Genome sequencing reveals evidence of adaptive variation in the genus Zea

Lu Chen^#^{1

2}, Jingyun Luo^#¹, Minliang Jin^#¹, Ning Yang^#^{3

4}, Xiangguo Liu⁵, Yong Peng¹, Wenqiang Li¹, Alyssa Phillips^{6

7}, Brenda Cameron⁷, Julio S Bernal⁸, Rubén Rellán-Álvarez⁹, Ruairidh J H Sawers¹⁰, Qing Liu⁵, Yuejia Yin⁵, Xinnan Ye⁵, Jiali Yan¹, Qinghua Zhang¹, Xiaoting Zhang¹, Shenshen Wu¹, Songtao Gui¹, Wenjie Wei¹, Yuebin Wang¹, Yun Luo¹, Chenglin Jiang¹, Min Deng¹, Min Jin¹, Liumei Jian¹, Yanhui Yu¹, Maolin Zhang¹, Xiaohong Yang¹¹, Matthew B Hufford¹², Alisdair R Fernie¹³, Marilyn L Warburton¹⁴, Jeffrey Ross-Ibarra¹⁵, Jianbing Yan^{16

17}

Affiliations

¹ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
² State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
³ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. ningy@mail.hzau.edu.cn.
⁴ Hubei Hongshan Laboratory, Wuhan, China. ningy@mail.hzau.edu.cn.
⁵ Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China.
⁶ Center for Population Biology, University of California Davis, Davis, CA, USA.
⁷ Department of Evolution and Ecology, University of California Davis, Davis, CA, USA.
⁸ Department of Entomology, Texas A&M University, College Station, TX, USA.
⁹ Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA.
¹⁰ Department of Plant Science, The Pennsylvania State University, State College, PA, USA.
¹¹ National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China.
¹² Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
¹³ Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
¹⁴ United States Department of Agriculture-Agricultural Research Service: Western Regional Plant Introduction Station, Washington State University, Pullman, WA, USA.
¹⁵ Department of Evolution and Ecology, Center for Population Biology, Genome Center, University of California Davis, Davis, CA, USA. rossibarra@ucdavis.edu.
¹⁶ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. yjianbing@mail.hzau.edu.cn.
¹⁷ Hubei Hongshan Laboratory, Wuhan, China. yjianbing@mail.hzau.edu.cn.

^# Contributed equally.

PMID: 36266506
DOI: 10.1038/s41588-022-01184-y

Genome sequencing reveals evidence of adaptive variation in the genus Zea

Lu Chen et al. Nat Genet. 2022 Nov.

. 2022 Nov;54(11):1736-1745.

doi: 10.1038/s41588-022-01184-y. Epub 2022 Oct 20.

Authors

Affiliations

¹ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
² State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
³ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. ningy@mail.hzau.edu.cn.
⁴ Hubei Hongshan Laboratory, Wuhan, China. ningy@mail.hzau.edu.cn.
⁵ Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China.
⁶ Center for Population Biology, University of California Davis, Davis, CA, USA.
⁷ Department of Evolution and Ecology, University of California Davis, Davis, CA, USA.
⁸ Department of Entomology, Texas A&M University, College Station, TX, USA.
⁹ Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA.
¹⁰ Department of Plant Science, The Pennsylvania State University, State College, PA, USA.
¹¹ National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China.
¹² Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
¹³ Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
¹⁴ United States Department of Agriculture-Agricultural Research Service: Western Regional Plant Introduction Station, Washington State University, Pullman, WA, USA.
¹⁵ Department of Evolution and Ecology, Center for Population Biology, Genome Center, University of California Davis, Davis, CA, USA. rossibarra@ucdavis.edu.
¹⁶ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. yjianbing@mail.hzau.edu.cn.
¹⁷ Hubei Hongshan Laboratory, Wuhan, China. yjianbing@mail.hzau.edu.cn.

^# Contributed equally.

PMID: 36266506
DOI: 10.1038/s41588-022-01184-y

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 wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

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References

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Genome sequencing reveals evidence of adaptive variation in the genus Zea

Affiliations

Genome sequencing reveals evidence of adaptive variation in the genus Zea

Authors

Affiliations

Abstract

References

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LinkOut - more resources

Full Text Sources

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