Intra-regional diversity of rice bacterial blight pathogen, Xanthomonas oryzae pv. oryzae, in the Andaman Islands, India: revelation by pathotyping and multilocus sequence typing

K. Sakthivel, A. Kumar*, R. K. Gautam, K. Manigundan, G. S. Laha, R. Velazhahan, R. Singh, I. S. Yadav

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


Aim: To investigate the genetic and pathogenic variability of Xanthomonas oryzae pv. oryzae causing bacterial blight in rice on the remote Andaman Islands, India. Methods and Results: A total of 27 yellow-pigmented bacterial isolates representing rice fields of Andaman Islands incited blight on the susceptible-rice cultivar, C14-8. Phenotypic, pathogenic traits and 16S rRNA gene sequences revealed their identity as X. oryzae pv. oryzae. Virulence profiling indicated the prevalence of seven pathotypes of X. oryzae pv. oryzae on the Islands. Pathotypes-VI and -VII were highly virulent, whereas the pathotype-I was less virulent. Multilocus sequence typing based on nucleotide sequence polymorphism in nine housekeeping genes dnaK; fyuA; gyrB (two loci): rpoD; fusA; gapA; gltA and lepA clustered 27 isolates into 17 sequence types (STs) segregated into two clonal-complexes (CC). While CC-I comprised of isolates from Andaman Island, the CC-II is a mixture of isolates representing mainland India and Andaman Island. The data revealed trans-boundary pathogen introduction and a consequent intra-regional diversification on these islands due to the deployment of different rice cultivars in different regions. Conclusions: Genotyping and pathotyping of sland isolates revealed seven pathotypes distributed in two clonal complexes with strong indications for trans-boundary movement and consequent diversification of the bacterial pathogen. Highly virulent pathotypes of X. oryzae pv. oryzae that could overcome combinations of R-genes, xa13+Xa21 as well as xa5+xa13 were found prevalent in the Andaman Islands. Significance and Impact of the Study: Genetic and virulence analysis of X. oryzae pv. oryzae in the Andaman Islands revealed introduction and host-mediated regional diversification and local adaptation of X oryzae pv. oryzae. The study calls for the need of multi-gene pyramiding for durable disease resistance and establishing stringent quarantine measures for safeguarding island agricultural practices in the future.

Original languageEnglish
Pages (from-to)1259-1272
Number of pages14
JournalJournal of Applied Microbiology
Issue number4
Publication statusPublished - Apr 2021
Externally publishedYes


  • Andaman Islands
  • bacterial blight
  • diversity
  • multilocus sequence typing
  • pathotyping
  • rice
  • Xanthomonas oryzae

ASJC Scopus subject areas

  • Biotechnology
  • Applied Microbiology and Biotechnology

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