• Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Pathogen-plant host coevolutionary interactions exert strong natural selection on both organisms, specifically on the genes coding for effectors (pathogens), as well as on those coding for effector targets and R proteins (plant hosts). Natural selection leaves behind DNA sequence signatures on such genes and on linked genomic regions. These signatures can readily be detected by studying the patterns of intraspecies polymorphisms and interspecies divergence of the DNA sequences. Recent developments in DNA sequencing technology have made whole-genome studies on patterns of DNA polymorphisms : divergence possible. This type of analysis, called 'population genomics', appears to be powerful enough to identify novel effector-effector target genes. Here, we provide an overview of the statistical tools used for population genomics and their applications. This is followed by a brief review of evolutionary studies on plant genes involved in host-pathogen interactions. Finally we provide an example from our study on Magnaporthe oryzae.
    Full-text · Article · Sep 2010 · New Phytologist
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Salinity is a major abiotic stress which affects crop plants around the world, resulting in substantial loss of yield and millions of dollars of lost revenue. High levels of Na(+) in shoot tissue have many adverse effects and, crucially, yield in cereals is commonly inversely proportional to the extent of shoot Na(+) accumulation. We therefore need to identify genes, resistant plant cultivars and cellular processes that are involved in salinity tolerance, with the goal of introducing these factors into commercially available crops. Through the use of an Arabidopsis thaliana mapping population, we have identified a highly significant quantitative trait locus (QTL) linked to Na(+) exclusion. Fine mapping of this QTL identified a protein kinase (AtCIPK16), related to AtSOS2, that was significantly up-regulated under salt stress. Greater Na(+) exclusion was associated with significantly higher root expression of AtCIPK16, which is due to differences in the gene's promoter. Constitutive overexpression of the gene in Arabidopsis leads to plants with significant reduction in shoot Na(+) and greater salinity tolerance. amiRNA knock-downs of AtCIPK16 in Arabidopsis show a negative correlation between the expression levels of the gene and the amount of shoot Na(+) . Transgenic barley lines overexpressing AtCIPK16 show increased salinity tolerance.
    Full-text · Article · Aug 2012 · Plant Cell and Environment
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Despite the increasing number of genomic tools, identifying the genetics underlying adaptive complex traits remains challenging in the model species Arabidopsis thaliana. This is due, at least in part, to the lack of data on the geographical scale of adaptive phenotypic variation. The aims of this study were (i) to tease apart the historical roles of adaptive and nonselective processes in shaping phenological variation in A. thaliana in France and (ii) to gain insights into the spatial scale of adaptive variation by identifying the putative selective agents responsible for this selection. Forty-nine natural stands from four climatically contrasted French regions were characterized (i) phenologically for six traits, (ii) genetically using 135 SNP markers and (iii) ecologically for 42 variables. Up to 63% of phenological variation could be explained by neutral genetic diversity. The remaining phenological variation displayed stronger associations with ecological variation within regions than among regions, suggesting the importance of local selective agents in shaping adaptive phenological variation. Although climatic conditions have often been suggested as the main selective agents acting on phenology in A. thaliana, both edaphic conditions and interspecific competition appear to be strong selective agents in some regions. In a first attempt to identify the genetics of phenological variation at different geographical scales, we phenotyped worldwide accessions and local polymorphic populations from the French RegMap in a genome-wide association (GWA) mapping study. The genomic regions associated with phenological variation depended upon the geographical scale considered, stressing the need to account for the scale of adaptive phenotypic variation when choosing accession panels for GWAS.
    Full-text · Article · Jul 2013 · Molecular Ecology