Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection

Kumar, Ashish and Naik, Y D and Gautam, V and Sahu, S and Valluri, V K and Channale, S and Bhatt, J and Sharma, Stuti and Ramakrishnan, R S and Sharma, Radheshyam and Kudapa, H and Zwart, R S and Punnuri, S M and Varshney, R K and Thudi, M (2024) Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection. The Plant Genome (TSI), 18 (1). pp. 1-13. ISSN 1940-3372

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Abstract

Root-lesion nematodes (RLN) pose a significant threat to chickpea (Cicer arietinum L.) by damaging the root system and causing up to 25% economic losses due to reduced yield. Worldwide commercially grown chickpea varieties lack significant genetic resistance to RLN, necessitating the identification of genetic variants contributing to natural resistance. This study identifies genomic loci responsible for resistance to the RLN, Pratylenchus thornei Sher & Allen, in chickpea by utilizing high-quality single nucleotide polymorphisms from whole-genome sequencing data of 202 chickpea accessions. Phenotypic evaluations of the genetically diverse set of chickpea accessions in India and Australia revealed a wide range of responses from resistant to susceptible. Genome-wide association studies (GWAS) employing Fixed and Random Model Circulating Probability Unification (FarmCPU) and Bayesian-Information and Linkage-Disequilibrium Iteratively Nested Keyway (BLINK) models identified 44 marker-trait associations distributed across all chromosomes except Ca1. Crucially, genomic regions on Ca2 and Ca5 consistently display significant associations across locations. Of 25 candidate genes identified, five genes were putatively involved in RLN resistance response (glucose-6-phosphate dehydrogenase, heat shock proteins, MYB-like DNA-binding protein, zinc finger FYVE protein and pathogenesis-related thaumatin-like protein). One notably identified gene (Ca_10016) presents four haplotypes, where haplotypes 1–3 confer moderate susceptibility, and haplotype 4 contributes to high susceptibility to RLN. This information provides potential targets for marker development to enhance breeding for RLN resistance in chickpea. Additionally, five potential resistant genotypes (ICC3512, ICC8855, ICC5337, ICC8950, and ICC6537) to P. thornei were identified based on their performance at a specific location. The study's significance lies in its comprehensive approach, integrating multiple-location phenotypic evaluations, advanced GWAS models, and functional genomics to unravel the genetic basis of P. thornei resistance. The identified genomic regions, candidate genes, and haplotypes offer valuable insights for breeding strategies, paving the way for developing chickpea varieties resilient to P. thornei attack.

Item Type:	Article
Divisions:	Center of Excellence in Genomics and Systems Biology
CRP:	UNSPECIFIED
Uncontrolled Keywords:	root-lesion nematode resistance, chickpea, genetics and genomics
Subjects:	Mandate crops > Chickpea Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	23 Apr 2025 10:57
Last Modified:	23 Apr 2025 10:57
URI:	http://oar.icrisat.org/id/eprint/13045
Official URL:	https://acsess.onlinelibrary.wiley.com/doi/full/10...
Projects:	UNSPECIFIED
Funders:	Science Engineering Research Board
Acknowledgement:	Mahendar Thudi is grateful to Science and Engineering Research Board (SERB), Department of Science and Technology, Government of India (CRG/2018/003056), and University of Southern Queensland, Toowoomba, Australia for financial support. Open access publishing facilitated by University of Southern Queensland, as part of the Wiley - University of Southern Queensland agreement via the Council of Australian University Librarians.
Links:	Google Scholar

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