title: Nucleotide diversity analysis of three major bacterial blight resistance genes in rice.
abstract: 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.
authors: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India.
authors: Waikhom
authors: W
authors: Bimolata
authors: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India.
authors: Anirudh
authors: A
authors: Kumar
authors: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India.
authors: Sai Kiran Reddy
authors: SK
authors: M
authors: Crop Improvement Section, Directorate of Rice Research, Rajendranagar, Hyderabad, 500030, India.
authors: Raman Meenakshi
authors: RM
authors: Sundaram
authors: Crop Protection Section, Directorate of Rice Research, Rajendranagar, Hyderabad, 500030, India.
authors: Gouri Sankar
authors: GS
authors: Laha
authors: Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India.
authors: Insaf Ahmed
authors: IA
authors: Qureshi
authors: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India.
authors: Irfan Ahmad
authors: IA
authors: Ghazi
mesh_terms: D020413:3' Untranslated Regions; D000483:Alleles; D018744:DNA, Plant / Q000032:analysis; D060467:Disease Resistance / Q000235:genetics*; D019143:Evolution, Molecular; D017343:Genes, Plant; D056426:Genetic Loci; D014644:Genetic Variation; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D020413:3' Untranslated Regions; D018744:DNA, Plant; D010940:Plant Proteins