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Analysis of elite variety tag SNPs reveals an important allele in upland rice

Author

Listed:
  • Jun Lyu

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences)

  • Shilai Zhang

    (Food Crops Research Institute, Yunnan Academy of Agricultural Sciences)

  • Yang Dong

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences)

  • Weiming He

    (BGI-Shenzhen, Beishan Industrial Zone)

  • Jing Zhang

    (Food Crops Research Institute, Yunnan Academy of Agricultural Sciences)

  • Xianneng Deng

    (Food Crops Research Institute, Yunnan Academy of Agricultural Sciences)

  • Yesheng Zhang

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences)

  • Xin Li

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences)

  • Baoye Li

    (Food Crops Research Institute, Yunnan Academy of Agricultural Sciences)

  • Wangqi Huang

    (Food Crops Research Institute, Yunnan Academy of Agricultural Sciences)

  • Wenting Wan

    (Food Crops Research Institute, Yunnan Academy of Agricultural Sciences)

  • Yang Yu

    (Food Crops Research Institute, Yunnan Academy of Agricultural Sciences)

  • Qiong Li

    (Food Crops Research Institute, Yunnan Academy of Agricultural Sciences)

  • Jun Li

    (BGI-Shenzhen, Beishan Industrial Zone)

  • Xin Liu

    (BGI-Shenzhen, Beishan Industrial Zone)

  • Bo Wang

    (BGI-Shenzhen, Beishan Industrial Zone)

  • Dayun Tao

    (Food Crops Research Institute, Yunnan Academy of Agricultural Sciences)

  • Gengyun Zhang

    (BGI-Shenzhen, Beishan Industrial Zone
    BGI-Yunnan, Haiyuan Road, Kunming Hi-Tech Development Zone)

  • Jun Wang

    (BGI-Shenzhen, Beishan Industrial Zone)

  • Xun Xu

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences
    BGI-Shenzhen, Beishan Industrial Zone
    BGI-Yunnan, Haiyuan Road, Kunming Hi-Tech Development Zone)

  • Fengyi Hu

    (Food Crops Research Institute, Yunnan Academy of Agricultural Sciences)

  • Wen Wang

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences)

Abstract

Elite crop varieties usually fix alleles that occur at low frequencies within non-elite gene pools. Dissecting these alleles for desirable agronomic traits can be accomplished by comparing the genomes of elite varieties with those from non-elite populations. Here we deep-sequence six elite rice varieties and use two large control panels to identify elite variety tag single-nucleotide polymorphism alleles (ETASs). Guided by this preliminary analysis, we comprehensively characterize one protein-altering ETAS in the 9-cis-epoxycarotenoid dioxygenase gene of the IRAT104 upland rice variety. This allele displays a drastic frequency difference between upland and irrigated rice, and a selective sweep is observed around this allele. Functional analysis indicates that in upland rice, this allele is associated with significantly higher abscisic acid levels and denser lateral roots, suggesting its association with upland rice suitability. This report provides a potential strategy to mine rare, agronomically important alleles.

Suggested Citation

  • Jun Lyu & Shilai Zhang & Yang Dong & Weiming He & Jing Zhang & Xianneng Deng & Yesheng Zhang & Xin Li & Baoye Li & Wangqi Huang & Wenting Wan & Yang Yu & Qiong Li & Jun Li & Xin Liu & Bo Wang & Dayun , 2013. "Analysis of elite variety tag SNPs reveals an important allele in upland rice," Nature Communications, Nature, vol. 4(1), pages 1-9, October.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3138
    DOI: 10.1038/ncomms3138
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