基于转录组的鳜鱼（Tinca tinca L.）新型 SNP 芯片。

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

机构信息

Research Institute of Fish Culture and Hydrobiology, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Czech Republic.

Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa-Bilbao, Bizkaia, Spain.

出版信息

PLoS One. 2019 Mar 19;14(3):e0213992. doi: 10.1371/journal.pone.0213992. eCollection 2019.

DOI:10.1371/journal.pone.0213992

PMID:30889192

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6424483/

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.

摘要

由于其高繁殖率和长寿命，丁鱥（Tinca tinca L.）具有巨大的经济潜力。基于同工酶、微卫星、PCR-RFLP 以及基因和 DNA 片段序列分析的种群遗传研究揭示了存在东、西两个进化群。然而，由于该物种缺乏基因组资源，遗传标记的开发变得复杂。在这项研究中，通过高通量测序对丁鱥的转录组和基因组进行了测序。使用计算管道在丁鱥转录组中鉴定了 60414 个假定的 SNP。选择了 96 个 SNP 进行验证，总共验证了 92 个 SNP，这是迄今为止获得的非模式物种的最高转换和验证率（95.83%）。验证的 SNP 用于对属于两个丁鱥品种（塔博尔和匈牙利）的 140 个个体进行基因分型，表明两个丁鱥品种之间存在低（FST = 0.0450）但显著（<0.0001）的遗传分化。这意味着，验证的 SNP 可以用于区分丁鱥品种，并且可能有助于研究 DNA 序列与重要性状之间的一系列关联。为丁鱥创建的这些基因组资源将为种群遗传学、保护鱼类种群管理和水产养殖提供深入的了解。