Age estimates derived from hard parts of swordfish Xiphias gladius from the north-western Mediterranean Sea

Accurate age estimates for fish are critical for properly understanding stock dynamics and health; this is particularly true for larger billfishes. Here we determined the most accurate aging estimation methods for swordfish (Xiphias gladius). We compared age estimates obtained from fin-ray sections, otolith sections, whole otoliths, and vertebrae collected from 87 swordfish off the east coast of Corsica. Age estimates from otolith sections were most consistently estimated across different readers (lowest average percentage error), followed by fin-ray sections, third vertebrae, and whole otoliths. When the age estimates from the otolith sections were compared with the other three age sclerochronological methods, we found the average percentage error to be lowest between the otolith section and fin-ray methods. However, age estimates from fin rays proved most useful for estimating swordfish younger than 6 years, as the fin ray-based age diverged from that of the otolith sections as the swordfish aged. Combining fin ray and otolith section techniques, we estimated the growth parameters of 1-12-year-old females (L∞  = 259.412, k = 0.113, t0  = -2.499) and 1-7-year-old males (L∞  = 175.543, k = 0.202, t0  = -2.239). We found that females grew significantly faster than males after 3 years and remained larger thereafter. Our calculated growth rates for this region of the north-western Mediterranean Sea were lower than those of the Atlantic, Pacific, and eastern Mediterranean Sea swordfish populations, and similar to growth rates recorded for the western Mediterranean Sea populations. Our study provides critical knowledge on biological-related parameters to serve as a guide for preserving the swordfish population in the Mediterranean Sea.

Whole-genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass

BACKGROUND

Viral nervous necrosis (VNN) is a major disease that affects European sea bass, and understanding the biological mechanisms that underlie VNN resistance is important for the welfare of farmed fish and sustainability of production systems. The aim of this study was to identify genomic regions and genes that are associated with VNN resistance in sea bass.

RESULTS

We generated a dataset of 838,451 single nucleotide polymorphisms (SNPs) identified from whole-genome sequencing (WGS) in the parental generation of two commercial populations (A: 2371 individuals and B: 3428 individuals) of European sea bass with phenotypic records for binary survival in a VNN challenge. For each population, three cohorts were submitted to a red-spotted grouper nervous necrosis virus (RGNNV) challenge by immersion and genotyped on a 57K SNP chip. After imputation of WGS SNPs from their parents, quantitative trait loci (QTL) were mapped using a Bayesian sparse linear mixed model (BSLMM). We found several QTL regions that were specific to one of the populations on different linkage groups (LG), and one 127-kb QTL region on LG12 that was shared by both populations and included the genes ZDHHC14, which encodes a palmitoyltransferase, and IFI6/IFI27-like, which encodes an interferon-alpha induced protein. The most significant SNP in this QTL region was only 1.9 kb downstream of the coding sequence of the IFI6/IFI27-like gene. An unrelated population of four large families was used to validate the effect of the QTL. Survival rates of susceptible genotypes were 40.6% and 45.4% in populations A and B, respectively, while that of the resistant genotype was 66.2% in population B and 78% in population A.

CONCLUSIONS

We have identified a genomic region that carries a major QTL for resistance to VNN and includes the ZDHHC14 and IFI6/IFI27-like genes. The potential involvement of the interferon pathway, a well-known anti-viral defense mechanism in several organisms (chicken, human, or fish), in survival to VNN infection is of particular interest. Our results can lead to major improvements for sea bass breeding programs through marker-assisted genomic selection to obtain more resistant fish.