Analysis of the diversity and function of the alleles of the rice blast resistance genes Piz-t, Pita and Pik in 24 rice cultivars

Wang, Yan; Zhao, Jiaming; Zhang, Lixia; Ping, Wang; Wang, Shiwei; Wang, Hui; Wang, Xiaoxi; Liu, Zhiheng; Zheng, Wenjing

doi:10.1016/s2095-3119(15)61207-2

Cited by 10 publications

(7 citation statements)

References 22 publications

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“…Huang et al [ 24 ] studied the molecular evolution of Pi-ta gene in wild rice O. rufipogon and identified two haplogroups, H1 and H2, with the amino acid Ala-918 present in H1 of the LRR domain of Pi-ta gene displaying a close relationship with the resistant phenotype. Yan et al [ 25 ] analyzed the Pi-ta gene diversity and reported 78 polymorphic nucleotide sites which leading to 22 amino acid variations with mutations reported at the 148th, 158th, 176th, and 641st amino acid positions failing to have an impact on the resistance phenotype. Among the Pi-ta variants reported by Wang et al [ 4 ], 105 polymorphic sites were identified with 27 sites resulting in amino acid substitutions, where the higher number of polymorphism was observed in intron regions rather than in exons.…”

Section: Discussionmentioning

confidence: 99%

In silico molecular and morphological analysis of rice blast resistant gene Pi-ta in Sri Lankan rice germplasm

Terensan

Fernando²,

Silva³

et al. 2021

Journal of Genetic Engineering and Biotechnology

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Background Pi-ta is a major blast resistant gene, introgressed from indica rice varieties. In this study, diversity of the Pi-ta gene of 47 Sri Lankan rice accessions was studied by bioinformatics, and the results were validated with molecular and disease reaction assays. Sequences of rice accessions at the locus Os12g0281300 were retrieved from Rice SNP-Seek Database, and the coding sequence of reference Pi-ta gene of cultivar Tetep (accession no. GQ918486.1) was obtained from GenBank. Comparisons were made at nucleotide, amino acid, and protein structure level, and the 3D models predicted using Phyre2 software were superimposed using TM-align software. Results In silico analysis revealed that 10 accessions possessed resistant allele of the Pi-ta gene. The remaining accessions recorded high polymorphism in the leucine-rich domain resulting in 9 allele types, leading to single–amino acid substitutions at 27 different positions including a functional mutation of alanine to serine at the 918th amino acid position. None of the genotypes led to truncations in the amino acid sequence. The in silico analysis results were validated on 23 accessions comprising resistant and susceptible genotypes and another 25 cultivars from Northern Sri Lanka, by molecular assay using YL183/YL87 and YL155/YL87 resistant and susceptible allele-specific markers. Resistance of Pi-ta gene for the causal fungus, Magnaporthe oryzae, was further validated through pathogenicity assay. Conclusion The Pi-ta gene, especially the LRD region, revealed significant variations within Sri Lankan rice cultivars leading to high levels of resistance against blast. This information would be highly useful in breeding programmes for resistance against rice blast.

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Section: Discussionmentioning

confidence: 99%

In silico molecular and morphological analysis of rice blast resistant gene Pi-ta in Sri Lankan rice germplasm

Terensan

Fernando²,

Silva³

et al. 2021

Journal of Genetic Engineering and Biotechnology

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“…A total number of 565 polymorphic sites and 46 haplotypes were identified in the 2.9 kb sequence of all the Piz-t alleles in forty-five rice land races in Indian ( Thakur et al, 2013 ). Seventeen Piz-t allelic types were identified among 24 cultivars in China ( Wang Y. et al, 2016 ). Higher variance levels of Piz-t gene suggested that AvrPiz-t gene experienced some degree of selection pressure.…”

Section: Discussionmentioning

confidence: 99%

Novel Variation and Evolution of AvrPiz-t of Magnaporthe oryzae in Field Isolates

Wang

Lü

et al. 2020

Front. Genet.

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The product of the avirulence (Avr) gene of Magnaporthe oryzae can be detected by the product of the corresponding resistance (R) gene of rice and activates immunity to rice mediated by the R gene. The high degree of variability of M. oryzae isolates in pathogenicity makes the control of rice blast difficult. That resistance of the R gene in rice has been lost has been ascribed to the instability of the Avr gene in M. oryzae. Further study on the variation of the Avr genes in M. oryze field isolates may yield valuable information on the durable and effective deployment of R genes in rice production areas. AvrPiz-t and Piz-t are a pair of valuable genes in the Rice-Magnaporthe pathosystem. AvrPiz-t is detectable by Piz-t and determines the effectiveness of Piz-t. To effectively deploy the R gene Piz-t, the distribution, variation, and evolution of the corresponding Avr gene AvrPiz-t were found among 312 M. oryzae isolates collected from Yunnan rice production areas of China. PCR amplification and pathogenicity assays of AvrPiz-t showed that 202 isolates (64.7%) held AvrPiz-t alleles and were avirulent to IRBLzt-T (holding Piz-t). There were 42.3-83.3% avirulent isolates containing AvrPiz-t among seven regions in Yunnan Province. Meanwhile, 11 haplotypes of AvrPiz-t encoding three novel AvrPiz-t variants were identified among 100 isolates. A 198 bps insertion homologous to solo-LTR of the retrotransposon inago2 in the promoter region of AvrPizt in one isolate and a frameshift mutation of CDS in another isolate were identified among 100 isolates, and those two isolates had evolved to virulent from avirulent. Synonymous mutation and non-AUG-initiated N-terminal extensions keeps the AvrPizt gene avirulence function in M. oryzae field isolates in Yunnan. A haplotype network showed that H3 was an ancestral haplotype. Structure variance for absence (28.2%) or partial fragment loss (71.8%) of AvrPiz-t was found among 39 virulent isolates and may cause the AvrPiz-t avirulence function to be lost. Overall, AvrPiz-t evolved to virulent from avirulent forms via point mutation, retrotransposon, shift mutation, and structure variance under field conditions.

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“…Pyramiding multiple blast resistance genes is an effective way to improve resistance (Jiang et al 2012;Zhao et al 2018). It was reported that Pi2/Pi9/Pigm allele clusters mainly occur in indica rice with increased rice blast resistance (Deng et al 2017;Xie et al 2019), however, in the northeast, Pita presents a great opportunity to improve rice blast resistance due to the corresponding avirulence gene Avr-Pita, which is widespread in the area (Wang et al 2014(Wang et al , 2016Xie et al 2019). Furthermore, owing to the prevalence of blast strain ZB15 in the area in recent years (Liu et al 2014;Li et al 2017), its corresponding high resistance gene Pid2 should be considered a good application prospect.…”

Section: Introductionmentioning

confidence: 99%

Superior japonica rice variety YJ144 with improved rice blast resistance, yield, and quality achieved using molecular design and multiple breeding strategies

et al. 2021

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Pib, and Pid2, all of which afford broad-spectrum resistance to blast. A collection of 91 japonica rice germplasms with similar ecological characteristics to YF47 were screened, and Wuyunjing 27 (WYJ27) with Pita and Pib alleles and P135 with the Pid2 allele were identified. Furthermore, the corresponding positive Pita, Pib, and Pid2 alleles were transferred into YF47 using single, mutual, and backcrosses, together with molecular marker-assisted selection (MAS) and anther culture technology. These genetic materials, carrying one, two, or three functional alleles, were generated within 3 years, and compared to YF47, they all showed improved resistance to naturally inoculated rice blast. Further improved lines (IL) 1 to 5 (all containing Pita, Pib, and Pid2 alleles) were evaluated for yield performance, and when no fungicide was applied, all lines except IL-4 showed increased traits compared with those of YF47. IL-5, renamed Yanjing 144 (YJ144), showed yield increases in the Liaoning province regional variety comparison test and superior appearance quality compared to YF47. Our work provides a molecular design strategy for pyramiding multiple beneficial genes to rapidly improve rice blast resistance, yield, and quality using multiple breeding strategies.

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Analysis of the diversity and function of the alleles of the rice blast resistance genes Piz-t, Pita and Pik in 24 rice cultivars

Cited by 10 publications

References 22 publications

In silico molecular and morphological analysis of rice blast resistant gene Pi-ta in Sri Lankan rice germplasm

In silico molecular and morphological analysis of rice blast resistant gene Pi-ta in Sri Lankan rice germplasm

Novel Variation and Evolution of AvrPiz-t of Magnaporthe oryzae in Field Isolates

Superior japonica rice variety YJ144 with improved rice blast resistance, yield, and quality achieved using molecular design and multiple breeding strategies

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