Biology subjects

Lagarde, H.

Publications and source records attributed to Lagarde, H..

3 recordsLinked to original sources

bioRxiv2023

Links between behaviour and resistances to acute hyperthermia and hypoxia using rainbow trout isogenic lines

In the context of adaptation to climate change, acute hyperthermia and hypoxia resistance are traits of growing interest in aquaculture. The feasibility of genetic improvement of these resistance traits through selection has been demonstrated in rainbow trout (Oncorhynchus mykiss). The present paper aims to test whether behaviour may be associated with acute hyperthermia and hypoxia resistance to better characterize these resistance phenotypes. For this, six rainbow trout isogenic lines were phenotyped for behaviour variables and for acute hyperthermia and hypoxia resistance, using different individuals for each phenotype. The behaviour variables of the fish were phenotyped using an individual test in a new environment. The experimental design used 150 fish phenotyped per isogenic line for each resistance trait and 18 fish per isogenic line for behavioural traits, distributed in triplicates. Relations between acute hyperthermia and hypoxia resistance phenotypes and behaviour phenotypes were tested at the level of isogenic lines. Significant differences in behaviour between isogenic lines were found, with some behaviour variables being highly associated with hypoxia resistance and moderately associated with acute hyperthermia resistance. Travelling distance, frequency of change between a risky and a safe zone of the tank and the percentage of time in movement in the behaviour test were strongly positively associated with acute hypoxia resistance. Travelling distance and frequency of change between a risky and a safe zone of the tank in the behaviour test were slightly negatively associated with acute hyperthermia resistance. This previously unstudied link between behaviour and resistance phenotypes also suggests that some behaviour variables could be used as predictors for acute hyperthermia and hypoxia resistance in fish. This result could lead to more ethical acute hyperthermia and hypoxia resistance phenotyping protocols, as the current protocols in use are classified as severe by French ethics committees.

animal behavior and cognition↗

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

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↗