An Australian chickpea pan-genome provides insights into genome organization and offers opportunities for enhancing drought adaptation for crop improvement

Vanika Garg; Rutwik Barmukh; Yan Huang; Annapurna Chitikineni; Kristy Hobson; Bicheng Yang; Yong Jia; Shengnan Bi; Sukhjiwan Kaur; Muhammad Ahsan Asif; Matthew Hayden; Sally Norton; Darshan L Sharma; Kadambot H M Siddique; Xin Liu; Chengdao Li; Rajeev K Varshney

doi:10.1111/pbi.70192

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An Australian chickpea pan-genome provides insights into genome organization and offers opportunities for enhancing drought adaptation for crop improvement

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An Australian chickpea pan-genome provides insights into genome organization and offers opportunities for enhancing drought adaptation for crop improvement

Vanika Garg, Rutwik Barmukh, Yan Huang, Annapurna Chitikineni, Kristy Hobson, Bicheng Yang, Yong Jia, Shengnan Bi, Sukhjiwan Kaur, Muhammad Ahsan Asif, …

Plant biotechnology journal, Vol.23(9), pp.3967-3983

2025

DOI: https://doi.org/10.1111/pbi.70192

PMID: 40534107

Appears in Open Access via Read & Publish Agreements

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Abstract

drought tolerance

genetic variation

graph pan‐genome

flowering time

haplotype‐based breeding

QTL‐hotspot

Chickpea (Cicer arietinum L.) is an important legume crop that has been subjected to intensive breeding, resulting in limited genetic diversity. Australia is the world's second largest producer and the leading exporter of chickpea; the genomic architecture of its cultivars remains largely unexplored. This knowledge gap hinders efforts to enhance their genetic potential for production, protection, and stress adaptation. To address this, we generated high-quality genome assemblies and annotations for 15 leading Australian chickpea cultivars using single-tube long-fragment read technology. The pan-genome analysis identified 34 345 gene families, including 13 986 dispensable families enriched for genes associated with key agronomic traits. Comparative genomic analysis revealed ~2.5 million single-nucleotide polymorphisms, nearly 200 000 insertions/deletions, and over 280 000 structural variations. These variations were found in key flowering time genes, seed weight-related genes, and disease resistance genes, providing insights into the genetic diversity underlying these critical traits. Haplotype analysis of key genes within the 'QTL-hotspot' region revealed the absence of superior haplotypes in Australian cultivars. Validation using Kompetitive allele-specific PCR markers confirmed these findings, highlighting the need to introduce beneficial haplotypes from diverse accessions to enhance drought tolerance in Australian chickpea cultivars. The genomic resources generated in this study provide valuable insights into chickpea genetic diversity and offer potential avenues for crop improvement.

Details

Title: An Australian chickpea pan-genome provides insights into genome organization and offers opportunities for enhancing drought adaptation for crop improvement
Authors/Creators: Vanika Garg - Murdoch University, Centre for Crop and Food Innovation
Rutwik Barmukh - Murdoch University, Centre for Crop and Food Innovation
Yan Huang - BGI Group (China)
Annapurna Chitikineni - Murdoch University
Kristy Hobson - New South Wales Department of Primary Industries
Bicheng Yang - BGI (United States)
Yong Jia - Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, Murdoch, Western Australia, Australia
Shengnan Bi - BGI (United States)
Sukhjiwan Kaur - Agriculture Victoria
Muhammad Ahsan Asif - New South Wales Department of Primary Industries
Matthew Hayden - La Trobe University
Sally Norton - Agriculture Victoria
Darshan L Sharma - Department of Primary Industries and Regional Development
Kadambot H M Siddique - The University of Western Australia
Xin Liu - BGI Research
Chengdao Li - Murdoch University, Centre for Crop and Food Innovation
Rajeev K Varshney - Murdoch University, Food Futures Institute
Publication Details: Plant biotechnology journal, Vol.23(9), pp.3967-3983
Publisher: Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
Number of pages: 17
Grant note: UMU2303-003RTX / Grains Research and Development Corporation UMU2403-009RTX / Grains Research and Development Corporation
Identifiers: 991005788074807891
Murdoch Affiliation: Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre; Food Futures Institute
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.1543 Flow Cytometry
Web Of Science research areas: Biotechnology & Applied Microbiology; Plant Sciences
ESI research areas: Plant & Animal Science