname: Deng
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Tong
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Qingchun
authors.initials: Q
authors.lastname: Pan
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: yjianbing@mail.hzau.edu.cn.
authors.forename: Jianbing
authors.initials: J
authors.lastname: Yan
mesh_terms: D000222:Adaptation, Physiological; D005075:Biological Evolution; D001947:Breeding; D018745:Genome, Plant; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics*; D012641:Selection, Genetic; D059467:Transcriptome; D003313:Zea mays / Q000235:genetics* / Q000502:physiology
chemical_list: D010940:Plant Proteins
keywords: Zea mays; positive selection; regulatory evolution; temperate adaptation