title: Analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene Xa27 in cultivars of rice (Oryza sativa) and its wild relatives.
abstract: 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.
authors: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, India. bimowai@gmail.com
authors: Waikhom
authors: W
authors: Bimolata
authors: Anirudh
authors: A
authors: Kumar
authors: Raman Meenakshi
authors: RM
authors: Sundaram
authors: Gouri Shankar
authors: GS
authors: Laha
authors: Insaf Ahmed
authors: IA
authors: Qureshi
authors: Gajjala Ashok
authors: GA
authors: Reddy
authors: Irfan Ahmad
authors: IA
authors: Ghazi
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D056426:Genetic Loci; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D010641:Phenotype; D010802:Phylogeny; D010935:Plant Diseases / Q000276:immunology* / Q000382:microbiology; D057865:Plant Immunity / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014974:Xanthomonas / Q000502:physiology*
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins
references: Proc Natl Acad Sci U S A. 1979 Oct;76(10):5269-73
references: 291943
references: Plant Cell. 1998 Nov;10(11):1833-46
references: 9811792
references: Bioinformatics. 2009 Jun 1;25(11):1451-2
references: 19346325
references: Genome Biol. 2008;9(3):R49
references: 18315873
references: New Phytol. 2012 Sep;195(4):883-893
references: 22747776
references: Nature. 2005 Jun 23;435(7045):1122-5
references: 15973413
references: Mol Biol Evol. 1996 May;13(5):685-90
references: 8676743
references: Plant Cell. 1998 May;10(5):765-79
references: 9596635
references: Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11270-4
references: 12172004
references: Proc Natl Acad Sci U S A. 2004 Dec 14;101(50):17444-9
references: 15583124
references: Proc Natl Acad Sci U S A. 1999 Jan 5;96(1):302-6
references: 9874813
references: Curr Opin Plant Biol. 2010 Aug;13(4):394-401
references: 20570209
references: Nucleic Acids Res. 1988 Nov 25;16(22):10881-90
references: 2849754
references: Theor Popul Biol. 1975 Apr;7(2):256-76
references: 1145509
references: Plant Mol Biol. 1994 Jul;25(4):633-48
references: 7914758
references: Nature. 1999 Aug 12;400(6745):667-71
references: 10458161
references: PLoS One. 2011;6(10):e26260
references: 22043312
references: Genetics. 2008 Jul;179(3):1527-38
references: 18622033
references: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W465-8
references: 19429891
references: Nat Methods. 2011 Sep 29;8(10):785-6
references: 21959131
references: Genetics. 2004 Mar;166(3):1517-27
references: 15082565
references: Mol Plant Pathol. 2009 Nov;10(6):829-35
references: 19849788
references: Mol Biol Evol. 2007 Mar;24(3):875-88
references: 17218640
references: Genome Res. 2000 Apr;10(4):516-22
references: 10779491
references: Genes Genet Syst. 2009 Apr;84(2):121-36
references: 19556706
references: PLoS Genet. 2006 Nov 17;2(11):e199
references: 17112320
references: Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9519-24
references: 19470492
references: Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):531-6
references: 11149938
references: Mol Biol Evol. 1986 Sep;3(5):418-26
references: 3444411
references: PLoS One. 2010 Dec 06;5(12):e14234
references: 21151911
references: J Genet Genomics. 2009 Nov;36(11):667-77
references: 19932463
references: Plant Cell. 2004 Nov;16(11):2870-94
references: 15494555
references: Annu Rev Plant Biol. 2004;55:141-72
references: 15377217
references: Mol Biol Evol. 2007 Aug;24(8):1596-9
references: 17488738
references: Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20526-31
references: 19910532
references: Science. 2001 Jun 22;292(5525):2281-5
references: 11423651
references: Proc Natl Acad Sci U S A. 1998 May 12;95(10):5637-42
references: 9576936
references: Trends Genet. 2006 Dec;22(12):662-70
references: 17011664
references: Genetics. 2008 Apr;178(4):2031-43
references: 18245336
references: Genetics. 2007 Mar;175(3):1307-19
references: 17179076
references: Mol Biol Evol. 1997 Dec;14(12):1303-15
references: 9402740
references: Genetics. 1989 Nov;123(3):585-95
references: 2513255
references: Genetics. 2003 Feb;163(2):735-46
references: 12618410
references: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references: 9396791
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Nat Protoc. 2009;4(7):1073-81
references: 19561590
references: Genetics. 1993 Mar;133(3):693-709
references: 8454210
references: Theor Appl Genet. 2004 Mar;108(5):800-7
references: 15118822