Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection
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...
| Autores principales: | , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2025
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| Acceso en línea: | https://hdl.handle.net/10568/180018 |
| _version_ | 1855520712127676416 |
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| author | Kumar, Ashish Naik, Yogesh Dashrath Gautam, Vedant Sahu, Sunanda Valluri, Vinod Channale, Sonal Bhatt, Jayant Sharma, Stuti Ramakrishnan, R. S. Sharma, Radheshyam Kudapa, Himabindu Zwart, Rebecca S. Punnuri, Somashekhar M. Varshney, Rajeev K. Thudi, Mahendar |
| author_browse | Bhatt, Jayant Channale, Sonal Gautam, Vedant Kudapa, Himabindu Kumar, Ashish Naik, Yogesh Dashrath Punnuri, Somashekhar M. Ramakrishnan, R. S. Sahu, Sunanda Sharma, Radheshyam Sharma, Stuti Thudi, Mahendar Valluri, Vinod Varshney, Rajeev K. Zwart, Rebecca S. |
| author_facet | Kumar, Ashish Naik, Yogesh Dashrath Gautam, Vedant Sahu, Sunanda Valluri, Vinod Channale, Sonal Bhatt, Jayant Sharma, Stuti Ramakrishnan, R. S. Sharma, Radheshyam Kudapa, Himabindu Zwart, Rebecca S. Punnuri, Somashekhar M. Varshney, Rajeev K. Thudi, Mahendar |
| author_sort | Kumar, Ashish |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace180018 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1800182026-01-17T02:04:41Z Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection Kumar, Ashish Naik, Yogesh Dashrath Gautam, Vedant Sahu, Sunanda Valluri, Vinod Channale, Sonal Bhatt, Jayant Sharma, Stuti Ramakrishnan, R. S. Sharma, Radheshyam Kudapa, Himabindu Zwart, Rebecca S. Punnuri, Somashekhar M. Varshney, Rajeev K. Thudi, Mahendar crop yield genetic variants genome sequencing breeding methods chickpea 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. 2025-01-10 2026-01-16T18:18:25Z 2026-01-16T18:18:25Z Journal Article https://hdl.handle.net/10568/180018 en Open Access application/pdf Wiley Kumar, Ashish; Naik, Yogesh Dashrath; Gautam, Vedant; Sahu, Sunanda; Valluri, Vinod; Channale, Sonal; Bhatt, Jayant; Sharma, Stuti; Ramakrishnan, R. S.; Sharma, Radheshyam; Kudapa, Himabindu; Zwart, Rebecca S.; Punnuri, Somashekhar M.; Varshney, Rajeev K.; & Thudi, Mahendar. 2025. Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection. The Plant Genome, 18, e20508. https://doi.org/10.1002/tpg2.20508 |
| spellingShingle | crop yield genetic variants genome sequencing breeding methods chickpea Kumar, Ashish Naik, Yogesh Dashrath Gautam, Vedant Sahu, Sunanda Valluri, Vinod Channale, Sonal Bhatt, Jayant Sharma, Stuti Ramakrishnan, R. S. Sharma, Radheshyam Kudapa, Himabindu Zwart, Rebecca S. Punnuri, Somashekhar M. Varshney, Rajeev K. Thudi, Mahendar Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection |
| title | Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection |
| title_full | Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection |
| title_fullStr | Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection |
| title_full_unstemmed | Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection |
| title_short | Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection |
| title_sort | genome wide association mapping reveals novel genes and genomic regions controlling root lesion nematode resistance in chickpea mini core collection |
| topic | crop yield genetic variants genome sequencing breeding methods chickpea |
| url | https://hdl.handle.net/10568/180018 |
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