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Article|05 Jan 2022|OPEN
Genome sequencing and population resequencing provide insights into the genetic basis of domestication and diversity of vegetable soybean
Na Liu1 , , Yongchao Niu2 , Guwen Zhang1 , Zhijuan Feng1 , Yuanpeng Bo1 , Jinmin Lian2 , Bin Wang1 and Yaming Gong,1 ,
1State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
2Biozeron Shenzhen, Inc., Shenzhen, 518081, China
*Corresponding author. E-mail: ln200811@163.com,gongym07@126.com

Horticulture Research 9,
Article number: uhab052 (2022)
doi: https://doi.org/10.1093/hr/uhab052
Views: 291

Received: 21 May 2021
Revised: 26 Jul 2021
Accepted: 26 Aug 2021
Published online: 05 Jan 2022

Abstract

Vegetable soybean is one of the most important vegetables in China, and the demand for this vegetable has markedly increased worldwide over the past two decades. Here, we present a high-quality de novo genome assembly of the vegetable soybean cultivar Zhenong 6 (ZN6), which is one of the most popular cultivars in China. The 20 pseudochromosomes cover 94.57% of the total 1.01 Gb assembly size, with contig N50 of 3.84 Mb and scaffold N50 of 48.41 Mb. A total of 55 517 protein-coding genes were annotated. Approximately 54.85% of the assembled genome was annotated as repetitive sequences, with the most abundant long terminal repeat transposable elements. Comparative genomic and phylogenetic analyses with grain soybean Williams 82, six other Fabaceae species and Arabidopsis thaliana genomes highlight the difference of ZN6 with other species. Furthermore, we resequenced 60 vegetable soybean accessions. Alongside 103 previously resequenced wild soybean and 155 previously resequenced grain soybean accessions, we performed analyses of population structure and selective sweep of vegetable, grain, and wild soybean. They were clearly divided into three clades. We found 1112 and 1047 genes under selection in the vegetable soybean and grain soybean populations compared with the wild soybean population, respectively. Among them, we identified 134 selected genes shared between vegetable soybean and grain soybean populations. Additionally, we report four sucrose synthase genes, one sucrose-phosphate synthase gene, and four sugar transport genes as candidate genes related to important traits such as seed sweetness and seed size in vegetable soybean. This study provides essential genomic resources to promote evolutionary and functional genomics studies and genomically informed breeding for vegetable soybean.