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Isolation and characterization of single nucleotide polymorpisms (SNPs) in Atlantic bluefin tuna (Thunnus thynnus)

Final Report Summary - ABFT SNP (Isolation and characterization of single nucleotide polymorpisms (SNPs) in Atlantic bluefin tuna (Thunnus thynnus))


Executive Summary:

The majority of recent studies suggest population structuring of bluefin tuna in the Mediterranean, but evidence is still not conclusive.

Genetic characterization of this important fishery species was until recently very limited.

We sequenced the bluefin tuna transcriptome with the aims of isolating polymorphic SNPs and providing a genomic resource for this species.

Results

The sequencing and characterization of the bluefin tuna transcriptome has uncovered a high level of polymorphism. Combining functional annotation and information on synonymous and non-synonymous substitutions allows to select polymorphic markers based on their putative biological significance.

Based on the results we selected 128 SNP loci for designing a custom OpenArray® genotyping chip:

14 experimentally validated SNP loci with annotations
19 annotated loci with synonymous SNPs
20 annotated loci with non-synonymous SNP mutations from or to stop codons
29 loci annotated as enzymes with non-synonymous SNP mutations from or to polar and non polar amino acids
23 annotated loci with non-synonymous SNP mutations from the 17 least likely amino acid changes in a PAM2 matrix
23 annotated loci with other non-synonymous SNP mutations

Despite initial difficulties due to sample unavailability, except for the delaying of genotyping, the objectives of the project have been achieved or exceeded: a number of SNPs much larger than anticipated has been discovered and characterized in detail. This has allowed to select polymorphic markers for genotyping based on expected biological function inferred from the annotation; furthermore, the genomic resource obtained allows the selection of marker panels covering specific genes from a pool of more then 12,000, enabling the study of population variability for traits relevant to fitness and survival. A draft transcriptome has been produced; and a reference genome based assembly has just been completed. Other classes of polymorphism such as SSRs and SINEs have been discovered and their characterization is still in progress. Finally, the availability of a large pool of well characterized polymorphic markers constitutes an important resource for this species, enabling to address a broad range of questions.