From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon

Autor: Marie-Laure Acolas, Emilie Chancerel, Maud Pierre, Séverine Roques, Christophe Boury
Přispěvatelé: Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA)
Jazyk: angličtina
Rok vydání: 2019
Předmět:
0106 biological sciences
relatedness
protection of species
inbreeding
Single-nucleotide polymorphism
PROGRAMME DE RECHERCHE
Biology
010603 evolutionary biology
01 natural sciences
DNA sequencing
03 medical and health sciences
PROTECTION DES ESPECES
lcsh:QH540-549.5
Acipenser sturio
conservation program
high‐throughput sequencing
parentage assignment
research programme
Genotyping
Ecology
Evolution
Behavior and Systematics
Original Research
030304 developmental biology
Nature and Landscape Conservation
0303 health sciences
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]
Ecology
population genetics
biology.organism_classification
humanities
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics
Evolutionary biology
Genetic marker
Microsatellite
lcsh:Ecology
GENETIQUE DES POPULATIONS
[SDE.BE]Environmental Sciences/Biodiversity and Ecology
Inbreeding
Genetic monitoring
Zdroj: Ecology and Evolution, Vol 9, Iss 12, Pp 7017-7029 (2019)
Ecology and Evolution
Ecology and Evolution, Wiley Open Access, 2019, 9 (12), pp.7017-7029. ⟨10.1002/ece3.5268 ⟩
Ecology and Evolution, Wiley Open Access, 2019, 9 (12), pp.7017-7029. ⟨10.1002/ece3.5268⟩
Ecology and Evolution 12 (9), 7017-7029. (2019)
ISSN: 2045-7758
DOI: 10.1002/ece3.5268
Popis: International audience; The use of genetic information is crucial in conservation programs for the establishment of breeding plans and for the evaluation of restocking success. Short tandem repeats (STRs) have been the most widely used molecular markers in such programs, but next‐generation sequencing approaches have prompted the transition to genome‐wide markers such as single nucleotide polymorphisms (SNPs). Until now, most sturgeon species have been monitored using STRs. The low diversity found in the critically endangered European sturgeon (Acipenser sturio), however, makes its future genetic monitoring challenging, and the current resolution needs to be increased. Here, we describe the discovery of a highly informative set of 79 SNPs using double‐digest restriction‐associated DNA (ddRAD) sequencing and its validation by genotyping using the MassARRAY system. Comparing with STRs, the SNP panel proved to be highly efficient and reproducible, allowing for more accurate parentage and kinship assignments' on 192 juveniles of known pedigree and 40 wild‐born adults. We explore the effectiveness of both markers to estimated relatedness and inbreeding, using simulated and empirical datasets. Interestingly, we found significant correlations between STRs and SNPs at individual heterozygosity and inbreeding that give support to a reasonable representation of whole genome diversity for both markers. These results are useful for the conservation program of A. sturio in building a comprehensive studbook, which will optimize conservation strategies. This approach also proves suitable for other case studies in which highly discriminatory genetic markers are needed to assess parentage and kinship.
Databáze: OpenAIRE
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