Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding
Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding
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).
Njaci, Isaac
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Waweru, Bernice
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Kamal, Nadia
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Muktar, Meki Shehabu
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Fisher, David
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Gundlach, Heidrun
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Muli, Collins
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Muthui, Lucy
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Maranga, Mary
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Kiambi, Davies
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Maass, Brigitte L.
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Emmrich, Peter M. F.
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Domelevo Entfellner, Jean-baka
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Spannagl, Manuel
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Chapman, Mark A.
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Shorinola, Oluwaseyi
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Jones, Chris S.
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17 April 2023
Njaci, Isaac
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Waweru, Bernice
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Kamal, Nadia
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Muktar, Meki Shehabu
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Fisher, David
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Gundlach, Heidrun
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Muli, Collins
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Muthui, Lucy
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Maranga, Mary
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Kiambi, Davies
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Maass, Brigitte L.
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Emmrich, Peter M. F.
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Domelevo Entfellner, Jean-baka
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Spannagl, Manuel
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Chapman, Mark A.
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Shorinola, Oluwaseyi
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Jones, Chris S.
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Njaci, Isaac, Waweru, Bernice, Kamal, Nadia, Muktar, Meki Shehabu, Fisher, David, Gundlach, Heidrun, Muli, Collins, Muthui, Lucy, Maranga, Mary, Kiambi, Davies, Maass, Brigitte L., Emmrich, Peter M. F., Domelevo Entfellner, Jean-baka, 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 (1), [1915].
(doi:10.1038/s41467-023-37489-7).
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).
Text
s41467-023-37489-7
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Accepted/In Press date: 17 March 2023
e-pub ahead of print date: 17 April 2023
Published date: 17 April 2023
Additional Information:
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). We also thank Prof Cristobal Uauy for proofreading the manuscript.
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). We also thank Prof Cristobal Uauy for proofreading the manuscript.
Publisher Copyright:
© 2023, The Author(s).
Identifiers
Local EPrints ID: 476453
URI: http://eprints.soton.ac.uk/id/eprint/476453
ISSN: 2041-1723
PURE UUID: 3e1f93a9-93b6-4cde-9b26-d523ceeb9d8f
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Date deposited: 02 May 2023 16:34
Last modified: 18 Mar 2024 03:59
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Contributors
Author:
Isaac Njaci
Author:
Bernice Waweru
Author:
Nadia Kamal
Author:
Meki Shehabu Muktar
Author:
Heidrun Gundlach
Author:
Collins Muli
Author:
Lucy Muthui
Author:
Mary Maranga
Author:
Davies Kiambi
Author:
Brigitte L. Maass
Author:
Peter M. F. Emmrich
Author:
Jean-baka Domelevo Entfellner
Author:
Manuel Spannagl
Author:
Oluwaseyi Shorinola
Author:
Chris S. Jones
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