Use of chloroplast microsatellites to differentiate oak populations

Abstract

-The possibility to use chloroplast microsatellites (cpSSRs) instead of restriction analysis of PCR-amplified DNA fragments to differentiate oak populations was tested in two economically important tree species: Quercus petraea and Quercus robur. The level and pattern of inter-and intraspecific cpDNA variation were studied over 48 French populations using a total of 24 cpSSR loci. The same pattern of low intrapopulation diversity and high population differentiation was noted with both types of markers, since there was an almost total redundancy of haplotypes identified with both techniques. Overall, our results indicate that chloroplast microsatellites can be used for haplotype discrimination in many contexts including certification or traceability of oak material. microsatellites / cpSSR / PCR-RFLP / haplotypic diversity / population geneticsRésumé -Utilisation des microsatellites chloroplastiques pour différencier des populations de chênes. Nous avons cherché à comparer l'efficacité de deux types de marqueurs chloroplastiques, les marqueurs microsatellites (cpSSR) et marqueurs PCR-RFLP (cpRFLP), à différencier des populations de chênes sessiles et pédonculés, deux espèces d'arbres forestiers économiquement importantes. Le niveau et la structuration de la diversité inter et intra-spécifique ont été mesurés au sein de 48 populations françaises au travers de l'analyse de 24 microsatellites chloroplastiques. Une faible diversité intra-population, ainsi qu'une forte différenciation des populations de chênes ont pu être mesurées à l'aide des deux types de marqueurs, du fait d'une redondance quasi-complète des haplotypes identifiés par les deux techniques. Nos résultats indiquent donc que les marqueurs microsatellites chloroplastiques peuvent être utilisés pour la distinction d'haplotypes et de populations de chênes dans le cadre de la certification ou de la traçabilité de matériel forestier (graines, plants, bois). microsatellites / cpSSR / PCR-RFLP / diversité haplotypique / génétique des populations

Contrasting patterns of historical colonization in white oaks (Quercusspp.) in California and Europe

“…1995), allowing us to track recolonization processes through seeds. A previous study showed that chloroplast simple sequence repeats (cpSSRs) yield similar genetic patterns to chloroplast polymerase chain reaction‐restriction fragment length polymorphism (cpPCR‐RFLP) at the French scale for Q. petraea and Q. robur (Deguilloux et al . 2004) and, thus, constitute appropriate markers to infer historical recolonization processes in oaks.…”

Chloroplast microsatellites as a tool for phylogeographic studies: the case of white oaks in Poland

“…Defining such relatedness is necessary if new phylogeographic studies based on cpSSRs are to be compared to earlier works carried out using PCR-RFLPs. Deguilloux et al (2004) found almost complete redundancy between the haplotypes identified using the two types of markers in French oak populations. Other studies related haplotypes from the two marker systems only partially (Gailing et al 2007b, Neophytou & Michiels 2013.…”

“…Therefore, they may reveal incomplete concordance with PCR-RFLP when studying the genetic structure of populations. Nonetheless, direct relationships between cpSSR and PCR-RFLP haplotypes is expected since they are fully linked in the chloroplast genome, as previously reported (Deguilloux et al 2004, Gailing et al 2007b, Neophytou & Michiels 2013. However, PCR-RFLPs have low mutation rates and are primarily useful for reconstructing patterns at large geographical scales, while they lack the resolution needed for fine spatial scales studies.…”

“…Chloroplast microsatellites have already been used for studying phylogeography in oaks (Grivet et al 2006, Magri et al 2007, Pakkad et al 2008, revealing patterns of variation similar to PCR-RFLP markers (Deguilloux et al 2004, Gailing et al 2007a). However, recent studies of cpSSR diversity in European white oaks based on chloroplast polymorphisms indicated a smaller number of haplotypes compared with this study (Grivet et al 2006, Neophytou & Michiels 2013.…”

“…CpDNA variation can be alternatively mapped with microsatellite sequences (cpSSR - Deguilloux et al 2004). Several universal cpSSR loci have been identified for angiosperm taxa (Weising & Gardner 1999).…”