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Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice
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Document Title
Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice
Author
Danaisilichaichon C., Vejchasarn P., Patarapuwadol S., Tondelli A., Valè G., Toojinda T., Jantasuriyarat C.
Affiliations
Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand; Rice Department, Ministry of Agriculture, Bangkok, 10900, Thailand; Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, 73140, Thailand; Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, 29017, Italy; Department for Sustainable Development and Ecological Transition–DiSSTE, University of Piemonte Orientale, Piazza S. Eusebio 5, Vercelli, 13100, Italy; National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathumthani12120, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart (CASTNAR, NRU-KU), Kasetsart University, Bangkok, 10900, Thailand
Type
Article
Source Title
Agronomy
ISSN
20734395
Year
2023
Volume
13
Issue
5
Page
-
Open Access
All Open Access, Gold
Publisher
MDPI
DOI
10.3390/agronomy13051286
Format
Abstract
Bacterial leaf blight (BLB) is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which poses a significant threat to global rice production. In this study, a genome-wide association study (GWAS) was conducted using the genotyping-by-sequencing (GBS) approach to identify candidate single nucleotide polymorphisms (SNPs) associated with BLB resistance genes. The study utilized 200 indica rice accessions inoculated with seven distinct Xoo isolates and filtered highly significant SNPs using a minor allele frequency (MAF) of >5% and a call rate of 75%. Four statistical models were used to explore potential SNPs associated with BLB resistance, resulting in the identification of 32 significant SNPs on chromosomes 1–8 and 12 in the rice genome. Additionally, 179 genes were located within ±100 kb of the SNP region, of which 49 were selected as candidate genes based on their known functions in plant defense mechanisms. Several candidate genes were identified, including two genes in the same linkage disequilibrium (LD) decay as the well-known BLB resistance gene (Xa1). These findings represent a valuable resource for conducting further functional studies and developing novel breeding strategies to enhance the crop’s resistance to this disease. © 2023 by the authors.
Funding Sponsor
National Research Council of Thailand; Agricultural Research Development Agency; Kasetsart University Research and Development Institute
Publication Source
WOS