Search

Background: Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, to determine the genetic architecture of these traits by the identification of quantitative trait loci (QTL), and to assess the expected efficiency of a pedigree-based selection (BLUP) or genomic selection for these traits. Results: A pedigreed population of 1343 trout were genotyped for 57,000 SNP markers and phenotyped for seven traits at 2 years of age: spawning date, female body weight before and after spawning, the spawn weight and the egg number of the spawn, the egg average weight and average diameter. Genetic parameters were estimated in multi-trait linear animal models. Heritability estimates were moderate, varying from 0.27 to 0.44. The female body weight was not genetically correlated to any of the reproduction traits. Spawn weight showed strong and favourable genetic correlation with the number of eggs in the spawn and individual egg size traits, but the egg number was uncorrelated to the egg size traits. The genome-wide association studies showed that all traits were very polygenic since less than 10% of the genetic variance was explained by the cumulative effects of the QTLs: for any trait, only 2 to 4 QTLs were detected that explained in-between 1 and 3% of the genetic variance. Genomic selection based on a reference population of only one thousand individuals related to candidates would improve the efficiency of BLUP selection from 16 to 37% depending on traits. Conclusions: Our genetic parameter estimates made unlikely the hypothesis that selection for growth could induce any indirect improvement for female reproduction traits. It is thus important to consider direct selection for spawn weight for improving egg production traits in rainbow trout breeding programs. Due to the low proportion of genetic variance explained by the few QTLs detected for each reproduction traits, marker assisted selection cannot be effective. However genomic selection would allow significant gains of accuracy compared to pedigree-based selection. [ABSTRACT FROM AUTHOR]

Sea bass is a major species in Mediterranean aquaculture, and is now being subject to selective breeding programmes for faster growth. In terrestrial species, it was demonstrated that fast growth may be linked to a correlated degradation of fitness traits. In this experiment, we evaluated 600 young sea bass from a factorial mating of 76 sires and 13 dams. The sires were from four genetic groups, wild (W), domesticated (D), and selected for growth (2 groups, M and P). The 600 offspring were submitted to two acute confinement stress challenges at 6 weeks intervals, and plasma cortisol at one hour post stress was measured. The same fish were also submitted to two swimming challenges at a 5 days interval, where the maximum sustained swimming speed ( U max ) of each fish was evaluated. Parentage was assessed by genotyping of 12 microsatellites. 554 fish had both valid parentage and phenotypes. Cortisol had a low repeatability (r = 0.30 between the two successive measurements) while repeatability was moderate for U max (r = 0.62). However, genetic correlations between successive measurements were very high (> 0.96) for both traits, indicating that successive measurements were related to the same trait. Heritability was moderate for mean post-stress cortisol (h 2 = 0.34 ± 0.09) and U max (h 2 = 0.48 ± 0.08). When U max was expressed in m.s − 1 , it was negatively correlated to cortisol (r A = − 0.48 ± 0.08) and weakly correlated to body weight (r A = 0.12 ± 0.16), but figures changed when it was expressed in Body Lengths.s − 1 (h 2 = 0.55 ± 0.08, r A = − 0.10 ± 0.19 with cortisol and r A = − 0.64 ± 0.07 with body weight, respectively). Cortisol was moderately negatively correlated with body weight (r A = − 0.36 ± 0.18). The four lines did not differ for cortisol or U max , but when U max was expressed in BL.s − 1 it tended to be lower in the two selected lines — which were also significantly larger. However, this is likely due to a phenotypic decrease of relative U max with increasing body size. We conclude that selection for growth and/or domestication should not impact maximum sustained swimming speed in the European sea bass, but may tend to favour animals with low cortisol responsiveness. These traits could be used to orientate functional capabilities other than productivity in sea bass. Statement of relevance We estimate heritability of cortisol stress response and (for the first time) in European sea bass, as well as their correlations with growth. We show moderate correlations, and no correlated response to selection for growth. We also provide methods to evaluate these traits on large number of fishes. This can be useful to monitor and design breeding programmes. [ABSTRACT FROM AUTHOR]

Hypoxia is one of the major threats to the aquaculture sector resulting in substantial economic losses to the fish farmers. Thus, tolerance to hypoxia is of high economic interest to be genetically improved by breeding programs. Rainbow trout (Oncorhynchus mykiss) is one of the most cultured salmonid species worldwide, with well-developed breeding programs. Still, studies of genetic potential to improve hypoxia tolerance in this species are rare. In the present study, 1320 individuals of rainbow trout were used for a genome-wide association study of acute hypoxia tolerance based on imputed high-density genotypes to explore the genetic architecture and related candidate genes affecting hypoxia response. Three significant (Omy31_1, Omy31_2, Omy20) and two putative (Omy15, Omy28) quantitative trait loci (QTLs) were detected, but each of them only explained between 0.2% and 0.8% of the genetic variance of acute hypoxia tolerance. However, heritability was estimated at a moderate value of 0.24–0.28, that suggests a solid potential to improve hypoxia tolerance in the studied rainbow trout population by genetic selection. Moreover, it was shown that genomic prediction for hypoxia tolerance would lead to a relative increase of ∼11% for genomic selection (GS) accuracy compared to the pedigree-based selection, considering a reference population of 1000 individuals. Finally, fifteen genes (ids, fmr1, arx, lonrf3, commd5, map4k4, smu1, b4galt1, re1, abca1, noa1, igfbp7, noxo1, bcl2a, mylk3) were proposed as potential functional candidates involved in hypoxia tolerance. Taking all proposed candidate genes (6 out of 15 genes) and high linkage disequilibrium (r 2) values within the main QTL (Omy31_1), we may hypothesize that the complex response to acute hypoxia in rainbow trout, i.e., the interplay between behavioural, morphological, and physiological responses, is primarily encoded by a supergene. However, further functional validation of their effects may help to specify the biological mechanisms triggering a response to acute hypoxia in rainbow trout. • First report of genetic architecture for acute hypoxia tolerance in rainbow trout. • Moderate heritability of acute hypoxia tolerance was observed. • Three significant and two putative QTLs were identified. • Fifteen genes were highlighted as potential functional candidates. • Six candidate genes on Omy31_1 might be encoded by a supergene. [ABSTRACT FROM AUTHOR]

Abstract: Application of DNA parentage assignment for commercial selection in aquaculture is still rare. An experiment was performed to quantify and to minimize maternal effects on growth in rainbow trout. Six hundred families were reared until 198 day post fertilization (dpf) according to two different procedures. In the first procedure (NORM), all families were pooled at eyed stage. In the second procedure (MIN), where maternal effects due to differences in egg size were expected to be minimal, the spawns were divided into sub-groups with similar mean egg weight at eyed stage. These sub-groups were then pooled when they achieved the same mean body length (147dpf). Genetic parameters were estimated for body weight, body length and condition factor at 198dpf, with 2964 fish assigned to their parents using microsatellites. Significant maternal effects were observed in the NORM group for body weight and body length (m²=0.08±0.03). The heritability of body weight was 0.16±0.07 in the NORM group and 0.36±0.06 in the MIN group, in which maternal effects were not significant. It is concluded that, when eggs of different females are mixed at eyed stage, maternal effects persist at least until 198dpf. The proposed procedure efficiently limits maternal effects, substantially increasing the heritability for growth, and therefore the expected selection response. [Copyright &y& Elsevier]