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

Abstract

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.

Genomic characterization of dryland adaptation in endangered Anxi cattle in China

“…ENOPH1 is a recently discovered enzyme in the methionine salvage pathway (Wang et al., 2005) that plays a critical role in modulating stress responses and contributing to cellular metabolic processes (Barth et al., 2014; Zhuang et al., 2019). The PDHX gene is a component of the pyruvate dehydrogenase complex and participates in both ATP synthesis and catabolic processes (Lagarde et al., 2023; Li et al., 2021). The SLC16A7 gene encodes a proton–monocarboxylate cotransporter that plays a role in transporting short‐chain fatty acids, ketone bodies, and lactic acid (Zhao et al., 2001).…”

Genome-wide detection of positive and balancing selection signatures shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

“…Maintaining genetic diversity in regions related to the immune system may be essential to resilience against various pathogens. In addition, this region of chromosome 13 has been recently detected as a significant QTL playing a role on resistance to temperature (Lagarde et al, 2022).…”

“…Thus, genotype data must be phased before their calculation. We used FImpute3 (Sargolzaei et al, 2014) to phase the genotypes of the study females, considering all parents (including our study females) and offspring genotyped in LB, LC, and SY populations for different purposes (see respectively Prchal et al, 2022, Lagarde et al, 2022 and Paul et al, 2022). All parents (except 8 SY sires) were genotyped with the HD chip (Bernard et al, 2022), while offsprings (and 8 SY sires) were genotyped with a 57K chip only (Palti et al, 2015).…”