IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-37489-7.html
   My bibliography  Save this article

Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding

Author

Listed:
  • Isaac Njaci

    (International Livestock Research Institute
    John Innes Centre, Norwich Research Park)

  • Bernice Waweru

    (International Livestock Research Institute)

  • Nadia Kamal

    (Helmholtz Zentrum München, Plant Genome and Systems Biology)

  • Meki Shehabu Muktar

    (International Livestock Research Institute)

  • David Fisher

    (University of Southampton, School of Biological Sciences)

  • Heidrun Gundlach

    (Helmholtz Zentrum München, Plant Genome and Systems Biology)

  • Collins Muli

    (International Livestock Research Institute)

  • Lucy Muthui

    (International Livestock Research Institute)

  • Mary Maranga

    (Jomo Kenyatta University of Agriculture and Technology)

  • Davies Kiambi

    (Pwani University)

  • Brigitte L. Maass

    (Georg-August-University Göttingen)

  • Peter M. F. Emmrich

    (John Innes Centre, Norwich Research Park
    University of East Anglia)

  • Jean-Baka Domelevo Entfellner

    (International Livestock Research Institute)

  • Manuel Spannagl

    (Helmholtz Zentrum München, Plant Genome and Systems Biology)

  • Mark A. Chapman

    (University of Southampton, School of Biological Sciences)

  • Oluwaseyi Shorinola

    (International Livestock Research Institute
    John Innes Centre, Norwich Research Park)

  • Chris S. Jones

    (International Livestock Research Institute)

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).

Suggested Citation

  • Isaac Njaci & Bernice Waweru & Nadia Kamal & Meki Shehabu Muktar & David Fisher & Heidrun Gundlach & Collins Muli & Lucy Muthui & Mary Maranga & Davies Kiambi & Brigitte L. Maass & Peter M. F. Emmrich, 2023. "Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37489-7
    DOI: 10.1038/s41467-023-37489-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-37489-7
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-37489-7?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Jeremy Schmutz & Steven B. Cannon & Jessica Schlueter & Jianxin Ma & Therese Mitros & William Nelson & David L. Hyten & Qijian Song & Jay J. Thelen & Jianlin Cheng & Dong Xu & Uffe Hellsten & Gregory , 2010. "Genome sequence of the palaeopolyploid soybean," Nature, Nature, vol. 463(7278), pages 178-183, January.
    2. Jeremy Schmutz & Steven B. Cannon & Jessica Schlueter & Jianxin Ma & Therese Mitros & William Nelson & David L. Hyten & Qijian Song & Jay J. Thelen & Jianlin Cheng & Dong Xu & Uffe Hellsten & Gregory , 2010. "Erratum: Genome sequence of the palaeopolyploid soybean," Nature, Nature, vol. 465(7294), pages 120-120, May.
    3. Min Xie & Claire Yik-Lok Chung & Man-Wah Li & Fuk-Ling Wong & Xin Wang & Ailin Liu & Zhili Wang & Alden King-Yung Leung & Tin-Hang Wong & Suk-Wah Tong & Zhixia Xiao & Kejing Fan & Ming-Sin Ng & Xinpen, 2019. "A reference-grade wild soybean genome," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    4. ThankGod Echezona Ebenezer & Anne W. T. Muigai & Simplice Nouala & Bouabid Badaoui & Mark Blaxter & Alan G. Buddie & Erich D. Jarvis & Jonas Korlach & Josiah O. Kuja & Harris A. Lewin & Roksana Majews, 2022. "Africa: sequence 100,000 species to safeguard biodiversity," Nature, Nature, vol. 603(7901), pages 388-392, March.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Weidong Wang & Liyang Chen & Kevin Fengler & Joy Bolar & Victor Llaca & Xutong Wang & Chancelor B. Clark & Tomara J. Fleury & Jon Myrvold & David Oneal & Maria Magdalena Dyk & Ashley Hudson & Jesse Mu, 2021. "A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    2. Yukari Nagatoshi & Kenta Ikazaki & Yasufumi Kobayashi & Nobuyuki Mizuno & Ryohei Sugita & Yumiko Takebayashi & Mikiko Kojima & Hitoshi Sakakibara & Natsuko I. Kobayashi & Keitaro Tanoi & Kenichiro Fuj, 2023. "Phosphate starvation response precedes abscisic acid response under progressive mild drought in plants," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Shichen Li & Zhihui Sun & Qing Sang & Chao Qin & Lingping Kong & Xin Huang & Huan Liu & Tong Su & Haiyang Li & Milan He & Chao Fang & Lingshuang Wang & Shuangrong Liu & Bin Liu & Baohui Liu & Xiangdon, 2023. "Soybean reduced internode 1 determines internode length and improves grain yield at dense planting," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Aron Park & Se-Hee Kang & Byeong-Hee Kang & Sreeparna Chowdhury & Seo-Young Shin & Won-Ho Lee & Jeong-Dong Lee & Sungwoo Lee & Yu-Mi Choi & Bo-Keun Ha, 2023. "Identification of a Novel KTi-1 Allele Associated with Reduced Trypsin Inhibitor Activity in Soybean Accessions," Agriculture, MDPI, vol. 13(11), pages 1-14, October.
    5. Rahul Kumar & Prashant Swapnil & Mukesh Meena & Shweta Selpair & Bal Govind Yadav, 2022. "Plant Growth-Promoting Rhizobacteria (PGPR): Approaches to Alleviate Abiotic Stresses for Enhancement of Growth and Development of Medicinal Plants," Sustainability, MDPI, vol. 14(23), pages 1-16, November.
    6. David Wickell & Li-Yaung Kuo & Hsiao-Pei Yang & Amra Dhabalia Ashok & Iker Irisarri & Armin Dadras & Sophie de Vries & Jan de Vries & Yao-Moan Huang & Zheng Li & Michael S. Barker & Nolan T. Hartwick , 2021. "Underwater CAM photosynthesis elucidated by Isoetes genome," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    7. Zilong Guo & Hongrui Cao & Jing Zhao & Shuang Bai & Wenting Peng & Jian Li & Lili Sun & Liyu Chen & Zhihao Lin & Chen Shi & Qing Yang & Yongqing Yang & Xiurong Wang & Jiang Tian & Zhichang Chen & Hong, 2022. "A natural uORF variant confers phosphorus acquisition diversity in soybean," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    8. Octavio R. Salazar & Ke Chen & Vanessa J. Melino & Muppala P. Reddy & Eva Hřibová & Jana Čížková & Denisa Beránková & Juan Pablo Arciniegas Vega & Lina María Cáceres Leal & Manuel Aranda & Lukasz Jare, 2024. "SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    9. Wolfgang Goettel & Hengyou Zhang & Ying Li & Zhenzhen Qiao & He Jiang & Dianyun Hou & Qijian Song & Vincent R. Pantalone & Bao-Hua Song & Deyue Yu & Yong-qiang Charles An, 2022. "POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    10. Jerzy H. Czembor & Elzbieta Czembor & Marcin Krystek & Juliusz Pukacki, 2023. "AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank," Agriculture, MDPI, vol. 13(1), pages 1-16, January.
    11. Jiaqi Sun & Shiyu Huang & Qing Lu & Shuo Li & Shizhen Zhao & Xiaojian Zheng & Qian Zhou & Wenxiao Zhang & Jie Li & Lili Wang & Ke Zhang & Wenyu Zheng & Xianzhong Feng & Baohui Liu & Fanjiang Kong & Fe, 2023. "UV-B irradiation-activated E3 ligase GmILPA1 modulates gibberellin catabolism to increase plant height in soybean," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    12. Xiao Feng & Qipian Chen & Weihong Wu & Jiexin Wang & Guohong Li & Shaohua Xu & Shao Shao & Min Liu & Cairong Zhong & Chung-I Wu & Suhua Shi & Ziwen He, 2024. "Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    13. Jessen V. Bredeson & Jessica B. Lyons & Ibukun O. Oniyinde & Nneka R. Okereke & Olufisayo Kolade & Ikenna Nnabue & Christian O. Nwadili & Eva Hřibová & Matthew Parker & Jeremiah Nwogha & Shengqiang Sh, 2022. "Chromosome evolution and the genetic basis of agronomically important traits in greater yam," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    14. Qingnan Hao & Hongli Yang & Shuilian Chen & Chanjuan Zhang & Limiao Chen & Dong Cao & Songli Yuan & Wei Guo & Zhonglu Yang & Yi Huang & Yanhui Qu & Lucy Qin & Xiaoyan Sheng & Xueyan Wang & Chandrani M, 2024. "A pair of atypical NLR-encoding genes confers Asian soybean rust resistance in soybean," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    15. Oluwaseyi Shorinola & Rose Marks & Peter Emmrich & Chris Jones & Damaris Odeny & Mark A. Chapman, 2024. "Integrative and inclusive genomics to promote the use of underutilised crops," Nature Communications, Nature, vol. 15(1), pages 1-4, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37489-7. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.