Genome-wide detection of genes under positive selection in worldwide populations of the barley scald pathogen

Norfarhan Mohd Assa`Ad, Bruce A. McDonald, Daniel Croll

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abiotic factors could lead to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. Rhynchosporium commune, the pathogen causing barley scald disease, interacts at least partially in a gene-for-gene manner with its host. We analyzed global field populations of 125 R. commune isolates to identify candidate genes for local adaptation. Whole genome sequencing data showed that the pathogen is subdivided into three genetic clusters associated with distinct geographic and climatic regions. Using haplotype-based selection scans applied independently to each genetic cluster, we found strong evidence for selective sweeps throughout the genome. Comparisons of loci under selection among clusters revealed little overlap, suggesting that ecological differences associated with each cluster led to variable selection regimes. The strongest signals of selection were found predominantly in the two clusters composed of isolates from Central Europe and Ethiopia. The strongest selective sweep regions encoded protein functions related to biotic and abiotic stress responses. Selective sweep regions were enriched in genes encoding functions in cellular localization, protein transport activity, and DNA damage responses. In contrast to the prevailing view that a small number of gene-for-gene interactions govern plant pathogen evolution, our analyses suggest that the evolutionary trajectory is largely determined by spatially heterogeneous biotic and abiotic selection pressures.

Original languageEnglish
Pages (from-to)1315-1332
Number of pages18
JournalGenome Biology and Evolution
Volume10
Issue number5
DOIs
Publication statusPublished - 1 May 2018

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Hordeum
barley
genome
pathogen
Genome
gene
pathogens
Population
Genes
genes
plant pathogens
local adaptation
Rhynchosporium
scald diseases
genotype
Genotype
loci
gene interaction
protein transport
Plant Genome

Keywords

  • Fungi
  • Genome-wide selection scans
  • Plant pathogen
  • Population genomics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Genome-wide detection of genes under positive selection in worldwide populations of the barley scald pathogen. / Mohd Assa`Ad, Norfarhan; McDonald, Bruce A.; Croll, Daniel.

In: Genome Biology and Evolution, Vol. 10, No. 5, 01.05.2018, p. 1315-1332.

Research output: Contribution to journalArticle

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