Pubblicazione scientifica

A novel transcriptome-derived SNPs array for tench (Tinca tinca L.)

FILONE TECNOLOGICO	TEMA
economia circolare e sostenibilità
trasformazione e commercializzazione

RIASSUNTO

Tench (Tinca tinca L.) has great economic potential due to its high rate of fecundity and long-life span. Population genetic studies based on allozymes, microsatellites, PCR-RFLP and sequence analysis of genes and DNA fragments have revealed the presence of Eastern and Western phylogroups. However, the lack of genomic resources for this species has complicated the development of genetic markers. In this study, the tench transcriptome and genome were sequenced by high-throughput sequencing. A total of 60,414 putative SNPs were identified in the tench transcriptome using a computational pipeline. A set of 96 SNPs was selected for validation and a total of 92 SNPs was validated, resulting in the highest conversion and validation rate for a non-model species obtained to date (95.83%). The validated SNPs were used to genotype 140 individuals belonging to two tench breeds (Tabor and Hungarian), showing low (FST = 0.0450) but significant (<0.0001) genetic differentiation between the two tench breeds. This implies that set of validated SNPs array can be used to distinguish the tench breeds and that it might be useful for studying a range of associations between DNA sequence and traits of importance. These genomic resources created for the tench will provide insight into population genetics, conservation fish stock management, and aquaculture.

DATA

Data di pubblicazione: 19/03/2019

AUTORI

KUMAR GIRISH
LANGA JORGE
MONTES IRATXE
CONKLIN DARRELL
KOCOUR MARTIN
KOHLMANN KLAUS
ESTONBA ANDONE

ENTE DI AFFERENZA

RESEARCH INST FISH CULTURE & HYDROBIOLOGY SOUTH BOHEMIAN RSCH CTR AQUACULTURE & BIODIVERSITY OF HYDROCENOSES FACULTY OF FISHERIES & PROTECTION OF WATERS UNIV SOUTH BOHEMIA IN CESKE BUDEJOVICE CZECH REPUBLIC
DEPT GENETICS PHYSICAL ANTHROPOLOGY & ANIMAL PHYSIOLOGY UNIV BASQUE COUNTRY UPV EHU LEIOA BILBAO BIZKAIA SPAIN
DEPT COMPUTER SCIENCE & ARTIFICIAL INTELLIGENCE UNIV BASQUE COUNTRY UPV EHU SAN SEBASTIAN GIPUZKOA SPAIN
IKERBASQUE BASQUE FNDN SCIENCE BILBAO BIZKAIA SPAIN
DEPT AQUACULTURE & ECOPHYSIOLOGY LEIBNIZ INST FRESHWATER ECOLOGY & INLAND FISHERIES BERLIN GERMANY
NATL CHENG KUNG UNIV TAIWAN

RIVISTA

PLoS ONE, 14(3), e0213992

IMPACT FACTOR

2,870

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