Promoter variants of Xa23 alleles affect bacterial blight resistance and evolutionary pattern

PLOS ONE, Nov 2019

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most important bacterial disease in rice (Oryza sativa L.). Our previous studies have revealed that the bacterial blight resistance gene Xa23 from wild rice O. rufipogon Griff. confers the broadest-spectrum resistance against all the naturally occurring Xoo races. As a novel executor R gene, Xa23 is transcriptionally activated by the bacterial avirulence (Avr) protein AvrXa23 via binding to a 28-bp DNA element (EBEAvrXa23) in the promoter region. So far, the evolutionary mechanism of Xa23 remains to be illustrated. Here, a rice germplasm collection of 97 accessions, including 29 rice cultivars (indica and japonica) and 68 wild relatives, was used to analyze the evolution, phylogeographic relationship and association of Xa23 alleles with bacterial blight resistance. All the ~ 473 bp DNA fragments consisting of promoter and coding regions of Xa23 alleles in the germplasm accessions were PCR-amplified and sequenced, and nine single nucleotide polymorphisms (SNPs) were detected in the promoter regions (~131 bp sequence upstream from the start codon ATG) of Xa23/xa23 alleles while only two SNPs were found in the coding regions. The SNPs in the promoter regions formed 5 haplotypes (Pro-A, B, C, D, E) which showed no significant difference in geographic distribution among these 97 rice accessions. However, haplotype association analysis indicated that Pro-A is the most favored haplotype for bacterial blight resistance. Moreover, SNP changes among the 5 haplotypes mostly located in the EBE/ebe regions (EBEAvrXa23 and corresponding ebes located in promoters of xa23 alleles), confirming that the EBE region is the key factor to confer bacterial blight resistance by altering gene expression. Polymorphism analysis and neutral test implied that Xa23 had undergone a bottleneck effect, and selection process of Xa23 was not detected in cultivated rice. In addition, the Xa23 coding region was found highly conserved in the Oryza genus but absent in other plant species by searching the plant database, suggesting that Xa23 originated along with the diversification of the Oryza genus from the grass family during evolution. This research offers a potential for flexible use of novel Xa23 alleles in rice breeding programs and provide a model for evolution analysis of other executor R genes.

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Promoter variants of Xa23 alleles affect bacterial blight resistance and evolutionary pattern

October Promoter variants of Xa23 alleles affect bacterial blight resistance and evolutionary pattern Hua Cui☯ 0 1 2 Chunlian Wang☯ 0 1 2 Tengfei Qin☯ 0 1 2 Feifei Xu 0 1 2 Yongchao Tang 0 1 2 Ying Gao 0 1 2 Kaijun Zhao 0 1 2 ☯ These authors contributed equally to this work. 0 1 2 0 1 2 0 National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS) , Beijing , China 1 the Major Science and Technology Project to Create New Crop Cultivars using Gene Transfer Technology (2014ZX0801001B, 2016ZX08001002-009) and the Innovation Program of Chinese Academy of Agricultural Sciences 2 Editor: Zonghua Wang, Fujian Agriculture and Forestry University , CHINA Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most important bacterial disease in rice (Oryza sativa L.). Our previous studies have revealed that the bacterial blight resistance gene Xa23 from wild rice O. rufipogon Griff. confers the broadestspectrum resistance against all the naturally occurring Xoo races. As a novel executor R gene, Xa23 is transcriptionally activated by the bacterial avirulence (Avr) protein AvrXa23 via binding to a 28-bp DNA element (EBEAvrXa23) in the promoter region. So far, the evolutionary mechanism of Xa23 remains to be illustrated. Here, a rice germplasm collection of 97 accessions, including 29 rice cultivars (indica and japonica) and 68 wild relatives, was used to analyze the evolution, phylogeographic relationship and association of Xa23 alleles with bacterial blight resistance. All the ~ 473 bp DNA fragments consisting of promoter and coding regions of Xa23 alleles in the germplasm accessions were PCR-amplified and sequenced, and nine single nucleotide polymorphisms (SNPs) were detected in the promoter regions (~131 bp sequence upstream from the start codon ATG) of Xa23/xa23 alleles while only two SNPs were found in the coding regions. The SNPs in the promoter regions formed 5 haplotypes (Pro-A, B, C, D, E) which showed no significant difference in geographic distribution among these 97 rice accessions. However, haplotype association analysis indicated that Pro-A is the most favored haplotype for bacterial blight resistance. Moreover, SNP changes among the 5 haplotypes mostly located in the EBE/ebe regions (EBEAvrXa23 and corresponding ebes located in promoters of xa23 alleles), confirming that the EBE region is the key factor to confer bacterial blight resistance by altering gene expression. Polymorphism analysis and neutral test implied that Xa23 had undergone a bottleneck effect, and selection process of Xa23 was not detected in cultivated rice. In addition, the Xa23 coding region was found highly conserved in the Oryza genus but absent in other plant species by searching the plant database, suggesting that Xa23 originated along with the diversification of the Oryza genus from the grass family during evolution. This research offers a potential for flexible use of novel Xa23 alleles in rice breeding programs and provide a model for evolution analysis of other executor R genes. - Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Competing interests: The authors have declared that no competing interests exist. Introduction Plants could co-evolve in response to changes of pathogens [ 1 ]. Resistance of a plant to a pathogen with Avr protein effectors, which can be secreted and internalized into the plant cells through type-III secretion pathway, is due to the recognition by plant surveillance system [ 2 ]. Accordingly, plants have evolved resistance (R) genes to interact with their cognate avr genes and activate host immune responses [ 3, 4 ]. However, intensive diversifying selection allowed the pathogen to diversify its effector genes and escape recognition by the plant resistance gene, resulting in loss of the R gene-mediated resistance [1]. The constant interactions between hosts and pathogens are thought to play an important role in the evolution of R genes in plants and avr genes in pathogens. Thus, an in-depth study of the molecular evolution of R genes will be of significance for identifying novel or ªhiddenº resistant alleles and unravelling the role of pathogen-imposed selection of R genes [5±8]. The polymorphism and molecular evolution of plant R genes have been extensively studied [9±13] and found three kinds of distinctly regular patterns [8, 14±16]. The first is conserved type with little variation in the population or species, which identifies conservative avr genes and accounts for 63% of the R genes of rice genome, such as Pi-ta [ 17 ]. The second is the opposite type with abundant variation in population or species, which shares the mutations among different alleles by recombination and identifies conservative and non-conservative avr genes, such as Rpp13 and Rpp8 [ 18, 19 ]. The third is present and absent R genes, such as Rpm (...truncated)


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Hua Cui, Chunlian Wang, Tengfei Qin, Feifei Xu, Yongchao Tang, Ying Gao, Kaijun Zhao. Promoter variants of Xa23 alleles affect bacterial blight resistance and evolutionary pattern, PLOS ONE, 2017, Volume 12, Issue 10, DOI: 10.1371/journal.pone.0185925