Genome sequencing and population resequencing provide insights into the genetic basis of domestication and diversity of vegetable soybean
Genome sequencing and population resequencing provide insights into the genetic basis of domestication and diversity of vegetable soybean
复制标题
基因组测序和群体重测序为了解菜用大豆驯化和多样性的遗传基础提供了见解
DOI：
10.1093/hr/uhab052
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发表时间：
2022-01-05
影响因子：
8.7
通讯作者：
Gong, Yaming
中科院分区：
文献类型：
--
作者：
Liu, Na;Niu, Yongchao;Gong, Yaming
菜用大豆是中国最重要的蔬菜之一，在过去的二十年里，世界范围内对这种蔬菜的需求显著增加。在这里，我们提出了一个高质量的从头基因组组装菜用大豆品种浙农6号（ZN 6），这是在中国最受欢迎的品种之一。20条假染色体覆盖了1.01 Gb总组装大小的94.57%，重叠群N50为3.84 Mb，骨架N50为48.41 Mb。共注释了55517个蛋白质编码基因。大约54.85%的组装基因组被注释为重复序列，具有最丰富的长末端重复转座元件。通过对籽粒大豆威廉姆斯82、其他6种豆科植物和拟南芥基因组的比较基因组学和系统发育分析，突出了ZN 6与其他物种的差异。此外，我们对60份菜用大豆材料进行了重测序。除了103以前重测序的野生大豆和155以前重测序的粮食大豆种质，我们进行了群体结构和蔬菜，粮食和野生大豆的选择扫描分析。它们明显分为三个分支。与野生大豆群体相比，菜用大豆和粮用大豆群体中分别有1112和1047个基因处于选择状态。其中，我们鉴定了134个菜用大豆和粒用大豆群体间共有的选择基因。此外，我们报告了四个蔗糖合成酶基因，一个蔗糖磷酸合成酶基因，和四个糖转运基因作为候选基因相关的重要性状，如种子甜度和种子大小的菜用大豆。本研究为促进菜用大豆的进化和功能基因组学研究以及基因组信息育种提供了必要的基因组资源。
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.