Temporal and region‐specific variations in genome‐wide inbreeding effects on female size and reproduction traits of rainbow trout

Abstract

Recent studies have shown that current levels of inbreeding, estimated by runs of homozygosity (ROH), are moderate to high in farmed rainbow trout lines. Based on ROH metrics, the aims of our study were to (i) quantify inbreeding effects on female size (postspawning body weight, fork length) and reproduction traits (spawning date, coelomic fluid weight, spawn weight, egg number, average egg weight) in rainbow trout, and (ii) identify both the genomic regions and inbreeding events affecting performance. We analysed the performance of 1346 females under linear animal models including random additive and dominance genetics effects, with fixed covariates accounting for inbreeding effects at different temporal and genomic scales. A significant effect of genome‐wide inbreeding ( F ) was only observed for spawning date and egg weight, with performance variations of +12.3% and −3.8%, respectively, for 0.1 unit increase in F level. At different local genomic scales, we observed highly variable inbreeding effects on the seven traits under study, ranging from increasing to decreasing trait values. As widely reported in the literature, the main scenario observed during this study was a negative impact of recent inbreeding. However, other scenarios such as positive effects of recent inbreeding or negative impacts of old inbreeding were also observed. Although partial dominance appeared to be the main hypothesis explaining inbreeding depression for all the traits studied, the overdominance hypothesis might also play a significant role in inbreeding depression affecting fecundity (egg number and mass) traits in rainbow trout. These findings suggest that region‐specific inbreeding can strongly impact performance without necessarily observing genome‐wide inbreeding effects. They shed light on the genetic architecture of inbreeding depression and its evolution along the genome over time. The use of region‐specific metrics may enable breeders to more accurately manage the trade‐off between genetic merit and the undesirable side effects associated with inbreeding.

Genomics applied to livestock and aquaculture breeding

“…Similarly, the first application of genomic selection and genome‐wide association studies for growth traits in rock bream ( Oplegnathus fasciatus ), a valued species for marine aquaculture in Asia, has been recently reported (Gong et al, 2021 ). Incorporation of genomic information can also be a useful approach to assess the levels of inbreeding, their effect on economically important traits and even the genomic regions affecting changes in performance of breeding populations, as it has been recently demonstrated for female size and reproduction traits in rainbow trout (Paul et al, 2021 ).…”

Aquaponics as a Promising Strategy to Mitigate Impacts of Climate Change on Rainbow Trout Culture

“…Loss of genetic variability influences the long-term survival of populations associated with reduced fitness and an eventual higher risk of extinction. For instance, in a small population of rainbow trout, in successive generations and without gene flow, the probability of mating with closely related individuals is very high, leading to inbreeding and specifically a decrease in the population structure [ 43 , 44 , 45 , 46 , 47 ]. The assessment of reproductive values in all generations showed that multi-leaf selection (with a low rate of inbreeding) has brought an average of 7% genetic gain per generation in the development of rainbow trout of market size [ 48 ].…”

“…is needed in the context of a circular economy. Aquaponics, in combination with selective breeding and thermal acclimation, are promising management strategies that may contribute to the development of a new form of rainbow trout farming [ 47 , 48 , 155 , 156 , 157 ]. Nevertheless, climate change remains a difficult obstacle for examining the genetic diversity of rainbow trout populations, a species sensitive to climate change.…”

Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

“…A first commercial medium-density Axiom ® Trout Genotyping array (hereafter termed 57 K chip) has then been developed ( Palti et al, 2015 ) and produced by Affymetrix (Thermofisher). Since then it has been largely used in population genetics studies ( Larson et al, 2018 ; D’Ambrosio et al, 2019 ; Paul et al, 2021 ), GWAS and GS accuracy works for various traits in farmed populations ( Gonzalez-Pena et al, 2016 ; Vallejo et al, 2017 ; Vallejo et al, 2019 ; Reis Neto et al, 2019 ; Rodríguez et al, 2019 ; Yoshida et al, 2019 ; Fraslin et al, 2019 ; Fraslin et al, 2020 ; Karami et al, 2020 ; D’Ambrosio et al, 2020 ; Blay et al, 2021a ; Blay et al, 2021b ). However, out of the 57,501 SNPs included in this chip, nearly 20,000 were found to be unusable because they were either duplicated due to the ancestral genome duplication or showing primer polymorphism in five French commercial or experimental lines ( D’Ambrosio et al, 2019 ).…”