Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

Abstract

The optimal management of the commercially important, but mostly over-exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded FST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between-ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17-SNP panel was developed in Atlantic BFT by cross-species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (FST = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.

Crossing the line: migratory and homing behaviors of Atlantic bluefin tuna

“…Under the assumption of natal homing, we expect that female-mediated gene flow between eastern and western populations of bluefin tuna would be limited, resulting in genetically distinct populations. Longitudinal patterns of genetic structuring (west to east) have been reported recently for bluefin tuna, and individuals from eastern (Mediterranean Sea) and western (Gulf of Mexico) spawning grounds are genetically distinct based on analysis of mtDNA control region sequence data (Φ st ) (Boustany et al 2008), microsatellites (Carlsson et al 2007), and single nucleotide polymorphisms (Albaina et al 2013). In response, the natal homing scenario proposed here for bluefin tuna based on δ 13 C and δ…”

Otolith shape variation provides a marker of stock origin for north Atlantic bluefin tuna (Thunnus thynnus)

“…Analyses of DNA microsatellites (Carlsson et al 2007), mitochondrial DNA (Boustany et al 2008) and single nucleotide polymorphisms (Albaina et al 2013) all show significant genetic divergence of the two populations. In addition, there is evidence of genetic heterogeneity within the Mediterranean, and the existence of separate spawning populations in the western and eastern Mediterranean has been proposed (Carlsson et al 2004;Riccioni et al 2010).…”

Development of gene-associated single nucleotide polymorphisms for Japanese anchovy Engraulis japonicus through cross-species amplification

“…Therefore, flanking sequences are highly conserved between species and suitable for designing primers/probes that successfully cross-amplify in closely related species [45]. Most of the previous studies for non-model species (Table 3) have discovered SNPs through cross-species amplification based on the emulsion, paired isolation, and concatenation polymerase chain reaction (EPIC-PCR) method [46][47][48], in which primers are designed on exon regions to amplify the intron [49]. However, the EPIC-PCR has been ousted by transcriptome sequencing through high throughput sequencing, the strategy chosen in the present study, which allows the discovery of thousands of potential SNPs that can be used for cross-species amplification [50,51].…”

“…Nevertheless, the validation rate obtained in the present study was high compared to that of previous studies (Table 3). Albaina et al [47] conducted a cross-species amplification of SNPs from albacore to Atlantic bluefin tuna, and obtained a validation rate of 18%; the reciprocal cross resulted in a validation success of 24.2% [51]. Cross-amplification success between Atlantic and Pacific herring, Clupea harengus and Clupea pallasii respectively, is even lower, 11.9% [50].…”