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An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations

文献类型： 外文期刊

作者： Hofinger, Bernhard J. 1 ; Russell, Joanne R. 2 ; Bass, Chris G. 1 ; Baldwin, Thomas 1 ; Dos Reis, Mario 3 ; Hedley, 1 ;

作者机构： 1.Rothamsted Res, Dept Plant Pathol & Microbiol, Harpenden AL5 2JQ, Herts, England

2.James Hutton Inst, Genet Programme, Dundee DD2 5DA, Scotland

3.UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England

4.Jilin Acad Agr Sci, Biotechnol Res Ctr, Changchun 130033, Peoples R China

关键词： eIF4E;Hordeum vulgare;positive selection;resistance to viruses;single nucleotide polymorphism

期刊名称：MOLECULAR ECOLOGY （ 影响因子：6.185； 五年影响因子：6.801 ）

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收录情况： SCI

摘要： In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognized as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars, two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study, the sequence of eIF4E was analysed in 1090 barley landraces and noncurrent cultivars originating from 84 countries. An exceptionally high nucleotide diversity was evident in the coding sequence of eIF4E but not in either the adjacent MCT-1 gene or the sequence-related eIF(iso)4E gene situated on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in the coding sequence of eIF4E resulted in amino acid changes. A total of 47 eIF4E haplotypes were identified, and phylogenetic analysis using maximum likelihood provided evidence of strong positive selection acting on this barley gene. The majority of eIF4E haplotypes were found to be specific to distinct geographic regions. Furthermore, the eI4FE haplotype diversity (uh) was found to be considerably higher in East Asia, whereas SNP genotyping identified a comparatively low degree of genome-wide genetic diversity in 16 of 17 tested accessions (each carrying a different eIF4E haplotype) from this same region. In addition, selection statistic calculations using coalescent simulations showed evidence of non-neutral variation for eIF4E in several geographic regions, including East Asia, the region with a long history of the bymovirus-induced yellow mosaic disease. Together these findings suggest that eIF4E may play a role in barley adaptation to local habitats.

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