Parinthawong, Nonglak

Preferred name

Alternative Name

Parinthawong, N.

Main Affiliation

School of Agricultural Technology

nonglak.pa@kmitl.ac.th

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Development of novel InDel markers by whole-genome sequence comparison and genetic diversity assessment of Thailand rice blast fungus populations
(2025-12-01)
Thamkirati, Napassorn
;
Suktrakul, Worrawit
;
Ngernmuen, Athipat
;
Toojinda, Theerayut
;
Katengam, Sureeporn
InDel markers are commonly used to assess genetic relationships among populations. In this study, we employed a whole-genome sequence comparison method to identify and develop InDel markers for the rice blast fungus Pyricularia oryzae. We analyzed 152 whole-genome sequences of P. oryzae isolates from diverse global regions, including Brazil, Burundi, China, Colombia, Côte d'Ivoire, France, Ghana, Hungary, India, Japan, Korea, Laos, Madagascar, Mali, Morocco, Nepal, the Philippines, Portugal, Spain, Suriname, Thailand, the UK, the USA, and Zambia. Our analysis identified a total of 233,595 InDel loci distributed across the seven chromosomes of P. oryzae. From these, 82 loci were selected based on their high polymorphism across the 152 genome sequences. The effectiveness of these 82 loci was assessed by analyzing the genetic diversity of 47 Thai rice blast isolates alongside two reference isolates, GUY11 (France) and KJ201 (Korea). Of the 82 InDel loci, 33 exhibited polymorphisms, with 2–4 alleles per locus and polymorphic information content (PIC) scores ranging from 0.04 to 0.67. Principal coordinate and structure analyses revealed two genetic subgroups among the Thai rice blast isolates, categorized according to host specificity. Genetic relationships highlighted disparities among rice blast populations based on their respective hosts: rice and grassy weeds. This finding suggests a correlation between genetic relatedness and the plant hosts susceptible to rice blast disease. The newly developed InDel markers provide a valuable resource for future research in this field.
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High nucleotide sequence variation of avirulent gene, AVR-Pita1, in Thai rice blast fungus population
(2020-12-01)
Damchuay, Katanyutita
;
Longya, Apinya
;
Sriwongchai, Tanee
;
Songkumarn, Pattavipha
;
Parinthawong, Nonglak
Rice blast disease, caused by Magnaporthe oryzae, is one of the most importance diseases of rice production worldwide. The key role of defense mechanism to combat this fungus in rice follows the gene-for-gene concept, which a plant resistant (R) gene product recognizes a fungal avirulent (AVR) effector and triggers the hypersensitive response. However, the AVR genes have been shown to be rapidly evolving resulting in high level of genetic diversity. The aims of this study were to examine the nucleotide sequence variation of AVR-Pita1 gene in Thai rice blast isolates and to identify the severity of blast disease using isogenic line of Pita gene. Seventy-six rice blast isolates collected from different parts of Thailand were used. Gene specific primers for AVR-Pita1 gene coding sequence were designed and used for identifying the genetic diversity of AVR-Pita1 gene by PCR amplification and sequencing. The obtained sequences were analysed for genetic variation and genetic relationship. Our results revealed the association between the sequence variations of AVR-Pita1 and selective forces from Pita gene. This phenomenon demonstrated the coevolution between rice blast resistant gene in rice and avirulent gene in blast fungus. The information about variation and evolutionary mechanisms of AVR gene obtained from this study can be used in rice blast resistant breeding programme.
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Genetic variation of avirulence genes (AVR-Pi9, AVR-Pik, AVR-Pita1) and genetic diversity of rice blast fungus, Pyricularia oryzae, in Thailand
(2022-02-01)
Sutthiphai, Thanathip
;
Damchuay, Katanyutita
;
Neupane, Ram Chandra
;
Longya, Apinya
;
Sriwongchai, Tanee
Genetic variation of the rice blast (Pyricularia oryzae) population in Thailand was investigated based on the nucleotide sequence of three avirulence genes, AVR-Pi9, AVR-Pik, and AVR-Pita1. Sixty rice blast isolates were collected from rice-growing areas around Thailand. Gene-specific primers were used to amplify these AVR genes and AVR-Pi9, AVR-Pik, and AVR-Pita1 were detected in 60, 57, and 23 isolates, respectively. Based on the AVR-Pi9 sequences, we identified one rice blast isolate containing an amino acid change from glutamic acid to aspartic acid. Moreover, two rice blast isolates had identical sequences to the rice blast strain originating in Japan, indicating a potential movement of this isolate from Japan to Thailand. Three AVR-Pik alleles were found, including AVR-PikA (3.51%), AVR-PikD (71.93%), and isolates with two copies of AVR-PikD and AVR-PikF (24.56%). AVR-PikA and AVR-PikF are virulent to Thai rice variety Jao Hom Nin. Six haplotypes of AVR-Pita1 were identified with one deletion and 12 amino acid substitutions. This study revealed that different AVR genes in Thai rice blast populations have different levels of genetic variation: AVR-Pi9 and AVR-Pik genes have a relatively low genetic diversity, while the AVR-Pita1 gene has high genetic diversity. We found AVR-Pi9 was not under selection pressure, while AVR-Pita1 was under purifying selection pressure. In addition, geographic location has influenced the distribution of genetic variation of AVR-Pita1. The information obtained from this study is valuable for the future development of breeding strategies for rice blast resistance in Thailand.
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Whole-Genome Sequencing Reveals SNP-Based Genetic Diversity and Population Structure of the Thai Rice Blast Fungus
(2026-01-01)
Longya, Apinya
;
Suktrakul, Worrawit
;
Suksirt, Mantira
;
Korinsak, Siripar
;
Pootakham, Wirulda
Rice blast, caused by Magnaporthe oryzae, is a devastating disease threatening global rice production. While Southeast Asia is a centre of origin, the pathogen's population dynamics in Thailand are not well understood. We analysed whole-genome sequences from 191 M. oryzae isolates (60 from Thailand and 131 global) to investigate their genetic diversity, structure and pathogenicity. Phylogenomic analysis revealed that Thai isolates cluster with other Asian populations but exhibit greater within-population diversity, forming two major genetic clusters. We found that Thai rice isolates from rain-fed lowland and irrigated rice in the northeast and central regions cluster in World Group 3, while isolates from upland rice in northern Thailand cluster in World Group 1. This revised interpretation provides a more accurate representation of the population structure and highlights previously uncharacterised diversity. To link molecular data with phenotypes, we performed avirulence gene profiling and pathogenicity assays on 31 rice blast resistance near-isogenic lines. A correlation analysis showed a strong relationship for key gene pairs, including AvrPik and AvrPi9, highlighting their functional importance. In contrast, the correlation was low for Pii, Pizt and Pib due to the low frequency of their corresponding avirulence genes. The Avr-Pita interaction displayed a complex, haplotype-specific correlation. Our findings provide new insights into the genomic and pathogenic variation of M. oryzae in Thailand, establishing a robust link between avirulence gene profiles and observed pathogenicity phenotypes. This work offers a refined foundation for region-specific resistance breeding and disease management strategies.

Parinthawong, Nonglak

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