Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea.

Autor: Khan AW; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.; School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.; Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA., Garg V; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.; Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia., Sun S; BGI Research, Qingdao, China., Gupta S; Curtin Health Innovation Research Institute (CHIRI), Curtin Medical School, Curtin University, Perth, Western Australia, Australia., Dudchenko O; Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA., Roorkiwal M; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.; Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates., Chitikineni A; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.; Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia., Bayer PE; School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia., Shi C; BGI Research, Qingdao, China., Upadhyaya HD; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.; Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA., Bohra A; Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia., Bharadwaj C; ICAR- Indian Agricultural Research Institute (IARI), New Delhi, India., Mir RR; Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir,Wadura Campus, Kashmir, India., Baruch K; NRGene Ltd, Park HaMada, Ness Ziona, Israel., Yang B; BGI-Australia, Herston, Queensland, Australia., Coyne CJ; USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, USA., Bansal KC; National Academy of Agricultural Sciences (NAAS), NASC Complex, New Delhi, India., Nguyen HT; Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA., Ronen G; NRGene Ltd, Park HaMada, Ness Ziona, Israel., Aiden EL; Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA., Veneklaas E; School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia., Siddique KHM; UWA Institute of Agriculture, and School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia., Liu X; BGI Research, Qingdao, China. liuxin@genomics.cn.; BGI Research, Shenzhen, China. liuxin@genomics.cn., Edwards D; School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia. dave.edwards@uwa.edu.au., Varshney RK; Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India. rajeev.varshney@murdoch.edu.au.; Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia. rajeev.varshney@murdoch.edu.au.
Jazyk: angličtina
Zdroj: Nature genetics [Nat Genet] 2024 Jun; Vol. 56 (6), pp. 1225-1234. Date of Electronic Publication: 2024 May 23.
DOI: 10.1038/s41588-024-01760-4
Abstrakt: 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.
(© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Databáze: MEDLINE
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