Planta

, Volume 238, Issue 2, pp 293–305

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

  • Waikhom Bimolata
  • Anirudh Kumar
  • Raman Meenakshi Sundaram
  • Gouri Shankar Laha
  • Insaf Ahmed Qureshi
  • Gajjala Ashok Reddy
  • Irfan Ahmad Ghazi
Original Article

DOI: 10.1007/s00425-013-1891-3

Cite this article as:
Bimolata, W., Kumar, A., Sundaram, R.M. et al. Planta (2013) 238: 293. doi:10.1007/s00425-013-1891-3

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 ‘θw’ = 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 Oryzanivara 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.

Keywords

Allele miningAllelic diversityBacterial blightSynonymous mutationNonsynonymous mutationTrans-membrane domain

Abbreviations

BB

Bacterial blight

NBS-LRR

Nucleotide binding site leucine rich repeats

RLL

Relative lesion length

TSS

Transcription start site

UTR

Untranslated region

UPT

Upregulated by transcriptional activator

NJ

Neighbor joining

Supplementary material

425_2013_1891_MOESM1_ESM.pdf (82 kb)
The accessions used for isolating Xa27 alleles are indicated by asterisks (*). S† and P denote disease score and phenotype of the plant against respective Xoo strains. Scoring of disease was performed following standard evaluation system (SES, IRRI). R = Resistant and S = susceptible. (PDF 81 kb)
425_2013_1891_MOESM2_ESM.pdf (85 kb)
Multiple alignment of protein coding region of Xa27 alleles. Deletion of three nucleotides ‘TAC’ from eight genotypes is shown. Nucleotide changes in other genotypes is also indicated with different colors. (PDF 85 kb)

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Waikhom Bimolata
    • 1
  • Anirudh Kumar
    • 1
  • Raman Meenakshi Sundaram
    • 2
  • Gouri Shankar Laha
    • 3
  • Insaf Ahmed Qureshi
    • 4
  • Gajjala Ashok Reddy
    • 2
  • Irfan Ahmad Ghazi
    • 1
  1. 1.Department of Plant Sciences, School of Life SciencesUniversity of HyderabadHyderabadIndia
  2. 2.Crop Improvement SectionDirectorate of Rice ResearchHyderabadIndia
  3. 3.Crop Protection SectionDirectorate of Rice ResearchHyderabadIndia
  4. 4.Department of Biotechnology, School of Life SciencesUniversity of HyderabadHyderabadIndia