Abstract
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.
Highlights
Tench (Tinca tinca L.) is a freshwater fish species within the Cyprinidae family that spawns and grows ideally at water temperatures of 20–29 ̊C [1, 2]
In this study, using the validated SNPs we have demonstrated that the two tench breeds show low but significant genetic differentiation, even with their similar genetic structure concerning their phylogroup based gene pool
We showed that the SNPs array in tench is strong enough to distinguish tench breeds and that it might be useful for studies focused on searching the range of associations between DNA sequence and traits of importance
Summary
Tench (Tinca tinca L.) is a freshwater fish species within the Cyprinidae family that spawns and grows ideally at water temperatures of 20–29 ̊C [1, 2]. Its native distribution is Eurasia; due to human-mediated movement, tench can be found in temperate and tropic freshwater regions across the globe [3]. Transcriptome-derived SNPs array for tench of the Czech Republic, and by the Genomic Resources Research Group from the Basque University System (IT558-10) funded by the Department of Education, Universities and Research of the Basque Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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