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Portrait of a genus: the genetic diversity of Zea

Lu Chen, Jingyun Luo, Minliang Jin, Ning Yang, Xiangguo Liu, Yong Peng, Wenqiang Li, Liu Qing, Yuejia Yin, Xinnan Ye, Jiali Yan, Qinghua Zhang, Xiaoting Zhang, Songtao Gui, Shenshen Wu, Yuebin Wang, Yun Luo, Chengling Jiang, Min Deng, Min Jin, Liumei Jian, Yanhui Yu, Maolin Zhang, Xiaohong Yang, Matthew B. Hufford, Alisdair R. Fernie, Marilyn L. Warburton, Jeffrey Ross-Ibarra, Jianbing Yan
doi: https://doi.org/10.1101/2021.04.07.438828
Lu Chen
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Jingyun Luo
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Minliang Jin
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Ning Yang
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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  • For correspondence: yjianbing@mail.hzau.edu.cn rossibarra@ucdavis.edu yangningyingji@126.com
Xiangguo Liu
2Biotechnology Research Centre, Jilin Academy of Agricultural Sciences, Changchun 130033, China
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Yong Peng
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Wenqiang Li
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Liu Qing
2Biotechnology Research Centre, Jilin Academy of Agricultural Sciences, Changchun 130033, China
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Yuejia Yin
2Biotechnology Research Centre, Jilin Academy of Agricultural Sciences, Changchun 130033, China
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Xinnan Ye
2Biotechnology Research Centre, Jilin Academy of Agricultural Sciences, Changchun 130033, China
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Jiali Yan
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Qinghua Zhang
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Xiaoting Zhang
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Songtao Gui
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Shenshen Wu
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Yuebin Wang
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Yun Luo
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Chengling Jiang
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Min Deng
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Min Jin
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Liumei Jian
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Yanhui Yu
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Maolin Zhang
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Xiaohong Yang
3National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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Matthew B. Hufford
4Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
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Alisdair R. Fernie
5Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Marilyn L. Warburton
6United States Department of Agriculture-Agricultural Research Service: Corn Host Plant Resistance Research Unit, Box 9555, Mississippi State, MS, 39762, USA
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Jeffrey Ross-Ibarra
7Department of Evolution and Ecology, Center for Population Biology, and Genome Center, University of California Davis, Davis, California 95616, USA
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  • For correspondence: yjianbing@mail.hzau.edu.cn rossibarra@ucdavis.edu yangningyingji@126.com
Jianbing Yan
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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  • For correspondence: yjianbing@mail.hzau.edu.cn rossibarra@ucdavis.edu yangningyingji@126.com
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Abstract

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in the wild relatives of maize. Here, we characterize a high-density genomic variation map from ~700 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 65 million single nucleotide polymorphisms (SNPs), 8 million Insertion/Deletion (InDel) polymorphisms, and over one thousand novel inversions. The variation map reveals evidence of selection within taxa displaying novel adaptations such as perenniality and regrowth. We focus in detail on evidence of convergent adaptation in highland teosinte and temperate maize. This study not only indicates the key role of hormone related pathways in highland adaptation and flowering time related pathways in high latitude adaptation, but also identifies significant overlap in the genes underlying adaptations to both environments. To show how this data can identify useful genetic variants, we generated and characterized novel mutant alleles for two flowering time candidate genes. This work provides the most extensive sampling to date of the genetic diversity inherent in the genus Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 09, 2021.
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Portrait of a genus: the genetic diversity of Zea
Lu Chen, Jingyun Luo, Minliang Jin, Ning Yang, Xiangguo Liu, Yong Peng, Wenqiang Li, Liu Qing, Yuejia Yin, Xinnan Ye, Jiali Yan, Qinghua Zhang, Xiaoting Zhang, Songtao Gui, Shenshen Wu, Yuebin Wang, Yun Luo, Chengling Jiang, Min Deng, Min Jin, Liumei Jian, Yanhui Yu, Maolin Zhang, Xiaohong Yang, Matthew B. Hufford, Alisdair R. Fernie, Marilyn L. Warburton, Jeffrey Ross-Ibarra, Jianbing Yan
bioRxiv 2021.04.07.438828; doi: https://doi.org/10.1101/2021.04.07.438828
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Portrait of a genus: the genetic diversity of Zea
Lu Chen, Jingyun Luo, Minliang Jin, Ning Yang, Xiangguo Liu, Yong Peng, Wenqiang Li, Liu Qing, Yuejia Yin, Xinnan Ye, Jiali Yan, Qinghua Zhang, Xiaoting Zhang, Songtao Gui, Shenshen Wu, Yuebin Wang, Yun Luo, Chengling Jiang, Min Deng, Min Jin, Liumei Jian, Yanhui Yu, Maolin Zhang, Xiaohong Yang, Matthew B. Hufford, Alisdair R. Fernie, Marilyn L. Warburton, Jeffrey Ross-Ibarra, Jianbing Yan
bioRxiv 2021.04.07.438828; doi: https://doi.org/10.1101/2021.04.07.438828

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