Whole-genome assembly and re-sequencing reveal genomic imprint and key genes of rapid domestication in narrow-leafed lupin.

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 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 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 narrow-leafed lupin cultivar Tanjil, comprising 20 chromosomes with a total genome size of 615.8 Mb and contig N50 = 5.65 Mb. We characterised the original mutation and putative biological pathway resulting in low seed alkaloid level that initiated the de novo domestication of narrow-leafed lupin. We identified an 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 predicted precisely by the original model of the bottleneck effect on genetic variability in populations. Our results identify the key domestication genetic loci and provide the 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.