RESUMO
Understanding the genetic architecture of phenotypic traits can provide important information about the mechanisms and genomic regions involved in local adaptation and speciation. Here, we used genotyping-by-sequencing and a combination of previously published and newly generated data to construct sex-specific linkage maps for sockeye salmon (Oncorhynchus nerka). We then used the denser female linkage map to conduct quantitative trait locus (QTL) analysis for 4 phenotypic traits in 3 families. The female linkage map consisted of 6322 loci distributed across 29 linkage groups and was 4082 cM long, and the male map contained 2179 loci found on 28 linkage groups and was 2291 cM long. We found 26 QTL: 6 for thermotolerance, 5 for length, 9 for weight, and 6 for condition factor. QTL were distributed nonrandomly across the genome and were often found in hotspots containing multiple QTL for a variety of phenotypic traits. These hotspots may represent adaptively important regions and are excellent candidates for future research. Comparing our results with studies in other salmonids revealed several regions with overlapping QTL for the same phenotypic trait, indicating these regions may be adaptively important across multiple species. Altogether, our study demonstrates the utility of genomic data for investigating the genetic basis of important phenotypic traits. Additionally, the linkage map created here will enable future research on the genetic basis of phenotypic traits in salmon.
Assuntos
Mapeamento Cromossômico , Locos de Características Quantitativas , Salmão/genética , Análise de Sequência de DNA , Animais , Feminino , Ligação Genética , Genótipo , Masculino , Fenótipo , Polimorfismo de Nucleotídeo ÚnicoRESUMO
BACKGROUND: Meiotic maps are a key tool for comparative genomics and association mapping studies. Next-generation sequencing and genotyping by sequencing are speeding the processes of SNP discovery and the development of new genetic tools, including meiotic maps for numerous species. Currently there are limited genetic resources for sockeye salmon, Oncorhynchus nerka. We develop the first dense meiotic map for sockeye salmon using a combination of novel SNPs found in restriction site associated DNA (RAD tags) and SNPs available from existing expressed sequence tag (EST) based assays. RESULTS: We discovered and genotyped putative SNPs in 3,430 RAD tags. We removed paralogous sequence variants leaving 1,672 SNPs; these were combined with 53 EST-based SNP genotypes for linkage mapping. The map contained 29 male and female linkage groups, consistent with the haploid chromosome number expected for sockeye salmon. The female map contains 1,057 loci spanning 4,896 cM, and the male map contains 1,118 loci spanning 4,220 cM. Regions of conservation with rainbow trout and synteny between the RAD based rainbow trout map and the sockeye salmon map were established. CONCLUSIONS: Using RAD sequencing and EST-based SNP assays we successfully generated the first high density linkage map for sockeye salmon.
Assuntos
Mapeamento Cromossômico/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Meiose/genética , Salmão/genética , Análise de Sequência de DNA , Animais , Feminino , Loci Gênicos/genética , Marcadores Genéticos/genética , Técnicas de Genotipagem , Masculino , Polimorfismo de Nucleotídeo Único/genéticaRESUMO
The production and trade of objects manufactured from the skeletal axis of coralid precious corals is a historically, culturally and economically important global industry. Coralids are members of the diverse Coralliidae family, which contains several species complexes and morphospecies. For most precious coral found in the jewelry trade, the color remains the sole clue and link to the taxonomic identity of the individual. Different coralid species have however similar or overlapping colors resulting in difficulty to taxonomically identify jewelry objects, including four species listed by the Convention on the International Trade of Endangered Species (CITES) whose international transport and trade requires species-specific and country of origin documentation. We aimed at developing a reliable method to taxonomically identify coralid material with the objective of distinguishing CITES protected species from their non-protected counterparts. We present Coral-ID, a genetic assay to taxonomically classify coralid objects using quasi non-destructive sampling. The assay classifies the analyzed sample in one of six taxonomic categories and performs at least presumptive separation of CITES-listed and non-listed species in all cases. Developmental validation experiments prove that Coral-ID is a specific, accurate and very sensitive method. As the first attempt to randomly sample corals in the trade to identify them, we applied Coral-ID on 20 precious coral objects seized by custom authorities upon import to in Switzerland. Thirteen (65%) of these samples could be analyzed; three of these were found to be presumptively CITES-listed, and 10 of them have proven to originate from non-CITES-listed species.
Assuntos
Antozoários , Animais , Antozoários/genética , Comércio , Testes Genéticos , Humanos , Internacionalidade , Especificidade da EspécieRESUMO
Deep-sea corals are a critical component of habitat in the deep-sea, existing as regional hotspots for biodiversity, and are associated with increased assemblages of fish, including commercially important species. Because sampling these species is so difficult, little is known about the connectivity and life history of deep-sea octocoral populations. This study evaluates the genetic connectivity among 23 individuals of the deep-sea octocoral Swiftia simplex collected from Eastern Pacific waters along the west coast of the United States. We utilized high-throughput restriction-site associated DNA (RAD)-tag sequencing to develop the first molecular genetic resource for the deep-sea octocoral, Swiftia simplex. Using this technique we discovered thousands of putative genome-wide SNPs in this species, and after quality control, successfully genotyped 1,145 SNPs across individuals sampled from California to Washington. These SNPs were used to assess putative population structure across the region. A STRUCTURE analysis as well as a principal coordinates analysis both failed to detect any population differentiation across all geographic areas in these collections. Additionally, after assigning individuals to putative population groups geographically, no significant FST values could be detected (FST for the full data set 0.0056), and no significant isolation by distance could be detected (p = 0.999). Taken together, these results indicate a high degree of connectivity and potential panmixia in S. simplex along this portion of the continental shelf.
Assuntos
Antozoários/genética , Fluxo Gênico , Técnicas de Genotipagem , Análise de Sequência de DNA , Animais , Sequência de Bases , Genética Populacional , Geografia , Heterozigoto , Metadados , Oceanos e Mares , Filogenia , Polimorfismo de Nucleotídeo Único/genética , Análise de Componente Principal , Reprodutibilidade dos Testes , Mapeamento por Restrição , Tamanho da Amostra , Especificidade da Espécie , Estados UnidosRESUMO
Understanding how organisms interact with their environments is increasingly important for conservation efforts in many species, especially in light of highly anticipated climate changes. One method for understanding this relationship is to use genetic maps and QTL mapping to detect genomic regions linked to phenotypic traits of importance for adaptation. We used high-throughput genotyping by sequencing (GBS) to both detect and map thousands of SNPs in haploid Chinook salmon (Oncorhynchus tshawytscha). We next applied this map to detect QTL related to temperature tolerance and body size in families of diploid Chinook salmon. Using these techniques, we mapped 3534 SNPs in 34 linkage groups which is consistent with the haploid chromosome number for Chinook salmon. We successfully detected three QTL for temperature tolerance and one QTL for body size at the experiment-wide level, as well as additional QTL significant at the chromosome-wide level. The use of haploids coupled with GBS provides a robust pathway to rapidly develop genomic resources in nonmodel organisms; these QTL represent preliminary progress toward linking traits of conservation interest to regions in the Chinook salmon genome.
RESUMO
Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.
RESUMO
The long-term effect of hypoxia is to decrease both the production and use of ATP and thus decrease the reliance on mitochondrial oxidative energy production. Yet, recent studies include more immediate affects of hypoxia on gene expression and these data suggest the maintenance of mitochondrial function. To better understand the short-term physiological response to hypoxia, we quantified metabolic mRNA expression in the heart ventricles and livers of the teleost fish Fundulus grandis exposed to partial oxygen pressure of 2.8 kPa (-13.5% air saturation).Twenty-eight individuals from a single population were exposed to hypoxia for 0, 4, 8, 12, 24, 48, and 96 hr. Liver and cardiac tissues were sampled from the same individuals at 0-48 hr. At 96 hr, only cardiac tissue was assayed. Gene expression was significantly different (ANOVA, P < 0.05) for 17 of 226 metabolic genes (7.5%) in cardiac tissue and for 20 of 256 (7.8%) metabolic genes in hepatic tissue. For the two tissues examined in this study, the maximum response occurred at different times. For cardiac tissue, using Dunnett's post hoc test, most of these significant differences occurred at 96 hr of exposure. For liver, all but one significant difference occurred at 4 hr. Surprisingly, too many (relative to random expectations) of the genes with significant increase in mRNA are involved in the oxidative phosphorylation pathway: 44% of the significant genes at 96 hr in the heart and 33% of the significant genes at 4 hr in the liver are involved in the oxidative phosphorylation pathway. These data indicate that there are tissue-specific differences in the timing of the response to hypoxia, yet both cardiac and hepatic tissues have increases in mRNA that code for enzyme in the oxidative phosphorylation pathway. If these changes in mRNA produce a similar change in protein, then these data suggest that the initial response to hypoxia involves an increase in the oxidative pathway potentially as a mechanism to maintain ATP production.
Assuntos
Regulação da Expressão Gênica , Hipóxia/metabolismo , Animais , Fundulidae/metabolismo , Fundulidae/fisiologia , Ventrículos do Coração/metabolismo , Fígado/metabolismo , Hibridização de Ácido Nucleico , Análise de Sequência com Séries de Oligonucleotídeos , Oxirredução , RNA Mensageiro/metabolismo , Fatores de TempoRESUMO
Hypoxia has significant effects on organisms, from metabolic reduction to death, and could be an important evolutionary force affecting the variation among populations within a species. To determine intraspecific variation in hypoxic metabolism and the effect of body mass, we examine rates of oxygen consumption (M(O2)) at seven oxygen concentrations among seven populations of Fundulus grandis that inhabit a mosaic of habitats with different frequencies and intensities of hypoxia. For M(O2), there is a significant interaction (P< 0.05) between body mass and oxygen concentrations: log(10) body mass: log(10) M(O2) slopes were steeper at intermediate oxygen partial pressures (Po(2)) than either normoxic or lowest Po(2) (ANCOVA, P<0.001). Additionally, the PO(2crit) (Po(2) where M(O2) can no longer be maintained) was a negative function of body mass (P < 0.04). At the lowest Po(2) (1.8 kPa), there was a significant difference in M(O2) among populations: one of the populations from environments more frequently stressed by hypoxia has greater M(O2) at the lowest oxygen concentrations. With few differences among populations, the most important effects were how body mass affected M(O2) at intermediate Po(2) and the negative relationship between body mass and PO(2crit). These findings suggest that an increase in body size is a useful strategy to minimize the effect of hypoxia.
Assuntos
Fundulidae/metabolismo , Hipóxia/metabolismo , Oxigênio/metabolismo , Adaptação Fisiológica/fisiologia , Animais , Tamanho Corporal/fisiologia , Masculino , Consumo de Oxigênio/fisiologia , Análise de Regressão , Água do Mar , Sudeste dos Estados UnidosRESUMO
Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.