The differentiation of plant vascular tissue is regulated by plant hormones and transcription factors. One of the key plant hormones involved in this process is auxin. Auxin signals are mediated by auxin response factor transcription factors (ARFs). These transcription factors are involved in the perception of auxin signals and the subsequent activation or deactivation of suites of downstream genes. Based on its mutant phenotype, one of the most interesting members of this family is the ARF MONOPTEROS (MP). This thesis investigates the role played by MP in secondary vascular differentiation, as well as taking a look at other molecular aspects of secondary vascular differentiation, with a focus on the model plants Arabidopsis thaliana and poplar (Populus trichocarpa and hybrid poplar). A dexamethasone inducible RNAi silencing strategy was developed, and transgenic Arabidopsis lines produced. When silencing was induced in these lines from germination, a phenotype closely resembling the mp mutant was observed. When MP silencing was induced in bolting stems, early senescence, as well as a dramatic reduction in interfascicular fibre production was observed, and these stems were thinner and less rigid than empty vector controls. RNA from these stems was isolated and used in a global transcript profiling microarray experiment. This experiment showed that several auxin-related genes, as well as several transcription factors, were differentially regulated in response to MP silencing. Because Arabidopsis is not a typical woody plant, further investigation into the role played by MP in wood formation was done using the model tree poplar. A BLAST search of a poplar xylem EST database identified a single promising partial sequence. Based on this sequence information, a poplar MP homolog was isolated and named PopMP1. The full-length sequence of this gene demonstrated remarkable structural conservation when compared with that of Arabidopsis. Subsequent complete sequencing of the poplar genome revealed a second copy of the MP gene in poplar and named PopMP2. Expression profiling across a range of tissues suggests that subfunctionalization has occurred between the two copies. Overexpression transgenic lines for PoptrMP1 were developed. AtHB8 is known to be regulated by MP in Arabidopsis, and a poplar HB8 homolog was upregulated in the transgenic lines. However, no obvious physical phenotype in these lines was apparent. To investigate the transcriptome-wide changes associated with initiation of cambium formation in poplar stems, a global transcript profiling experiment was performed. Out of 15400 genes tested, 2320 met an arbitrary cutoff of >1.3 fold and p-value <0.05 and were labeled differentially expressed (DE). These included several transcription factors and showed remarkable similarity to analogous data from Arabidopsis. The conclusions drawn from this thesis support the hypothesis that MP plays roles in later development, and do not rule out the possibility that MP is directly involved in wood development. The data reported also offer a large number of candidate for further investigation into the genetic control of wood development.

The differentiation of plant vascular tissue is regulated by plant hormones and transcription factors. One of the key plant hormones involved in this process is auxin. Auxin signals are mediated by auxin response factor transcription factors (ARFs). These transcription factors are involved in the perception of auxin signals and the subsequent activation or deactivation of suites of downstream genes. Based on its mutant phenotype, one of the most interesting members of this family is the ARF MONOPTEROS (MP). This thesis investigates the role played by MP in secondary vascular differentiation, as well as taking a look at other molecular aspects of secondary vascular differentiation, with a focus on the model plants Arabidopsis thaliana and poplar (Populus trichocarpa and hybrid poplar). A dexamethasone inducible RNAi silencing strategy was developed, and transgenic Arabidopsis lines produced. When silencing was induced in these lines from germination, a phenotype closely resembling the mp mutant was observed. When MP silencing was induced in bolting stems, early senescence, as well as a dramatic reduction in interfascicular fibre production was observed, and these stems were thinner and less rigid than empty vector controls. RNA from these stems was isolated and used in a global transcript profiling microarray experiment. This experiment showed that several auxin-related genes, as well as several transcription factors, were differentially regulated in response to MP silencing. Because Arabidopsis is not a typical woody plant, further investigation into the role played by MP in wood formation was done using the model tree poplar. A BLAST search of a poplar xylem EST database identified a single promising partial sequence. Based on this sequence information, a poplar MP homolog was isolated and named PopMP1. The full-length sequence of this gene demonstrated remarkable structural conservation when compared with that of Arabidopsis. Subsequent complete sequencing of the poplar genome revealed a second copy of the MP gene in poplar and named PopMP2. Expression profiling across a range of tissues suggests that subfunctionalization has occurred between the two copies. Overexpression transgenic lines for PoptrMP1 were developed. AtHB8 is known to be regulated by MP in Arabidopsis, and a poplar HB8 homolog was upregulated in the transgenic lines. However, no obvious physical phenotype in these lines was apparent. To investigate the transcriptome-wide changes associated with initiation of cambium formation in poplar stems, a global transcript profiling experiment was performed. Out of 15400 genes tested, 2320 met an arbitrary cutoff of >1.3 fold and p-value <0.05 and were labeled differentially expressed (DE). These included several transcription factors and showed remarkable similarity to analogous data from Arabidopsis. The conclusions drawn from this thesis support the hypothesis that MP plays roles in later development, and do not rule out the possibility that MP is directly involved in wood development. The data reported also offer a large number of candidate for further investigation into the genetic control of wood development.

<p>Renewable fibers produced by forest trees provide excellentraw material of high economic value for industrialapplications. Despite this, the genes and corresponding enzymesinvolved in wood fiber biosynthesis in trees are poorlycharacterized. This thesis describes a functional genomicsapproach for the identification of carbohydrate-active enzymesinvolved in secondary cell wall (wood) formation in hybridaspen.</p><p>First, a 3' target amplification method was developed toenable microarray-based gene expression analysis on minuteamounts of RNA. The amplification method was evaluated usingboth a smaller microarray containing 192 cDNA clones and alarger microarray containing 2995 cDNA clones that werehybridized with targets isolated from xylem and phloem.Moreover, a gene expression study of phloem differentiation wasperformed to show the usefulness of the amplificationmethod.</p><p>A microarray containing 2995 cDNA clones representing aunigene set of a cambial region EST library was used to studygene expression during wood formation. Transcript populationsfrom thin tissue sections representing different stages ofxylem development were hybridized onto the microarrays. It wasdemonstrated that genes encoding lignin and cellulosebiosynthetic enzymes, as well as a number of genes withoutassigned function, were differentially expressed across thedevelopmental gradient.</p><p>Microarrays were also used to track changes in geneexpression in the developing xylem of transgenic, GA-20 oxidaseoverexpressing hybrid aspens that had increased secondarygrowth. The study revealed that a number of genes encoding cellwall related enzymes were upregulated in the transgenic trees.Moreover, most genes with high transcript changes could beassigned a role in the early events of xylogenesis.</p><p>Ten genes encoding putative cellulose synthases (CesAs) wereidentified in our own<i>Populus</i>ESTdatabase. Full length cDNA sequences wereobtained for five of them. Expression analyses performed withreal-time PCR and microarrays in normal wood undergoingxylogenesis and in tension wood revealed xylem specificexpression of four putative CesA isoenzymes.</p><p>Finally, an approach combining expressionprofiling,bioinformatics as well as EST and full length sequencing wasadopted to identify secondary cell wall related genes encodingcarbohydrate-active enzymes, such as glycosyltransferases andglycoside hydrolases. As expected, glycosyltransferasesinvolved in the carbohydrate biosynthesis dominated thecollection of the secondary cell wall related enzymes that wereidentified.</p><p><b>Key words:</b>Populus, xylogenesis, secondary cell wall,cellulose, hemicellulose, microarrays, transcript profiling,carbohydrate-active enzyme, glycosyltransferase, glycosidehydrolase</p>

<p>Forest biotechnology is a fast emerging field of research. The application of biotechnological tools will enhance the quality of the forest products. The resultant value added and environmentally sustainable products are an absolute necessity in the future. The study of wood biosynthesis and degradation will result in enormous knowledge resources, which can be used for exploiting wood properties. This thesis addresses questions representing both wood degradation and biosynthesis.</p><p>The wood degrading fungus <i>Phanerochaete chrysosporium</i> is expression profiled with the microarray technology. The objective is to understand the expression pattern of the extracellular carbohydrate active enzymes (CAZymes) secreted by the organism. The data obtained increases our understanding of gene expression upon growth on cellulose.</p><p>Wood biosynthesis is studied with the model wood forming tree species, <i>Populus</i>. The plentiful data resources from the expression profiling during wood formation in Populus are used as the platform of this work. One of the wood specific genes, <i>PttMAP20</i>, previously with an unknown function is studied in this thesis. The immunolocalisation of PttMAP20 with specific antibodies is demonstrated. The putative microtubule-targeting domain of the protein is demonstrated microscopically and by using a biochemical binding assay. </p>

The detection of non-protein-coding RNA (ncRNA) genes in bacteria and their diverse regulatory mode of action moved the experimental and bio-computational analysis of ncRNAs into the focus of attention. Regulatory ncRNA transcripts are not translated to proteins but function directly on the RNA level. These typically small RNAs have been found to be involved in diverse processes such as (post-)transcriptional regulation and modification, translation, protein translocation, protein degradation and sequestration. Bacterial ncRNAs either arise from independent primary transcripts or their mature sequence is generated via processing from a precursor. Besides these autonomous transcripts, RNA regulators (e.g. riboswitches and RNA thermometers) also form chimera with protein-coding sequences. These structured regulatory elements are encoded within the messenger RNA and directly regulate the expression of their “host” gene. The quality and completeness of genome annotation is essential for all subsequent analyses. In contrast to protein-coding genes ncRNAs lack clear statistical signals on the sequence level. Thus, sophisticated tools have been developed to automatically identify ncRNA genes. Unfortunately, these tools are not part of generic genome annotation pipelines and therefore computational searches for known ncRNA genes are the starting point of each study. Moreover, prokaryotic genome annotation lacks essential features of protein-coding genes. Many known ncRNAs regulate translation via base-pairing to the 5’ UTR (untranslated region) of mRNA transcripts. Eukaryotic 5’ UTRs have been routinely annotated by sequencing of ESTs (expressed sequence tags) for more than a decade. Only recently, experimental setups have been developed to systematically identify these elements on a genome-wide scale in prokaryotes. The first part of this thesis, describes three experimental surveys of exploratory field studies to analyze transcript organization in pathogenic bacteria. To identify ncRNAs in Pseudomonas aeruginosa we used a combination of an experimental RNomics approach and ncRNA prediction. Besides already known ncRNAs we identified and validated the expression of six novel RNA genes. Global detection of transcripts by next generation RNA sequencing techniques unraveled an unexpectedly complex transcript organization in many bacteria. These ultra high-throughput methods give us the appealing opportunity to analyze the complete RNA output of any species at once. The development of the differential RNA sequencing (dRNA-seq) approach enabled us to analyze the primary transcriptome of Helicobacter pylori and Xanthomonas campestris. For the first time we generated a comprehensive and precise transcription start site (TSS) map for both species and provide a general framework for the analysis of dRNA-seq data. Focusing on computer-aided analysis we developed new tools to annotate TSS, detect small protein-coding genes and to infer homology of newly detected transcripts. We discovered hundreds of TSS in intergenic regions, upstream of protein-coding genes, within operons and antisense to annotated genes. Analysis of 5’ UTRs (spanning from the TSS to the start codon of the adjacent protein-coding gene) revealed an unexpected size diversity ranging from zero to several hundred nucleotides. We identified and validated the expression of about 60 and about 20 ncRNA candidates in Helicobacter and Xanthomonas, respectively. Among these ncRNA candidates we found several small protein-coding genes that have previously evaded annotation in both species. We showed that the combination of dRNA-seq and computational analysis is a powerful method to examine prokaryotic transcriptomes. Experimental setups are time consuming and often combined with huge costs. Another limitation of experimental approaches is that genes which are expressed in specific developmental stages or stress conditions are likely to be missed. Bioinformatic tools build an alternative to overcome such restraints. General approaches usually depend on comparative genomic data and evolutionary signatures are used to analyze the (non-)coding potential of multiple sequence alignments. In the second part of my thesis we present our major update of the widely used ncRNA gene finder RNAz and introduce RNAcode, an efficient tool to asses local protein-coding potential of genomic regions. RNAz has been successfully used to identify structured RNA elements in all domains of life. However, our own experience and the user feedback not only demonstrated the applicability of the RNAz approach, but also helped us to identify limitations of the current implementation. Using a much larger training set and a new classification model we significantly improved the prediction accuracy of RNAz. During transcriptome analysis we repeatedly identified small protein-coding genes that have not been annotated so far. Only a few of those genes are known to date and standard proteincoding gene finding tools suffer from the lack of training data. To avoid an excess of false positive predictions, gene finding software is usually run with an arbitrary cutoff of 40-50 amino acids and therefore misses the small sized protein-coding genes. We have implemented RNAcode which is optimized for emerging applications not covered by standard protein-coding gene annotation software. In addition to complementing classical protein gene annotation, a major field of application of RNAcode is the functional classification of transcribed regions. RNA sequencing analyses are likely to falsely report transcript fragments (e.g. mRNA degradation products) as non-coding. Hence, an evaluation of the protein-coding potential of these fragments is an essential task. RNAcode reports local regions of high coding potential instead of complete protein-coding genes. A training on known protein-coding sequences is not necessary and RNAcode can therefore be applied to any species. We showed this with our analysis of the Escherichia coli genome where the current annotation could be accurately reproduced. We furthermore identified novel small protein-coding genes with RNAcode in this extensively studied genome. Using transcriptome and proteome data we found compelling evidence that several of the identified candidates are bona fide proteins. In summary, this thesis clearly demonstrates that bioinformatic methods are mandatory to analyze the huge amount of transcriptome data and to identify novel (non-)coding RNA genes. With the major update of RNAz and the implementation of RNAcode we contributed to complete the repertoire of gene finding software which will help to unearth hidden treasures of the RNA World.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2018-03-02T23:09:14Z No. of bitstreams: 1 VivianeBritoNogueira_DISSERT.pdf: 3038632 bytes, checksum: 6b375d3a8d8d5af0979152bdca538728 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2018-03-13T18:02:38Z (GMT) No. of bitstreams: 1 VivianeBritoNogueira_DISSERT.pdf: 3038632 bytes, checksum: 6b375d3a8d8d5af0979152bdca538728 (MD5) / Made available in DSpace on 2018-03-13T18:02:38Z (GMT). No. of bitstreams: 1 VivianeBritoNogueira_DISSERT.pdf: 3038632 bytes, checksum: 6b375d3a8d8d5af0979152bdca538728 (MD5) Previous issue date: 2017-12-14 / O sagui comum (Callithrix jacchus), um pequeno primata de novo mundo, tem sido amplamente empregado como modelo biol?gico, n?o apenas para decifrar disfun??es em transtornos neuropsiqui?tricos como tamb?m para compreender circuitos neurais envolvidos no comportamento social humano. A este respeito, a disponibilidade de dados de express?o g?nica advindos de tecnologias nextgeneration sequencing (NGS) representam uma oportunidade para novos estudos aprofundados na gen?tica e na epigen?tica desta esp?cie. Uma das fronteiras na neuroci?ncia ? manusear esses dados em larga escala a fim de conectar vias moleculares ao comportamento do sistema nervoso. Para tornar esses dados mais acess?veis para a comunidade cient?fica sem forma??o em bioinform?tica, foi criado o CajaDB, um banco de dados que fornece uma interface web para dados de gen?mica, express?o g?nica e splicing alternativo, incluindo ferramentas para an?lises biol?gicas. Com os dados processados para esta plataforma foram realizadas duas an?lises distintas: (1) Express?o diferencial de genes nos hemisf?rios direito e esquerdo, uma vez que lateraliza??o ? um aspecto crucial do funcionamento da arquitetura cerebral para habilidades cognitivas, onde foram encontrados 49 genes diferencialmente expressos, sendo 24 para o hemisf?rio esquerdo e 25 para o hemisf?rio direito; (2) Express?o diferencial de genes entre machos e f?meas, com foco em c?rtex frontal e compara??o com dados equivalentes de humanos. Neste ?ltimo caso, foi verificado que genes com express?o enviesada para machos s?o conservados e enriquecidos para fun??es de manuten??o celular. J? genes com express?o enviesada para f?mea foram relacionados a fun??es de plasticidade neural, envolvidos com remodelamento dos circuitos sin?pticos, cascatas de estresse e comportamento visual. Com base em conhecimentos sobre dimorfismo comportamental entre sexos de saguis, ? sugerido que estas express?es diferenciais podem estar relacionadas a determinadas circuitarias neurais associadas ?s estrat?gias adaptativas de sobreviv?ncia e reprodu??o para cada sexo. Diante do exposto, espera-se que os dados dispon?veis no banco de dados associados ?s ferramentas biol?gicas dispon?veis facilitem a gera??o de hip?teses e a interpreta??o de resultados sobre o funcionamento cerebral nesta esp?cie que ? um modelo biol?gico largamente utilizado, abrindo perspectivas de investiga??o e desenvolvimento de novos tratamentos para doen?as neuropsiqui?tricas no futuro. CajaDB est? dispon?vel em cajadb.neuro.ufrn.br. / Common marmoset (Callithrix jacchus), a small New World monkey, has been widely used as a biological model not only to elucidate brain dysfunction in neuropsychiatric disorders, but also for deciphering neural circuits involved in human social behaviors. In this regard, the availability of gene expression data derived from next-generation sequencing (NGS) technologies represents an opportunity for deeper studies on the genetic and epigenetic architecture of this species. One of the frontiers in neuroscience field requires handling omics large-scale data sets for connecting molecular pathways to nervous system behavior. To make these omics datasets more accessible for the scientific community without a solid bioinformatics background, we have created CajaDB, a database that provides a friendly interface for genomic, expression and alternative splicing data, including tools for biological analyses. Using the processed data two analysis were conducted: (1) Differential expression between right and left hemispheres, once lateralization is a crucial aspect of the functional brain architecture for cognitive abilities. It was found 49 differentially expressed genes, where 24 genes had left hemisphere bias and 25 genes had right hemisphere bias. (2) Sex-biased gene expression with focus in frontal comparing to humans. It was found that genes whose expression is male biased are conserved between marmosets and humans and enriched with "housekeeping" functions. On the other hand, female-biased genes are more related to neural plasticity functions involved in remodeling of synaptic circuits, stress cascades and visual behavior. Based on knowledge of dimorphic social behavior of male and female common marmosets we discuss that these differences might be linked to neuronal circuitry underlying the expression of the adaptive strategies in each sex and related to survival and reproductive behavior traits. Hence, it is expected that data available in the webpage associated with available biological tools will facilitate generation of hypotheses and interpretation of results on brain functioning, facilitating improvements in neurological diseases treatment in the future. CajaDB is available at cajadb.neuro.ufrn.br.

Esta dissertação apresenta uma edição anotada de um livro inédito de contos de Valdomiro Silveira, Mucufos. A introdução situa historicamente esse livro, expõe as visões críticas a respeito do conjunto da obra do escritor, que envolvem aspectos sociais, humanos, estéticos e lingüísticos. Descreve o conjunto de contos de Mucufos encontrados em duas pastas denominadas Mucufos e Originaes manuscriptos de Papae (preciosíssimos), no Arquivo Valdomiro Silveira, no IEB/ USP, e explicita os critérios adotados na edição. Tal edição tem por finalidade estabelecer, a partir do confronto entre o apógrafo de CLSD (Carmen Lydia de Souza Dias), os autógrafos, os datiloscritos e os impressos encontrados nas pastas e no Arquivo do Estado, uma edição fidedigna. Para tanto, além do confronto referido, foi escolhida a transcrição crítica dos contos, procurando preservar os arcaísmos e os regionalismos presentes neles. A partir da transcrição, foram estabelecidos dois tipos de notas de rodapé. O primeiro, denominado de Nota CLSD, indica jornais de época em que foi publicada a maior parte dos contos, local e data de publicação, assim como local e data da escritura dos contos. O segundo, denominado Nota da edição, indica a pasta onde foi encontrado o conto e explica algumas palavras de cunho regional. Nas análises dos contos, buscou-se problematizar o teor de realismo, com a contribuição da categoria do realismo, segundo Georg Lukács; também foram analisadas as características estéticas, o grau de descrição de elementos da natureza e os principais temas e motivos. Entre estes últimos, destaca-se a violência e seu tratamento estético. Das análises, depreende-se a visão de Brasil por parte do escritor. A presente dissertação, pelo que foi exposto, busca resgatar uma parte do legado artístico de um escritor que muito se preocupou em humanizar um sujeito até então marginalizado em nossa literatura, o caipira, e discutir as principais questões estéticas e ideológicas surgidas nas análises dos 24 contos que constituem a edição. / This dissertation focuses on the annotated edition of an unpublished book of short stories, Mucufos, by Valdomiro Silveira. The introduction situates this book in a historical context, explaining critical views on the collected works of the writer, involving social, human, esthetical and linguistic aspects. It describes the short story collection of Mucufos found in two files named Mucufos and Originaes manuscriptos de Papae (especially valuable) in the Valdomiro Silveira Archive (IEB/ USP), and explains the criteria adopted for the edition. The aim of this edition was to establish an authentic edition emanating from a comparison between a reproduction by CLSD (Carmen Lydia de Souza Dias), autographs, typewritten sheets and printed papers found in the files and in the Office of Public Records. Apart from this comparison, a critical transcript of the short stories was chosen, in an attempt to preserve archaisms and regionalisms in these stories. Two types of footnotes were established from the transcript. The first note, named CLSD Note, indicates newspapers of the time period when most of the short stories were published, with publication date and location, as well as location and date when the stories were written. The second note, named Edition Note, indicates the file where the story was found, explaining some words of regional character. In an analysis of the short stories, there was an attempt to put in doubt the tenor of realism, with contribution from the category of realism, according to Georg Lukács; esthetical features, description of the elements, and main topics and motives were also analyzed. In the latter, violence and its esthetical treatment are highlighted. The writer\'s view of Brazil can be inferred from the analyses. Therefore, the current dissertation seeks to salvage part of the artistic legacy of a writer who was very concerned with humanizing an individual who had been marginalized in our literature until then, i.e. the hillbilly, and discuss the main esthetical and ideological issues that appear in the analyses of the 24 short stories of the edition.

In the modern world, Internet has become a popular place, people with speech hearing disabilities and search engines can't take part of speech content in podcast les. In order to solve the problem partially, the Sphinx decoders such as Sphinx-3, Sphinx-4 can be used to implement a Auto Transcript Generator application, by coupling already existing large acoustic model, language model and a existing dictionary, or by training your own large acoustic model, language model and creating your own dictionary to support continuous speaker independent speech recognition system.

CADASIL is a neurodegenerative autosomal dominant hereditary disease with late onset. Main symptoms are migraines with aura, cerebral ischemic events, cognitive impairment and dementia. The disease is caused by a mutation in the NOTCH3 gene. The major mutation type changes the number of cysteine residues in the EGF-like repeats of the Notch3 protein. In Czech Republic, currently used methods for molecular genetic analysis of the CADASIL disease are Sanger sequencing and MLPA. But there are patients with CADASIL-like symptoms who were not confirmed by these methods. Therefore, the aim of this thesis was to implement transcript analysis by Sanger sequencing of cDNA PCR products and quantitative real-time PCR (qPCR) to analyze gross deletions and duplications to clarify the molecular genetic basis of the disease. By transcript analysis, the existence of the transcript variant X1 was experimentally confirmed in control samples. Moreover, the results from transcript analysis showed that non-typical missense mutation c.1725G>A (p.T575=) which does not directly change the number of cysteine residues, can cause the CADASIL disease via missplicing and subsequent causing deletion including cysteine residues. The other tested variants did not show any changes in the transcript level. The qPCR method did not...

Atlantic salmon (Salmo salar L.) has been domesticated since the 1960s and has undergone over 10 generations of artificial selection for economically important traits. As a result, domesticated salmon have diverged with respect to a number of phenotypic, genotypic and behavioural traits from their wild counterparts. Since the selection pressures that are present in the wild differ greatly from the ones that shape salmon under culture conditions, domesticated salmon stocks are considered to be maladapted to natural conditions. Despite strict regulations, insoluble issues pertaining to large-scale cage rearing of farmed fish mean that there is a continuous presence of farm escapees in the wild. Gene flow from escapees has been perceived as a factor in the decline of wild populations, suggested to occur through disruption of local adaptation. This study aims to improve understanding of the genetic differences between wild and domesticated stocks by comparing the transcriptomes of Figgjo (wild) and Mowi (domesticated) strains. A series of common garden experiments have been performed, utilizing pure and reciprocal hybrid crosses of the wild and domesticated stocks, reared under two different conditions and sampled at four time points and three distinct life stages (embryo, sac-fry and feeding fry). Microarray interrogations were performed employing a 44K custom microarray design to identify genes and gene pathways that are differentially expressed between the stocks. KEGG-based functional analyses have been implemented using different gene set enrichment packages, and dominance and additive parameters were calculated from normalized expression values to predict the mode of heritability of the genes identified as differentially expressed between stocks. Most biological functions represented in wild and domesticated crosses were consistent across life stages and environments. The transcriptomic differences detected between stocks in multiple developmental stages likely reflected adaptations to selection pressures differing between natural and aquaculture environments. Down-regulated environmental information processing and immune and nervous system functions in domesticated vs. wild fish may be due to local adaptation to captivity. These included reduced information acquisition and processing systems, altered stress responsiveness and changes in feeding behaviour. In line with the resource allocation theory of production trait animals, reduced immune function was coupled with increased expression of growth and development related pathways in domesticated salmon, compared to wild counterparts. Although there is support for this trade-off in all life-stages, resource allocation showed a shift over time; possibly reflecting variation in the utilization of energy sources during the transition from endogenous to exogenous feeding. Differences in cell communication and signalling pathways between wild and domesticated stocks, associated with organogenesis during the embryo stage, reflect sampling time and are indicative of altered organ development in response to domestication. Stress responses common across stocks included the down-regulation of cellular processes, including cell cycle and meiosis, and genetic information processing, such as replication and repair, transcription and translation pathways, probably reflecting the reallocation of energy resources away from growth and towards the restoration of homeostasis. Moreover, the mobilization of energy to cover the increased demands of maintaining homeostasis was indicated by the up-regulation of some metabolic pathways, mostly involved in energy, lipid and carbohydrate metabolism in response to stress. The analysis also revealed cross-specific stress responses, including indicators of a non-additive stress response in hybrid crosses. Most differentially expressed transcripts exhibited additive (31-59%) or maternal dominant (19-33%) inheritance patterns, although maternal over-dominance (23-26%) was also significant in the embryo stage. The mode of heritability of some immune transcripts was suggestive of maternal environmental influence having been affected by aquaculture. This study has demonstrated that biological functions affected by domestication include those associated with allocation of resources, involve reduction of information acquisition and processing systems and may lead to loss of local adaptation to wild conditions. Since such changes may affect key systems, such as immunity and responsiveness to stress, they can potentially have serious negative consequences under natural conditions. Transcriptomic differences observed between wild and domesticated stocks primarily exhibited additive and maternal dominant inheritance modes. Since gene-flow from farmed fish can be frequent and primarily concerns farmed females, this suggests that introgression due to repeated large scale escape events has the capacity to significantly erode local adaptation.