Genetics Selection Evolution · 2023

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

Delpuech E, Vandeputte M, Morvezen R, Bestin A, Besson M, Brunier J, Bajek A, Imarazene B, François Y, Bouchez O, Cousin X, Poncet C, Morin T, Bruant JS, Chatain B, Haffray P, Phocas F, Allal F

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In European sea bass, this study looks for genomic regions associated with resistance to viral nervous necrosis. It identifies a region shared by two populations and candidate genes, including IFI6/IFI27-like. The results open prospects for selection, without being a treatment for the disease.

The question: Which regions and genes are associated with VNN resistance in European sea bass?
The approach: Genome sequencing, genotyping and imputation, QTL mapping in two populations and validation of the effect of a region in an independent population.
What the article brings: A region on linkage group 12 is associated with resistance and contains in particular ZDHHC14 and IFI6/IFI27-like.
The limits: An associated QTL and a candidate gene do not, on their own, demonstrate the biological mechanism, and do not promise absolute resistance.

Figures from the article

Fig. 1, Whole-genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass — Fig. 1. Evolution of the Kaplan–Meier cumulative survival to a VNN infection challenge for each cohort from two commercial populations and a validation population. Results are in purple for pop A (A_1, A_2, A_3), in green for pop B (B_1, B_2, B_3), and in yellow for the validation populationOriginal caption. Delpuech E et al. (2023), Genetics Selection Evolution. CC BY 4.0

Fig. 2, Whole-genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass — Fig. 2. Manhattan plots of for VNN resistance in European sea bass populations A(a) and B(b). The red dashed line represents the logBF threshold of 10, corresponding to strong evidence for the presence of a QTLOriginal caption. Delpuech E et al. (2023), Genetics Selection Evolution. CC BY 4.0

Fig. 4, Whole-genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass — Fig. 4. Results for the LG12_QTL_2 region showing the SNPs with their genomic positions and the identified genes. The graph displays the logBF value on the y-axis and the physical position on the x-axis. Each point represents a variant in the QTL region, colored according to their LD (based on the squared coefficient of correlation, r 2 measure) with the characteristic variant of this QTL (red point). The red dashed lines indicate the logBF = 10 thresholdOriginal caption. Delpuech E et al. (2023), Genetics Selection Evolution. CC BY 4.0

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

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