Vigna unguiculata is an important legume crop worldwide. The subsp. sesquipedalis and unguiculata are the two major types grown; the former is mainly grown in Asia to produce fresh pods, while the latter is mainly grown in Africa to produce seeds. Here, a chromosome-scale genome for subsp. sesquipedalis was generated by combining high-fidelity (HiFi) long-read sequencing with high-throughput chromosome conformation capture (Hi-C) technology. The genome size for all contigs and N50 were 594 and 18.5 Mb, respectively. The Hi-C interaction map helped cluster 91% of the contigs into 11 chromosomes. Genome comparisons between subsp. sesquipedalis and unguiculata revealed extensive genomic variations, and some variations resulted in gene loss. A germplasm panel with 315 accessions of V. unguiculata was resequenced, and a genomic variation map was constructed. Population structure and phylogenetic analyses suggested that subsp. sesquipedalis originated from subsp. unguiculata. Highly differentiated genomic regions were also identified, and a number of genes functionally enriched in adaptations were located in these regions. Two traits, pod length (PL) and pod width (PW), were observed for this germplasm, and genome-wide association analysis of these traits was performed. The quantitative trait loci (QTLs) for these two traits were identified, and their candidate genes were uncovered. Interestingly, genomic regions of PL QTLs also showed strong signals of artificial selection. Taken together, the results of this study provide novel insights into the population differentiation and genetic basis of key agricultural traits in V. unguiculata.

中文翻译：

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豇豆的全面基因组分析为了解种群分化和关键农业性状的遗传基础提供了见解

豇豆是世界范围内重要的豆科作物。亚种。esquipedalis和unguiculata是种植的两种主要类型；前者主要种植在亚洲，用于生产新鲜豆荚，后者主要种植在非洲，用于生产种子。在这里，亚种的染色体规模基因组。sesquipedalis是通过将高保真 (HiFi) 长读长测序与高通量染色体构象捕获 (Hi-C) 技术相结合而产生的。所有重叠群和 N50 的基因组大小分别为 594 和 18.5 Mb。Hi-C 相互作用图谱帮助 91% 的重叠群聚集成 11 条染色体。亚种之间的基因组比较。倍足目和有爪目揭示了广泛的基因组变异，有些变异导致基因丢失。对具有 315 个V. unguiculata材料的种质组进行了重新测序，并构建了基因组变异图谱。种群结构和系统发育分析表明亚种。sesquipedalis起源于亚种。有蹄类。还鉴定了高度分化的基因组区域，并且许多在适应方面功能丰富的基因位于这些区域。观察到该种质的两个性状，荚长度（PL）和荚宽度（PW），并对这些性状进行了全基因组关联分析。鉴定了这两个性状的数量性状基因座（QTL），并发现了它们的候选基因。有趣的是，PL QTL 的基因组区域也显示出强烈的人工选择信号。总而言之，本研究的结果为V. unguiculata的种群分化和关键农业性状的遗传基础提供了新的见解。