Analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene Xa27 in cultivars of rice (Oryza sativa) and its wild relatives

• Published in: Planta Vol. 238; no. 2; pp. 293 - 305
• Main Authors: Bimolata, Waikhom, Kumar, Anirudh, Sundaram, Raman Meenakshi, Laha, Gouri Shankar, Qureshi, Insaf Ahmed, Reddy, Gajjala Ashok, Ghazi, Irfan Ahmad
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.08.2013; Springer Berlin Heidelberg; Springer Nature B.V
• Subjects: Agriculture; Alleles; Amino Acid Sequence; Amino acids; Bacteria; Biomedical and Life Sciences; blight; chemistry; Cultivars; Disease resistance; DNA, Plant; DNA, Plant - chemistry; DNA, Plant - genetics; Ecology; Evolution; Evolution, Molecular; Forestry; gene expression regulation; Gene Expression Regulation, Plant; genetic distance; Genetic diversity; Genetic Loci; genetics; immunology; Life Sciences; metabolism; microbiology; Molecular Sequence Data; Nucleotides; Original Article; Oryza; Oryza - genetics; Oryza - immunology; Oryza - microbiology; Oryza nivara; Oryza sativa; Pathogens; Phenotype; Phylogeny; physiology; Plant Diseases; Plant Diseases - immunology; Plant Diseases - microbiology; Plant Immunity; Plant Immunity - genetics; Plant Proteins; Plant Proteins - genetics; Plant Proteins - metabolism; Plant Sciences; Polymorphism, Genetic; Promoter regions; Promoter Regions, Genetic; Rice; Sequence Alignment; Sequence Analysis, DNA; Species Specificity; transcription factors; wild relatives; Xanthomonas; Xanthomonas - physiology; Xanthomonas oryzae; Xanthomonas oryzae pv. oryzae; Allele mining; Allelic diversity; Synonymous mutation; Trans-membrane domain; Nonsynonymous mutation; Bacterial blight
• ISSN: 0032-0935; 1432-2048; 1432-2048
• DOI: 10.1007/s00425-013-1891-3

Xa27 is one of the important R-genes, effective against bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Using natural population of Oryza, we analyzed the sequence variation in the functionally important domains of Xa27 across the Oryza species. DNA sequences of Xa27 alleles from 27 rice accessions revealed higher nucleotide diversity among the reported R-genes of rice. Sequence polymorphism analysis revealed synonymous and non-synonymous mutations in addition to a number of InDels in non-coding regions of the gene. High sequence variation was observed in the promoter region including the 5'UTR with 'π' value 0.00916 and 'θ w ' = 0.01785. Comparative analysis of the identified Xa27 alleles with that of IRBB27 and IR24 indicated the operation of both positive selection (Ka/Ks > 1) and neutral selection (Ka/Ks ≈ 0). The genetic distances of alleles of the gene from Oryza nivara were nearer to IRBB27 as compared to IR24. We also found the presence of conserved and null UPT (upregulated by transcriptional activator) box in the isolated alleles. Considerable amino acid polymorphism was localized in the trans-membrane domain for which the functional significance is yet to be elucidated. However, the absence of functional UPT box in all the alleles except IRBB27 suggests the maintenance of single resistant allele throughout the natural population.