Genome-wide association study and genomic prediction of tolerance to acute hypoxia in rainbow trout

Prchal, Martin; d'Ambrosio, Jonathan; Lagarde, Henri; Lallias, Delphine; Patrice, Pierre; François, Yoannah; Poncet, Charles; Desgranges, Alexandre; Haffray, Pierrick; Dupont‐Nivet, Mathilde; Phocas, Florence

doi:10.1016/j.aquaculture.2022.739068

Cited by 9 publications

(7 citation statements)

References 133 publications

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“…Our lower estimate of heritability is associated with the inclusion of the maternal effect, explaining 6-7% of TLE phenotypic variance. A maternal effect of similar magnitude was also detected for acute hypoxia resistance at 270 dpf in rainbow trout [60]. Ignoring the random maternal effect, the pedigree- and genomic-based estimates of heritability were increased to 0.39 ± 0.06 and 0.35 ± 0.04, i.e.…”

Section: Discussionmentioning

confidence: 68%

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

Lagarde

Lallias

Patrice

et al. 2022

Preprint

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Background: Selective 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. Results: The heritability estimate of resistance to acute hyperthermia in juveniles was 0.29, 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. Conclusions: This 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.

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Section: Discussionmentioning

confidence: 68%

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

Lagarde

Lallias

Patrice

et al. 2022

Preprint

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“…A multi-trait genome-wide association study in Nile tilapia associated variations in proximity to this gene with fillet trait [ 50 ]. Interleukin 1 receptor accessory protein-like 2 ( IL1RAPL2 ), included in a genomic region that emerged in the comparison between nuclei A and B and present in the enriched gene list for cellular process (GO: 0009987), was suggested to be involved in the main QTL explaining 0.8% of variation for the acute hypoxia tolerance in a rainbow trout population [ 51 ]. The solute carrier family 4 member 8 ( SLC4A8 ), having a large impact variation in the comparison between nuclei A and B, encodes for an electroneutral Na + -driven Cl − /HCO 3 − exchanger whose expression in the gills seems to be reduced in salt water, as shown in Spotted seabass [ 52 ].…”

Section: Resultsmentioning

confidence: 99%

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei

Bertolini

Ribani

Capoccioni

et al. 2023

Genes

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The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.

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“…The correlations found between some behaviour variables and acute hyperthermia or hypoxia resistances at the level of the isogenic line possibly reveal genetic correlations between some behavioural variables and resistance phenotypes. Therefore, selection for resistance to acute hyperthermia or hypoxia stress as proposed by Perry et al (2005); Lagarde et al (2023a); Prchal et al (2023) could result in indirect selection on certain behavioural variables. This is not surprising as, in practice, selected fish over several generations are known to exhibit different behaviours, such as swimming, foraging, predator avoidance, social behaviour, personality, reproduction and cognitive learning, compared to the wild type (Pasquet 2019).…”

Section: Discussionmentioning

confidence: 99%

“…The resistance time or the temperature/O2 saturation at loss of equilibrium are considered as the resistance phenotypes (Beitinger et al 2000;Roze et al 2013). Previously, genetic determinism for acute hyperthermia and hypoxia resistances have been demonstrated in rainbow trout (Perry et al 2005;Lagarde et al 2023a;Prchal et al 2023). Especially, Lagarde et al (2023b) showed that some genotypes were more resistant to acute hyperthermia or hypoxia using rainbow trout isogenic lines but without exploring the physiological mechanisms underlying this observed genetic variability.…”

Section: Introductionmentioning

confidence: 99%

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

Lagarde,

Lallias,

Phocas

et al. 2023

Preprint

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Acute hyperthermia and hypoxia resistances are traits of growing interest in aquaculture in the context of adaptation to climate change. The feasibility of genetic improvement of these traits through selection was demonstrated in rainbow trout (Oncorhynchus mykiss) and other fish species. It is now important to understand what makes a genotype resistant by identifying the mechanisms underlying these resistances, which are still under debate. In the present study, we investigated links between resistances to acute hyperthermia and hypoxia and some behaviour variables measured in moderately stressful conditions. For this purpose, we used rainbow trout isogenic lines, previously phenotyped for acute hyperthermia and hypoxia resistances. Behaviour of fish was phenotyped using an individual test as well as a group test, respectively response to a novel environment and evaluation of shoaling combined with response to a moderate thermal challenge. The use of isogenic lines allowed to relate resistance to acute hyperthermia with behaviour phenotypes. There were significant differences in behaviour between isogenic lines. Some behaviour variables were found to be highly correlated with acute hyperthermia and hypoxia resistances. Isogenic lines with a higher activity level were found to be more sensitive to acute hyperthermia and more resistant to acute hypoxia than lines with a lower activity level. This encouraging link between behaviour and resistance phenotypes also suggest that some behaviour variables could be used as predictors for acute hyperthermia and hypoxia resistances in fish, leading to more ethical phenotyping methods than classical ones.

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Genome-wide association study and genomic prediction of tolerance to acute hypoxia in rainbow trout

Cited by 9 publications

References 133 publications

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

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

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei

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

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