Biology subjects

Quillet, E.

Publications and source records attributed to Quillet, E..

7 recordsLinked to original sources

bioRxiv2026

Insights into the genetic architecture of resistance to viral haemorrhagic septicaemia virus in rainbow trout from a genome-wide association study to in vitro CRISPR-Cas9 functional evaluation

Viral haemorrhagic septicaemia (VHS) is a severe disease affecting rainbow trout (Oncorhynchus mykiss) and a wide range of wild freshwater and marine fish species. VHSV threatens rainbow trout aquaculture, as it may cause 100% mortality in fry. Previous studies identified a quantitative trait locus (QTL) on chromosome 3 associated with resistance to VHSV waterborne challenge and reduced viral replication in fin explants, although these findings were obtained using limited genetic diversity. The objective of this study was to validate and extend the identification of genomic regions associated with resistance to VHSV in the genetically diverse rainbow trout line designated "synthetic." A genome-wide association study (GWAS) was conducted using whole-genome sequences from parents of progeny classified as resistant or susceptible to a VHSV waterborne challenge. While the QTL on chromosome 3 was not validated in the synthetic line, four novel suggestive SNPs associated with survival following VHSV waterborne challenge were identified on chromosomes 6, 8, 17, and 32. Notably, one SNP on chromosome 17 was located within a gene potentially involved in antiviral defence, a paralog of lrp1 (low-density lipoprotein receptor-related protein 1). To further investigate its role, lrp1 function was analysed in vitro using CRISPR-Cas9 genome editing. Three independent lrp1-/- CHSE-EC cell lines were generated and challenged with VHSV. The results showed that lrp1 is not essential for viral entry but may modulate the inflammatory response during VHSV infection in epithelial cell lines.

genetics↗

bioRxiv2024

In-depth investigation of genome to refine QTL positions for spontaneous sex-reversal in XX rainbow trout

Sex determination is a flexible process in fish, controlled by genetics or environmental factors or a combination of both depending on the species. Revealing the underlying molecular mechanisms may have important implications for research on reproductive development in vertebrates, as well as sex-ratio control and selective breeding in fish. Phenotypic sex in rainbow trout is primarily controlled by a XX/XY male heterogametic sex determination system. Unexpectedly in genetically XX all-female farmed populations, a small proportion of males or intersex individuals are regularly observed. This spontaneous masculinisation is a highly heritable trait, controlled by minor sex-modifier genes that remain unknown, although several QTL regions were detected in previous studies. In this work we used genome-based approaches and various statistical methods to investigate these QTL regions. We validated in six different French farmed populations DNA markers we had previously identified in a different commercial population on chromosomes Omy1, Omy12 and Omy20. We also identified functional candidate genes located that may be involved in spontaneous masculinisation by reducing germ cell proliferation and repressing oogenesis of XX-rainbow trout in the absence of the master sex determining gene. In particular, syndig1, tlx1 and hells on Omy1, as well as khdrbs2 and csmd1 on Omy20 deserve further investigation as potential sex-modifier genes to precise their functional roles as well as their interaction with rearing temperature. Those findings could be used to produce all-female populations that are preferred by farmers due to a delayed maturation of females and higher susceptibility of male trout to diseases.

genetics↗

bioRxiv2023

From the third to the seventh generation of selection for muscle fat content in rainbow trout: Consequences for flesh quality

Muscle lipid content was shown to affect many quality features in salmonids in both raw and processed fillets. The objective of the present work was to assess the consequences of 7 generations of divergent selection for muscle adiposity on some rainbow trout flesh quality and muscle parameters. Fish from Lean (L) and Fat (F) lines had a similar body weight but L fish were longer and had consequently lower condition factor values. Carcass yield was not affected by selective breeding, but L fish had lower hepato- and gonado-somatic indexes, a bigger head, and lower fillet yield than F fish. A difference of more than 15 points in mean fat-meter(R) values (genetic selection criteria) was measured between the two lines. Mean muscle lipid content was 5.0{+/-}1.0% for L line vs 13.5{+/-}2.2% for F line. An absolute difference of more than 6% was measured in fillet dry matter content between the two lines, for raw, cooked, and smoked fillets. Raw fillets from F fish were lighter (L*>) and more colorful (a* and b*>), but softer than those from the L line. Quality parameters of cooked fillets were very similar between the two lines, whereas smoked fillets exhibited, between the two lines, similar differences than raw fillets. A large difference in white muscle fiber size was observed, fish from F line having higher fiber mean diameter, a lower proportion of small fibers, and a higher proportion of large fibers. Sex effects were observed on these immature fish, on classically sex-related traits (GSI and head development), but also on muscle fiber size. Moreover, these effects were more marked in F line. Correlation analysis showed that raw fillet color was positively related to muscle adiposity whereas mechanical resistance was negatively related. Raw fillet mechanical resistance was also negatively correlated to white muscle fiber size. Moreover, smoked fillet quality parameters were correlated to raw fillet ones. The relationships between muscle adiposity, but also muscle cellularity, and fillet quality were discussed. HighlightsO_LI7 generations of adiposity divergent selection affect raw and smoked fillet quality. C_LIO_LISelective breeding led to a noteworthy response in white muscle cellularity. C_LIO_LISome differences between male and female was measured in immature pan-size trout. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/569019v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@10b25f6org.highwire.dtl.DTLVardef@e9402aorg.highwire.dtl.DTLVardef@173b1f9org.highwire.dtl.DTLVardef@a9898b_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2023

Interplay between a bacterial pathogen and its host in rainbow trout isogenic lines with contrasted susceptibility to Cold Water Disease

Infectious diseases are a major constraint on aquaculture. Genetic lines with different susceptibilities to diseases are useful models to identify resistance mechanisms to pathogens and to improve prophylaxis. Bacterial cold-water disease (BCWD) caused by Flavobacterium psychrophilum represents a major threat for freshwater salmonid farming worldwide. A collection of rainbow trout (Oncorhynchus mykiss) isogenic lines was previously produced from a French domestic population. Here, we compared BCWD resistance phenotypes using a subset of isogenic lines chosen for their contrasted susceptibilities to F. psychrophilum. We applied individual monitoring to document the infection process, including time-course quantification of bacteremia and innate immune response. Strikingly, BCWD resistance was correlated with a lower bacterial growth rate in blood. Several immune genes were expressed at higher levels in resistant fish regardless of infection: the Type II arginase (arg2), a marker for M2 macrophages involved in anti-inflammatory responses and tissue repair, and two Toll-like receptors (tlr2/tlr7), responsible for pathogen detection and inflammatory responses. This study highlights the importance of innate and intrinsic defense mechanisms in determining the outcome of F. psychrophilum infections, and illustrates that non-lethal time-course blood sampling for individual monitoring of bacteremia is a powerful tool to resolve within-host pathogen behavior in bacterial fish diseases.

pathology↗

bioRxiv2023

Isogenic lines of rainbow trout (Oncorhynchus mykiss) as a tool to assess how growth and feeding behaviour are correlated to feed efficiency in fish

Accurately measuring individual feed intake is required to include feed efficiency (FE) as an objective in commercial breeding programs. Phenotyping individual feed intake through direct measurements remains complex in fish reared in groups. One way to overcome this challenge is to find proxies for estimating FE. This study aimed to investigate the correlations between fish FE and potential predictive criteria in rainbow trout Oncorhynchus mykiss. As predictive criteria, we considered the variations of body weight assessed as thermal growth coefficients (TGC) and the feeding behaviour assessed as the number of feed demands over a period and the proportion of the demands made before noon. Feed intake was assessed over three different periods in ten isogenic lines allowing a recording for each of the ten genotypes while keeping fish in groups. The protocol consisted of two successive feed deprivation and refeeding phases after initial basal growth periods. Correlations were then calculated between FE, measured either as feed conversion ratio (FCR) or residual feed intake (RFI), and the different indirect criteria. We found positive phenotypic correlations between FCR and RFI over the feed intake measurement periods (r [>=] 0.79, P < 0.001). Assessment of the relationship between FE traits (FCR and RFI) calculated over the three measurement periods and TGC revealed no significant association. We found significant positive correlations between RFI calculated from the first feed intake measurement period and feeding behaviour, assessed as the number of feed demands (r = 0.42-0.49, P [<=] 0.022). Nevertheless, such correlations were not established for the two other measurement periods following feed deprivation. While we demonstrated that the weight variations during feed deprivation are not a good proxy for FE (FCR or RFI) in rainbow trout, we also highlighted the interest in exploring more the relationships between FE and feeding behaviour in fish.

genetics↗

bioRxiv2022

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

Single nucleotide polymorphism (SNP) arrays, also named << SNP chips >>, enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2 kb to 10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50 kb to 100 kb which are usual distances between markers of the medium-density chip.

genomics↗

bioRxiv2020

Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing

Rainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY. Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenotypic sex of 20,210 XX-rainbow trout from a French farm at 10 and 15 months post-hatching. The masculinisation rate was 1.45%. We performed two genome-wide association studies (GWAS) using both medium-throughput genotyping (31,811 SNPs) and whole-genome sequencing (WGS, 8.7 million SNPs) on a subsample of 1,139 individuals classified as females, intersex or males. The genomic heritability of maleness ranged between 0.48 and 0.62 depending on the method and number of SNPs used for estimation. At the 31K SNPs level, we detected four QTLs on three chromosomes (Omy1, Omy12 and Omy20). Using WGS information, we narrowed down the positions of the two QTLs detected on Omy1 to 96 kb and 347 kb respectively, with the second QTL explaining up to 14% of the total genetic variance of maleness. Within this QTL, we detected three putative candidate genes, fgfa8, cyp17a1 and an uncharacterised protein (LOC110527930), which might be involved in spontaneous maleness of XX-female rainbow trout.

genomics↗