Abstract
Temperature tolerance is an important trait from both an economic and evolutionary perspective in fish. Because of difficulties with measurements, genome-wide selection using quantitative trait loci (QTLs) affecting Upper temperature tolerance may be an alternative for genetic improvement. Turbot Scophthalmus maximus (L.) is a cold-water marine fish with high economic value in Europe and Asia. The genetic bases of upper temperature tolerance (UTTs) traits have been rarely studied. In this study, we constructed a genetic linkage map of turbot using simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers. A total of 190 SSR and 8,123 SNP were assigned to 22 linkage groups (LGs) of a consensus map, which spanned 3,648.29 cM of the turbot genome, with an average interval of 0.44 cM. Moreover, we re-anchored genome sequences, allowing 93.8% physical sequences to be clustered into 22 turbot pseudo-chromosomes. A high synteny was observed between two assemblies from the literature. QTL mapping and validation analysis identified thirteen QLTs which are major effect QTLs, of these, 206 linked SNP loci, and two linked SSR loci were considered to have significant QTL effects. Association analysis for UTTs with 129 QTL markers was performed for different families, results showed that eight SNP loci were significantly correlated with UTT, which markers could be helpful in selecting thermal tolerant breeds of turbot. 1,363 gene sequences were genomically annotated, and 26 QTL markers were annotated. We believe these genes could be valuable candidates affecting high temperatures, providing valuable genomic resources for the study of genetic mechanisms regulating thermal stress. Similarly, they may be used in marker-assisted selection (MAS) programs to improve turbot performance.
Highlights
Turbot Scophthalmus maximus (L.) is a cold-water marine fish, which was introduced to China in 1992, and is an important economic species of wild fisheries
Before QTLs are used for marker-assisted selection, several issues must be addressed: Are genetic effects identified by these QTLs stable? Which markers are shared among different families? Are there specific markers? Answers to these questions are crucial for MAS programs
Our study provides a genetic analysis of turbot upper thermal tolerance traits, and valuable genomic resources for molecular breeding programs in this commercially vital fish
Summary
Turbot Scophthalmus maximus (L.) is a cold-water marine fish, which was introduced to China in 1992, and is an important economic species of wild fisheries. From an economic and evolutionary point of view, temperature tolerance is an important trait of fish, especially for cool- and cold-water turbot. Turbot is difficult to culture in Northern China during the summer, where natural seawater temperatures often exceed 26 °C5. Such high temperatures can cause stress responses in these fishes, resulting in increased mortality, decreased growth rate and disease resistance[6]. The construction of high-density genetic linkage maps, and the analysis of quantitative trait loci (QTLs) for marker-assisted selection (MAS) is of significant value, as it accelerates breeding processes, reduces population sizes and breeding costs of bringing progeny to m aturity[11,12]. Before QTLs are used for marker-assisted selection, several issues must be addressed: Are genetic effects identified by these QTLs stable? Which markers are shared among different families? Are there specific markers? Answers to these questions are crucial for MAS programs
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