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Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection
Journal article   Open access   Peer reviewed

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

S Sahu, R S Ramakrishnan, R K Varshney, Y D Naik, Stuti Sharma, V Gautam, S Channale, H Kudapa, R S Zwart, Radheshyam Sharma, …
The plant genome, Vol.18(1), e20508
2024
DOI: https://doi.org/10.1002/tpg2.20508
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Published1.05 MBDownloadView
Published (Version of Record)CC BY V4.0,  Open Access

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. Plain Language Summary Chickpeas are vital crops for India and Australia but face threats from root-lesion nematodes (RLN), which cause significant yield losses. We aim to identify new sources of resistance and understand its genetic basis. Significant variations in RLN reproduction were observed in the chickpea diversity panel. Promising genotypes, including ICC3512, ICC8855, ICC5337, ICC8950, and ICC6537 were identified for further genetic investigation. Association studies revealed 44 genetic markers associated with RLN responses. Functional analysis identified 24 genes involved in plant-nematode responses, including G6PDH, heat shock proteins (HSPs), MYB-like DNA-binding protein, zinc finger FYVE protein, and thaumatin-like proteins. Notably, gene Ca_10016 displayed four variations, three conferring moderate susceptibility and one conferring high susceptibility. These findings offer opportunities for marker development, accelerating breeding efforts for RLN-resistant varieties, ensuring stable production, and enhancing food security in both nations.

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Collaboration types
Domestic collaboration
International collaboration
Citation topics
3 Agriculture, Environment & Ecology
3.97 Plant Pathology
3.97.1108 Nematode Management
Web Of Science research areas
Genetics & Heredity
Plant Sciences
ESI research areas
Plant & Animal Science
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