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ToolsNjaci, Isaac, Waweru, Bernice, Kamal, Nadia, Muktar, Meki Shehabu, Fisher, David, Gundlach, Heidrun, Muli, Collins, Muthui, Lucy, Maranga, Mary, Kiambi, Davies, Maass, Brigitte L., Domelevo Entfellner, Jean-Baka, Emmrich, Peter M. F., Spannagl, Manuel, Chapman, Mark A., Shorinola, Oluwaseyi and Jones, Chris S. (2023) Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding. Nature Communications, 14. ISSN 2041-1723
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Abstract
Under-utilised orphan crops hold the key to diversified and climate-resilient food systems. Here, we report on orphan crop genomics using the case of Lablab purpureus (L.) Sweet (lablab) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led plant genome collaboration produces a high-quality chromosome-scale assembly of the lablab genome. Our assembly highlights the genome organisation of the trypsin inhibitor genes - an important anti-nutritional factor in lablab. We also re-sequence cultivated and wild lablab accessions from Africa confirming two domestication events. Finally, we examine the genetic and phenotypic diversity in a comprehensive lablab germplasm collection and identify genomic loci underlying variation of important agronomic traits in lablab. The genomic data generated here provide a valuable resource for lablab improvement. Our inclusive collaborative approach also presents an example that can be explored by other researchers sequencing indigenous crops, particularly from low and middle-income countries (LMIC).
| Item Type: | Article |
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| Additional Information: | Data availability statement: Nanopore long reads used for the reference assembly are available from NCBI SRA under BioProject PRJNA824307. Illumina reads for the resequencing samples are available from the NCBI SRA under project number PRJNA834808. The lablab genome and annotation files are available at the Plant Genomics and Phenomics Research Data Repository (e!DAL) [https://doi.org/10.5447/ipk/2022/26]114 and ILRI (International Livestock Research Institute) [https://hpc.ilri.cgiar.org/~bngina/lablab_longread_sequencing_March_2022/]. All lablab accessions are available by request [https://genebank.ilri.org/gringlobal/] Source data are provided with this paper. Funding information: This research was conducted as part of the CGIAR Research Programme on Livestock, supported by CGIAR Fund Donors. O.S. was supported by the Royal Society FLAIR award (FLR_R1_191850), N.K., H.G. and M.S. were supported by the German Federal Ministry of Education and Research (De.NBI, FKZ 031A536). D.F. was supported by the SoCoBio DTP (grant number BB/T008768/1; BBSRC, UK) to carry out a PhD rotation project in the lab of MAC. D.F. and M.A.C. acknowledge the use of the IRIDIS High Performance Computing Facility, and associated support services at the University of Southampton. I.N., B.W., M.M., D.K. were supported by a Bioinformatics Community of Practice training grant from UK Research and Innovation (UKRI, BB/R020272/1). |
| Faculty \ School: | Faculty of Science > School of Biological Sciences Faculty of Social Sciences > School of Global Development (formerly School of International Development) |
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| Depositing User: | LivePure Connector |
| Date Deposited: | 05 Oct 2024 00:06 |
| Last Modified: | 12 Nov 2024 13:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/96880 |
| DOI: | 10.1038/s41467-023-37489-7 |
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