Genetic diversity and population structure of rice pathogen Ustilaginoidea virens in China

PLoS One. 2013 Sep 30;8(9):e76879. doi: 10.1371/journal.pone.0076879. eCollection 2013.

Abstract

Rice false smut caused by the fungal pathogen Ustilaginoidea virens is becoming a destructive disease throughout major rice-growing countries. Information about its genetic diversity and population structure is essential for rice breeding and efficient control of the disease. This study compared the genome sequences of two U. virens isolates. Three SNP-rich genomic regions were identified as molecular markers that could be used to analyze the genetic diversity and population structure of U. virens in China. A total of 56 multilocus sequence types (haplotypes) were identified out of 162 representative isolates from 15 provinces covering five major rice-growing areas in China. However, the phylogeny, based on sequences at individual SNP-rich regions, strongly conflicted with each other and there were significant genetic differences between different geographical populations. Gene flow between the different geographical populations and genetic differentiation within each geographical population were also detected. In addition, genetic recombination and genetic isolation resulting from geographic separation was also found.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Breeding / methods
  • China
  • DNA Primers / genetics
  • Demography
  • Gene Flow / genetics*
  • Genetic Variation*
  • Genetics, Population
  • Haplotypes / genetics
  • Likelihood Functions
  • Models, Genetic
  • Molecular Sequence Data
  • Oryza / microbiology*
  • Phylogeny
  • Polymorphism, Single Nucleotide / genetics
  • Sequence Analysis, DNA
  • Species Specificity
  • Ustilaginales / genetics*

Substances

  • DNA Primers

Grants and funding

This project is supported by the Special Fund for Agro-scientific Research in the Public Interest of China (No. 200903039-8) and a “100 Talent Program” grant from Chinese Academy of Sciences (to Shaojie Li). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.