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Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding

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  • Jiantao Guan

    (Chinese Academy of Agricultural Sciences
    Beijing Academy of Agriculture and Forestry Sciences
    Chinese Academy of Agricultural Sciences)

  • Jintao Zhang

    (Chinese Academy of Agricultural Sciences
    Yangtze University)

  • Dan Gong

    (Chinese Academy of Agricultural Sciences
    Yangtze University)

  • Zhengquan Zhang

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Yang Yu

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Gaoling Luo

    (Guangxi Academy of Agricultural Sciences)

  • Prakit Somta

    (Kasetsart University)

  • Zheng Hu

    (Chinese Academy of Agricultural Sciences)

  • Suhua Wang

    (Chinese Academy of Agricultural Sciences)

  • Xingxing Yuan

    (Jiangsu Academy of Agricultural Sciences)

  • Yaowen Zhang

    (Shanxi Agricultural University)

  • Yanlan Wang

    (Crop Research Institute of Hunan Province)

  • Yanhua Chen

    (Guangxi Academy of Agricultural Sciences)

  • Kularb Laosatit

    (Kasetsart University)

  • Xin Chen

    (Jiangsu Academy of Agricultural Sciences)

  • Honglin Chen

    (Chinese Academy of Agricultural Sciences)

  • Aihua Sha

    (Yangtze University)

  • Xuzhen Cheng

    (Chinese Academy of Agricultural Sciences)

  • Hua Xie

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Lixia Wang

    (Chinese Academy of Agricultural Sciences)

Abstract

Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean.

Suggested Citation

  • Jiantao Guan & Jintao Zhang & Dan Gong & Zhengquan Zhang & Yang Yu & Gaoling Luo & Prakit Somta & Zheng Hu & Suhua Wang & Xingxing Yuan & Yaowen Zhang & Yanlan Wang & Yanhua Chen & Kularb Laosatit & X, 2022. "Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33515-2
    DOI: 10.1038/s41467-022-33515-2
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    References listed on IDEAS

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