High nucleotide sequence variation of avirulent gene, AVR-Pita1, in Thai rice blast fungus population

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

“…In contrast to the other AVR genes investigated, the AVR ‐ Pita1 gene exhibited a high level of genetic variation. Our finding is similar to those of Kasetsomboon et al (2013), Huang et al (2014), and Damchuay et al (2020), who reported a high level of nucleotide substitution and haplotype diversity in the AVR ‐ Pita1 gene of 62 China rice blast isolates, 44 Thai rice blast isolates, and 151 isolates collected in the USA, China, and Colombia. The high level of variation or, in some isolates, the absence of this gene in Thai rice blast isolates may be due to the location of the gene in the highly unstable telomeric region of chromosome 3, which might have conferred low stability and high genetic recombination (Orbach et al, 2000).…”

“…Several studies have provided evidence for positive selection pressure on the AVR ‐ Pita1 gene (Damchuay et al, 2020; Kasetsomboon et al, 2013; Zhou et al, 2007) suggesting that selection pressure is a common mechanism for AVR ‐ Pita1 gene variation. The resistance gene Pi ‐ ta has been widely used in the germplasm of major rice‐producing countries, including China, Colombia, Japan, Vietnam, Philippines, Thailand, and the USA, which has driven the high selection pressure on the AVR ‐ Pita1 gene (Wang et al, 2007).…”

“…The switching of selection pressure from positive selection to purifying selection was proven by the decreasing genetic variation of AVR ‐ Pita1 in the Thai rice blast population. Damchuay et al (2020) found the rice blast population collected from Thai rice in 2018 showed lower haplotype diversity and nucleotide diversity than the population collected in 2006–2013. Moreover, Kasetsomboon et al (2013) and Singh et al (2014) reported that the selection of AVR ‐ Pita1 alleles favourable to the pathogen may occur through recurrent selective sweeps, leading to a reduction or elimination of genetic variation in this gene.…”

“…The assay was performed to evaluate the effect on avirulence of a nonsynonymous substitution in AVR ‐ Pi9 in a rice blast isolate, NST61103, collected during the study. The methods for fungal cultivation and spore preparation were described by Damchuay et al (2020). The spore suspension, 2 × 10 5 conidia/ml in 0.01% Tween, was sprayed onto leaves of 21‐day‐old plants.…”

“…JHN contains the Pik gene and has been widely used as a resistant donor in the development of blast resistant rice cultivars (Chaipanya et al, 2017). In previous studies, the rice blast resistant genes, Pi9 , Pik , and Pita1 were identified to be effective R genes for controlling rice blast disease in Thailand and were employed for the development of the blast resistant rice varieties (Chaipanya et al, 2017; Damchuay et al, 2020). The variation of the AVR gene sequence in the rice blast population in Thailand, including AVR ‐ Pita1 , AVR ‐ Pik , AVR ‐ Pii , Avr ‐ Piz ‐ t , and PWL ‐ 2 , has been analysed by several investigators (Damchuay et al, 2020; Kasetsomboon et al, 2013; Longya et al, 2019; Sirisathaworn et al, 2017).…”