Fisheries and aquaculture
Assessing the health status of farmed mussels (Mytilus galloprovincialis) through histological, microbiological and biomarker analyses
Autori: Matozzo V, Ercolini C, Serracca L, Battistini R, Rossini I, Granato G, Quaglieri E, Perolo A, Finos L, Arcangeli G, Bertotto D, Radaelli G, Chollet B, Arzul I, Quaglio F
Riferimenti: Journal of Invertebrate Pathology (2018) 153, pp. 165-179
Summary: The Gulf of La Spezia (northern Tyrrhenian Sea, Italy) is a commercially important area both as a shipping port and for mussel farming. Recently, there has been increased concern over environmental disturbances caused by anthropogenic activities such as ship traffic and dredging and the effects they have on the health of farmed mussels. This paper reports the results of microbiological and histological analyses, as well as of measurement of several biomarkers which were performed to assess the health status of mussels (Mytilus galloprovincialis) from four rearing sites in the Gulf of La Spezia. Mussels were collected between October 2015 and September 2016 and histological analyses (including gonadal maturation stage), as well as the presence of pathogenic bacteria (Vibrio splendidus clade, V. aestuarianus and V. harveyi), viruses (Herpes virus and ostreid Herpes virus 1) and protozoa (Marteilia spp., in the summer season only) were carried out on a monthly basis. Conversely, biomarker responses in haemocyte/haemolymph (total haemocyte count, haemocyte diameter and volume, lysozyme and lactate dehydrogenase activities in cell-free haemolymph, and micronuclei frequency) and in gills and digestive gland (cortisol-like steroids and lipid peroxidation levels), were evaluated bimonthly. Microbiological data indicated that mussels contain a reservoir of potentially pathogenic bacteria, viruses and protozoa that in certain environmental conditions may cause a weakening of the immune system of animals leading to mortality episodes. The percentage of parasites detected in the mussels was generally low (9.6% for Steinhausia mytilovum, that is 17 samples out of 177 examined females; 3.4% for Proctoeces maculatus; 0.9% for Mytilicola intestinalis and 2% for ciliated protozoa), while symbiont loads were higher (31% for Eugymnanthea inquilina and Urastoma cyprinae). Interestingly, a previously undescribed haplosporidian was detected in a single mussel sample (0.2%) and was confirmed by in situ hybridization. Cells morphologically similar to Perkinsus sp. trophozoites were observed in 0.7% of the mussels analysed; however, infection with Perkinsus spp. could neither be confirmed by ISH nor by PCR. Different pathological aspects, such as host defence responses and regressive/progressive changes were detected in the gills, digestive glands, gonads and mantle. Only one single case of disseminated neoplasia (0.2%) was observed. As for the biomarker evaluation, the MANOVA analysis revealed the statistically significant effect that the variable “sampling site” had on the biological parameter measured, thus suggesting that the multibiomarker approach was able to differentiate the rearing sites.
Link: https://www.sciencedirect.com/science/article/pii/S0022201117304111?via%3Dihub
A microarray-based analysis of oocyte quality in the European clam Ruditapes decussatus
Autori: de Sousa JT, Milan M, Pauletto M, Bargelloni L, Joaquim S, Matias D, Matias AM, Quillien V, Leitão A, Huvet A.
Riferimenti: Aquaculture 446 (2015) 17–24.
Summary: A microarray-based analysis was performed with the objective of describing genomic features of oocytes and looking for potential markers of oocyte quality in the economically important European clam, Ruditapes decussatus. Oocytes of 25 females from Ria de Aveiro, western coast of Portugal (40°42′N; 08°40′W) were selected for this study and oocyte quality was estimated by success of D-larval rate under controlled conditions, which appeared to vary from 0 to 95%. By genome-wide expression profiling with a DNA microarray, 526 probes appeared differentially expressed between two groups representing the largest and smallest value of D larval rates, named good (represented by a mean D-larval yield of 57 ± 22%) and poor (9 ± 5%) quality oocytes. Enrichment analysis showed “lysosome” (dre04142) as the single pathway represented in the enriched KEGG pathway terms, with 8 genes coding for putative cathepsins. Furthermore, differentially expressed genes involved in oocyte protection (DnaJ (Hsp40), Hsp70, cyclophilin B, PDI), maturation (Cam-PDE1C, PRDM9, G protein), sperm–egg interaction (PDI, G protein) and apoptosis (TNF) were also identified. From these, the apoptosis pathway was supposed to assume an important role in oocyte quality as the mRNA level of caspase 8 appeared also negatively correlated with the D-larval yield. Finally, a G-protein transcript was identified as more abundant in poor quality oocytes, which underlines the importance of release prophase I block and meiotic maturation in the oocytes of this species. This study provided new highly valuable information on genes specifically expressed by mature oocytes of R. decussatus, for further understanding of the mechanisms of early development in this species.
Link: https://www.sciencedirect.com/science/article/pii/S0044848615002227
Transcriptomic profiling of male European eel (Anguilla anguilla) livers at sexual maturity
Autori: Churcher AM, Pujolar JM, Milan M, Huertas M, Hubbard PC, Bargelloni L, Patarnello T, Marino IA, Zane L, Canário AV
Riferimenti: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics. 2015 Dec;16:28-35. doi: 10.1016/j.cbd.2015.07.002. Epub 2015 Jul 23.
Summary: The European eel Anguilla anguilla has a complex life cycle that includes freshwater, seawater and morphologically distinct stages as well as two extreme long distance migrations. Eels do not feed as they migrate across the Atlantic to the Sargasso Sea but nevertheless reach sexual maturity before spawning. It is not yet clear how existing energy stores are used to reach the appropriate developmental state for reproduction. Since the liver is involved in energy metabolism, protein biosynthesis and endocrine regulation it is expected to play a key role in the regulation of reproductive development. We therefore used microarrays to identify genes that may be involved in this process. Using this approach, we identified 231 genes that were expressed at higher and 111 genes that were expressed at lower levels in sexually mature compared with immature males. The up-regulated set includes genes involved in lipid metabolism, fatty acid synthesis and transport, mitochondrial function, steroid transport and bile acid metabolism. Several genes with putative enzyme functions were also expressed at higher levels at sexual maturity while genes involved in immune system processes and protein biosynthesis tended to be down-regulated at this stage. By using a high-throughput approach, we have identified a subset of genes that may be linked with the mobilization of energy stores for sexual maturation and migration. These results contribute to an improved understanding of eel reproductive biology and provide insight into the role of the liver in other teleosts with a long distance spawning migrations.
Link: https://www.sciencedirect.com/science/article/pii/S1744117X15000507?via%3Dihub
Transcriptomic features of Pecten maximus oocyte quality and maturation.
Autori: Pauletto M, Milan M, Huvet A, Corporeau C, Suquet M, Planas JV, Moreira R, Figueras A, Novoa B, Patarnello T, Bargelloni L
Riferimenti: Plos One. March 2 2017: DOI:10.1371/journal.pone.0172805.
Summary: The king scallop Pecten maximus is a high valuable species of great interest in Europe for both fishery and aquaculture. Notably, there has been an increased investment to produce seed for enhancement programmes of wild scallop populations. However, hatchery production is a relatively new industry and it is still underdeveloped. Major hurdles are spawning control and gamete quality. In the present study, a total of 14 scallops were sampled in the bay of Brest (Brittany, France) to compare transcriptomic profiles of mature oocytes collected by spawning induction or by stripping. To reach such a goal, a microarray analysis was performed by using a custom 8x60K oligonucleotide microarray representing 45,488 unique scallop contigs. First we identified genes that were differentially expressed depending on oocyte quality, estimated as the potential to produce D-larvae. Secondly, we investigated the transcriptional features of both stripped and spawned oocytes. Genes coding for proteins involved in cytoskeletal dynamics, serine/threonine kinases signalling pathway, mRNA processing, response to DNA damage, apoptosis and cell-cycle appeared to be of crucial importance for both oocyte maturation and developmental competence. This study allowed us to dramatically increase the knowledge about transcriptional features of oocyte quality and maturation, as well as to propose for the first time putative molecular markers to solve a major bottleneck in scallop aquaculture.
A microarray study of carpet-shell clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression differences in gills and digestive gland
Autori: Saavedra C, Milan M, Leite RB, Cordero D, Patarnello T, Cancela L, Bargelloni L
Riferimenti: Frontiers in Physiology | doi: 10.3389/fphys.2017.00943.
Summary: Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG) were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC), i.e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/insulin-like growth factor signaling pathway (IIS), enzymes of four additional signaling pathways (Raf/Ras/Mapk, Jnk, TOR, and Hippo), and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in the microarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO) annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO term enrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others, some genes related to the IIS, such as the ParaHox gene Xlox, CCAR and the CCN family of secreted proteins, in the regulation of growth in bivalves.
Link: https://www.frontiersin.org/articles/10.3389/fphys.2017.00943/full#h1
Genetic variability of the striped venus Chamelea gallina in the northern Adriatic Sea.
Autori: Papetti C, Schiavon L, Milan M, Lucassen M, Caccavo AJ, Paterno M, Boscari E, Marino IAM, Congiu L, Zane L.
Riferimenti: Fisheries research Volume 201, May 2018, Pages 68-78.
Summary: Chamelea gallina is a valuable commercial species in the Mediterranean Sea. The strong fishing pressure on C. gallina in the northern and central Adriatic Sea has paralleled a clear-cut decrease in clam population density and the occurrence of several irregular mortality events. Despite the commercial interest in this species, nothing is known about its genetic sub-structuring at the geographic and/or temporal scale, nor its levels of genetic variability. Analyzing microsatellite genotypes for samples collected in the Adriatic Sea, we detected large geographic genetic homogeneity with gene flow guided by broad scale circulation in the north-south direction. Our results also indicate weak genetic differentiation among size classes at the local and temporal scale. These small genetic differences might be determined by variability of local circulation and reproductive success, partial overlapping generations and high larval mortality rates as suggested by our estimates of the effective number of breeders. In fact, global effective population size estimates over multiple generations are medium-high, but a low number of breeders are responsible for the small clams size class recruitment. Notwithstanding, it was not possible to detect signatures of bottleneck. Future efforts in fishery management should aim to maintain genetic diversity – essential to the long-term sustainability of the resource – and limit effective population size fluctuations while considering the need to improve water quality to avoid mass mortality events.
Link: https://www.sciencedirect.com/science/article/pii/S0165783618300134
Bivalve transcriptomics reveal pathogen sequences and a powerful immune response of the Mediterranean mussel (Mytilus galloprovincialis).
Autori: Moreira R, Balseiro P, Forn-Cunì G, Milan M, Bargelloni L, Novoa B, Figueras A
Riferimenti: Marine Biology, April 2018, 165:61.
Summary: Bivalves have colonized the interface between land and sea for the last 500 million years. Although bivalves lack an adaptive immune system, they are extraordinarily well adapted to adverse environmental conditions. Bivalves are valuable aquaculture resources worldwide and are used as sentinels for monitoring pollution. In this work, the immune transcriptomes of mussels (Mytilus galloprovincialis and edulis) and clam (Ruditapes decussatus) were sequenced. For comparative purposes, an already published transcriptome dataset of Ruditapes philippinarum was also included in the analyses. The 454 pyrosequencing of stimulated hemocytes resulted in more than 400,000 reads for each transcriptome. The percentage of annotated sequences ranges from 50% for mussels to 30–40% for clams. Considering the 28,061 non-redundant sequences from the four transcriptomes, the four species share 785 genes. Moreover, sequences related to different putative pathogens were found in the four bivalves. A high number of bivalve herpesvirus ORFs were found, which confirms the value of NGSs as tools to detect and quantify pathogen RNA. Based on an examination of the immune-enriched transcriptomes of these four species, we can conclude that bivalves present an immune system that differs from its conventional characterization as a simple innate immune response against invading pathogens. Enrichment analyses showed that species in the Mytilus genus, especially M. galloprovincialis, possesses a significantly higher number of sequences related to immune processes and killing molecules than species in the Ruditapes genus. This could be related to the broader ecological niche occupied by mussels and the scarcity of reported mussel mass mortalities compared to the high number of mass mortalities reported for clams.
Link: https://link.springer.com/article/10.1007/s00227-018-3308-0
Proteomic-based comparison between populations of the Great Scallop, Pecten maximus
Autori: Artigaud S, Lavaud R, Thébault J, Jean F, Strand O, Strohmeier T, Milan M, Pichereau V.
Riferimenti: Journal of Proteomics. 2014 Apr 3. pii: S1874-3919(14)00148-1. doi: 10.1016/j.jprot.2014.03.026.
Summary: Comparing populations residing in contrasting environments is an efficient way to decipher how organisms modulate their physiology. Here we present the proteomic signatures of two populations in a non-model marine species, the great scallop Pecten maximus, living in the northern (Hordaland, Norway) and in the center (Brest, France) of this species' latitudinal distribution range. The results showed 38 protein spots significantly differentially accumulated in mantle tissues between the two populations. We could unambiguously identify 11 of the protein spots by Maldi TOF–TOF mass spectrometry. Eight proteins corresponded to different isoforms of actin, two were identified as filamin, another protein related to the cytoskeleton structure, and one was the protease elastase. Our results suggest that scallops from the two populations assayed may modulate their cytoskeleton structures through regulation of intracellular pools of actin and filamin isoforms to better adapt to their environment.
Link: https://www.sciencedirect.com/science/article/pii/S1874391914001481?via%3Dihub
Insights into Molecular Features of Venerupis decussata Oocytes: A Microarray-Based Study
Autori: Pauletto M, Milan M, de Sousa JT, Huvet A, Joaquim S, Matias D, Leitão A, Patarnello T, Bargelloni L
Riferimenti: PLoS One. 2014 Dec 3;9(12):e113925. doi: 10.1371/journal.pone.0113925. eCollection 2014.
Summary: The production of Venerupis decussata relies on wild seed collection, which has been recently compromised due to recruitment failure and severe mortalities. To address this issue and provide an alternative source of seed, artificial spawning and larval rearing programs were developed. However, hatchery-based seed production is a relatively new industry and it is still underdeveloped. A major hurdle in the European clam seed production is the control of spawning and reproduction, which is further hindered by the impossibility of obtaining fertile gametes by gonadal “stripping”, as meiosis re-initiation is constrained to a maturation process along the genital ducts. In the present study, oocytes were collected from 15 females and microarray analyses was performed to investigate gene expression profiles characterizing released and stripped ovarian oocytes. A total of 198 differentially expressed transcripts between stripped and spawned oocytes were detected. Functional analysis carried out on these transcripts highlighted the importance of a few biological processes, which are most probably implicated in the control of oocyte competence. Significant differences were observed for transcripts encoding proteins involved in meiosis progression (e.g. dual specificity phosphatase CDC25), WNT signalling (e.g. frizzled class receptor 8, wingless-type MMTV integration site family member 4), steroid synthesis (e.g. progestin and adipoQ receptor family member 3, cytochrome P450-C17), mRNA processing (e.g. zinc finger protein XlCOF28), calcium regulation (e.g. regucalcin, calmodulin) and ceramide metabolism (ceramidase B, sphingomyelinase). This study provides new information on transcriptional profiles putatively associated with ovarian egg infertility, and suggests potential mechanisms regulating early oocyte development in clams. Genes which were differentially expressed between stripped and spawned oocytes might have a pivotal role during maturation process in the gonadal duct and could be interesting targets for further functional studies aiming to make ovarian oocytes fertilizable.
Link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113925
A Microarray-Based Analysis of Gametogenesis in Two Portuguese Populations of the European Clam Ruditapes decussatus
Autori: de Sousa JT, Milan M, Bargelloni L, Pauletto M, Matias D, Joaquim S, Matias AM, Quillien V, Leitão A, Huvet A.
Riferimenti: PLoS One. 2014 Mar 18;9(3):e92202. doi: 10.1371/journal.pone.0092202. eCollection 2014.
Summary: The European clam, Ruditapes decussatus is a species with a high commercial importance in Portugal and other Southern European countries. Its production is almost exclusively based on natural recruitment, which is subject to high annual fluctuations. Increased knowledge of the natural reproductive cycle of R. decussatus and its molecular mechanisms would be particularly important in providing new highly valuable genomic information for better understanding the regulation of reproduction in this economically important aquaculture species. In this study, the transcriptomic bases of R. decussatus reproduction have been analysed using a custom oligonucleotide microarray representing 51,678 assembled contigs. Microarray analyses were performed in four gonadal maturation stages from two different Portuguese wild populations, characterized by different responses to spawning induction when used as progenitors in hatchery. A comparison between the two populations elucidated a specific pathway involved in the recognition signals and binding between the oocyte and components of the sperm plasma membrane. We suggest that this pathway can explain part of the differences in terms of spawning induction success between the two populations. In addition, sexes and reproductive stages were compared and a correlation between mRNA levels and gonadal area was investigated. The lists of differentially expressed genes revealed that sex explains most of the variance in gonadal gene expression. Additionally, genes like Foxl2, vitellogenin, condensing 2, mitotic apparatus protein p62, Cep57, sperm associated antigens 6, 16 and 17, motile sperm domain containing protein 2, sperm surface protein Sp17, sperm flagellar proteins 1 and 2 and dpy-30, were identified as being correlated with the gonad area and therefore supposedly with the number and/or the size of the gametes produced.
Link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092202
Understanding the mechanisms involved in the high sensitivity of Pecten maximus larvae to aeration
Autori: Pauletto M, Di Camillo B, Miner P, Huvet A, Quillien V,Milan M, Ferraresso S, Pegolo S, Patarnello T, Bargelloni L.
Riferimenti: Aquaculture 497 (2018) 189–199.
Summary: Among reared bivalves, some “novel species”, such as the great scallop, Pecten maximus, have experienced more difficulty with routine reproduction due to their high sensitivity to biological, chemical, and physical stress during stages of early development. Working with high larval densities requires the use of aeration systems to provide optimal larval suspension and feed distribution. The high susceptibility of the great scallop to aeration in small-volume systems may impose an important limitation in hatchery-based practices. The present study aimed to investigate the processes impacted by aeration in P. maximus veliger larvae exposed to continuous aeration in small-volume tanks (10 L). Aeration appeared as major stressor that was responsible for early mortality among exposed animals (at 96 h after aeration started, haa) when exposure started 13 days after fertilization. Exposed larvae and controls were collected at 12, 24 and 72 haa, and a total of 18 cDNA libraries, each representing a pool of approximately 7,500 larvae, were sequenced, obtaining 358,817,016 raw reads. RNA-seq data were first used to build a de novo transcriptome assembly, and differential transcript abundance was assessed in exposed and control groups; thus, the molecular mechanisms involved in high sensitivity to aeration were deciphered. More than 2,000 transcripts were differentially expressed between exposed and control larvae across the entire time series (logFC > 1, FDR < 5%). Functional analysis revealed that transcriptional changes in larvae exposed to aeration mainly involved the genes that regulate digestive activity and energy metabolism, immune defense, inflammation, apoptosis, larval growth, and development. The results of this study demonstrate that, overall, aeration affects the feeding capacity and energy metabolism of larvae, with expected consequences on the animal's fitness, including its swimming efficiency. Aeration also triggered immune responses and apoptosis, which then increased through opportunistic infections. Notably, infections may be a consequence of a bacterial bloom triggered by the first mortality events that occurred in the culture. This study provides insights into the interactions between environmental variables and great scallop larvae physiology, and the results may contribute to the development of strategies for improving larval rearing practices and ensuring long-term sustainability of P. maximus aquaculture.
Link: https://www.sciencedirect.com/science/article/pii/S0044848617324869
Gene expression profile analysis of Manila clam (Ruditapes philippinarum) hemocytes after a Vibrio alginolyticus challenge using an immune-enriched oligo-microarray
Autori: Moreira R, Milan M, Balseiro P, Romero A, Babbucci M, Figueras A, Bargelloni L, Novoa B.
Riferimenti: BMC Genomics 2014, 15(1):267. doi: 10.1186/1471-2164-15-267.
Summary: Background The Manila clam (Ruditapes philippinarum) is a cultured bivalve with worldwide commercial importance, and diseases cause high economic losses. For this reason, interest in the immune genes in this species has recently increased. The present work describes the construction of the first R. philippinarum microarray containing immune-related hemocyte sequences and its application to study the gene transcription profiles of hemocytes from clams infected with V. alginolyticus through a time course.
Results The complete set of sequences from R. philippinarum available in the public databases and the hemocyte sequences enriched in immune transcripts were assembled successfully. A total of 12,156 annotated sequences were used to construct the 8 ×15 k oligo-microarray. The microarray experiments yielded a total of 579 differentially expressed transcripts. Using the gene expression results, the associated Gene Ontology terms and the enrichment analysis, we found different response mechanisms throughout the experiment. Genes related to signaling, transcription and apoptosis, such as IL-17D, NF-κB or calmodulin, were typically expressed as early as 3 hours post-challenge (hpc), while characteristic immune genes, such as PGRPs, FREPs and defense proteins appeared later at 8 hpc. This immune-triggering response could have affected a high number of processes that seemed to be activated 24 hpc to overcome the Vibrio challenge, including the expression of many cytoskeleton molecules, which is indicative of the active movement of hemocytes. In fact functional studies showed an increment in apoptosis, necrosis or cell migration after the infection. Finally, 72 hpc, activity returned to normal levels, and more than 50% of the genes were downregulated in a negative feedback of all of the previously active processes.
Conclusions Using a new version of the R. philippinarum oligo-microarray, a putative timing for the response against a Vibrio infection was established. The key point to overcome the challenge seemed to be 8 hours after the challenge, when we detected immune functions that could lead to the destruction of the pathogen and the activation of a wide variety of processes related to homeostasis and defense. These results highlight the importance of a fast response in bivalves and the effectiveness of their innate immune system.
Link: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-267
Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature
Autori: Alba N Mininni, Massimo Milan, Serena Ferraresso, Tommaso Petochi, Patrizia Di Marco, Giovanna Marino, Silvia Livi, Chiara Romualdi, Luca Bargelloni & Tomaso Patarnello
Riferimenti: BMC Genomics. 2014 Sep 6;15:765. doi: 10.1186/1471-2164-15-765
Summary: Background Water temperature greatly influences the physiology and behaviour of teleost fish as other aquatic organisms. While fish are able to cope with seasonal temperature variations, thermal excursions outside their normal thermal range might exceed their ability to respond leading to severe diseases and death. Profound differences exist in thermal tolerance across fish species living in the same geographical areas, promoting for investigating the molecular mechanisms involved in susceptibility and resistance to low and high temperatures toward a better understanding of adaptation to environmental challenges. The gilthead sea bream, Sparus aurata, is particularly sensitive to cold and the prolonged exposure to low temperatures may lead to the "winter disease", a metabolic disorder that significantly affects the aquaculture productions along the Northern Mediterranean coasts during winter-spring season. While sea bream susceptibility to low temperatures has been extensively investigated, the cascade of molecular events under such stressful condition is not fully elucidated.
Results In the present study two groups of wild sea bream were exposed for 21 days to two temperature regimes: 16 ± 0.3°C (control group) and 6.8 ± 0.3°C (cold-exposed group) and DNA microarray analysis of liver transcriptome was carried out at different time points during cold exposure.
A large set of genes was found to be differentially expressed upon cold-exposure with increasingly relevant effects being observed after three weeks at low temperature. All major known responses to cold (i.e. anti-oxidant response, increased mitochondrial function, membrane compositional changes) were found to be conserved in the gilthead sea bream, while, evidence for a key role of unfolded protein response (UPR) to endoplasmic reticulum (ER) stress, during short- and long-term exposure to cold is reported here for the first time.
Conclusions Transcriptome data suggest a scenario where oxidative stress, altered lipid metabolism, ATP depletion and protein denaturation converge to induce ER stress. The resulting UPR activation further promotes conditions for cell damage, and the inability to resolve ER stress leads to severe liver dysfunction and potentially to death.
Link: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-765
Range-wide population structure of European sea bass Dicentrarchus labrax
Autori: EL Souche, B Hellemans, M Babbucci, E MacAoidh, B Guinand, et al.
Riferimenti: BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 116 (1), 86-105
Summary: The euryhaline European sea bass Dicentrarchus labrax L., inhabiting the coasts of the eastern Atlantic Ocean and Mediterranean Sea, has had many opportunities for differentiation throughout its large natural range. However, evidence for this has been incompletely documented geographically and with an insufficient number of markers. Therefore, its full range was sampled at 22 sites and individuals were genotyped with a suite of mapped markers, including 14 microsatellite loci (N = 536) and 46 neutral or gene‐linked single nucleotide polymorphisms (SNPs; N = 644). We confirm that the Atlantic and Mediterranean basins harbour two distinct lineages. Within the Atlantic Ocean no pattern was obvious based on the microsatellite and SNP genotypes, except for a subtle difference between South‐eastern and North‐eastern Atlantic sea bass attributed to limited introgression of alleles of Mediterranean origin. SNP genotypes of the Mediterranean lineage differentiated into three groups, probably under the influence of geographical isolation. The Western Mediterranean group showed genetic homogeneity without evidence for outlier loci. The Adriatic group appeared as a distinct unit. The Eastern Mediterranean group showed a longitudinal gradient of genotypes and most interestingly an outlier locus linked to the somatolactin gene. Overall, the spatial pattern fits those observed with other taxa of between‐basin segregation and within‐basin connectivity, which concurs well with the swimming capabilities of European sea bass. Evidence from a few outlier loci in this and other studies encourages further exploration of its regional connectivity and adaptive evolution.
Link: https://onlinelibrary.wiley.com/doi/full/10.1111/bij.12572
Second generation genetic linkage map for the gilthead sea bream Sparus aurata
Autori: Tsigenopoulos CS, Louro B, Chatziplis D, Lagnel J, Vogiatzi E, Loukovitis D, Franch R, Sarropoulou E, Power DM, Patarnello T, Mylonas CC, Magoulas A, Bargelloni L, Canario A, Kotoulas G
Riferimenti: MARINE GENOMICS. 2014 Dec;18 Pt A:77-82. doi: 10.1016/j.margen.2014.09.008. Epub 2014 Oct 7.
Summary: An updated second linkage map was constructed for the gilthead sea bream, Sparus aurata L., a fish species of great economic importance for the Mediterranean aquaculture industry. In contrast to the first linkage map which mainly consisted of genomic microsatellites (SSRs), the new linkage map is highly enriched with SSRs found in Expressed Sequence Tags (EST-SSRs), which greatly facilitates comparative mapping with other teleosts. The new map consists of 321 genetic markers in 27 linkage groups (LGs): 232 genomic microsatellites, 85 EST-SSRs and 4 SNPs; of those, 13 markers were linked to LGs but were not ordered. Eleven markers (5 SSRs, 5 EST-SSRs and 1 SNP) are not assigned to any LG. The total length of the sex-averaged map is 1769.7 cM, 42% longer than the previously published one, and the number of markers in each LG ranges from 2 to 30. The inter-marker distance varies from 0 to 75.6 cM, with an average of 5.75 cM. The male and female maps have a length of 1349.2 and 2172.1 cM, respectively, and the average distance between markers is 4.38 and 7.05 cM, respectively. Comparative mapping with the three-spined stickleback (Gasterosteus acuulatus) chromosomes and scaffolds showed conserved synteny with 132 S. aurata markers (42.9% of those mapped) having a hit on the stickleback genome.
Link: https://www.sciencedirect.com/science/article/pii/S1874778714001093?via%3Dihub
The population genomics of yellowfin tuna (Thunnus albacares) at global geographic scale challenges current stock delineation
Autori: Carlo Pecoraro, Massimiliano Babbucci, Rafaella Franch, Ciro Rico, Chiara Papetti, Emmanuel Chassot, Nathalie Bodin, Alessia Cariani, Luca Bargelloni & Fausto Tinti
Riferimenti: Scientific ReportsOpen AccessVolume 8, Issue 1, 1 December 2018, Article number 13890
Summary: Yellowfin tuna, Thunnus albacares, is one of the most important seafood commodities in the world. Despite its great biological and economic importance, conflicting evidence arises from classical genetic and tagging studies concerning the yellowfin tuna population structure at local and global oceanic scales. Access to more powerful and cost effective genetic tools would represent the first step towards resolving the population structure of yellowfin tuna across its distribution range. Using a panel of 939 neutral Single Nucleotide Polymorphisms (SNPs), and the most comprehensive data set of yellowfin samples available so far, we found genetic differentiation among the Atlantic, Indian and Pacific oceans. The genetic stock structure analysis carried out with 33 outlier SNPs, putatively under selection, identified discrete populations within the Pacific Ocean and, for the first time, also within the Atlantic Ocean. Stock assessment approaches that consider genetic differences at neutral and adaptive genomic loci should be routinely implemented to check the status of the yellowfin tuna, prevent illegal trade, and develop more sustainable management measures.
Applications of genotyping by sequencing in aquaculture breeding and genetics
Autori: Diego Robledo Christos Palaiokostas Luca Bargelloni Paulino Martínez Ross Houston
Riferimenti: Reviews in Aquaculture, Volume 10, Issue 3, August 2018, Pages 670-682
Summary: Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing (RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.
Link: https://onlinelibrary.wiley.com/doi/full/10.1111/raq.12193
Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing
Autori: Muhammad L Aslam , Roberta Carraro, Anastasia Bestin, Sophie Cariou, Anna K. Sonesson, Jean-Sébastien Bruant, Pierrick Haffray, Luca Bargelloni and Theo H. E. Meuwissen
Riferimenti: BMC GeneticsOpen AccessVolume 19, Issue 1, 11 July 2018, Article number 4
Summary: Background Photobacteriosis is an infectious disease developed by a Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp), which may cause high mortalities (90–100%) in sea bream. Selection and breeding for resistance against infectious diseases is a highly valuable tool to help prevent or diminish disease outbreaks, and currently available advanced selection methods with the application of genomic information could improve the response to selection. An experimental group of sea bream juveniles was derived from a Ferme Marine de Douhet (FMD, Oléron Island, France) selected line using ~ 109 parents (~ 25 females and 84 males). This group of 1187 individuals represented 177 full-sib families with 1–49 sibs per family, which were challenged with virulent Phdp for a duration of 18 days, and mortalities were recorded within this duration. Tissue samples were collected from the parents and the recorded offspring for DNA extraction, library preparation using 2b-RAD and genotyping by sequencing. Genotypic data was used to develop a linkage map, genome wide association analysis and for the estimation of breeding values.
Results The analysis of genetic variation for resistance against Phdp revealed moderate genomic heritability with estimates of ~ 0.32. A genome-wide association analysis revealed a quantitative trait locus (QTL) including 11 SNPs at linkage group 17 presenting significant association to the trait with p-value crossing genome-wide Bonferroni corrected threshold P ≤ 2.22e-06. The proportion total genetic variance explained by the single top most significant SNP was ranging from 13.28–16.14% depending on the method used to compute the variance. The accuracies of predicting breeding values obtained using genomic vs. pedigree information displayed 19–24% increase when using genomic information.
Conclusion The current study demonstrates that SNPs-based genotyping of a sea bream population with 2b-RAD approach is effective at capturing the genetic variation for resistance against Phdp. Prediction accuracies obtained using genomic information were significantly higher than the accuracies obtained using pedigree information which highlights the importance and potential of genomic selection in commercial breeding programs.
Link: https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-018-0631-x
Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species
Autori: Maroso F., Hillen J.E., Pardo B.G., Gkagkavouzis K., Coscia I., Hermida M, Franch R.,Hellemans B, Van Houdt J, Simionati B.g, Taggart J.B., Nielsen E.E., Maes G.b, Ciavaglia S.A., Webster L.M.I., Volckaert F.A.M., Martinez P.c, Bargelloni L., Ogden R.
Riferimenti: Marine Genomics Volume 39, June 2018, Pages 64-72
Summary: The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in “non-model” species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double digest Restriction enzyme Associated DNA (ddRAD) sequencing in SNP genotyping studies including high number of samples. Datasets of sequence data were generated from three marine teleost species (>5500 samples, >2.5 × 1012 bases in total), using a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use of a reference genome and a posteriori genotype correction improved genotyping precision. Individual read coverage was a key variable for reproducibility; variance in sequencing depth between loci in the same individual was also identified as an important factor and found to correlate to tag length. A comparison of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select and improve approaches to the analysis of large datasets based on RAD-like methodologies.
Link: https://www.sciencedirect.com/science/article/pii/S1874778717301411?via%3Dihub
Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly
Autori: F Maroso, M Hermida, A Millán, A Blanco, M Saura, A Fernández, G Dalla Rovere, L Bargelloni, Cabaleiro, B Villanueva, C Bouza, and P Martínez
Riferimenti: DNA ResearchOpen AccessVolume 25, Issue 4, 2018, Pages 439-450
Summary: Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.
Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105115/pdf/dsy015.pdf
Long dsRNAs promote an anti-viral response in Pacific oyster hampering ostreid herpesvirus 1 replication
Autori: Marianna Pauletto, Amélie Segarra, Caroline Montagnani, Virgile Quillien, Nicole Faury, Jacqueline Le Grand, Philippe Miner, Bruno Petton, Yannick Labreuche, Elodie Fleury, Caroline Fabioux, Luca Bargelloni, Tristan Renault, Arnaud Huvet
Riferimenti: journal of Experimental BiologyVolume 220, Issue 20, 15 October 2017, Pages 3671-3685
Summary: Double-stranded RNA (dsRNA)-mediated genetic interference (RNAi) is a widely used reverse genetic tool for determining the loss-of-function phenotype of a gene. Here, the possible induction of an immune response by long dsRNA was tested in a marine bivalve (Crassostrea gigas), as well as the specific role of the subunit 2 of the nuclear factor κB inhibitor (IκB2). This gene is a candidate of particular interest for functional investigations in the context of oyster mass mortality events, as Cg-IκB2 mRNA levels exhibited significant variation depending on the amount of ostreid herpesvirus 1 (OsHV-1) DNA detected. In the present study, dsRNAs targeting Cg-IκB2 and green fluorescent protein genes were injected in vivo into oysters before being challenged by OsHV-1. Survival appeared close to 100% in both dsRNA-injected conditions associated with a low detection of viral DNA and a low expression of a panel of 39 OsHV-1 genes as compared with infected control. Long dsRNA molecules, both Cg-IκB2- and GFP-dsRNA, may have induced an anti-viral state controlling the OsHV-1 replication and precluding the understanding of the specific role of Cg-IκB2. Immune-related genes including Cg-IκB1, Cg-Rel1, Cg-IFI44, Cg-PKR and Cg-IAP appeared activated in the dsRNA-injected condition, potentially hampering viral replication and thus conferring a better resistance to OsHV-1 infection. We revealed that long dsRNA-mediated genetic interference triggered an anti-viral state in the oyster, emphasizing the need for new reverse genetics tools for assessing immune gene function and avoiding off-target effects in bivalves.
Ontogenetic onset of immune-relevant genes in the common sole (Solea solea)
Autori: Ferraresso S, Bonaldo A, Parma L, Buonocore F, Scapigliati G, Gatta PP, Bargelloni L.
Riferimenti: Fish and Shellfish Immunology, Volume 57, 1 October 2016, Pages 278-292
Summary: Fish are free-living organisms since initial stages of development and are exposed to numerous pathogens before their lymphoid organs have matured and adaptive immunity has developed. Susceptibility to diseases and juvenile mortality represent key critical factors for aquaculture. In this context, the characterization of the appearance kinetics of the immune system key members will be useful in understanding the ability of a particular species in generating immune protection against invading pathogens at different developmental stages. The present study characterized, for the first time, the transcriptional onset of un-explored relevant genes of both innate and adaptive immune system during the Solea solea ontogenesis. Gene expression profiles of immune relevant genes was investigated, by means of DNA microarray, in ten developmental stages, from hatching (1 day post-hatching, dph) to accomplishment of the juvenile form (33 dph). The obtained results revealed that transcripts encoding relevant members of innate immune repertoire, such as lysozyme, AMPs (hepcidin, β-defensin), PPRs and complement components are generally characterized by high expression levels at first stages (i.e. hatch and first feeding) indicating protection from environmental pathogens even at early development. Transcription of adaptive immune genes (i.e. Class I and class II MHC, TCRs) differs from that of the innate immune system. Their onset coincides with metamorphosis and larvae-to-juvenile transition, and likely overlaps with the appearance and maturation of the main lymphoid organs. Finally, data collected suggest that at the end of metamorphosis S. solea cell-mediated immune system hasn't still undergone full maturation.
Link: https://www.sciencedirect.com/science/article/pii/S1050464816305198?via%3Dihub
A comprehensive survey on selective breeding programs and seed market in the European aquaculture fish industry
Autori: Hervé Chavanne, Kasper JanssenJohann HofherrFranca ContiniPierrick HaffrayAquatrace ConsortiumHans KomenEinar Eg NielsenLuca Bargelloni
Riferimenti: Aquaculture InternationalVolume 24, Issue 5, 1 October 2016, Pages 1287-1307
Summary: The use of selective breeding is still relatively limited in aquaculture species.Information on such activities is sparse, hindering an overall evaluation of their success.Here, we report on the results of an online survey of the major aquaculture breedingcompanies operating in Europe. Six main reared fish species were targeted. A total of 31respondents contributed to the survey, representing 75 % of European breeding organi-zations. Family-based breeding schemes were predominant, but individual selection wasmore frequently applied in marine species. Artificial fertilization is the preferred means ofreproduction; however, mass spawning is often used as a fallback method. The mostfrequently selected trait is growth performance, but the number of selected traits has beenincreasing over the years through the addition of traits such as disease resistance or productquality. The use of molecular tools is now common in all programs, mainly for pedigreetraceability. An increasing number of programs use either genomic or marker-assistedselection. Results related to the seed production market confirmed that for Atlantic salmonthere are a few dominant players at the European level, with 30–50 % market share. Onlypart of the European fish aquaculture industry today fully exploits selective breeding to thebest advantage. A larger impact assessment still needs to be made by the remainder,particularly on the market share of fish seed (eggs, larvae or juveniles) and its conse-quences for hatchery stability.
Link: https://link.springer.com/content/pdf/10.1007%2Fs10499-016-9985-0.pdf
RAD SNP markers as a tool for conservation of dolphinfish Coryphaena hippurus in the Mediterranean Sea: Identification of subtle genetic structure and assessment of populations sex-ratios
Autori: Maroso F, Franch R, Dalla Rovere G, Arculeo M, Bargelloni L
Riferimenti: Mar Genomics. 2016 Aug;28:57-62. doi: 10.1016/j.margen.2016.07.003. Epub 2016 Jul 19.
Summary: Dolphinfish is an important fish species for both commercial and sport fishing, but so far limited information is available on genetic variability and pattern of differentiation of dolphinfish populations in the Mediterranean basin. Recently developed techniques allow genome-wide identification of genetic markers for better understanding of population structure in species with limited genome information. Using restriction-site associated DNA analysis we successfully genotyped 140 individuals of dolphinfish from eight locations in the Mediterranean Sea at 3324 SNP loci. We identified 311 sex-related loci that were used to assess sex-ratio in dolphinfish populations. In addition, we identified a weak signature of genetic differentiation of the population closer to Gibraltar Strait in comparison to other Mediterranean populations, which might be related to introgression of individuals from Atlantic. No further genetic differentiation could be detected in the other populations sampled, as expected considering the known highly mobility of the species. The results obtained improve our knowledge of the species and can help managing dolphinfish stock in the future.
Link: https://www.sciencedirect.com/science/article/pii/S1874778716300630
Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (Thunnus albacares)
Autori: Pecoraro C, Babbucci M, Villamor A, Franch R, Papetti C, Leroy B, Ortega-Garcia S, Muir J, Rooker J, Arocha F, Murua H, Zudaire I, Chassot E, Bodin N, Tinti F, Bargelloni L, Cariani A
Riferimenti: Mar Genomics. 2016 Feb;25:43-48. doi: 10.1016/j.margen.2015.12.002. Epub 2015 Dec 23.
Summary: Global population genetic structure of yellowfin tuna (Thunnus albacares) is still poorly understood despite its relevance for the tuna fishery industry. Low levels of genetic differentiation among oceans speak in favour of the existence of a single panmictic population worldwide of this highly migratory fish. However, recent studies indicated genetic structuring at a much smaller geographic scales than previously considered, pointing out that YFT population genetic structure has not been properly assessed so far. In this study, we demonstrated for the first time, the utility of 2b-RAD genotyping technique for investigating population genetic diversity and differentiation in high gene-flow species. Running de novo pipeline in Stacks, a total of 6772 high-quality genome-wide SNPs were identified across Atlantic, Indian and Pacific population samples representing all major distribution areas. Preliminary analyses showed shallow but significant population structure among oceans (FST = 0.0273; P-value < 0.01). Discriminant Analysis of Principal Components endorsed the presence of genetically discrete yellowfin tuna populations among three oceanic pools. Although such evidence needs to be corroborated by increasing sample size, these results showed the efficiency of this genotyping technique in assessing genetic divergence in a marine fish with high dispersal potential.
Link: https://www.sciencedirect.com/science/article/pii/S1874778715300581?via%3Dihub
Genomic prediction of resistance to pasteurellosis in gilthead sea bream (Sparus aurata) using 2B-RAD sequencing
Autori: Palaiokostas C, Ferraresso S, Franch R, Houston RD, Bargelloni L.
Riferimenti: G3 (Bethesda). 2016 Nov 8;6(11):3693-3700. doi: 10.1534/g3.116.035220.
Summary: Gilthead sea bream (Sparus aurata) is a species of paramount importance to the Mediterranean aquaculture industry, with an annual production exceeding 140,000 metric tons. Pasteurellosis due to the Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp) causes significant mortality, especially during larval and juvenile stages, and poses a serious threat to bream production. Selective breeding for improved resistance to pasteurellosis is a promising avenue for disease control, and the use of genetic markers to predict breeding values can improve the accuracy of selection, and allow accurate calculation of estimated breeding values of nonchallenged animals. In the current study, a population of 825 sea bream juveniles, originating from a factorial cross between 67 broodfish (32 sires, 35 dams), were challenged by 30 min immersion with 1 × 105 CFU virulent Phdp. Mortalities and survivors were recorded and sampled for genotyping by sequencing. The restriction-site associated DNA sequencing approach, 2b-RAD, was used to generate genome-wide single nucleotide polymorphism (SNP) genotypes for all samples. A high-density linkage map containing 12,085 SNPs grouped into 24 linkage groups (consistent with the karyotype) was constructed. The heritability of surviving days (censored data) was 0.22 (95% highest density interval: 0.11–0.36) and 0.28 (95% highest density interval: 0.17–0.4) using the pedigree and the genomic relationship matrix respectively. A genome-wide association study did not reveal individual SNPs significantly associated with resistance at a genome-wide significance level. Genomic prediction approaches were tested to investigate the potential of the SNPs obtained by 2b-RAD for estimating breeding values for resistance. The accuracy of the genomic prediction models (r = 0.38–0.46) outperformed the traditional BLUP approach based on pedigree records (r = 0.30). Overall results suggest that major quantitative trait loci affecting resistance to pasteurellosis were not present in this population, but highlight the effectiveness of 2b-RAD genotyping by sequencing for genomic selection in a mass spawning fish species.
Link: http://www.g3journal.org/cgi/pmidlookup?view=long&pmid=27652890
Evaluating genetic traceability methods for captive-bred marine fish and their applications in fisheries management and wildlife forensics
Autori: BYLEMANS Jonas, MAES Gregory, CARIANI Alessia, BARGELLONI Luca, CARVALHO Gary R., NIELSEN Einar Eg, TINTI Fausto, VOLCKAERT Filip, OGDEN Rob, MARTINSOHN Jann, DIOPERE Eveline, SENN Helen, TAYLOR Martin, HELYAR Sarah, BONALDO Alessio, GUANIERO Ilaria, KOMEN Hans.
Riferimenti: Aquaculture Environment InteractionsOpen AccessVolume 8, 2016, Pages 131-145
Summary: Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in aquaculture production. Consequently, more captive-bred fish are released into the wild through accidental escape or deliberate releases. The increased mixing of captive-bred and wild fish may affect the ecological and/or genetic integrity of wild fish populations. Unambiguous identification tools for captive-bred fish will be highly valuable to manage risks (fisheries management) and tracing of escapees and seafood products (wildlife forensics). Using single nucleotide polymorphism (SNP) data from captive-bred and wild populations of Atlantic cod Gadus morhua L. and sole Solea solea L., we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive-bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterized the broodstock and escapees originated from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive-bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case-by-case strategy when choosing the best method.
Link: https://orbit.dtu.dk/files/125151001/Publishers_version.pdf
Proteomic responses to hypoxia at different temperatures in the great scallop (Pecten maximus)
Autori: Artigaud S, Lacroix C, Richard J, Flye-Sainte-Marie J, Bargelloni L, Pichereau V.
Riferimenti: PeerJ. 2015 Mar 31;3:e871. doi: 10.7717/peerj.871. eCollection 2015.
Summary: Hypoxia and hyperthermia are two connected consequences of the ongoing global change and constitute major threats for coastal marine organisms. In the present study, we used a proteomic approach to characterize the changes induced by hypoxia in the great scallop, Pecten maximus, subjected to three different temperatures (10 °C, 18 °C and 25 °C). We did not observe any significant change induced by hypoxia in animals acclimated at 10 °C. At 18 °C and 25 °C, 16 and 11 protein spots were differentially accumulated between normoxia and hypoxia, respectively. Moreover, biochemical data (octopine dehydrogenase activity and arginine assays) suggest that animals grown at 25 °C switched their metabolism towards anaerobic metabolism when exposed to both normoxia and hypoxia, suggesting that this temperature is out of the scallops’ optimal thermal window. The 11 proteins identified with high confidence by mass spectrometry are involved in protein modifications and signaling (e.g., CK2, TBK1), energy metabolism (e.g., ENO3) or cytoskeleton (GSN), giving insights into the thermal-dependent response of scallops to hypoxia.
Range-wide population structure of European sea bass Dicentrarchus labrax
Autori: Souche, E.L., Hellemans, B., Babbucci, M., Macaoidh, E., Guinand, B., Bargelloni, L., Chistiakov, D.A., Patarnello, T., Bonhomme, F., Martinsohn, J.T., Volckaert, F.A.M.
Riferimenti: Biological Journal of the Linnean SocietyVolume 116, Issue 1, 1 September 2015, Pages 86-105
Summary: The euryhaline European sea bass Dicentrarchus labrax L., inhabiting the coasts of the eastern Atlantic Ocean and Mediterranean Sea, has had many opportunities for differentiation throughout its large natural range. However, evidence for this has been incompletely documented geographically and with an insufficient number of markers. Therefore, its full range was sampled at 22 sites and individuals were genotyped with a suite of mapped markers, including 14 microsatellite loci (N = 536) and 46 neutral or gene‐linked single nucleotide polymorphisms (SNPs; N = 644). We confirm that the Atlantic and Mediterranean basins harbour two distinct lineages. Within the Atlantic Ocean no pattern was obvious based on the microsatellite and SNP genotypes, except for a subtle difference between South‐eastern and North‐eastern Atlantic sea bass attributed to limited introgression of alleles of Mediterranean origin. SNP genotypes of the Mediterranean lineage differentiated into three groups, probably under the influence of geographical isolation. The Western Mediterranean group showed genetic homogeneity without evidence for outlier loci. The Adriatic group appeared as a distinct unit. The Eastern Mediterranean group showed a longitudinal gradient of genotypes and most interestingly an outlier locus linked to the somatolactin gene. Overall, the spatial pattern fits those observed with other taxa of between‐basin segregation and within‐basin connectivity, which concurs well with the swimming capabilities of European sea bass. Evidence from a few outlier loci in this and other studies encourages further exploration of its regional connectivity and adaptive evolution.
Link: https://onlinelibrary.wiley.com/doi/full/10.1111/bij.12572
Effect of stocking density of fish on water quality and growth performance of European Carp and leafy vegetables in a low-tech aquaponic system
Autori: Maucieri C., Nicoletto C., Zanin G., Birolo M., Trocino A., Sambo P., Borin M., Xiccato G. 2019
Riferimenti: PLoS ONE, 14 (5), art. no. e0217561
Summary: Aquaponics (AP) is a semi-closed system of food production that combines aquaculture and hydroponics and represents a new agricultural system integrating producers and consumers. The aim of this study was to test the effect of stocking densities (APL, 2.5 kg m-3; APH, 4.6 kg m-3) on water quality, growth performance of the European Carp (Cyprinus carpio L.), and yield of leafy vegetables (catalogna, lettuce, and Swiss Chard) in a low-technology AP pilot system compared to a hydroponic cultivation. The AP daily consumption of water due to evapotranspiration was not different among treatments with an average value of 8.2 L d-1, equal to 1.37% of the total water content of the system. Dissolved oxygen was significantly (p < 0.05) different among treatments with the lowest median value recorded with the highest stocking density of fish (5.6 mg L-1) and the highest median value in the hydroponic control (8.7 mg L-1). Marketable yield of the vegetables was significantly different among treatments with the highest production in the hydroponic control for catalogna (1.2 kg m-2) and in the APL treatment for Swiss Chard (5.3 kg m-2). The yield of lettuce did not differ significantly between hydroponic control and APL system (4.0 kg m-2 on average). The lowest production of vegetables was obtained in the APH system. The final weight (515 g vs. 413 g for APL and APH, respectively), specific growth rate (0.79% d-1 vs. 0.68% d-1), and feed conversion (1.55 vs. 1.86) of European Carp decreased when stocking density increased, whereas total yield of biomass was higher in the APH system (4.45 kg m-3 vs. 6.88 kg m-3). A low mortality (3% on average) was observed in both AP treatments. Overall, the results showed that a low initial stocking density at 2.5 kg m-3 improved the production of European Carp and of leafy vegetables by maintaining a better water quality in the tested AP system.
Link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217561
Sperm quality in wild-caught and farmed males of the European eel (Anguilla anguilla)
Autori: Locatello, L., Bertotto, D., Cerri, R., Parmeggiani, A., Govoni, N., Trocino, A., Xiccato, G., Mordenti, O.
Riferimenti: Animal Reproduction Science 198, 167-176.
Summary: Sperm density and performance of wild and farmed male European eels were evaluated to investigate the effect of maintenance in captivity on ejaculate quality. Hormonal stimulation (with human chorionic gonadotropin) lasted for 17 weeks. Different origins of the male European eels partially influenced the quality of the ejaculates. Indeed, wild animals (i.e., collected at a natural site) had greater sperm longevity during the hormonal stimulation, whereas there was no significant effect of the origin on sperm density, spermatocrit, the percentage of motile sperm, and plasma testosterone concentrations. The different origins of the males also affected fatty acid sperm content, with greater unsaturated fatty acid and omega-6 concentrations in wild eels and lesser concentrations of saturated fatty acids and omega-3 fatty acids in farmed eels. Regarding sperm quality of European eels, this is the first study that takes into account the effect of different origins of stimulated males (wild-caught compared with farmed) on sperm quality, and these findings may help to improve the production of high-quality gametes in this endangered species.
Link: https://www.sciencedirect.com/science/article/pii/S0378432018301155
