Integrative Biology Journals
Plant Diversity

Plant Diversity ›› 2026, Vol. 48 ›› Issue (01): 59-74.DOI: 10.1016/j.pld.2025.10.002

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Integrative analysis of plastome, single-copy nuclear gene Pgk1 and SLAF-seq data uncovers multiple-origin and introgression history in polyploid Agropyron cristatum

Hao Yana, Yihao Zhanga, Hailun Shia, Xuande Xua, Shuangbing Yua, Lijun Yanb, Yan Zhaoc, Dandan Wua, Yue Zhanga, Yiran Chenga, Yi Wanga, Houyang Kanga, Xiao Mad, Haiqin Zhangd, Yonghong Zhoua, Wenjie Chene, Lina Shad, Xing Fana   

  1. a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China;
    b Sichuan Academy of Grassland Science, Chengdu, Sichuan, China;
    c Key Laboratory of Grassland Resources, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China;
    d College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China;
    e Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
  • Received:2025-05-13 Revised:2025-10-14 Online:2026-03-05 Published:2026-01-25
  • Contact: Wenjie Chen,E-mail:wjchen@nwipb.cas.cn;Lina Sha,E-mail:shalina@sicau.edu.cn;Xing Fan,E-mail:fanxing9988@163.com
  • Supported by:
    This work was funded by the following projects: the National Natural Science Foundation of China (Nos. 31870360 and 32171603); Xining Science and Technology Major Project (2023-Z- 13); Qinghai Provincial Science and Technology Major Project (2023-SF-A5); Youth Innovation Promotion Association (Chinese Academy of Sciences, Grant/Award Number: Y2023116) and the Qinghai Provincial central guide local science and technology development funds project (2025ZY002).

Integrative analysis of plastome, single-copy nuclear gene Pgk1 and SLAF-seq data uncovers multiple-origin and introgression history in polyploid Agropyron cristatum

Hao Yana, Yihao Zhanga, Hailun Shia, Xuande Xua, Shuangbing Yua, Lijun Yanb, Yan Zhaoc, Dandan Wua, Yue Zhanga, Yiran Chenga, Yi Wanga, Houyang Kanga, Xiao Mad, Haiqin Zhangd, Yonghong Zhoua, Wenjie Chene, Lina Shad, Xing Fana   

  1. a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China;
    b Sichuan Academy of Grassland Science, Chengdu, Sichuan, China;
    c Key Laboratory of Grassland Resources, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China;
    d College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China;
    e Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
  • 通讯作者: Wenjie Chen,E-mail:wjchen@nwipb.cas.cn;Lina Sha,E-mail:shalina@sicau.edu.cn;Xing Fan,E-mail:fanxing9988@163.com
  • 基金资助:
    This work was funded by the following projects: the National Natural Science Foundation of China (Nos. 31870360 and 32171603); Xining Science and Technology Major Project (2023-Z- 13); Qinghai Provincial Science and Technology Major Project (2023-SF-A5); Youth Innovation Promotion Association (Chinese Academy of Sciences, Grant/Award Number: Y2023116) and the Qinghai Provincial central guide local science and technology development funds project (2025ZY002).

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Abstract: Elucidating the origins and mechanisms of polyploidization requires tracing the evolutionary history of polyploid species, particularly those with complex origins. Agropyron cristatum, traditionally regarded as an autopolyploid, exhibits characteristics indicative of a segmental allopolyploid. Here, we used phylogenetic analysis based on a low-copy nuclear gene (i.e., Pgk1), SLAF-seq, and plastome data from 20 diploid and 120 tetraploid Agropyron individuals to determine whether tetraploid A. cristatum arose from an allopolyploid or autopolyploid event. Phylogenetic analyses based on Pgk1 and SLAF-seq data identified two distinct A. cristatum lineages that corresponded to the two main Agropyron habitats in Central Asia–Europe and East Asia–Qinghai-Tibet Plateau. These findings, taken together with molecular dating and gene flow analyses, suggest that the East Asian tetraploid A. cristatum originated via both autopolyploidy from A. cristatum and hybridization between diploid A. cristatum and A. mongolicum, with each diploid cytotype acting as a maternal donor. Furthermore, the Central Asia–Europe tetraploid A. cristatum originated solely via autopolyploidy of diploid A. cristatum. Our findings also indicate that rapid diversification of Agropyron was likely driven by climate oscillations, geographic isolation, introgressive hybridization, and chloroplast capture. These findings challenge simplistic views of autopolyploids and underscore substantial potential for achieving high levels of genetic and adaptive diversity through recurrent hybridization and reticulate evolution.

Key words: Polyploidy, Agropyron, SLAF-seq, Plastome, Diversification, Pgk1

摘要： Elucidating the origins and mechanisms of polyploidization requires tracing the evolutionary history of polyploid species, particularly those with complex origins. Agropyron cristatum, traditionally regarded as an autopolyploid, exhibits characteristics indicative of a segmental allopolyploid. Here, we used phylogenetic analysis based on a low-copy nuclear gene (i.e., Pgk1), SLAF-seq, and plastome data from 20 diploid and 120 tetraploid Agropyron individuals to determine whether tetraploid A. cristatum arose from an allopolyploid or autopolyploid event. Phylogenetic analyses based on Pgk1 and SLAF-seq data identified two distinct A. cristatum lineages that corresponded to the two main Agropyron habitats in Central Asia–Europe and East Asia–Qinghai-Tibet Plateau. These findings, taken together with molecular dating and gene flow analyses, suggest that the East Asian tetraploid A. cristatum originated via both autopolyploidy from A. cristatum and hybridization between diploid A. cristatum and A. mongolicum, with each diploid cytotype acting as a maternal donor. Furthermore, the Central Asia–Europe tetraploid A. cristatum originated solely via autopolyploidy of diploid A. cristatum. Our findings also indicate that rapid diversification of Agropyron was likely driven by climate oscillations, geographic isolation, introgressive hybridization, and chloroplast capture. These findings challenge simplistic views of autopolyploids and underscore substantial potential for achieving high levels of genetic and adaptive diversity through recurrent hybridization and reticulate evolution.

关键词: Polyploidy, Agropyron, SLAF-seq, Plastome, Diversification, Pgk1

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