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

文献类型： 外文期刊

第一作者： Guan, Jiantao

作者： Guan, Jiantao;Zhang, Jintao;Gong, Dan;Hu, Zheng;Wang, Suhua;Chen, Honglin;Cheng, Xuzhen;Wang, Lixia;Guan, Jiantao;Zhang, Zhengquan;Yu, Yang;Xie, Hua;Guan, Jiantao;Zhang, Jintao;Gong, Dan;Luo, Gaoling;Chen, Yanhua;Laosatit, Kularb;Chen, Xin;Zhang, Yaowen;Wang, Yanlan

作者机构：

期刊名称：NATURE COMMUNICATIONS （ 影响因子：17.694； 五年影响因子：17.763 ）

ISSN：

年卷期： 2022 年 13 卷 1 期

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收录情况： SCI

摘要： Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits. 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.

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