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

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, Xin Chen, Honglin Chen, Aihua Sha, Xuzhen Cheng, Hua Xie () and Lixia Wang ()
Additional contact information
Jiantao Guan: Chinese Academy of Agricultural Sciences
Jintao Zhang: Chinese Academy of Agricultural Sciences
Dan Gong: Chinese Academy of Agricultural Sciences
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

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-33515-2

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