Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes

BACKGROUND: The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations. METHODS: Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. RESULTS: Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. CONCLUSIONS: Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-021-00680-9

High Expression Levels of the Genes cyclin-A2 and glucocorticoid receptor Are Associated with High-Quality Embryos in Gilthead Sea Bream (Sparus aurata L.)

Identifying early egg-quality predictors is a major challenge in finfish hatcheries, and relevant research is now focused on the development of molecular markers. In our study, we examined whether fertilization rates and early morphological abnormalities in sea bream egg batches of high (HQ) and low quality (LQ) are associated with mRNA levels of cathepsin D, cathepsin Z, cyclin-A2, and glucocorticoid receptor. Additionally, we examined whether these early quality descriptors were associated with the development of skeletal abnormalities during the larval period. HQ egg batches were characterized by significantly higher rates of normal embryos (95.8 ± 2.3%) and lower rates of unfertilized (2.8 ± 1.0%) and abnormal eggs (1.3 ± 1.4%), compared to LQ (84.2 ± 0.8% normal embryos, 12.3 ± 12.3 unfertilized eggs, and 3.5 ± 1.4% abnormal eggs) (p < 0.05, Mann–Whitney U test). Relative expression of cyclin-A2 and glucocorticoid receptor was found to be significantly higher in HQ embryos compared to those of LQ (respectively, p < 0.01 and p < 0.05, Mann–Whitney U test). No statistically significant differences were observed in the mRNA transcripts of cathepsin D and cathepsin Z (p > 0.05, Mann–Whitney U test). Differences in the rate of skeletal abnormalities between the two quality groups of larvae were not significant (p > 0.05, G-test), indicating that cyclin-A2 and glucocorticoid receptor may serve as reliable molecular markers for early prediction of fish egg quality but not for later larval stages

Parentage assignment, estimates of heritability and genetic correlation for growth-related traits in meagre Argyrosomus regius

Meagre is a relatively new aquaculture species with great potential in large scale European aquaculture. The primary objective of the study was to describe, for the first time, parentage allocation and assign offspring to their parents for an industrial scale production system. A total of 800 meagre fish were sampled from two large cages in January and May 2016, both part of a commercial farm site in Valencia, Spain. All fish originated from the same spawning event obtained from a broodstock of 6 females and 13 males. However, due to differential growth during the juvenile stage the fish were graded into two groups, a group of larger juveniles that was transferred to one cage (batch 1) and a group of smaller juveniles that were transferred to the second cage (batch 2). Total length and weight was measured for all fish that were genotyped with a 10 microsatellite loci multiplex to infer parentage based on parental genotypes. Parentage assignment rate was high (87.5% for batch 1 and 95% for batch 2) and provided evidence that offspring belonged to 20 families. Half of the broodstock was identified as probable parents of the offspring (five females and seven males).Between the two sea-cages, a slight differential composition for the same families was encountered. The fifteen shared families that the offspring were assigned to, were analyzed for statistical significant differences concerning body weight and total body length, differences which were observed in 3 families for both batches. We estimated the heritability for body weight and total body length, as well as the genetic and phenotypic correlations for these two traits. Batch 1 showed higher heritability estimates than batch 2 with the genetic and phenotypic correlation estimates being almost the same for both batches. Certain parents contributed more offspring and exhibited dominance in spawning. Similarly, the growth related traits of body weight and total body length of the dominant parents correlate, putatively, with the statistical important differences that are observed in these three families.info:eu-repo/semantics/acceptedVersio

Microbiota Succession of Whole and Filleted European Sea Bass (<i>Dicentrarchus labrax</i>) during Storage under Aerobic and MAP Conditions via 16S rRNA Gene High-Throughput Sequencing Approach

In the present work, the profiles of bacterial communities of whole and filleted European sea bass (Dicentrarchus labrax), during several storage temperatures (0, 4, 8 and 12 °C) under aerobic and Modified Atmosphere Packaging (MAP) conditions, were examined via the 16S rRNA High-Throughput Sequencing (HTS) approach. Sensorial attributes were also assessed to determine products’ shelf-life. Results indicated that shelf-life was strongly dependent on handling, as well as on temperature and atmosphere conditions. HTS revealed the undisputed dominance of Pseudomonas from the very beginning and throughout storage period in the majority of treatments. However, a slightly different microbiota profile was recorded in MAP-stored fillets at the middle stages of storage, which mainly referred to the sporadic appearance of some bacteria (e.g., Carnobacterium, Shewanella, etc.) that followed the dominance of Pseudomonas. It is noticeable that a major difference was observed at the end of shelf-life of MAP-stored fillets at 12 °C, where the dominant microbiota was constituted by the genus Serratia, while the relative abundance of Pseudomonas and Brochothrix was more limited. Furthermore, at the same temperature under aerobic storage of both whole and filleted fish, Pseudomonas almost co-existed with Acinetobacter, while the presence of both Erwinia and Serratia in whole fish was noteworthy. Overall, the present study provides useful information regarding the storage fate and spoilage status of whole and filleted European sea bass, suggesting that different handling and storage conditions influence the shelf-life of sea bass by favoring or delaying the dominance of Specific Spoilage Organisms (SSOs), affecting in parallel to some extent the formation of their consortium that is responsible for products’ sensorial deterioration. Such findings enrich the current knowledge and should be used as a benchmark to develop specific strategies aiming to delay spoilage and thus increase the products’ added value