Genomic dissection of maternal, additive and non-additive genetic effects for growth and carcass traits in Nile tilapia

International audienceAbstractBackgroundThe availability of both pedigree and genomic sources of information for animal breeding and genetics has created new challenges in understanding how they can be best used and interpreted. This study estimated genetic variance components based on genomic information and compared these to the variance components estimated from pedigree alone in a population generated to estimate non-additive genetic variance. Furthermore, the study examined the impact of the assumptions of Hardy–Weinberg equilibrium (HWE) on estimates of genetic variance components. For the first time, the magnitude of inbreeding depression for important commercial traits in Nile tilapia was estimated by using genomic data.ResultsThe study estimated the non-additive genetic variance in a Nile tilapia population of full-sib families and, when present, it was almost entirely represented by additive-by-additive epistatic variance, although in pedigree studies this non-additive variance is commonly assumed to arise from dominance. For body depth (BD) and body weight at harvest (BWH), the proportion of additive-by-additive epistatic to phenotypic variance was estimated to be 0.15 and 0.17 using genomic data (P < 0.05). In addition, with genomic data, the maternal variance (P < 0.05) for BD, BWH, body length (BL) and fillet weight (FW) explained approximately 10% of the phenotypic variances, which was comparable to pedigree-based estimates. The study also showed the detrimental effects of inbreeding on commercial traits of tilapia, which was estimated to reduce trait values by 1.1, 0.9, 0.4 and 0.3% per 1% increase in the individual homozygosity for FW, BWH, BD and BL, respectively. The presence of inbreeding depression but lack of dominance variance was consistent with an infinitesimal dominance model for the traits.ConclusionsThe benefit of including non-additive genetic effects for genetic evaluations in tilapia breeding schemes is not evident from these findings, but the observed inbreeding depression points to a role for reciprocal recurrent selection. Commercially, this conclusion will depend on the scheme’s operational costs and resources. The creation of maternal lines in Tilapia breeding schemes may be a possibility if the variation associated with maternal effects is heritable

Validation of reference genes for quantitative RT-qPCR studies of gene expression in Atlantic cod (Gadus morhua l.) during temperature stress

<p>Abstract</p> <p>Background</p> <p>One important physiological response to environmental stress in animals is change in gene expression. To obtain reliable data from gene expression studies using RT-qPCR it is important to evaluate a set of possible reference genes as normalizers for expression. The expression of these candidate genes should be analyzed in the relevant tissues during normal and stressed situations. To find suitable reference genes it was crucial that the genes were stably expressed also during a situation of physiological stress. For poikilotermic animals like cod, changes in temperature are normal, but if the changes are faster than physiological compensation, the animals respond with typical stress responses. It has previously been shown that Atlantic cod show stress responses when elevation of water temperature is faster than 1 degree/day, for this reason we chose hyperthermia as stress agent for this experiment.</p> <p>Findings</p> <p>We here describe the expression of eight candidate reference genes from Atlantic cod (<it>Gadus morhua l</it>.) and their stability during thermal stress (temperature elevation of one degree C/day for 5 days). The genes investigated were: Eukaryotic elongation factor 1 alpha, <it>ef1a</it>; 18s ribosomal RNA; <it>18s</it>, Ubiquitin conjugate protein; <it>ubiq</it>, cytoskeletal beta-actin; <it>actb</it>, major histcompatibility complex I; MHC-I light chain, beta-2 -microglobulin; <it>b2m</it>, cytoskeletal alpha-tubulin; <it>tba1c</it>, acidic ribosomal phosphoprotein; <it>rplp1</it>, glucose-6-phosphate dehydrogenase; <it>g6pd</it>. Their expression were analyzed in 6 tissues (liver, head kidney, intestine, spleen, heart and gills) from cods exposed to elevated temperature and compared to a control group. Although there were variations between tissues with respect to reference gene stability, four transcripts were more consistent than the others: <it>ubiq</it>, <it>ef1a</it>, <it>18s </it>and <it>rplp1</it>. We therefore used these to analyze the expression of stress related genes (heat shock proteins) induced during hyperthermia. We found that both transcripts were significantly upregulated in several tissues in fish exposed to increased temperature.</p> <p>Conclusion</p> <p>This is the first study comparing reference genes for RT-qPCR analyses of expression during hyperthermia in Atlantic cod. <it>ef1a, 18s, rplp1 </it>and <it>ubiq </it>transcripts were found to be well suited as reference genes during these experimental conditions.</p

Selection for improved stress tolerance in rainbow trout (Oncorhynchus mykiss) leads to reduced feed waste.

The magnitude of the cortisol response to a standardised stressor is a heritable trait in salmonid fishes, and selection for stress responsiveness induces differences in both behaviour and neuroendocrine function. For instance, in laboratory studies, fish with a high cortisol response show a greater propensity for stress induced anorexia. Some authors have, however, commented that controlled studies encompassing relatively small groups of fish hold little or no relevance to practical aquaculture. This notion may be flawed, since understanding the mechanisms behind the behaviour of individuals is a proviso to predict behaviour in groups even with the caveat that some behaviors may be modified by group size. As an example, optimal feeding regimes should be easier to predict in a population consisting of individuals whose appetite is relatively less affected by external stressors. In a fluctuating and potentially stressful environment, such a population should also generate less feed waste, if kept on fixed rations. In the present experiment, we tested this hypothesis by monitoring feed waste and feed onversion efficiency in lines of rainbow trout selected for a low (LR) or high (HR) cortisol response to stress. The study was carried out after fish had been transported between rearing sites in the United Kingdom and Norway. There was significantly more feed waste from rearing units containing HR fish, and these fish also showed lower feed efficiency (growth per unit feed consumed). The difference in feed waste became more apparent with increasing time after transport, as rations increased. Simultaneously, size was more variable and growth was slower in HR rearing units. These results suggest that there are several potential benefits of selection for low stress responsiveness in aquaculture