Whole‐genome assembly and resequencing reveal genomic imprint and key genes of rapid domestication in narrow‐leafed lupin

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