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

Lagarde, H.; Lallias, D.; Patrice, P.; Prchal, M.; Francois, Y.; D'Ambrosio, J.; Segret, E.; Acin-Perez, A.; Cachelou, F.; Haffray, P.; Dehaullon, A.; Dupont-Nivet, M.; Phocas, F.

doi:10.1101/2022.11.14.516387

bioRxiv · 10.1101/2022.11.14.516387

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

Lagarde, H.·Lallias, D.·Patrice, P.·Prchal, M.·Francois, Y.·D'Ambrosio, J.·Segret, E.·Acin-Perez, A.·Cachelou, F.·Haffray, P.·Dehaullon, A.·Dupont-Nivet, M.·Phocas, F.

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Abstract

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.

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Lagarde, H., Lallias, D., Patrice, P., Prchal, M., Francois, Y., D'Ambrosio, J., Segret, E., Acin-Perez, A., Cachelou, F., Haffray, P., Dehaullon, A., Dupont-Nivet, M., Phocas, F.. 2022-11-16. Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits. https://doi.org/10.1101/2022.11.14.516387

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