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Journal article
Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance
Frontiers in plant science, Vol.14, Art. 1139574
2023
PMID: 37035083
Abstract
Pratylenchus thornei is an economically important species of root-lesion nematode adversely affecting chickpea (Cicer arietinum) yields globally. Integration of resistant crops in farming systems is recognised as the most effective and sustainable management strategy for plant-parasitic nematodes. However, breeding for P. thornei resistance in chickpea is limited by the lack of genetic diversity. We deployed a genome-wide association approach to identify genomic regions and candidate genes associated with P. thornei resistance in 285 genetically diverse chickpea accessions. Chickpea accessions were phenotyped for P. thornei resistance in replicated glasshouse experiments performed for two years (2018 and 2020). Whole genome sequencing data comprising 492,849 SNPs were used to implement six multi-locus GWAS models. Fourteen chickpea genotypes were found to be resistant to P. thornei. Of the six multi-locus GWAS methods deployed, FASTmrMLM was found to be the best performing model. In all, 24 significant quantitative trait nucleotides (QTNs) were identified, of which 13 QTNs were associated with lower nematode population density and 11 QTNs with higher nematode population density. These QTNs were distributed across all of the chickpea chromosomes, except chromosome 8. We identified, receptor-linked kinases (RLKs) on chromosomes 1, 4 and 6, GDSL-like Lipase/Acylhydrolase on chromosome 3, Aspartic proteinase-like and Thaumatin-like protein on chromosome 4, AT-hook DNA-binding and HSPRO2 on chromosome 6 as candidate genes for P. thornei resistance in the chickpea reference set. New sources of P. thornei resistant genotypes were identified that can be harnessed into breeding programs and putative candidate P. thornei resistant genes were identified that can be explored further to develop molecular markers and accelerate the incorporation of improved P. thornei resistance into elite chickpea cultivars.
Details
- Title
- Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance
- Authors/Creators
- Sonal Channale - University of Southern QueenslandJohn P. Thompson - University of Southern QueenslandRajeev K. Varshney - Murdoch University, Food Futures InstituteMahendar Thudi - University of Southern QueenslandRebecca S. Zwart - University of Southern Queensland
- Publication Details
- Frontiers in plant science, Vol.14, Art. 1139574
- Publisher
- Frontiers Media Sa
- Number of pages
- 12
- Grant note
- Bioplatforms Australia University of Melbourne Galaxy Australia Australian Biocommons University of Southern Queensland Queensland Government RICF Australian Research Data Commons
- Identifiers
- 991005572569407891
- Copyright
- © 2023 Channale et al.
- Murdoch Affiliation
- Centre for Crop and Food Innovation
- Language
- English
- Resource Type
- Journal article
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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
- Plant Sciences
- ESI research areas
- Plant & Animal Science