Biology subjects

Francois, Y.

Publications and source records attributed to Francois, Y..

3 recordsLinked to original sources

bioRxiv2025

High-density genome-wide association study points out major candidate genes for resistance to infectious pancreatic necrosis in rainbow trout

BackgroundThis study focuses on genetic resistance to infectious pancreatic necrosis (IPN), a highly contagious disease caused by an aquatic birnavirus (IPNV) which especially affects salmonids worldwide. The objectives were to estimate the heritability of IPN resistance and to fine map quantitative trait loci (QTL) using a Bayesian Sparse Linear Mixed Model to identify candidate genes possibly linked to IPN resistance in two successive generations from a French commercial strain of rainbow trout. For each generation, 2,000 fish were experimentally exposed by bath to IPNV and mortalities were monitored daily during 5 weeks. All fish were genotyped using a medium-density 57K SNP chip and imputed to high-density genotypes (665K SNP). ResultsThe mean survival rate was 70% after 37 days, with a higher survival rate in the second generation compared to the first one (78% versus 61%). Heritability was moderate ([~]0.20). Approximately 74% of the genetic variance of IPN resistance was explained by a few tens of SNP. In total, 25 QTL were mapped on 10 chromosomes. Among them, 7 were detected with very strong evidence on chromosomes 1, 14, 16 and 28. The most interesting QTL were associated to top SNP with mean survival rate differences over 20% between the beneficial and detrimental homozygous genotypes. Those SNP were all located within promising functional candidate genes on chromosome 1 (uts2d, rc3h1, ga45b) and chromosome 16 (irf2bp, eif2ak2), all these genes being associated to the regulation of inflammatory pathways. A key factor of the genetic differences in susceptibility to IPNV among fish is PKR, the dsRNA-dependent serine/threonine-protein kinase encoded by the eif2ak2 gene. ConclusionsAll genes associated to the most significant QTL on chromosomes 1 and 16 are involved in the regulation of inflammatory pathways, strongly suggesting a central role of inflammation in the IPN resistance in rainbow trout. These findings offer the possibility of marker-assisted selection for rapid dissemination of genetic improvement for IPN resistance.

genetics↗

bioRxiv2022

Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits

BackgroundSelective breeding is a promising solution to reduce fish farms vulnerability to heat peaks which intensity and frequency are predicted to increase due to climate change. However, limited information about the genetic architecture of acute hyperthermia resistance in fish is available. Two batches of sibs from a rainbow trout commercial line were produced. The first batch (N=1,382) was phenotyped for acute hyperthermia resistance at nine months, and the second batch (N=1,506) was phenotyped for main production traits (growth, body length, muscle fat content and carcass yield) at twenty months. Fish were genotyped on a 57K SNP array, and their genotypes were imputed at high-density thanks to their parents being genotyped on a 665K SNP array. ResultsThe heritability estimate of resistance to acute hyperthermia in juveniles was 0.29 {+/-} 0.05, confirming the potential of selective breeding for this trait. Genetic correlations between acute hyperthermia resistance and main production traits at near harvest age were all close to zero. Hence, selecting for acute hyperthermia resistance should not impact the main production traits, and reversely. The genome-wide association study revealed that resistance to acute hyperthermia is highly polygenic; altogether, the six detected QTL explained less than 5% of the genetic variance. Two of these QTL, including the most significant one, might explain acute hyperthermia resistance differences across INRAE isogenic lines of rainbow trout. The phenotypic mean differences between homozygotes at peak SNP were up to 69% of the phenotypic standard deviation, showing promising potential for marker-assisted selection. We identified 89 candidate genes within the six QTL regions, among which the most convincing functional candidate genes were dnajc7, hsp70b, nkiras2, cdk12, phb, fkbp10, ddx5, cygb1, enpp7, pdhx and acly. ConclusionsThis study provides valuable insight on the genetic architecture of acute hyperthermia resistance in juvenile rainbow trout. The potential for the selective breeding of this trait was shown to be substantial and should not interfere with selection for main production traits. Identified functional candidate genes give a new insight on physiological mechanisms involved in acute hyperthermia resistance, such as protein chaperoning, oxidative stress response, homeostasis maintenance and cell survival.

genomics↗

bioRxiv2022

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

BackgroundViral Nervous Necrosis (VNN) is major disease affecting of European sea bass. Understanding the biological mechanisms that underlie VNN resistance is thus important for the welfare of farmed fish and the sustainability of production systems. This study aimed at identifying key genomic regions and genes that determine VNN resistance in sea bass. ResultsWe generated a dataset of around 900,000 single nucleotide polymorphisms (SNPs) identified from whole-genome sequencing (WGS) in the parental generation in two different commercial populations (pop A and pop B) comprising 2371 and 3428 European sea bass with phenotypic records for binary survival in a VNN challenge. In each commercial population, three cohorts were submitted to the redspotted grouper nervous necrosis virus (RGNNV) challenge by immersion and genotyped on a 57K SNP chip. After imputation of WGS SNPs from their parents, QTL mapping was performed using a Bayesian Sparse Linear Mixed Model (BSLMM). We found several QTL regions on different linkage groups (LG), most of which are specific to a single population, but a QTL region on LG12 was shared by both commercial populations. This QTL region is only 127 kB wide, and we identified IFI6, an interferon induced protein at only 1.9 kB of the most significant SNP. An unrelated validation population with 4 large families was used to validate the effect of the QTL, for which the survival of the susceptible genotype ranges from 39.8 to 45.4%, while that of the resistant genotype ranges from 63.8 to 70.8%. ConclusionsWe could precisely locate the genomic region implied in the main resistance QTL at less than 1.9 kb of the interferon alpha inducible protein 6 (IFI6), which has already been identified as a key player for other viral infections such as hepatitis B and C. This will lead to major improvements for sea bass breeding programs, allowing for greater genetic gain by using marker-assisted genomic selection to obtain more resistant fish. Further functional analyses are needed to evaluate the impact of the variant on the expression of this gene.

genetics↗