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Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea.
Khan, Aamir W; Garg, Vanika; Sun, Shuai; Gupta, Saurabh; Dudchenko, Olga; Roorkiwal, Manish; Chitikineni, Annapurna; Bayer, Philipp E; Shi, Chengcheng; Upadhyaya, Hari D; Bohra, Abhishek; Bharadwaj, Chellapilla; Mir, Reyazul Rouf; Baruch, Kobi; Yang, Bicheng; Coyne, Clarice J; Bansal, Kailash C; Nguyen, Henry T; Ronen, Gil; Aiden, Erez Lieberman; Veneklaas, Erik; Siddique, Kadambot H M; Liu, Xin; Edwards, David; Varshney, Rajeev K.
Affiliation
  • Khan AW; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
  • Garg V; School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.
  • Sun S; Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA.
  • Gupta S; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
  • Dudchenko O; Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
  • Roorkiwal M; BGI Research, Qingdao, China.
  • Chitikineni A; Curtin Health Innovation Research Institute (CHIRI), Curtin Medical School, Curtin University, Perth, Western Australia, Australia.
  • Bayer PE; Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.
  • Shi C; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
  • Upadhyaya HD; Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates.
  • Bohra A; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
  • Bharadwaj C; Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
  • Mir RR; School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.
  • Baruch K; BGI Research, Qingdao, China.
  • Yang B; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
  • Coyne CJ; Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA.
  • Bansal KC; Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
  • Nguyen HT; ICAR- Indian Agricultural Research Institute (IARI), New Delhi, India.
  • Ronen G; Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir,Wadura Campus, Kashmir, India.
  • Aiden EL; NRGene Ltd, Park HaMada, Ness Ziona, Israel.
  • Veneklaas E; BGI-Australia, Herston, Queensland, Australia.
  • Siddique KHM; USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, USA.
  • Liu X; National Academy of Agricultural Sciences (NAAS), NASC Complex, New Delhi, India.
  • Edwards D; Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA.
  • Varshney RK; NRGene Ltd, Park HaMada, Ness Ziona, Israel.
Nat Genet ; 56(6): 1225-1234, 2024 Jun.
Article in En | MEDLINE | ID: mdl-38783120
ABSTRACT
Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genome, Plant / Crops, Agricultural / Cicer / Quantitative Trait Loci Language: En Journal: Nat Genet Journal subject: GENETICA MEDICA Year: 2024 Document type: Article Affiliation country: Country of publication:
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genome, Plant / Crops, Agricultural / Cicer / Quantitative Trait Loci Language: En Journal: Nat Genet Journal subject: GENETICA MEDICA Year: 2024 Document type: Article Affiliation country: Country of publication: