What determines growth potential and juvenile quality of farmed fish species?

Enhanced production of high quality and healthy fry is a key target for a successful and competitive expansion of the aquaculture industry. Although large quantities of fish larvae are produced, survival rates are often low or highly variable and growth potential is in most cases not fully exploited, indicating significant gaps in our knowledge concerning optimal nutritional and culture conditions. Understanding the mechanisms that control early development and muscle growth are critical for the identification of time windows in development that introduce growth variation, and improve the viability and quality of juveniles. This literature review of the current state of knowledge aims to provide a framework for a better understanding of fish skeletal muscle ontogeny, and its impact on larval and juvenile quality as broadly defined. It focuses on fundamental biological knowledge relevant to larval phenotype and quality and, in particular, on the factors affecting the development of skeletal muscle. It also discusses the available methodologies to assess growth and larvae/juvenile quality, identifies gaps in knowledge and suggests future research directions. The focus is primarily on the major farmed non-salmonid fish species in Europe that include gilthead sea bream, European sea bass, turbot, Atlantic cod, Senegalese sole and Atlantic halibut

Selective genotyping for QTL detection using sib pair analysis in outbred populations with hierarchical structures

A simulation study illustrates the effects of the inclusion of half-sib pairs as well as the effects of selective genotyping on the power of detection and the parameter estimates in a sib pair analysis of data from an outbred population. The power of QTL detection obtained from samples of sib pairs selected according to their within family variance or according to the mean within family variance within half sib family was compared and contrasted with the power obtained when only full sib pair analysis was used. There was an increase in power (4–16%) and decrease in the bias of parameter estimates with the use of half-sib information. These improvements in power and parameter estimates depended on the number of the half sib pairs (half sib family size). Almost the same power as that obtained using all the available sib pairs could be achieved by selecting only 50–60% the animals. The most effective method was to select both full and half sib pairs on the basis of high within full sib family variance for the trait in question. The QTL position estimates were in general slightly biased towards the center of the chromosome and the QTL variance estimates were biased upwards, there being quite large differences in bias depending on the selection method

Advances in european sea bass genomics and future perspectives

Only recently available sequenced and annotated teleost fish genomes were restricted to a few model species, none of which were for aquaculture. Application of Marker Assisted Selection for improved production traits had been largely restricted to the salmon industry and genetic and Quantitative Trait Loci (QTL) maps were available for only a few species. With the advent of Next Generatio Sequencing the landscape is rapidly changing and today the genomes of several aquaculture species have been sequenced. The European sea bass, Dicentrarchus labrax, is a good example of a 17 commercially important aquaculture species in Europe for which in the last decade a wealth of genomic resources, including a chromosomal scale genome assembly, physical and linkage maps as well as relevant QTL have been generated. The current challenge is to stimulate the uptake of the resources by the industry so that the full potential of this scientific endeavour can be exploited and produce benefits for producers and the public alike

A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep

BACKGROUND: The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change. RESULTS: We detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h(2) = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response. CONCLUSIONS: Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-021-00682-7

Phenotypic and genetic characterisation of dairy sheep production resilience to climate fluctuations

Small ruminant milk production is of major importance for the Greek livestock sector and is challenged by climate change affecting the Mediterranean region. Breeding for resilience to climate change is a possible mitigation strategy. The resilience of milk yield to weather fluctuation was studied in one of the most productive Greek sheep breed, the Chios breed. Data included 364,173 test-day milk records of 29,331 ewes raised in 91 flocks. These records were matched with weather data from the nearest meteorological stations to the farms. Reaction norm functions were fitted to random regression models for the statistical analysis of the joint data to derive novel resilience phenotypes reflecting milk production response to weather fluctuations. Substantial phenotypic variation was observed among individuals. Significant heritability was estimated for the resilience phenotypes (0.19). A downstream genome-wide association study was conducted on 664 individuals genotyped with the Ovine SNP50KBead Chip. One genome and two chromosome-wise significant SNP markers were identified, indicating candidate genomic regions located at chromosome five associated with animal resilience. Subsequent functional annotation of the significant SNP markers revealed closely located genes related to animal adaptation to climate biological processes. Examination of the genetic and phenotypic correlations of the novel trait with other production and functional traits and incorporation in future breeding goals constitute the next steps

A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L.

The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60–90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal

Phenotypic and genetic characterisation of dairy sheep production resilience to climate fluctuations

Small ruminant milk production is of major importance for the Greek livestock sector and is challenged by climate change affecting the Mediterranean region. Breeding for resilience to climate change is a possible mitigation strategy. The resilience of milk yield to weather fluctuation was studied in one of the most productive Greek sheep breed, the Chios breed. Data included 364,173 test-day milk records of 29,331 ewes raised in 91 flocks. These records were matched with weather data from the nearest meteorological stations to the farms. Reaction norm functions were fitted to random regression models for the statistical analysis of the joint data to derive novel resilience phenotypes reflecting milk production response to weather fluctuations. Substantial phenotypic variation was observed among individuals. Significant heritability was estimated for the resilience phenotypes (0.19). A downstream genome-wide association study was conducted on 664 individuals genotyped with the Ovine SNP50KBead Chip. One genome and two chromosome-wise significant SNP markers were identified, indicating candidate genomic regions located at chromosome five associated with animal resilience. Subsequent functional annotation of the significant SNP markers revealed closely located genes related to animal adaptation to climate biological processes. Examination of the genetic and phenotypic correlations of the novel trait with other production and functional traits and incorporation in future breeding goals constitute the next steps

Understanding the seasonality of performance resilience to climate volatility in Mediterranean dairy sheep

11 Pág. Departamento de ​Mejora Genética AnimalAs future climate challenges become increasingly evident, enhancing performance resilience of farm animals may contribute to mitigation against adverse weather and seasonal variation, and underpin livestock farming sustainability. In the present study, we develop novel seasonal resilience phenotypes reflecting milk production changes to fluctuating weather. We evaluate the impact of calendar season (autumn, winter and spring) on animal performance resilience by analysing 420,534 milk records of 36,908 milking ewes of the Chios breed together with relevant meteorological data from eastern Mediterranean. We reveal substantial seasonal effects on resilience and significant heritable trait variation (h2 = 0.03-0.17). Resilience to cold weather (10 °C) of animals that start producing milk in spring was under different genetic control compared to autumn and winter as exemplified by negative genetic correlations (- 0.09 to - 0.27). Animal resilience to hot weather (25 °C) was partially under the same genetic control with genetic correlations between seasons ranging from 0.43 to 0.86. We report both favourable and antagonistic associations between animal resilience and lifetime milk production, depending on calendar season and the desirable direction of genetic selection. Concluding, we emphasise on seasonal adaptation of animals to climate and the need to incorporate the novel seasonal traits in future selective breeding programmes.The work was mainly funded by iSAGE Horizon 2020 project: “Innovation for Sustainable Sheep and Goat Production in Europe” (679302; https://www.isage.eu/). Additional support was received by the UK Biotechnology and Biological Sciences Research Council ISP3 (BBS/E/D/30002275) and the Rural & Environment Science & Analytical Services (RESAS) Division of the Scottish Government.Peer reviewe