Genome-wide association studies for bacterial leaf blight resistance gene in Thai Local Rice

Name: Chananton Danaisilichaichon

LCSH: Kasetsart University -- Dissertations. Ph.D. (Genetics) 2022

Classification :.LCCS: QK495.G74

LCSH: Kasetsart University. -- Department of Genetics -- Dissertations

LCSH: Rice -- Genetics

LCSH: Rice -- Disease and pest resistance

LCSH: Rice blast disease

LCSH: Xanthomonas diseases

LCSH: Xanthomonas

Abstract: Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a significant disease that can have a substantial impact on global rice production. The disease affects the vascular system of rice plants and can lead to the development of lesions on the leaf blade or leaf tips, resulting in symptoms such as yellowing, wilting, and drying. To identify candidate genes associated with BLB resistance in Thai local rice, this research conducted a genome-wide association study (GWAS) using genotyping-by-sequencing (GBS) on 200 local rice accessions inoculated with seven different Xoo isolates. Single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) of less than 5% and a call rate of less than 75% were filtered out. Finally, 25,338 high-quality SNPs were used for the GWAS analysis. The analysis led to the identification of 32 significant SNPs on chromosomes 1-8 and 12 in the rice genome. Additionally, 438 genes were located within ±100kb of the significant SNP region, and 23 candidate genes were selected based on their functions in plant defense mechanisms. Sixteen of the candidate genes were located in the flanking region of the well-known bacterial blight resistance gene (Xa1). Among these candidate genes were those encoding the nuclear factor Y C subunit 5 (NF-YC5) and three genes encoding nucleotide-binding site leucine-rich repeat (NLR) containing proteins. Furthermore, two of the 23 candidate genes were annotated as the well-known blast resistance genes, Pi21 and Pi33. The identification of these candidate genes provides valuable resources for future functional studies and breeding approaches aimed at enhancing BLB resistance in rice crops. These findings have significant implications for rice breeding programs.

Kasetsart University. Office of the University Library

Address: Bangkok

Email: tdckulib@ku.ac.th

Name: Chatchawan Jantasuriyarat

Role: Thesis Advisor

Name: Sujin Patarapuwado

Role: Thesis CO-Advisor

Created: 2022

Modified: 2025-07-27

Issued: 2025-07-27

วิทยานิพนธ์/Thesis

application/pdf

URL: https://www.lib.ku.ac.th/KUthesis/2565/chananton-dan-all.pdf

CallNumber: QK495.G74 .C44

eng

DegreeName: Doctor of Philosophy

Level: Doctoral Degraee

Descipline: Genetics

Grantor: Kasetsart University

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