Nucleotide diversity and linkage disequilibrium at 58 stress response and phenology candidate genes in a European beech (Fagus sylvatica L.) population from southeastern France
2014
Csilléry, Katalin | Oddou-Muratorio, Sylvie | Safrana, Jonathan | de Quattro, C. | Fady, Bruno | González-Martínez, Santiago C. | Vendramin, G. G. | Ecologie des Forêts Méditerranéennes (URFM) ; Institut National de la Recherche Agronomique (INRA) | Plant Genetics Institute ; National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR) | Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA) | EU Network of Excellence "EvolTree" [GOCE-016322]; ERA-Net BiodivERsA; ANR (France); MINECO (Spain); Italian MIUR [RBAP10A2T4]; INRA-EFPA; AdapCon project [CGL2011-30182-C02-01] | ANR-08-BDVA-0006,LINK TREE,Relations entre diversité génétique et réponse écologique aux changements environementaux : les arbres forestiers comme modèles d'étude(2008)
International audience
Afficher plus [+] Moins [-]anglais. European beech (Fagus sylvatica L.) is one of the most economically and ecologically important deciduous trees in Europe, yet little is known about its genomic diversity and its adaptive potential. Here, we detail the discovery and analysis of 573 single nucleotide polymorphisms (SNPs) from 58 candidate gene fragments that are potentially involved in abiotic stress response and budburst phenology using a panel of 96 individuals from southeastern France. The mean nucleotide diversity was low (theta (pi) = 2.2 x 10(-3)) but extremely variable among gene fragments (range from 0.02 to 10), with genes carrying insertion/deletion mutations exhibiting significantly higher diversity. The decay of linkage disequilibrium (LD) measured at gene fragments > 800 base pairs was moderate (the half distance of r (2) was 154 bp), consistent with the low average population-scaled recombination rate (rho = 5.4 x 10(-3)). Overall, the population-scaled recombination rate estimated in F. sylvatica was lower than for other angiosperm tree genera (such as Quercus or Populus) and similar to conifers. As a methodological perspective, we explored the effect of minimum allele frequency (MAF) on LD and showed that higher MAF resulted in slower decay of LD. It is thus essential that the same MAF is used when comparing the decay of LD among different studies and species. Our results suggest that genome-wide association mapping can be a potentially efficient approach in F. sylvatica, which has a relatively small genome size.
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