Shifting from a livestock‐based protein diet to a plant‐based protein diet has been proposed as an essential requirement to maintain global food sustainability, which requires the increased production of protein‐rich crops for direct human consumption. Meanwhile, the lack of sufficient genetic diversity in crop varieties is an increasing concern for sustainable food supplies. Countering this concern requires a clear understanding of the domestication process and dynamics. Narrow‐leafed lupin (Lupinus angustifolius L.) has experienced rapid domestication and has become a new legume crop over the past century, with the potential to provide protein‐rich seeds. Here, using long‐read whole‐genome sequencing, we assembled the third‐generation reference genome for the narrow‐leafed lupin cultivar Tanjil, comprising 20 chromosomes with a total genome size of 615.8 Mb and contig N50 = 5.65 Mb. We characterized the original mutation and putative biological pathway resulting in low seed alkaloid level that initiated the recent domestication of narrow‐leafed lupin. We identified a 1133‐bp insertion in the cis‐regulatory region of a putative gene that may be associated with reduced pod shattering (lentus). A comparative analysis of genomic diversity in cultivars and wild types identified an apparent domestication bottleneck, as precisely predicted by the original model of the bottleneck effect on genetic variability in populations. Our results identify the key domestication genetic loci and provide direct genomic evidence for a domestication bottleneck, and open up the possibility of knowledge‐driven de novo domestication of wild plants as an avenue to broaden crop plant diversity to enhance food security and sustainable low‐carbon emission agriculture.

中文翻译：

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全基因组装配和重新测序揭示了窄叶羽扇豆的基因组印记和快速驯化的关键基因

已提议从基于牲畜的蛋白质饮食转变为基于植物的蛋白质饮食，这是维持全球食品可持续性的一项基本要求，这要求增加富含蛋白质的农作物的产量，以供人类直接食用。同时，农作物品种缺乏足够的遗传多样性是对可持续粮食供应的日益关注。解决这一问题需要对驯化过程和动态有一个清晰的了解。窄叶羽扇豆（羽扇豆）L.）驯化迅速，在过去的一个世纪中已成为一种新的豆类作物，具有提供富含蛋白质的种子的潜力。在这里，我们使用长时程全基因组测序技术，为窄叶羽扇豆品种Tanjil组装了第三代参考基因组，其中包括20条染色体，总基因组大小为615.8 Mb，重叠群N50 = 5.65 Mb。我们对导致原始种子生物碱水平低的原始突变和推定的生物途径进行了表征，从而引发了最近窄叶羽扇豆的驯化。我们在推定基因的顺式调控区域中发现了一个1133 bp的插入片段，该插入片段可能与荚果碎裂的减少有关（扁豆）。品种和野生型基因组多样性的比较分析确定了明显的驯化瓶颈，正如瓶颈对种​​群遗传变异的原始模型所精确预测的那样。我们的结果确定了关键的驯化遗传基因座，并为驯化瓶颈提供了直接的基因组证据，并开辟了知识驱动的野生植物从头驯化的可能性，以此作为拓宽作物植物多样性，增强粮食安全和可持续低碳发展的途径排放农业。