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The Neotropical region hosts 4225 freshwater fish species, ranking first among the world's most diverse regions for freshwater fishes. Our NEOTROPICAL FRESHWATER FISHES data set is the first to produce a large-scale Neotropical freshwater fish inventory, covering the entire Neotropical region from Mexico and the Caribbean in the north to the southern limits in Argentina, Paraguay, Chile, and Uruguay. We compiled 185,787 distribution records, with unique georeferenced coordinates, for the 4225 species, represented by occurrence and abundance data. The number of species for the most numerous orders are as follows: Characiformes (1289), Siluriformes (1384), Cichliformes (354), Cyprinodontiformes (245), and Gymnotiformes (135). The most recorded species was the characid Astyanax fasciatus (4696 records). We registered 116,802 distribution records for native species, compared to 1802 distribution records for nonnative species. The main aim of the NEOTROPICAL FRESHWATER FISHES data set was to make these occurrence and abundance data accessible for international researchers to develop ecological and macroecological studies, from local to regional scales, with focal fish species, families, or orders. We anticipate that the NEOTROPICAL FRESHWATER FISHES data set will be valuable for studies on a wide range of ecological processes, such as trophic cascades, fishery pressure, the effects of habitat loss and fragmentation, and the impacts of species invasion and climate change. There are no copyright restrictions on the data, and please cite this data paper when using the data in publications.

Cobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first de novo transcriptome assembly of R. canadum liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyses with Danio rerio, Lates calcarifer, Seriola lalandi dorsalis, Seriola dumerili, or Echeneis naucrates. Finally, we identified 7894 microsatellites related to cobia’s putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.

Due to the morphological similarity between some billfish species, the International Commission for the Conservation of Atlantic Tunas (ICCAT) recommends the use of molecular tools to identify billfish at the species level to properly manage this imperiled group. In this study, species-specific swordfish and billfish identification was carried out by using PCR-RFLP and multiplex PCR of the mitochondrial COI gene. Samples were obtained during landings of the tuna fleet at the Public Fisheries Port of Santos (PFPS) and in the General Warehouse Company of Sao Paulo (CEAGESP), Brazil. A total of 87 samples from PFPS were identified: Kajikia albida, Tetrapturus georgii, T. pfluegeri, Makaira nigricans, and Istiophorus platypterus. At CEAGESP, 432 individuals were collected, and three species were detected: Xiphias gladius, I. platypterus and T. georgii. Some samples presented an unknown band pattern for PCR-RFLP, which were sequenced and identified as X. gladius. These findings demonstrate that billfishes protected by law are being caught by industrial fisheries, but they are not traded at the CEAGESP. We advocate continuous onboard and of landings fishing monitoring using molecular identification tools in accordance with ICCAT recommendations. We provided evidence that DNA-based methods are efficient in overcoming billfish misidentification in the Atlantic Ocean.

A coloração em peixes tem sido um objeto de estudo intrigante para muitos pesquisadores que procuram entender a função biológica de tal exuberância de cores nas inúmeras espécies de peixes que habitam os mares e os sistemas fluviais. O mosaico de cores presentes em peixes também nos fascina ao observarmos extasiados peixes de diversas formas e colorações em aquários ao redor do mundo. Os processos de formação de cores em peixes são eventos que envolvem mecanismos genéticos e fisiológicos que são intrinsecamente associados aos aspectos evolutivos das espécies. A compreensão de tais mecanismos tem possibilitado ao homem não somente entender processos adaptativos, como também manipular cores em peixes para fins ornamentais e para aumentar a atratividade de peixes como alimento.

Intermuscular bones (IBs) are mineralized spicules, present in the myosepta of many, but not all, teleost species. IBs are often small and sharp, and they consequently limit how the fish can be processed; the IBs may cause injury or trauma if lodged in consumers' throats or mouths, and therefore affect the appeal of the fish to many consumers. The development of IBs in teleosts is still not fully understood and the molecular basis of IB development remains to be established. Here, the characteristics of IB tissue are evaluated based on single-cell transcriptomics in wild-type zebrafish. The analysis defined 18 distinct cell types. Differentiation trajectories showed that IBs are derived from tendons and that a core tendon-osteoblast cell lineage is related to IB formation. In particular, the functions of 10 candidate genes were evaluated via CRISPR-Cas9 mutants. Among those

Colossoma macropomum known as “tambaqui” is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and great adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39X coverage of long reads and polished to a QV=36 with 130X coverage of short reads. The genome was assembled into 1,269 scaffolds to a total of 1,221,847,006 bases, with a scaffold N50 size of 40 Mb where 93% of all assembled bases were placed in the largest 54 scaffolds that corresponds to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced which benefits any groups interested in exploring unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for novel insights about ecological and evolutionary facets and is a helpful resource for aquaculture purposes.

Made available in DSpace on 2020-12-12T01:44:43Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-12-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Sharks developed life history traits that make them susceptible to overfishing. This is, in turn, a risk for extinction, and several species are affected. The high price of shark fins in the international trade has triggered the widespread capture of sharks at unsustainable levels, prompting illegal and unethical practices, such as finning. To address these concerns, the present study aimed to identify species composition using molecular techniques based on DNA barcoding and DNA polymorphism on samples taken from illegal shark fin seizures conducted by the Federal Environmental Agency of Brazil. A species-specific DNA-based identification from three finning seizures in Brazil found at least 20 species from 747 shark fins, some of which were identified as endangered and protected under Brazilian legislation, while others were representative of restricted catches, according to Appendix II of CITES. In the seizure from Belém, 338 fins were identified as belonging to at least 19 different species, while in the seizure from Natal 211, fins belonging to at least 8 different species were identified. Furthermore, 198 fins from Cananéia were identified through PCR-Multiplex as belonging to Isurus oxyrinchus. These results raise concerns about the environmental and socioeconomic effects of finning on developing countries. Furthermore, this study represents the first finning evaluation from Brazil in the Southwest Atlantic, highlighting the importance of developing policies aimed toward restricting and regulating the shark trade and detecting IUU fisheries and illegal trade of endangered species, mainly in developing countries, where fisheries management, surveillance, and species-specific fisheries catch data are often sporatic. Laboratório de Genética e Conservação Universidade Santa Cecília (UNISANTA), 277 Oswaldo Cruz Street Laboratório de Genética Pesqueira e Conservação (GenPesC) Instituto do Mar (IMar) Universidade Federal de São Paulo (UNIFESP), 144 Dr. Carvalho de Mendonça Street Laboratório de Biologia e Genética de Peixes (LBGP) Instituto de Biociências de Botucatu (IBB) Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 250 Prof. Dr. Antonio Celso Wagner Zanin Street Núcleo Integrado de Biotecnologia Universidade de Mogi das Cruzes, 200 Dr. Cândido Xavier de Almeida e Souza Avenue Fisheries Institute (IP), 192 Bartolomeu de Gusmão Avenue Laboratório de Biologia e Genética de Peixes (LBGP) Instituto de Biociências de Botucatu (IBB) Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 250 Prof. Dr. Antonio Celso Wagner Zanin Street FAPESP: 2009/54660-6 FAPESP: 2011/23787-0 FAPESP: 2017/02420-8

Estimating components of variance and genetic parameters of economically relevant traits is the first step towards planning a breeding program for aquaculture species. This study estimated the (co)variance components for growth rate and other body traits and then determined a multiple regression equation to assess the loin eye area (LEA) from morphometric traits of the Neotropical aquaculture species Colossoma macropomum. Estimation of variance components was performed using derivative‐free restricted maximum likelihood estimation using the MTDFREML package. Six predictive variables were tested to estimate the coefficient of regression equation and to select the most suitable model for predicting LEA. The estimated genetic parameter for body weight showed moderate‐to‐high heritability estimates of 0.26 (0.01) and 0.49 (0.01) at 221 and 623 days respectively. The genetic correlation (rg) estimates between body size measurements were positive and ranged from low to high at both ages. The heritability for LEA in this assessment was 0.39 (0.03). The genetic and phenotypic correlations between LEA and the other body measurements ranged from 0.16 to 0.94 and 0.75 and 0.90 respectively. The outcomes of this study can contribute to the development of a genetics‐based breeding program that will improve (tambaqui) productivity and carcass quality.

We describe key production-related traits of trahira (Hoplias malabaricus), an aquaculture candidate species, in a semi-intensive fish farming system. We quantified growth from hatch through grow-out at two stocking densities and evaluated fillet protein, lipids and fatty-acid content. We made 2430 observations of growth and morphometrics on 270 juvenile fish allocated to four fish ponds, two at 5 fish/m2 (90 animals) and two at 10 fish/m2 (180 animals) through 11 months. The fish reached an average length of 27.5 cm (±0.38) and 27.0 cm (±0.24), and weight of 263.0 g (±10.54) and 246.7 g (±6.89), respectively, at the low and high densities. There was no significant difference in weight (P > 0.05) between the densities for any of the parameters assessed, and hence the same growth curve applied to both densities (A = 292.9; B = 28.1; and K = 0.65). Standard length, however, differed significantly (P

The dusky grouper, Epinephelus marginatus, is a well-known and widespread marine fish assessed as endangered by the International Union for the Conservation of Nature. Analyzing the genetic diversity of this species is, therefore, of utmost importance and necessary for conservation purposes. Microsatellites are molecular tools with advantages that are ideal for population analyses. This study provides the first set of species-specific microsatellite loci for E. marginatus that can be applied when assessing both intra- and interpopulation genetic variation. Twenty microsatellite loci were isolated and characterized for the dusky grouper by genotyping 20 individuals obtained from the North Eastern Atlantic Ocean (n = 4) and from the South Western Atlantic Ocean (n = 16). The number of alleles per locus varied from 2 to 11, while the observed and expected heterozygosities ranged from 0.25 to 0.94 and 0.34 to 0.89, respectively. The polymorphic information content varied from moderately to highly informative. This suite of markers provides the first specific nuclear tools for E. marginatus and, thus, allows to assess with more specificity different populations’ structures.

Made available in DSpace on 2019-10-04T12:35:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-03-30 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Introgressive crossbreeding between Red-Stirling and Chitralada Nile tilapia was carried out to assess the association of polymorphisms of short tandem repeats loci located in the growth hormone-I promoter and first intron with growth performance. The growth of seven genetic groups was assessed using a mixed linear model. We considered sex, age, and initial weight class of each animal as fixed effects, while genetic group, and polymorphisms in the short tandem repeats in the promoter and in the intron were considered as random effects. We found six alleles in the promoter, which were arranged in 18 of the 21 genotypic possible combinations. Alleles 191 and 196 of the promoter correspond to 80% of the assessed individuals' total alleles, and genotypes 196/196, 191/196 and 196/201 were the most frequent. We found only three alleles in the intron. Allelic variation at the promoter locus showed a significant association with weight, genotypes 181/181, 181/191 and 196/206 showed higher average weight, and genotypes 196/201, 201/201 and 191/196 showed the lowest weight. The polymorphism in the intron was not associated with fish weight. The approach utilized is unprecedented for short tandem repeats found in the growth hormone-I gene. The observed association indicates that this gene's polymorphism could be used as a tool in tilapia breeding programs. Univ Mogi Das Cruzes, Unit Biotechnol, Mogi Das Cruzes, SP, Brazil Sao Paulo State Univ, Campus Registro, Registro, SP, Brazil Univ Fed Lavras, Dept Stat, Lavras, MG, Brazil Univ Fed Lavras, Dept Anim Sci, Lavras, MG, Brazil Univ Sao Paulo, Postgrad Program Biotechnol, Sao Paulo, Brazil Sao Paulo State Univ, Campus Registro, Registro, SP, Brazil FAPESP: 11/23752-2 CAPES: 142832/2010-3 CAPES: 052-11

Astyanax bimaculatus, a ubiquitous species in many Neotropical basins, is characterized by a complex taxonomy and are currently considered a species complex. The goal of this study was to analyze 31 populations (N = 136) of this species from southeastern Brazil using cytogenetic techniques: conventional staining, nucleolar organizer region (Ag-NOR), C-banding, and 18S and 5S recombinant DNA fluorescent in situ hybridization (FISH) probes; and molecular techniques: S72, RAG2, and COI. All populations were 2n = 50 (6m + 20sm +18st +6a); Ag-NORs were predominantly simple, C-banding revealed high variation levels within and among basins, and the FISH probes 18S and 5S were restricted to chromosome pairs 14 and 7, respectively. The S72 was uninformative for phylogenetic analyses, and RAG2 showed no variation among populations. The COI gene revealed three haplogroups. The most basal was composed of Pandeiros population (São Francisco Basin) that diverged in the Middle Miocene. The second was composed of A. altiparanae from the Upper Paraná Basin and Espírito Santo Stream (Paraíba do Sul Basin), whereas the third was composed of Astyanax lacustris from São Francisco and coastal basins. The second and third haplogroups diverged in the Pleistocene, indicating that diversification of the bimaculatus complex was driven by tectonic activity and sea-level fluctuations.

Brycon is a fish genus in the order Characiformes, distributed from southern Mexico to the La Plata River in Argentina. Several of its species, including Brycon nattereri, are threatened with extinction or considered vulnerable because they are highly sensitive to anthropogenic factors. The decline of these species may be related to the growth of agriculture and mining in the Brazilian Cerrado region, thus their recovery requires management plans. In this study, we use morphological, chromosomal, and genetic analysis to suggest that two distinct evolutionary units exist under the same denomination B. nattereri, indistinguishable by the descriptive morphological characters of the species until the present moment and show that the population of the Sao Francisco River is more diverse than that of the upper Parana River basin. These results may help with future management and conservation programs of Brycon species in the Parana and Sao Francisco river basins, two major Brazilian hydrographic basins.

While in all vertebrates, growth hormone (GH) promotes post-natal growth, in fishes it also affects such metabolic functions as foraging rate, digestion, osmoregulation, and reproduction. The promoter region of the GH gene is an important target for studies of mechanisms regulating its expression, and polymorphisms within the promoter have been associated with performance traits in fishes. We used Thermal Asymmetric Interlaced PCR (TAIL-PCR) to amplify and sequence the 5′-flanking regions of the Colossoma macropomum GH (cmGH) gene. Based on a sequence of 1,038 bp, we designed three specific nested primers (R-290, R-186 and R-26) which were used with shorter arbitrary degenerate primers to amplify the 5′ proximal region of the cmGH gene. We identified a tetranucleotide (ATCC)4 microsatellite motif in this region, exhibiting four alleles (118, 122, 126 and 130 bp) within the population study. Genotypes at this locus deviated significantly from Hardy–Weinberg expectations (p ≤.05) and showed a low level of polymorphism (polymorphic information content = 0.163). High homozygosity (FIS = 0.147) was observed in the overall population. The polymorphism at the microsatellite makes it an important candidate for association studies between the respective genotypes, growth rate and other traits in farmed populations. Such studies may contribute to future breeding programs using marker-assisted selection upon this aquaculturally important species. Accepted version

The dusky grouper Epinephelus marginatus is a large epinephelid species that occurs in the eastern and south-western Atlantic and western Indian Oceans. Late maturity, protogynous hermaphroditism, site fidelity, and overfishing have all contributed to its demographic decline. Connectivity and demography within a broad sampling of dusky grouper populations throughout its distribution were assessed. To do so, genetic variation at 11 polymorphic microsatellite loci and a partial sequence of the mitochondrial control region (mtCR) were evaluated. Two major mtCR lineages with a sequence divergence of 1.6% were found. The magnitude of genetic differentiation for mtCR among north and south Atlantic and Indian Ocean populations was high, with ΦST = 0.528. DEST and results of discriminant analysis of principal component revealed significant microsatellite genetic differentiation between all collection areas. Significant pairwise DEST showed moderate (0.084) to very great (0.603) differentiation. The effective population size was low for all localities, ranging between 25 (Azores Archipelago) and 311 (Rio Grande do Sul). The overall effective population size was estimated as 299 (confidence interval = 215–412), and there was no evidence of strong or recent bottleneck effects. Local and regional genetic structuring among dusky grouper populations is the consequence of the species' site fidelity, distribution across multiple oceanographic boundaries, and probably also of sequential hermaphroditism that contributes to the intensity of random genetic drift. The spatial pattern of genetic structuring of dusky groupers is such that fisheries management and conservation of population genetic integrity will have to be pursued at the local and regional scales. São Paulo Research Foundation (FAPESP), Grant/Award Numbers: 2015/23.883-0, 2016/20.208-3, 2017/02.420-8; Hatch Program of the National Institute of food and Agriculture, U.S. Departament of Agriculture Experiment Station; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/Brasil (CAPES). info:eu-repo/semantics/publishedVersion

Made available in DSpace on 2022-04-29T08:36:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-11-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Nile tilapia (Oreochromis niloticus) is a species of worldwide importance for aquaculture. A crossbred lineage was developed through introgressive backcross breeding techniques and combines the high growth performance of the Chitralada (CHIT) lwith attractive reddish color of the Red Stirling (REDS) strains. Since the crossbreed has an unknown genetically improved background, the objective of this work was to characterize expression signatures that portray the advantageous phenotype of the crossbreeds. We characterized the microRNA transcriptome by high throughput sequencing (RNA-seq) and the proteome through mass spectrometry (ESI-Q-TOF-MS) and applied bioinformatics for the comparative analysis of such molecular data on the three strains. Crossbreed expressed a distinct set of miRNAs and proteins compared to the parents. They comprised several microRNAs regulate traits of economic interest. Proteomic profiles revealed differences between parental and crossbreed in expression of proteins associated with glycolisis. Distinctive miRNA and protein signatures contribute to the phenotype of crossbreed. Department of Chemical and Biological Sciences Institute of Biosciences of Botucatu São Paulo State University (UNESP) Department of Biophysics and Pharmacology Institute of Biosciences of Botucatu São Paulo State University (UNESP) Division Molecular Biotechnology and Functional Genomics Technical University of Applied Sciences Wildau Center for the Study of Venoms and Venomous Animals (CEVAP) São Paulo State University (UNESP) Department of Structural and Functional Biology Institute of Biosciences of Botucatu São Paulo State University (UNESP) Unit of Biotechnology University of Mogi das Cruzes Department of Animal Sciences Federal University of Lavras Department of Chemical and Biological Sciences Institute of Biosciences of Botucatu São Paulo State University (UNESP) Department of Biophysics and Pharmacology Institute of Biosciences of Botucatu São Paulo State University (UNESP) Center for the Study of Venoms and Venomous Animals (CEVAP) São Paulo State University (UNESP) Department of Structural and Functional Biology Institute of Biosciences of Botucatu São Paulo State University (UNESP)

Cobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first de novo transcriptome assembly of R. canadum liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyzes with Danio rerio, Lates calcarifer, Seriola lalandi dorsalis, Seriola dumerili or Echeneis naucrates. Finally, we identified 7,894 microsatellites related to cobia's putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.

Made available in DSpace on 2021-06-25T12:18:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-10-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The present study aimed to evaluate two different methods of artificial reproduction induction, and characterize the embryonic development ofSalminus hilarii. Different than observed for other tropical fish species, artificial reproduction induction followed by hand-stripping of gametes was considered unfeasible forS.hilarii, as no gamete fertilization was observed. However, females that were induced and spawned naturally presented a fertilization rate of 65.64 +/- 0.54%. With a mean temperature of 26.20 +/- 0.90oC it was possible to clearly distinguish a large perivitelline space at 14 min after fertilization (AF) and at 49 min AF more than 50% of the embryos presented two blastomeres, and these cleavages occurred until 1 h 54 min AF. The gastrula phase was characterized at 3 h 56 min AF, and blastopore closure was observed at 8 h 31 min AF. At 9 h 1 min, organogenesis started, with a clear distinction of the yolk mass, embryonic axis, cephalic and caudal regions; at 11 h 51 min AF the embryos already had advanced segmentation and a free tail. Total hatching occurred at 21 h 17 min and after opening the mouth, which occurred at 33 h 9 min, the larvae ofS.hilariipresented a strong and characteristic cannibalism. This information can be considered fundamental to improvingS.hilariiproduction in captivity and for collaboration with a conservation programme in the upper Tiete river basin. Univ Mogi das Cruzes, Nucleo Integrad Biotecnoi, Av Dr Candido Xavier de Almeida Souza 200, BR-08780911 Mogi Das Cruzes, SP, Brazil Univ Estadual Paulista Julio de Mesquita Filho CA, Ctr Aquicultura, Via Acesso Prof Paulo Donato Castaane S-N, BR-14884900 Jaboticabal, SP, Brazil Univ Sao Paulo, Inst Biociencias, Dept Fisiol, Rua Matao,Trav 14,321, BR-05508090 Sao Paulo, SP, Brazil Univ Sao Paulo, Ctr Biol Marinha, Rodovia Manoel Hipolito do Rego,Km 131,5, BR-11612109 Sao Sebastiao, SP, Brazil Univ Estadual Paulista Julio de Mesquita Filho CA, Ctr Aquicultura, Via Acesso Prof Paulo Donato Castaane S-N, BR-14884900 Jaboticabal, SP, Brazil FAPESP: FAPESP 2001/10483-1 FAPESP: 2008/57687-0 FAPESP: 2014/16320-7 FAPESP: 2017/06765-0 CNPq: CNPq 134451/2005-8

The presence of intermuscular bones in fisheries products limits the consumption and commercialization potential of many fish species, including tambaqui (Colossoma macropomum). These bones have caused medical emergencies and are an undesirable characteristic for fish farming because their removal is labor-intensive during fish processing. Despite the difficulty in identifying genes related to the lack of intermuscular bone in diverse species of fish, the discovery of individuals lacking intermuscular bones in a Neotropical freshwater characiform fish has provided a unique opportunity to delve into the genetic mechanisms underlying the pathways of intermuscular bone formation. In this study, we carried out a GWAS among boneless and wt tambaqui populations to identify markers associated with a lack of intermuscular bone. After analyzing 11 416 SNPs in 360 individuals (12 boneless and 348 bony), we report 675 significant (Padj

The present study aimed to evaluate two different methods of artificial reproduction induction, and characterize the embryonic development of Salminus hilarii. Different than observed for other tropical fish species, artificial reproduction induction followed by hand-stripping of gametes was considered unfeasible for S. hilarii, as no gamete fertilization was observed. However, females that were induced and spawned naturally presented a fertilization rate of 65.64 ± 0.54%. With a mean temperature of 26.20 ± 0.90ºC it was possible to clearly distinguish a large perivitelline space at 14 min after fertilization (AF) and at 49 min AF more than 50% of the embryos presented two blastomeres, and these cleavages occurred until 1 h 54 min AF. The gastrula phase was characterized at 3 h 56 min AF, and blastopore closure was observed at 8 h 31 min AF. At 9 h 1 min, organogenesis started, with a clear distinction of the yolk mass, embryonic axis, cephalic and caudal regions; at 11 h 51 min AF the embryos already had advanced segmentation and a free tail. Total hatching occurred at 21 h 17 min and after opening the mouth, which occurred at 33 h 9 min, the larvae of S. hilarii presented a strong and characteristic cannibalism. This information can be considered fundamental to improving S. hilarii production in captivity and for collaboration with a conservation programme in the upper Tietê river basin.

Made available in DSpace on 2020-12-12T02:06:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-08-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The Nile tilapia (Oreochromis niloticus) is a prominent farmed fish in aquaculture worldwide. Crossbreeding has recently been carried out between the Red-Stirling and the wt Chitralada strains of Nile tilapia, producing a heterotic hybrid (7/8 Chitralada and 1/8 Red-Stirling) that combines the superior growth performance of the Chitralada with the reddish coloration of the Red-Stirling strain. While classical selective breeding and crossbreeding strategies are well known, the molecular mechanisms underlying the phenotypic expression of economically advantageous traits in tilapia remain largely unknown. Molecular investigations have shown that variable expression of growth hormone (gh), insulin-like growth factors (igf1 and 2) and somatolactin (smtla) – components of the growth hormone/insulin-like growth factor (GH/IGF) axis – and myostatin (mstn) genes can affect traits of economic relevance in farmed animals. The aim of this study was to assess and compare the gene expression signature among Chitralada, Red-Stirling and their backcross hybrid in order to gain insights into the effects of introgressive breeding in modulation of the GH/IGF axis. Gene expression analyses in distinct tissues showed that most genes of the GH/IGF axis were up-regulated and mstn was down-regulated in backcross animals in comparison with Red-Stirling and Chitralada animals. These gene expression profiles revealed that backcross animals displayed a distinctive expression signature, which attests to the effectiveness of the introgressive breeding technique. Our findings also suggest that the GH/IGF axis and mstn genes might be candidate markers for fish performance and prove useful within genetic improvement programs aimed at the production of superior-quality tilapia strains using introgressive breeding. Department of Genetics Institute of Biosciences of Botucatu São Paulo State University (UNESP) Unit of Biotechnology University of Mogi das Cruzes Department of Animal Sciences Federal University of Lavras São Paulo State University (UNESP) Department of Genetics Institute of Biosciences of Botucatu São Paulo State University (UNESP) São Paulo State University (UNESP) CNPq: 131265/2015-6 CNPq: 158284/2013-5 FAPESP: 2012/15589-7 FAPESP: 2014/03062-0 CNPq: 304662/2017-8 CNPq: 312046/2014-6 CNPq: 312273/2017-7 CNPq: 460608/2014-2

The Neotropical region harbors > 7000 species of freshwater fish, many of them important as genetic resources for fisheries and aquaculture. The myriad aquatic environments of the Neotropics and the fish living there raise challenging scientific issues regarding local adaptation and the physiological mechanisms underlying locally adapted phenotypes. The current technologies for exploring genomes are boosting our knowledge about the genetic mechanisms underlying adaptation and how they operate at the physiological level. This chapter explores how genetics and physiology interact to answer open biological questions concerning Neotropical fish life cycles.

The night shark, Carcharhinus signatus, is a mesopelagic, semi‐oceanic shark species found only in the Atlantic Ocean. It is one of the most frequently caught sharks in pelagic longline fisheries and is classified as Vulnerable by the International Union for the Conservation of Nature (IUCN). Despite their prevalence in commercial fisheries, the population genetic structure of the night shark has not been assessed. The present study investigated the genetic diversity, genetic connectivity, and phylogeography of the species throughout the western Atlantic Ocean, based on complete mitochondrial control region (mtCR) sequence data (n = 152) and genotypic data from nine nuclear microsatellites (n = 119). The mtCR sequence revealed 19 haplotypes, with overall haplotype and nucleotide diversities of 0.74 (±0.027) and 0.0034 (±0.0019), respectively, whereas the nuclear microsatellite observed and expected heterozygosities were 0.408 and 0.421, respectively. There was significant population structure (ФST = 0.429; P

Many populations of elasmobranchs (sharks and rays) are experiencing severe declines due to the high demand for shark fins in Asia, the activities of unregulated fisheries, and increases in shark and ray catches. Recently, the effects of the decline in the populations of marine fish species on genetic diversity have drawn increasing attention; however, only a few studies have addressed the genetic diversity of shark and ray populations. Here, we report the results of a quantitative analysis of the genetic diversity of shark and ray species over the past 20 years and discuss the importance and utility of this genetic information for fisheries management and conservation policies. Furthermore, we suggest future actions important for minimizing the gaps in our current knowledge of the genetic diversity of shark and ray species and to minimize the information gap between genetic scientists and policymakers. We suggest that shark and ray fisheries management and conservation policies consider genetic diversity information, such as the management unit, effective population size (Ne), haplotype and nucleotide diversity, observed heterozygosity, and allelic richness, because the long-term survival of a species is strongly dependent on the levels of genetic diversity within and between populations. In addition, sharks and rays are a group of particular interest for genetic conservation due to their remarkable life histories.

Este trabalho apresenta o primeiro registro de uma espécie exótica de ostra em Bertioga, Estado de São Paulo (sudeste da costa brasileira). As ostras exóticas foram encontradas fixadas em raí­­zes de mangue, costões rochosos, pedras e cascalhos no leito do rio, formando agrupamentos de 10í 20 indiví­­duos e coabitando com as espécies de ostras nativas (Crassostrea mangle, C. brasiliana e Ostrea spp.). Os resultados baseiam-se em análises moleculares de espécimes coletados no rio Itaguaré em junho de 2014. Foram utilizadas sequências parciais dos genes 16S e COI para avaliar a identidade taxonômica. As análises fenéticas foram realizadas pelo método de Neighbour-joining. A divergência genética foi calculada através das distí­¢ncias do parí­¢metro-2 de Kimura (K2P). As sequências agruparam-se com uma sequência de Saccostrea cucullata de Madagascar para ambos os genes (COI e 16S) e apresentaram uma distí­¢ncia genética de 1,7í 2,2% e 3,5í 5,3% de outras sequências do "grupo S. cucullata” para fragmentos de 16S e COI respectivamente. As distí­¢ncias genéticas de outras espécies de Saccostrea (S. palmula, S. glomerata e S. mordax) variaram de 4,7 a 9,1% para 16S e de 13,8 a 19,0% para COI. As distí­¢ncias genéticas de outras espécies de ostras dos gêneros Ostrea e Crassostrea foram superiores a 14,0% e 25,0% para 16S e COI respectivamente. O registro é discutido no contexto de possí­­veis consequências para o ambiente e prováveis vias de introdução. Este é o primeiro registro publicado de uma espécie de Saccostrea no sudoeste do Oceano Atlí­¢ntico.

Made available in DSpace on 2018-12-11T17:15:47Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-03-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Save Our Seas Foundation The silky shark, Carcharhinus falciformis, is a large-bodied, oceanic-coastal, epipelagic species found worldwide in tropical and subtropical waters. Despite its commercial importance, concerns about overexploitation, and likely ecological significance of this shark as an upper trophic-level predator, understanding of its population dynamics remains unclear for large parts of its distribution. We investigated the genetic diversity, population structure and demographic history of the silky shark along the western Atlantic Ocean based on the use of 707 bp of the mitochondrial DNA control region (mtCR). A total of 211 silky sharks were sampled, originating from five areas along the western Atlantic Ocean. The mitochondrial sequences revealed 40 haplotypes, with overall haplotype and nucleotide diversities of 0.88 (± 0.012) and 0.005 (± 0.003), respectively. The overall population structure was significantly different among the five western Atlantic Ocean regions. Phylogenetic analysis of mtCR sequences from globally sourced silky shark samples revealed two lineages, comprising a western Atlantic lineage and western Atlantic—Indo-Pacific lineage that diverged during the Pleistocene Epoch. In general, tests for the demographic history of silky sharks supported a population expansion for both the global sample set and the two lineages. Although our results showed that silky sharks have high genetic diversity, the current high level of overexploitation of this species requires long-term, scientifically informed management efforts. We recommend that fishery management and conservation plans be done separately for the two western Atlantic matrilineal populations revealed here. Universidade Estadual Paulista – UNESP Instituto de Biociências de Rio Claro, Av. 24-A, 1515 Laboratório de Pesquisa de Elasmobrânquios Instituto de Biociências Universidade Estadual Paulista – UNESP Campus do Litoral Paulista, Praça Infante D. Henrique, s/n Universidade de Mogi das Cruzes Núcleo Integrado de Biotecnologia., PO BOX 411 Save Our Seas Shark Research Center USA and Guy Harvey Research Institute Nova Southeastern University, 8000 North Ocean Drive Laboratório de Oceanografia Pesqueira Departamento de Pesca e Aquicultura Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos Universidade Estadual Paulista – UNESP Instituto de Biociências de Rio Claro, Av. 24-A, 1515 Laboratório de Pesquisa de Elasmobrânquios Instituto de Biociências Universidade Estadual Paulista – UNESP Campus do Litoral Paulista, Praça Infante D. Henrique, s/n FAPESP: #2009/59660-6 FAPESP: #2013/08675-7

Polymorphisms in the growth hormone (GH) gene that is associated with the growth rate of farmed fish have been the target of many breeding programmes. The present study aimed to identify single nucleotide polymorphisms (SNPs) in GH gene regions to evaluate the association of SNP variations with the growth rate of two Nile tilapia: Oreochromis niloticus (Linnaeus, 1758) strains. The targeted regions were amplified, sequenced, aligned and screened for the presence of SNPs; thereafter, performance tests were used to check for the association between SNPs and weight. Allele and genotype frequencies were estimated for each SNP and genotype. Genotype blocks or sets of SNP genotypes and frequencies were also estimated. Association between SNPs and growth rate was statistically evaluated using a univariate linear mixed model that included both fixed and random effects. A total of 10 SNPs were identified, nine in the proximal promoter and one located in the 5′ UTR, forming 10 genotype blocks. In all weight recordings, five genotype blocks were significantly associated with the highest weights. Single nucleotide polymorphisms 6-10 were also found to be significantly associated with growth (p-value

Brycon hilarii, a characid species endemic to the Upper Paraguay hydrographic basin, is important to regional artisanal and sports fisheries. To develop effective strategies for conservation of this species in the face of potential environmental changes in the Pantanal region, we characterized genetic structuring within and among six B. hilarii collections based on variation at five microsatellite DNA markers. Within-population genetic variability was high, with 75 different alleles; mean average allelic richness per locus per sample location ranged from 6.06 to 7.99. Nei’s gene diversity (hs) varied among drainages from 0.66 (±0.2) to 0.69 (±0.2), with an average across the four genetically identified populations of 0.68 (±0.02). Analyses of Jost’s D EST and F ST-like indices, AMOVA, and Structure-based clustering analyses indicated that B. hilarii populations exhibit a low level of genetic structure, with some indications that the Taquari River population is somewhat distinct from others. Results of K-means analysis suggested little or no structuring, with weakly differentiated populations above and below the confluence of the Paraguay and Taquari rivers. Because B. hilarii populations in the Pantanal are linked by high levels of gene flow, habitat alterations that would interfere with gene flow may jeopardize the long-term persistance of the species.

In order to develop a crossbred of Oreochromis niloticus with a high growth rate and coloration, a backcross breeding program was developed using Red-Stirling and Chitralada strains with 50%, 75%, and 87.5% of genic proportion to Chitralada. Seven genetic groups were obtained from Chitralada (C) and Red-Stirling (R): the hybrids F1, fish-female Red-Stirling × fish-male Chitralada (RC), and its reciprocal (CR), and the backcross breeding (BB1), fish-female CR × fish-male Chitralada (CR × C), and its reciprocal (C × CR) and BB2 [C(C × CR)]. Growth curves were adjusted using an exponential model for females and males. The curves show a distinct difference among genetic groups and between genders based on the backcross breddingapproach. The best ranking for red females was observed in BB1 [C × (CR)]. The gain observed is due to the action of a genetic additive effect of Chitralada (42.90 g), a maternal effect of Chitralada (41.48 g), and a non-additive effect, which is attributed to paternal heterosis (11.41 g). While the best ranking for red males was found in BB2, The observed gain may be attributed to an additive genetic effect of Chitralada (74.04 g) and maternal effect of Chitralada (57.68 g). Survival among females was average. Among males, a higher mortality in the Red-Stirling group was observed compared to the other groups. These results indicate that the backcross breeding program can be used to develop genetic lines of red tilapia for further genetic breeding programs mainly exploring paternal heterosis to produce dams. Statement of relevance The present study proposes a breeding methodology based in robust statistical analysis to develop genetically lines of red tilapia.

Made available in DSpace on 2019-10-04T12:40:28Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-15 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) An 8-week nutritional experiment was conducted with the aim of evaluating the influences of different arachidonic acid (ARA) levels and two different temperatures (29.5 degrees C and 26.5 degrees C) on the growth performance, tissue and whole-body fatty acid (FA) compositions, plasma prostaglandin concentration, liver morphology and expression of genes related to lipid metabolism in cobia juveniles. A basal fat-reduced diet was manufactured and subsequently coated with different FA sources, distinct levels of ARA (ARA1, 0.5%; ARA2, 1.2%; and ARA3, 1.9%) and fish oil (FO: 8.8%, as a control diet). All diets were formulated to be isoproteic and isolipidic. Cobia juveniles (5.86 +/- 0.40 g) were randomly divided into 24 tanks with 18 animals each. Twelve tanks were kept at 29.5 degrees C, and 12 tanks were kept at 26.5 degrees C. The animals were fed twice per day with each experimental diet until apparent satiation in triplicate tanks at both temperatures. The results revealed that the animals maintained at 26.5 degrees C and fed with the ARA diets exhibited better growth than those fed with the FO diet and kept at 29.5 degrees C. In contrast to observations in other teleost species, ARA excess did not reduce growth or survival. The FA compositions of the livers, fillets and whole bodies generally reflected the diet compositions, i.e., gradual increases in ARA were observed according to the diet level. Additionally, greater depositions of docosahexaenoic acid (DHA) in the fillets of the animals from the ARA2 group that was kept at 26.5 degrees C were observed. The plasma prostaglandin levels were greater in the animals that were kept at 29.5 degrees C for all experimental diets and in the ARA2 animals compared with the FO groups at both temperatures. The FAS and SREBP-1 expressions in the livers were down-regulated in the ARA1 and ARA2 animals that were maintained at 26.5 degrees C compared with the animals that were fed the same diets but kept at 29.5 degrees C. Additionally, SREBP-1 expression was up-regulated in the ARA2 animals compared with the FO animals at both temperatures. The results of this study indicated that ARA inclusion between 0.5 and 1.9% combined with a temperature of 26.5 degrees C can improve juvenile cobia growth performance and directly influence the modulation of prostaglandin synthesis and the relative expressions of lipid genes. Univ Mogi das Cruzes, Nucl Integrado Biotecnol, Av Dr Candido Xavier de Almeida Souza 200, BR-08780911 Mogi Das Cruzes, SP, Brazil Univ Sao Paulo CEBIMar USP, Ctr Biol Marinha, Rodovia Manoel Hipolito Rego Km 131,5, BR-11600000 Sao Sebastiao, SP, Brazil CSIRO, Agr & Food, Aquaculture Program, Bribie Isl Res Ctr, Woorim, Qld 4507, Australia Univ Estadual Paulista Julio de Mesquita Filho CA, Ctr Aquicultura, Via Acesso Prof Paulo Donato Castellane S-N, BR-14884900 Jaboticabal, SP, Brazil Univ Sao Paulo, Inst Biociencias, Dept Fisiol, Rua Matao,Trav 14,321, BR-05508090 Sao Paulo, SP, Brazil Univ Estadual Paulista Julio de Mesquita Filho CA, Ctr Aquicultura, Via Acesso Prof Paulo Donato Castellane S-N, BR-14884900 Jaboticabal, SP, Brazil FAPESP: 2014/16320-7 FAPESP: 2016/12435-0

Made available in DSpace on 2019-10-06T16:46:50Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-01-01 Red tilapia is a phenotype with potential value to the tilapia industry due to its attractive skin coloration. However, the presence of black blotches scattered on the body makes these fish less valuable than blemish-free red fish. The correlation between the degree of blotching and other economic traits is important for selective breeding programs including high-performance red fish without black blotches. Therefore, this study aimed to assess the magnitude and direct and indirect effects of blotching in crossbred red tilapia on the growth rate and body measure traits using path analysis methodology. Six genetic groups were evaluated in terms of body measurements, body weight rate, and proportion of black blotching over 250 days of growth: Chitralada and Red-Stirling; crossbred F1—♀ Red-Stirling × ♂ Chitralada and ♀ Chitralada × ♂ Red-Stirling, and the introgressive crossbreeding—♀ CR × ♂ Chitralada and ♀ Chitralada × ♂ CR (C × CR). All variables showed high and positive linear correlations. Individuals with black blotches had lower coefficients of correlation with other variables (body weight and measurements); the direct and indirect effects are near zero. The path analysis indicated a lack of genetic correlation between the degree of black blotches and the economic traits of red tilapia. This facilitates the development of high growth performance red fish with blotched-free reddish skin. Federal Institute of Education Science and Technology Baiano, Campus Santa Inês Department of Animal Sciences Federal University of Lavras São Paulo State University-UNESP Agrarian Sciences Center José do Rosário Vellano University-UNIFENAS Aquaculture Center São Paulo State University-UNESP Unit of Biotechnology University of Mogi das Cruzes São Paulo State University-UNESP Aquaculture Center São Paulo State University-UNESP

Astyanax fasciatus is a group of neotropical fish with two different diploid chromosome numbers, and in the wild, these individuals are found in sympatry. The annual reproductive cycles of adult females of species with different numbers of chromosomes (G1: 46 chromosomes, low responsiveness to induced spawning; G2: 48 chromosomes, responsive to induced spawning) were investigated in the wild and in captivity. Plasma estradiol (E2) levels, relative fecundity (RF), oocyte diameter, gonadosomatic index, and ovarian morpho-histology were evaluated to identify the ovarian maturation stage. The G1 females in both environments began the vitellogenic phase during winter, concurrent with increased plasma E2 levels. In wild G1 females, large numbers of vitellogenic oocytes were observed during spring and summer, when plasma E2 levels remained high. In contrast, captive G1 females showed higher E2 levels during the winter. They also retained significantly higher RF and vitellogenic oocyte numbers than wild females, but showed no spawning and slow yolk reabsorption. Wild G2 females began the vitellogenic phase in autumn and had progressively increasing E2 levels that peaked in the spring, with spawning occurring during the summer. In captive G2 females, the E2 levels and RF remained high throughout the year. These data suggest that A. aff. fasciatus with different numbers of chromosomes differ in their reproductive performance in the wild and show altered sensitivity to environmental cues in captivity. Our results indicate that G1 females likely respond best to artificial spawning just after winter, whereas G2 females should respond year-round.