Genetic variation of avirulence genes (AVR‐Pi9, AVR‐Pik, AVR‐Pita1) and genetic diversity of rice blast fungus, Pyricularia oryzae, in Thailand

Abstract

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.

Engineering effector‐triggered immunity in rice: Obstacles and perspectives

“…Liu, Zhu et al, 2021;Ning et al, 2020). The investigation of rice blast population and evolution has disclosed the effector distribution in different areas such as the Philippines (Lopez et al, 2019), Thailand (Sutthiphai et al, 2022), China (Hu et al, 2022) and Asia (Fukuta, 2020), which has facilitated the selection of R gene(s) to employ in each area.…”

“…In rice, several R genes, defence‐regulator genes and quantitative trait loci have been used to generate varieties with enhanced resistance against rice blast, sheath blight and bacterial blight (W. Li, Chern et al, 2019; Z. Liu, Zhu et al, 2021; Ning et al, 2020). The investigation of rice blast population and evolution has disclosed the effector distribution in different areas such as the Philippines (Lopez et al, 2019), Thailand (Sutthiphai et al, 2022), China (Hu et al, 2022) and Asia (Fukuta, 2020), which has facilitated the selection of R gene(s) to employ in each area. However, the drawbacks of this approach are that it is labour‐intensive and time‐consuming (W. Li et al, 2020); the appearance of unwanted traits by linkage drag; short life of the introduced R gene (W. Li et al, 2020); and reduced resistance caused by R gene interaction (Mundt, 2018).…”

Genetic diversity of an effector gene, AvrPi9, of rice blast pathogen in Thailand and characterization of its promoter

“…The corresponding effector gene of the Pi9 gene is AvrPi9 , which has been cloned by Wu et al (2015). The genetic variation and diversity levels of AvrPi9 were examined by Lin et al (2023) in Yunnan, China; Peng et al (2021) in Hunan, China; and Sutthiphai et al (2022) in Thailand. Their findings revealed that AvrPi9 remains widely conserved across rice blast isolates, exhibiting a substantially low degree of genetic variation.…”

“…Their findings revealed that AvrPi9 remains widely conserved across rice blast isolates, exhibiting a substantially low degree of genetic variation. Most observed mutations were single nucleotide substitutions, mainly occurring in noncoding sequences, and an insertion was found upstream of the start codon of AvrPi9 (Peng et al, 2021; Sutthiphai et al, 2022). According to Wu et al (2015), AvrPi9 exhibits specific expression during the early stage of infection, as determined by reverse transcription‐quantitative PCR (RT‐qPCR).…”

Emergence of Rice Blast AVR-Pi9 Resistance Breaking Haplotypes in Yunnan Province, China

“…Only a single amino acid change was detected in the AVR-Pi9 gene. The data suggested that AVR-Pi9 has relatively less genetic diversity compared to other AVR genes [ 20 ].…”