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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.

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, runx2b−/− mutants completely lost IBs, while swimming performance, growth and bone mineral density were not significantly different from runx2b+/+ zebrafish. Comparative single-cell RNA sequencing (scRNA-seq) analysis in runx2b−/− and runx2b+/+ zebrafish revealed the role of osteoblasts in IB formation. In addition, differentially expressed genes were enriched in the transforming growth factor β/bone morphogenetic protein (TGF-β/BMP) pathway after runx2b deletion. This study provides evidence for the crucial role of runx2b regulation in IB formation. Genetic breeding can target runx2b regulation and generate strains of commercial fish species without IBs, which can improve the safe consumption and economic value of many farmed fish species.

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.

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)

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

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 2018-12-11T17:20:34Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-12-01 MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identified, many of which seem to be teleost-specific, cichlid-specific or tilapia-specific. Abundant miRNA isoforms (isomiRs) were identified with modifications in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable differential ratio of miRNA arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs. Department of Genetics Institute of Biosciences of Botucatu Sao Paulo State University (UNESP) Department of Physics and Biophysics Institute of Biosciences of Botucatu Sao Paulo State University (UNESP) School of Biological Sciences University of East Anglia (UEA), Norwich Research Park Department of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU) Stevenson Center Vanderbilt University Unit of Biotechnology University of Mogi das Cruzes Department of Morphology Institute of Biosciences of Botucatu Sao Paulo State University (UNESP) Department of Genetics Institute of Biosciences of Botucatu Sao Paulo State University (UNESP) Department of Physics and Biophysics Institute of Biosciences of Botucatu Sao Paulo State University (UNESP) Department of Morphology Institute of Biosciences of Botucatu Sao Paulo State University (UNESP)

In the last decade, several studies have been focused on revealing the microRNA (miRNA) repertoire and determining their functions in farm animals such as poultry, pigs, cattle, and fish. These small non-protein coding RNA molecules (18–25 nucleotides) are capable of controlling gene expression by binding to messenger RNA (mRNA) targets, thus interfering in the final protein output. MiRNAs have been recognized as the main regulators of biological features of economic interest, including body growth, muscle development, fat deposition, and immunology, among other highly valuable traits, in aquatic livestock. Currently, the miRNA repertoire of some farmed fish species has been identified and characterized, bringing insights about miRNA functions, and novel perspectives for improving health and productivity. In this review, we summarize the current advances in miRNA research by examining available data on Neotropical and other key species exploited by fisheries and in aquaculture worldwide and discuss how future studies on Neotropical fish could benefit from this knowledge. We also make a horizontal comparison of major results and discuss forefront strategies for miRNA manipulation in aquaculture focusing on forward-looking ideas for forthcoming research.

Genetic variation of Salminus hilarii was assessed by screening microsatellite loci and mitochondrial D-loop DNA across four sampling in the upper rio Paraná basin of Brazil. Genetic diversity - measured as mean expected heterozygosity (0.904) and mean number of alleles across populations (13.7) - was reasonably high. Differentiation of microsatellite allele frequencies among populations was shown to be low but significant by AMOVA Φ ST (0.0192), and high by D EST (0.185). D-loop variation was high, with haplotypic diversity of 0.950 and nucleotide diversity of 0.011. Mitochondrial DNA-based estimates for population differentiation were high, with an overall Φ ST of 0.173. The results of tests of nuclear and mitochondrial variation yielded no unequivocal inference of historical demographic bottleneck or expansion. Genetic differentiation observed among S. hilarii populations in the rio Grande may be caused by a combination of historical differentiation and recent gene-flow disruption caused by the dams followed by reproduction of isolated spawning assemblages in mid-sized tributaries of the respective reservoirs. We present spatially more intensive sampling of S. hilarii populations across the rio Paraná basin in order to more effectively distinguish between historical and contemporary differentiation. A variabilidade genética de Salminus hilarii foi avaliada por lócus microssatélites e sequências D-Loop do DNA mitocondrial em quatro populações da região da bacia do Alto Paraná. A diversidade genética - medida pela heterozigosidade média (0,904) e número de alelos médios das populações (13,7) - foi razoavelmente alta. A diferenciação das frequências alélicas entre as populações foi baixa, mas significativa pela AMOVA Φ ST (0,0192), e alta pelo D EST (0,185). A variação mitocondrial foi alta com uma diversidade haplotípica de 0,950 e uma diversidade nucleotídica de 0,011. Estimativas de diferenciação populacional baseadas no DNA mitocondrial foram altas, com um valor global de Φ ST de 0,173. Os resultados dos testes da variação nuclear e mitocondrial demonstram nenhuma inequívoca inferência histórica de contração e expansão demográfica. A diferenciação genética observada entre as populações de S. hilarii no rio Grande pode ter sido causada pela combinação de diferenciação histórica e interrupção recente do fluxo gênico causada pela construção de barragens seguida por um isolamento reprodutivo de populações em tributários de médio porte dos respectivos reservatórios. Nós apresentamos uma amostragem mais ampla e intensiva de populações de S. hilarii ao longo da bacia do alto rio Paraná para se efetivamente distinguir se a diferenciação genética das populações encontrada é histórica ou contemporânea.

Homoplasmy is a feature usually found in the mtDNA of higher animal taxa. On the other hand, the presence of two classes of mtDNA in the same cell or organism is rare and may appear in length or site variation. Data from mtDNA RFLP analysis of Brycon opalinus populations (Cuvier, 1819; Characiformes, Characidae, Bryconinae) revealed site heteroplasmy from endonuclease NheI digestion. Southern blotting hybridization was used to survey a total of 257 specimens with 24 restriction enzymes. Three different restriction fragment patterns of mtDNA were obtained from NheI digestion. Two individuals from hatchery broodstock were found to have two of them. NheI digests of heteroplasmic individuals yielded two fragments of approximately 1180 and 1260 bp. Despite the low frequency of this type of heteroplasmy in the whole B. opalinus population, the presence of site heteroplasmy in this species supports the evidence of this phenomenon in lower vertebrate groups.

Made available in DSpace on 2019-09-12T16:56:55Z (GMT). No. of bitstreams: 0 Previous issue date: 1999 Proteína e DNA mitocondrial têm sido utilizados como marcadores moleculares para avaliar a variabilidade nos estudos de identificação de peixes. A proteína e o mt DNA utilizados para análise eletroforética são extraídos dos tecidos, o que geralmente leva à morte dos indivíduos. Neste estudo, apresentamos um procedimento de biópsia do músculo esquelético para extrair DNA mitocondrial que não requer sacrifício da amostra. Oitenta pirapitinga-do-sul ( Brycon opalinus ) foram biopsiadas pela presente técnica, sem mortalidade registrada. O DNA total foi extraído do músculo e digerido pelas enzimas de restrição Apa I e Hpa I. Os padrões de fragmentos de mt DNA foram hibridados com 32S ondas de mt DNA de pirapitinga-do-sul marcadas com P. A técnica descrita é simples e pode ser útil em protocolos que requerem extração de tecido para análises de DNA e proteínas sem perda do indivíduo investigado. Protein and mitochondrial DNA have been used as molecular markers to assess variability in stock identification studies of fishes. Protein and mtDNA used for electrophoretic analysis are extracted from tissues, which often leads to death of the individuals. In this study, we present a skeletal muscle biopsy procedure to extract mitochondrial DNA that does not require specimen sacrifice. Eighty pirapitinga-do-sul (Brycon opalinus) were biopsied by the present technique. with no mortalities recorded. Total DNA was extracted from muscle and digested by restriction enzymes ApaI and HpaI. The mtDNA fragment patterns were hybridized with P-32-labeled pirapitinga-do-sul mtDNA probes. The described technique is simple and may be useful in protocols requiring tissue extraction for DNA and protein analyses without loss of the individual investigated. FMUSP, Inst Coracao, Lab Genet & Cardiol Mol, BR-05403010 Sao Paulo, Brazil; FMUSP, Dept Clin Med, BR-05403010 Sao Paulo, Brazil; CESP, Estacao Hidrobiol & Piscicultura, Paraibuna, SP, Brazil; Universidade de Taubaté (Unitau), Dept Ciencias Agrarias

Made available in DSpace on 2013-08-12T18:37:09Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-09-01 Made available in DSpace on 2013-09-30T19:11:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-09-01 Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T15:30:30Z No. of bitstreams: 0 Made available in DSpace on 2014-05-20T15:30:30Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-09-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Premise of the study: Microsatellite markers were developed to study the genetic diversity and population structure of the carnivorous bladderwort Utricularia reniformis, which is endemic to the Atlantic Forest of southern and southeastern Brazil. Cross-species amplification was tested in U. gibba, U. neottioides, U. subulata, and Pinguicula benedicta.Methods and Results: The U. reniformis genome was sequenced in a 454 GS FLX sequencer, and eight primer sets were developed based on the microsatellites identified from the reads. All loci are polymorphic, showing 1.6 to 4.8 alleles per population. Preliminary results show that primer sets are suitable for population-level studies. Cross-species amplifi cation was successful in three other Utricularia species and one Pinguicula species.Conclusions: Markers developed in this study provide tools for analyses of intra- and interpopulation genetic diversity in Utricularia and Pinguicula. Univ Mogi das Cruzes, Nucleo Integrado Biotecnol, BR-08780911 São Paulo, Brazil Univ Florida, Dept Biol, Gainesville, FL 32611 USA Univ São Paulo, Dept Microbiol, BR-05508900 São Paulo, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Vet, BR-14884900 São Paulo, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Vet, BR-14884900 São Paulo, Brazil FAPESP: 08/22239-9 FAPESP: 07/58277-7 CAPES: 5316/10-3

Artificial reproduction and gamete fertilization were evaluated in Salminus hilarii wild and domesticated broodstocks. Wild and domesticated broodstocks were artificially induced to reproduction using a carp pituitary treatment. Four groups were considered: Group 1 (G1), fish caught in the wild maintained for three years in the same conditions as the domesticated broodstocks and spawned naturally; Group 2 (G2), broodstock born and raised in captivity and spawned naturally; Group 3 (G3), wild broodstocks, which were manually stripped for gamete collection and dry fertilization; and Group 4 (G4), domesticated males and females, also manually stripped. Oocytes, eggs, and larvae were sampled at different time intervals throughout embryonic development. Yolk sac absorption occurred approximately 24-29 h after hatching. Twenty-six h after hatching, the larvae mouths opened. Cannibalism was identified just 28-30 h after hatching. There was no morphological difference in embryonic development among all groups. The number of released eggs per gram of female was: G1: 83.3 ± 24.5 and G2: 103.8 ± 37.4; however, the fertilization success was lower in G2 (42.0 ± 6.37 %) compared with G1 (54.7 ± 3.02%) (P = 0.011). Hand-stripping of oocytes was not successful and the fertilization rate was zero. The reproduction of this species in captivity is viable, but it is necessary to improve broodstock management to enhance fertilization rates and obtain better fingerling production for restocking programs.A reprodução artificial e fertilização dos gametas foram avaliados em reprodutores selvagens e de cativeiro de Salminus hilarii. Reprodutores selvagens e de cativeiro foram induzidos artificialmente à reprodução utilizando hipófise de carpa. Quatros grupos foram considerados: Grupo 1 (G1), peixes capturados na natureza, mantidos por três anos nas mesmas condições de reprodutores de cativeiro e desovados naturalmente; Grupo 2 (G2), reprodutores nascidos e criados em cativeiro e desovados naturalmente; Grupo 3 (G3), reprodutores selvagens que foram extrusados manualmente para a coleta de gametas e fertilização a seco; e Grupo 4 (G4), com machos e fêmeas domesticadas, também extrusados manualmente. Oócitos, ovos e larvas foram amostrados em diferentes intervalos de tempo ao longo do desenvolvimento embrionário. A absorção do saco vitelínico ocorreu aproximadamente 24-29 h após a eclosão. Vinte e seis h após a eclosão, as larvas abriram a boca. O canibalismo foi identificado apenas 28-30 h após a eclosão. Não houve diferença morfológica no desenvolvimento embrionário entre todos os grupos. O número de ovos liberados por grama de fêmea foi: G1: 83,3 ± 24,5 e G2: 103,8 ± 37,4; embora, o sucesso na fertilização tenha sido menor no G2 (42,0 ± 6,37%) em comparação com G1 (54,7 ± 3,02%) (P = 0,011). A extrusão manual dos oócitos não foi bem sucedida e a taxa de fertilização foi zero. A reprodução em cativeiro desta espécie é viável, mas é necessário um melhor manejo dos reprodutores para aumentar as taxas de fertilização, visando a obtenção de uma melhor produção de alevinos para os programas de repovoamento.

Submitted by Guilherme Lemeszenski (guilherme@nead.unesp.br) on 2013-08-22T18:43:37Z No. of bitstreams: 1 S1679-62252010000100007.pdf: 13940739 bytes, checksum: e6c2e1ac0a6eb00dada6b6f290e4368e (MD5) Made available in DSpace on 2013-08-22T18:43:37Z (GMT). No. of bitstreams: 1 S1679-62252010000100007.pdf: 13940739 bytes, checksum: e6c2e1ac0a6eb00dada6b6f290e4368e (MD5) Previous issue date: 2010-03-01 Made available in DSpace on 2013-09-30T19:31:25Z (GMT). No. of bitstreams: 2 S1679-62252010000100007.pdf: 13940739 bytes, checksum: e6c2e1ac0a6eb00dada6b6f290e4368e (MD5) S1679-62252010000100007.pdf.txt: 32078 bytes, checksum: e1c3ac26c05c6967b1231a74ee106aa3 (MD5) Previous issue date: 2010-03-01 Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T15:08:37Z No. of bitstreams: 2 S1679-62252010000100007.pdf: 13940739 bytes, checksum: e6c2e1ac0a6eb00dada6b6f290e4368e (MD5) S1679-62252010000100007.pdf.txt: 32078 bytes, checksum: e1c3ac26c05c6967b1231a74ee106aa3 (MD5) Made available in DSpace on 2014-05-20T15:08:37Z (GMT). No. of bitstreams: 2 S1679-62252010000100007.pdf: 13940739 bytes, checksum: e6c2e1ac0a6eb00dada6b6f290e4368e (MD5) S1679-62252010000100007.pdf.txt: 32078 bytes, checksum: e1c3ac26c05c6967b1231a74ee106aa3 (MD5) Previous issue date: 2010-03-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) UMC/FAEP O padrão de coloração é reconhecido como uma característica importante para a diagnose das espécies do gênero Trichomycterus e no reconhecimento de suas relações de parentesco. A análise baseada em dados morfológicos e moleculares confirma a existência de uma única espécie de Trichomycterus no rio Itatinga, drenagem litorânea da Serra do Mar e no rio Claro, curso superior do rio Tietê. A única espécie do gênero encontrada, Trichomycterus iheringi, apresenta dois padrões de pigmentação do corpo bastante distintos e padrões de coloração intermediários relacionados ao tamanho corporal e ao micro-habitat. Color pattern is recognized as an important characteristic for diagnosing Trichomycterus species and for elucidating their relationships. An analysis based on morphological and molecular data confirms the existence of a single species of Trichomycterus in the rio Itatinga, a costal river drainage on the escarpment of the Serra do Mar and the rio Claro on the upper course of the rio Tietê. The only species found, Trichomycterus iheringi, shows two clearly distinct patterns of body pigmentation and intermediate color patterns related to body size and microhabitat preference. Universidade de Mogi das Cruzes Núcleo Integrado de Biotecnologia Laboratório de Genética de Organismos Aquáticos e Aquicultura Universidade Estadual Paulista Departamento de Zoologia e Botânica Laboratório de Ictiologia Universidade Estadual Paulista Departamento de Zoologia e Botânica Laboratório de Ictiologia CNPq: 306988/2008-9 CNPq: 152782/2007-9

Tambaqui (Colossoma macropomum) is the largest native Characiform species from the Amazon and Orinoco river basins of South America. Tambaqui farming is growing rapidly in Brazil, its production reached 139.209 tons in 2014, what corresponds to 57.7% of increase compared with 2013. However, few genetic studies of tambaqui are currently available. The tambaqui genetic studies for cultured and wild populations need a holistic approach for a rational action facing ecological and market challenges in aquaculture. Approaches based on genetic studies have provided important tools to understand population dynamics, local adaptation, and gene function to improve selection strategies to be applied in breeding programs. The next-generation sequencing (NGS) allowed a great advance in genomic and transcriptomic approaches, especially related to non-model species. The genotype-by-sequencing (GBS) is one of this approaches based on genome complexity reduction using restriction enzymes (REs). This thesis presents the application of these approaches to provide advances in the genetic background for tambaqui studies. The GBS approach provided a high-density SNPs panel that allowed us to develop the first linkage map, and association studies with environmental variables, local adaptation, and lack of intermuscular bones, both using tambaqui as a model. This work can give us many theoretical references to be applied in genetic breeding programs for tambaqui, allowing a better understanding of genetic processes related to traits of interest in aquaculture. O tambaqui (Colossoma macropomum) é a maior espécie nativa de Characiforme da América do Sul e é encontrado nas bacias do rio Amazonas e Orinoco. O cultivo do tambaqui está crescendo rapidamente no Brasil, sua produção atingiu 139.209 toneladas em 2014, o que corresponde a 57,7% de aumento em relação a 2013. No entanto, poucos estudos genéticos realizados com o tambaqui estão disponíveis atualmente. Estudos genéticos em tambaqui, tanto em populações cultivadas quanto em populações selvagens, necessitam de uma abordagem holística para uma ação racional frente aos desafios ecológicos e mercadológicos na aquicultura. Abordagens baseadas em estudos genéticos têm fornecido ferramentas importantes para se entender a dinâmica populacional, adaptação local e função gênica visando melhorar as estratégias de seleção a serem aplicadas em programas de melhoramento genético. O sequenciamento de nova geração (NGS) permitiu um grande avanço nas abordagens genômicas e transcriptômicas, especialmente relacionadas a espécies não-modelo. A genotipagem por sequenciamento (GBS) é uma dessas abordagens que utilizam enzimas de restrição (REs) para reduzir a complexidade do genoma. Esta tese apresenta a aplicação desta abordagem objetivando proporcionar avanços significativos nos estudos genéticos de base para tambaqui. A técnica de GBS forneceu um painel de SNPs de alta densidade que nos permitiu desenvolver o primeiro mapa de ligação e estudos de associação com variáveis ambientais, adaptação local e ausência de ossos intermusculares no tambaqui. Este trabalho pode nos dar muitas referências teóricas a serem aplicadas em programas de melhoramento genético do tambaqui, permitindo uma melhor compreensão dos processos genéticos relacionados a traços de interesse na aquicultura.