Next Article in Journal
The Impact of Foliar Fertilization on the Physiological Parameters, Yield, and Quality Indices of the Soybean Crop
Next Article in Special Issue
Comparison and Evaluation of Low-Temperature Tolerance of Different Soybean Cultivars during the Early-Growth Stage
Previous Article in Journal
Review of the Genesis of Plant Pathology and Its Relation to the Phytiatry as a Necessary Element in the Sustainable Development of Agronomy
Previous Article in Special Issue
Effect of NaCl on Morphophysiological and Biochemical Responses in Gossypium hirsutum L.
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Agronomy
Volume 13
Issue 5
10.3390/agronomy13051286
agronomy-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice

by
Chananton Danaisilichaichon
1,2,
Phanchita Vejchasarn
2,
Sujin Patarapuwadol
3,
Alessandro Tondelli
4,
Giampiero Valè
5,
Theerayut Toojinda
6 and
Chatchawan Jantasuriyarat
1,7,*
1
Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
2
Rice Department, Ministry of Agriculture, Bangkok 10900, Thailand
3
Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand
4
Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy
5
Department for Sustainable Development and Ecological Transition–DiSSTE, University of Piemonte Orientale, Piazza S. Eusebio 5, 13100 Vercelli, Italy
6
National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
7
Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart (CASTNAR, NRU-KU), Kasetsart University, Bangkok 10900, Thailand
*
Author to whom correspondence should be addressed.
Agronomy 2023, 13(5), 1286; https://doi.org/10.3390/agronomy13051286
Submission received: 22 March 2023 / Revised: 26 April 2023 / Accepted: 27 April 2023 / Published: 29 April 2023
(This article belongs to the Special Issue Genetic Identification and Characterisation of Crop Agronomic Traits and Stress Resistance)
Browse Figures
Versions Notes

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.
Keywords: genome-wide association; bacterial leaf blight; Xanthomonas oryzae pv. oryzae; resistance gene; indica rice genome-wide association; bacterial leaf blight; Xanthomonas oryzae pv. oryzae; resistance gene; indica rice

Share and Cite

MDPI and ACS Style

Danaisilichaichon, C.; Vejchasarn, P.; Patarapuwadol, S.; Tondelli, A.; Valè, G.; Toojinda, T.; Jantasuriyarat, C. Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice. Agronomy 2023, 13, 1286. https://doi.org/10.3390/agronomy13051286

AMA Style

Danaisilichaichon C, Vejchasarn P, Patarapuwadol S, Tondelli A, Valè G, Toojinda T, Jantasuriyarat C. Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice. Agronomy. 2023; 13(5):1286. https://doi.org/10.3390/agronomy13051286

Chicago/Turabian Style

Danaisilichaichon, Chananton, Phanchita Vejchasarn, Sujin Patarapuwadol, Alessandro Tondelli, Giampiero Valè, Theerayut Toojinda, and Chatchawan Jantasuriyarat. 2023. "Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice" Agronomy 13, no. 5: 1286. https://doi.org/10.3390/agronomy13051286

APA Style

Danaisilichaichon, C., Vejchasarn, P., Patarapuwadol, S., Tondelli, A., Valè, G., Toojinda, T., & Jantasuriyarat, C. (2023). Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice. Agronomy, 13(5), 1286. https://doi.org/10.3390/agronomy13051286

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop