Nucleotide diversity analysis of three major bacterial blight resistance genes in rice

• Published in: PloS one Vol. 10; no. 3; p. e0120186
• Main Authors: Bimolata, Waikhom, Kumar, Anirudh, M, Sai Kiran Reddy, Sundaram, Raman Meenakshi, Laha, Gouri Sankar, Qureshi, Insaf Ahmed, Ghazi, Irfan Ahmad
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 25.03.2015; Public Library of Science (PLoS)
• Subjects: 3' Untranslated Regions; Agricultural biotechnology; Alleles; Analysis; Arabidopsis; Arabidopsis thaliana; Bacterial genetics; Biodiversity; Blight; Crop diseases; Cultivars; Deoxyribonucleic acid; Disease Resistance - genetics; DNA; DNA sequencing; DNA, Plant - analysis; Domestication; Evolution; Evolution, Molecular; Gene expression; Gene frequency; Genes; Genes, Plant; Genetic diversity; Genetic Loci; Genetic Variation; Genomics; Host plants; Kinases; Life sciences; Multiculturalism & pluralism; Nucleotide sequence; Oryza - classification; Oryza - genetics; Oryza sativa; Pathogens; Phylogeny; Plant Proteins - genetics; Plant resistance; Plant sciences; Polymerase chain reaction; Polymorphism, Single Nucleotide; Proteins; Real-Time Polymerase Chain Reaction; Reverse transcription; Rice; Sequence Analysis, DNA; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Species diversity; Studies; Xanthomonas oryzae; United States > US; India
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0120186

Nucleotide sequence polymorphisms among R gene alleles influence the process of co-evolutionary interaction between host and pathogen by shaping the response of host plants towards invading pathogens. Here, we present the DNA sequence polymorphisms and diversities present among natural alleles of three rice bacterial blight resistance genes, Xa21, Xa26 and xa5. The diversity was examined across different wild relatives and cultivars of Oryza species. Functional significance of selected alleles was evaluated through semi-quantitative reverse transcription polymerase chain reaction and real time PCR. The greatest nucleotide diversity and singleton variable sites (SVS) were present in Xa26 (π = 0.01958; SVS = 182) followed by xa5 and Xa21 alleles. The highest frequency of single nucleotide polymorphisms were observed in Xa21 alleles and least in xa5. Transition bias was observed in all the genes and 'G' to 'A' transitions were more favored than other form of transitions. Neutrality tests failed to show the presence of selection at these loci, though negative Tajima's D values indicate the presence of a rare form of polymorphisms. At the interspecies level, O. nivara exhibited more diversity than O. sativa. We have also identified two nearly identical resistant alleles of xa5 and two sequentially identical alleles of Xa21. The alleles of xa5 showed basal levels of expression while Xa21 alleles were functionally not expressed.