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

Autor: Wang P; College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia.; Western Crop Genetics Alliance, Western Australian Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia., Zhou G; Western Crop Genetics Alliance, Western Australian Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.; Department of Primary Industries and Regional Development, Government of Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia., Jian J; BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China., Yang H; Department of Primary Industries and Regional Development, Government of Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia., Renshaw D; Department of Primary Industries and Regional Development, Government of Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia., Aubert MK; Australian Grain Technologies Pty Ltd, 100 Byfield Street, Northam, WA, 6041, Australia., Clements J; Green Blueprint Pty Ltd, 117C Hastings Street, Scarborough, WA, 6019, Australia.; Glycemic Lupin Company Pty Ltd, 33 Commercial St, Coorow, WA, 6515, Australia., He T; College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia.; Western Crop Genetics Alliance, Western Australian Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia., Sweetingham M; Department of Primary Industries and Regional Development, Government of Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia., Li C; College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia.; Western Crop Genetics Alliance, Western Australian Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.; Department of Primary Industries and Regional Development, Government of Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia.
Jazyk: angličtina
Zdroj: The Plant journal : for cell and molecular biology [Plant J] 2021 Mar; Vol. 105 (5), pp. 1192-1210. Date of Electronic Publication: 2021 Jan 11.
DOI: 10.1111/tpj.15100
Abstrakt: 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.
(© 2020 Society for Experimental Biology and John Wiley & Sons Ltd.)
Databáze: MEDLINE
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