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Bertolini F, Ribani A, Capoccioni F, Buttazzoni L, Bovo S, Schiavo G, Caggiano M, Rothschild MF, Fontanesi L. Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei. Genes (Basel) 2023; 14:genes14040839. [PMID: 37107597 PMCID: PMC10137967 DOI: 10.3390/genes14040839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.
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Affiliation(s)
- Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
- Correspondence:
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Fabrizio Capoccioni
- Centro di Ricerca “Zootecnia e Acquacoltura”, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), 00198 Roma, Italy
| | - Luca Buttazzoni
- Centro di Ricerca “Zootecnia e Acquacoltura”, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), 00198 Roma, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Massimo Caggiano
- Panittica Italia Società Agricola Srl, Torre Canne di Fasano, 72016 Brindisi, Italy
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
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Papadaki M, Karamanlidis D, Sigelaki E, Fakriadis I, Mylonas CC. Evolution of sex ratio and egg production of gilthead seabream (Sparus aurata) over the course of five reproductive seasons. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Naya-Català F, Piazzon MC, Calduch-Giner JA, Sitjà-Bobadilla A, Pérez-Sánchez J. Diet and Host Genetics Drive the Bacterial and Fungal Intestinal Metatranscriptome of Gilthead Sea Bream. Front Microbiol 2022; 13:883738. [PMID: 35602034 PMCID: PMC9121002 DOI: 10.3389/fmicb.2022.883738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota is now recognised as a key target for improving aquaculture profit and sustainability, but we still lack insights into the activity of microbes in fish mucosal surfaces. In the present study, a metatranscriptomic approach was used to reveal the expression of gut microbial genes in the farmed gilthead sea bream. Archaeal and viral transcripts were a minority but, interestingly and contrary to rRNA amplicon-based studies, fungal transcripts were as abundant as bacterial ones, and increased in fish fed a plant-enriched diet. This dietary intervention also drove a differential metatranscriptome in fish selected for fast and slow growth. Such differential response reinforced the results of previously inferred metabolic pathways, enlarging, at the same time, the catalogue of microbial functions in the intestine. Accordingly, vitamin and amino acid metabolism, and rhythmic and symbiotic processes were mostly shaped by bacteria, whereas fungi were more specifically configuring the host immune, digestive, or endocrine processes.
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Affiliation(s)
- Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain
| | - M. Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain
- M. Carla Piazzon,
| | - Josep A. Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain
- *Correspondence: Jaume Pérez-Sánchez,
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Selection for high growth improves reproductive performance of gilthead seabream Sparus aurata under mass spawning conditions, regardless of the dietary lipid source. Anim Reprod Sci 2022; 241:106989. [DOI: 10.1016/j.anireprosci.2022.106989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/13/2022] [Accepted: 05/01/2022] [Indexed: 11/19/2022]
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Erratum: Ferosekhan et al. Influence of Genetic Selection for Growth and Broodstock Diet n-3 LC-PUFA Levels on Reproductive Performance of Gilthead Seabream, Sparus Aurata. Animals 2021, 11, 519. Animals (Basel) 2021; 11:ani11102957. [PMID: 34680027 PMCID: PMC8532982 DOI: 10.3390/ani11102957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/21/2021] [Accepted: 10/09/2021] [Indexed: 11/17/2022] Open
Abstract
The authors wish to make the following corrections to this paper [...].
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