4 results on '"Bargelloni, Luca"'
Search Results
2. Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.
- Author
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Saura, María, Caballero, Armando, Santiago, Enrique, Fernández, Almudena, Morales-González, Elisabeth, Fernández, Jesús, Cabaleiro, Santiago, Millán, Adrián, Martínez, Paulino, Palaiokostas, Christos, Kocour, Martin, Aslam, Muhammad L., Houston, Ross D., Prchal, Martin, Bargelloni, Luca, Tzokas, Kostas, Haffray, Pierrick, Bruant, Jean-Sebastien, and Villanueva, Beatriz
- Subjects
CARP ,FISH breeding ,PSETTA maxima ,GENETIC variation ,EUROPEAN seabass ,FLATFISHES ,DNA sequencing - Abstract
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. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
3. Genome-wide analysis clarifies the population genetic structure of wild gilthead sea bream (Sparus aurata).
- Author
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Maroso F, Gkagkavouzis K, De Innocentiis S, Hillen J, do Prado F, Karaiskou N, Taggart JB, Carr A, Nielsen E, Triantafyllidis A, and Bargelloni L
- Subjects
- Animals, Atlantic Ocean, Europe, Genetic Markers genetics, Genetics, Population methods, Genome-Wide Association Study methods, Mediterranean Sea, Microsatellite Repeats genetics, Polymorphism, Single Nucleotide genetics, Sea Bream genetics
- Abstract
Gilthead sea bream is an important target for both recreational and commercial fishing in Europe, where it is also one of the most important cultured fish. Its distribution ranges from the Mediterranean to the African and European coasts of the North-East Atlantic. Until now, the population genetic structure of this species in the wild has largely been studied using microsatellite DNA markers, with minimal genetic differentiation being detected. In this geographically widespread study, 958 wild gilthead sea bream from 23 locations within the Mediterranean Sea and Atlantic Ocean were genotyped at 1159 genome-wide SNP markers by RAD sequencing. Outlier analyses identified 18 loci potentially under selection. Neutral marker analyses identified weak subdivision into three genetic clusters: Atlantic, West, and East Mediterranean. The latter group could be further subdivided into an Ionian/Adriatic and an Aegean group using the outlier markers alone. Seascape analysis suggested that this differentiation was mainly due to difference in salinity, this being also supported by preliminary genomic functional analysis. These results are of fundamental importance for the development of proper management of this species in the wild and are a first step toward the study of the potential genetic impact of the sea bream aquaculture industry., Competing Interests: The authors and the commercial company involved declare that they have no competing financial interests or personal relationships that could have influenced the work reported in this paper. The commercial affiliation with Fios Genomics Ltd. does not alter our adherence to PLOS ONE policies on sharing data and materials.
- Published
- 2021
- Full Text
- View/download PDF
4. Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.
- Author
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Milano I, Babbucci M, Panitz F, Ogden R, Nielsen RO, Taylor MI, Helyar SJ, Carvalho GR, Espiñeira M, Atanassova M, Tinti F, Maes GE, Patarnello T, and Bargelloni L
- Subjects
- Animals, Databases, Genetic, Europe, Gene Frequency genetics, Geography, Heterozygote, Molecular Sequence Annotation, ROC Curve, Reproducibility of Results, Sequence Analysis, DNA, Conservation of Natural Resources methods, Gadiformes genetics, Genomics methods, High-Throughput Nucleotide Sequencing methods, Polymorphism, Single Nucleotide genetics, Transcriptome genetics
- Abstract
The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).
- Published
- 2011
- Full Text
- View/download PDF
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