Microsatellites are highly polymorphic multi-allelic markers consisting of a sequence of a repeated motif, the number of repetitions of which varies between alleles.
The PGTB has developed a method for microsatellite genotyping using high-throughput sequencing which offers two major advantages:
(1) to identify all types of polymorphisms present in the repeat motif and in the surrounding region
(2) be based on the DNA sequence of the alleles, thereby enabling the nature of the alleles to be definitively determined and facilitating the sharing of genotype data between projects or laboratories.
You can find further details on this method developed by the PGTB in the associated publication and the list of species for which we have developed markers on this regularly updated dataverse.
Services
We offer a full service comprising:
- the development of microsatellite markers based on low-coverage random sequencing data generated by the PGTB or on existing genomic resources
- their amplification using highly multiplexed PCR (usually 60 microsatellites tested)
- the construction of libraries and Illumina sequencing (up to 1,140 individuals per run, including 95 repeat samples for data validation during the initial analysis used to develop the markers)
- the bioinformatics analysis used to generate the genotype table.
These steps can be adapted to suit specific requirements (such as the type of resources available, the number of individuals and markers to be analysed, etc.).
Requirements
Results
Sent by email or uploaded to a server.
The analysis results are sent in Excel format and include:
- the coverage of each locus
- the characteristics of each locus
- allelic information
- the genotype table
The FASTQ files and the run report (MultiQC) are also provided.
Associated publications
Allegue H., Guinet C., Patrick S.C., Ribout C., Bichet C., Lepais O., Réale D., 2024. Offspring sex ratio increases with paternal reproductive success in a colony of southern elephant seals. Marine Mammal Science. https://doi.org/10.1111/mms.13108
Belair M, Picot A, Lepais O, Masson C, Hébrard MN, Moronvalle A, Comont G, Gabri Martin VM, Tréguer S, Laloum Y, Corio-Costet MF, Michailides TJ, Moral J, Le Floch G, Pensec F., 2024. Genetic diversity and population structure of Botryosphaeria dothidea and Neofusicoccum parvum on English walnut (Juglans regia L.) in France. Sci Rep. DOI: 10.1038/s41598-024-67613-6
Schmitt S, Heuret P, Troispoux V, Beraud M, Cazal J, Chancerel E, Cravero C, Guichoux E, Lepais O, Loureiro J, Marande W, Martin-Ducup O, Vincent G, Chave J, Plomion C, Leroy T, Heuertz M, Tysklind N., 2024. Low-frequency somatic mutations are heritable in tropical trees Dicorynia guianensis and Sextonia rubra. Proc Natl Acad Sci U S A. DOI: 10.1073/pnas.2313312121
Clochard, G-J., Mbengue, A., Mettling, C., Diouf, B., Faurie, C., Sene, O., Chancerel, E., Guichoux, E., Hollard, G., Raymond, M., Willinger, M., 2023. The effect of the 7R allele at the DRD4 locus on risk tolerance is independent of background risk in Senegalese fishermen. Sci Rep 13, 622. https://doi.org/10.1038/s41598-022-27002-3
Laurent, B., Larue, C., Chancerel, E., Guichoux, E., Petit, R.J., Barreneche, T., Robin, C., Lepais, O., 2020a. Microhaplotype genotyping-by-sequencing of 98 highly polymorphic markers in three chestnut tree species. Conservation Genet Resour 12, 567–580. https://doi.org/10/ghxd3m
Lepais, O., Chancerel, E., Boury, C., Salin, F., Manicki, A., Taillebois, L., Dutech, C., Aissi, A., Bacles, C.F.E., Daverat, F., Launey, S., Guichoux, E., 2020. Fast sequence-based microsatellite genotyping development workflow. PeerJ 8. https://doi.org/10/ghxd3p