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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #405077
Research Project: Genetic Resource and Information Management for Pulse, Temperate Forage Legume, Oilseed, Vegetable, Grasses, Sugar, Ornamental, and Other Crops

Location: Plant Germplasm Introduction and Testing Research

Title: Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea (Cicer arietinum)

Author
item KAHN, AAMIR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item GARG, VANIKA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item SUN, SHUAI - Bgi Shenzhen
item GUPTA, SAURABH - Curtin University
item DUDCHENKO, OLGA - Baylor College
item ROORKIWAL, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item CHITIKINENI, ANNAPURNA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item BAYER, PHILIPP - The University Of Western Australia
item SHI, CHENGCHENG - Bgi Shenzhen
item UPADHYAYA, HARI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item BOHRA, ABHISHEK - Murdoch University
item BHARADWAJ, CHELLAPILLA - Indian Council Of Agricultural Research (ICAR)
item MIR, REYAZUL ROUF - University Of Kashmir
item BARUCH, KOBI - Nrgene
item YANG, BICHENG - Bgi Shenzhen
item Coyne, Clarice - Clare
item NGUYEN, HENRY - University Of Missouri
item RONEN, GIL - University Of Missouri
item AIDEN, EREZ LIEBERMAN - Baylor College
item VENEKLAAS, ERIK - The University Of Western Australia
item SIDDIQUE, KADAMBOT H - The University Of Western Australia
item XIN, LIU - Bgi Shenzhen
item EDWARDS, DAVID - The University Of Western Australia
item VARSHNEY, RAJEEV - Murdoch University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/18/2024
Publication Date: 5/23/2024
Citation: Kahn, A.W., Garg, V., Sun, S., Gupta, S., Dudchenko, O., Roorkiwal, M., Chitikineni, A., Bayer, P.E., Shi, C., Upadhyaya, H.D., Bohra, A., Bharadwaj, C., Mir, R., Baruch, K., Yang, B., Coyne, C.J., Nguyen, H.T., Ronen, G., Aiden, E., Veneklaas, E., Siddique, K.M., Xin, L., Edwards, D., Varshney, R. 2024. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea (Cicer arietinum). Nature Genetics. 56:1225-1234. https://doi.org/10.1038/s41588-024-01760-4.
DOI: https://doi.org/10.1038/s41588-024-01760-4

Interpretive Summary: Chickpea (Cicer arietinum L.) is a self-pollinated diploid annual legume grown predominantly in arid and semi-arid regions worldwide. It is one of the most widely grown legume crops, with an annual global production of over 17 million tonnes (FAO, 2020). Chickpea is a highly nutritious crop that can enhance soil fertility by fixing atmospheric nitrogen. It is a crop of high economic significance, but its production has not yet reached the anticipated level owing to several biotic and abiotic constraints. This study adds new genetic tools and information for chickpea plant breeders to use in developing new resilent chcikpea cultivars for farmer's fields.

Technical Abstract: Chickpea (Cicer arietinum L.) is one of the most important legume crops cultivated in arid and semi-arid regions of the world but the genetic diversity underlying its massive phenotypic variation remains largely unexplored. Here, we report Cicer super-pangenome based on genome assembly and annotation of eight Cicer annual wild species. Ortholog classification of the genes identified from the super-pangenome resulted in 25,008 gene families, of which 14,918 were core, 6378 were present in 2-8 genomes, and 871 were species-specific gene families. The dispensable genes were enriched for annotation related to agronomic traits, including disease resistance, biosynthesis of secondary metabolites, and flowering time. SVs identified between cultivated and wild Cicer genomes were used to construct a graph-based Cicer super-pangenome with ~20 million nodes and ~20 million edges. Pangenome analysis resulted in the identification of variation between genes controlling important traits such as flowering time, vernalization and disease resistance between the cultivated and Cicer wild genomes. The variation identified through Cicer super-pangenome analysis can support the transfer of traits from wild species into elite varieties for chickpea crop improvement through marker-assisted selection or gene-editing technologies.