Dataset Information

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

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.

SUBMITTER: Kumar G

PROVIDER: S-EPMC6424483 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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

Kumar Girish G Langa Jorge J Montes Iratxe I Conklin Darrell D Kocour Martin M Kohlmann Klaus K Estonba Andone A

PloS one 20190319 3

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 tot ...[more]

PMID: 30889192

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Project description:Jelena Lujić, Klaus Kohlmann, Petra Kersten, Zoran Marinović, Miroslav Ćirković, and Vladica Simić (2017) The tench, Tinca tinca, is an endangered freshwater fish species in the Balkans. However, there are no management and conservation strategies developed for this species so far. In order to be able to develop such strategies, we first determined the phylogeographic identity of 70 tench individuals from four countries (Serbia, FYRO Macedonia, Hungary and Croatia) by PCR-RFLP analyses of two nuclear markers (Act and RpS7) and one mitochondrial marker (Cytb). All makers enabled the identification of two major geographic clades of tench (Western and Eastern), while nuclear markers additionally enabled the identification of hybrids between the two clades. Based on the mitochondrial marker Cytb, tench populations can be separated into two distinct areas: areas north of the Danube River with the dominant Western origin, and areas south of the Danube River with the dominant Eastern origin. Data obtained for the Act gene demonstrated Eastern origin for most individuals (88.23%) while data obtained for the RpS7 gene demonstrated mixed origin with a high percentage of hybrids. The presence of high numbers of individuals with Western alleles for the RpS7 gene in areas south of the Danube may indicate a natural invasion of this phylogroup. According to these results, areas north and south of the Danube are identified as two main management units. Additionally, we identified the rare western haplotype W2 based on the Cytb marker which clearly indicated human-aided dispersals of tench in the investigated region and since some individuals with W2 origin were cultured, attention must be given to the genetic structure and identity of the introduced individuals, whether during introduction or reintroduction since biological and ecological consequences of the hybridization between the two major clades are still unknown. Finally, we propose and discuss management and conservation strategies for tench of both management areas.

Dataset Information

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

Publications

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

Similar Datasets

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