Growth, flesh adiposity and fatty acid composition of Atlantic salmon (Salmo salar) families with contrasting flesh adiposity: effects of replacement of dietary fish oil with vegetable oils

The present study compared the effects of diets formulated with reduced fishmeal (FM) content and either 100% fish oil (FO) or 100% of a vegetable oil (VO) blend in post-smolts of three family groups of Atlantic salmon. Two groups were selected as being either “Lean” or “Fat” based on estimated breeding values (EBV) for flesh adiposity of their parents derived from a breeding programme, while the third group (CAL) was a mix of non-pedigreed commercial families unrelated to the two groups above. The VO blend comprised rapeseed, palm and a new product, Camelina oil in a ratio of 5/3/2, and diets were fed to duplicate pens of each salmon group. After an ongrowing period of 55 weeks, to reach a mean weight of 3kg, the fish from all treatments were switched to a decontaminated FO for a further 24 weeks to follow restoration of long-chain n-3 polyunsaturated fatty acids (LC-PUFA) in the fish previously fed VO. Final weights were significantly affected by family group and there was also an interaction between diet and group with Fat and Lean FO fish being larger than the same fish fed VO. Specific growth rate (SGR) was highest in CAL fish (1.01), feed conversion ratio (FCR) was highest in the Lean fish but there were no significant effects on thermal growth coefficient (TGC). Condition Factor (CF) was lowest in CAL fish while the hepato-somatic index (HSI) was highest in Lean fish and viscero-somatic index (VSI) highest in Fat fish. Flesh and viscera lipid content was affected by both family group and diet with a significant interaction between the two. Flesh lipid in fish fed FO was in the order Fat > CAL > Lean although this order was Fat = Lean > CAL when fed VO. Flesh fatty acid compositions were affected mainly by diet although some minor fatty acids were also influenced by group. Fish fed VO had n-3 LC-PUFA reduced by ~65% compared to fish fed FO but this could be restored by a 16 week FO finishing diet phase. The differences observed in lipid and fatty acid deposition suggested that genetics affected lipid deposition and metabolism and that breeding programmes could select for fish that retained more n-3 LC-PUFA in their flesh, particularly when fed diets low in these fatty acids

Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle

International audienceAbstractBackgroundWhite spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein–Friesian cattle, and several previous studies have detected genetic loci with major effects for white spotting in animals with Holstein–Friesian ancestry. Here, our aim was to better understand the underlying genetic and molecular mechanisms of white spotting, by conducting the largest mapping study for this trait in cattle, to date.ResultsUsing imputed whole-genome sequence data, we conducted a genome-wide association analysis in 2973 mixed-breed cows and bulls. Highly significant quantitative trait loci (QTL) were found on chromosomes 6 and 22, highlighting the well-established coat color genes KIT and MITF as likely responsible for these effects. These results are in broad agreement with previous studies, although we also report a third significant QTL on chromosome 2 that appears to be novel. This signal maps immediately adjacent to the PAX3 gene, which encodes a known transcription factor that controls MITF expression and is the causal locus for white spotting in horses. More detailed examination of these loci revealed a candidate causal mutation in PAX3 (p.Thr424Met), and another candidate mutation (rs209784468) within a conserved element in intron 2 of MITF transcripts expressed in the skin. These analyses also revealed a mechanistic ambiguity at the chromosome 6 locus, where highly dispersed association signals suggested multiple or multiallelic QTL involving KIT and/or other genes in this region.ConclusionsOur findings extend those of previous studies that reported KIT as a likely causal gene for white spotting, and report novel associations between candidate causal mutations in both the MITF and PAX3 genes. The sizes of the effects of these QTL are substantial, and could be used to select animals with darker, or conversely whiter, coats depending on the desired characteristics

Automatic Text Generation: How to Write the Plot of a Novel with NooJ

Automatic Text Generation (ATG) is a Natural Language Processing (NLP) task that aims at writing acceptable and grammatical written text exploiting machine-representation systems, such as for instance knowledge bases, taxonomies and ontologies. In this sense, it is possible to state that an ATG system works like a translator that converts data into a natural-language written representation. The methods to produce the final texts may differ from those used by compilers, due to the inherent expressivity of natural languages. ATG is not a recent discipline, even if commercial ATG technology has only recently become widely available. Today, many software environments cope with ATG, as Text Spinner, DKB Lettere, or textOmatic*Composer, to mention just some of them. As a discipline strictly connected to NLP, ATG should be based strongly on morph-syntax formalization and semantic predicate use. However, in some cases it seems possible to avoid these steps. A simple example of ATG not involving the use of morph-syntactic and semantic rules may be the generation of texts using only simple alphabetic letters. This method can prove itself useful when the text to gener-ate is somehow generic in terms of semantics, and fix in terms of syntax. For in-stance, it can be used to generate a letter to a consumer stating that a credit card spending limit has been reached, or also to generate receipts from an ATM machine, or Social Media notifications. However, in theory and practice the automatic generation of more complex texts can only be based on a complete system of Natural Language Formalization (NLF), as for instance Maurice Gross’ Lexicon-Grammar. Therefore, in order to build an ATG procedure for novel plots, in this paper we will use both Lexicon-Grammar theoretical and practical framework and Max Silberztein’s NooJ NLP Environment , which as it is well known are in a strict connection. Starting from Gross’ definition of semantic predicates [1] and from the NooJ paraphrase generation routine [5,6], our aim will be to write automatically the basic plot of a novel. While achieving our aim, we will take into due account that the novel is a kind of writing difficult to define formally [7], and that the automatic writing of a novel plot is probably one of the most complex challenges an ATG routine can choose to tackle. Finally, in carrying out our research, we will also make extensive references to Text Linguistics (TL) and its theoretical and practical contact points with Formal Linguis-tics (FL)

Rapid Discovery of de Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species

In humans, the clinical and molecular characterization of sporadic syndromes is often hindered by the small number of patients and the difficulty in developing animal models for severe dominant conditions. Here we show that the availability of large data sets of whole-genome sequences, high-density SNP chip genotypes and extensive recording of phenotype offers an unprecedented opportunity to quickly dissect the genetic architecture of severe dominant conditions in livestock. We report on the identification of seven dominant de novo mutations in CHD7, COL1A1, COL2A1, COPA, and MITF and exploit the structure of cattle populations to describe their clinical consequences and map modifier loci. Moreover, we demonstrate that the emergence of recessive genetic defects can be monitored by detecting de novo deleterious mutations in the genome of bulls used for artificial insemination. These results demonstrate the attractiveness of cattle as a model species in the post genomic era, particularly to confirm the genetic aetiology of isolated clinical case reports in humans

Impact of a CD4 gene haplotype on the immune response in minipigs

The cluster of differentiation 4 (CD4) molecule functions as a co-receptor for MHC class II binding to TCR in T helper cells. A CD4 epitope deficiency was identified in the swine MeLiM (melanoblastoma-bearing Libechovminipig) strain, a model for spontaneous cutaneous melanoma development and regression. Extensive sequencing revealed a high genetic variability of CD4 and the existence of several haplotypes segregating in MeLiM. Forty polymorphisms were identified in the coding sequence, out of which 20 correspond to non-synonymous variants and 10 are located in the 3′UTR of CD4 transcripts. One of the haplotypes segregating in the MeLiM explained the epitope deficiency observed. An association analysis between CD4 genotype and several phenotypes related to tumor regression was performed in 267 animals. An association was evidenced between a MeLiM alternative CD4 haplotype and skin and eye depigmentation, as well as the extent of hair depigmentation. Also, seric IgG concentration was shown to be higher in pigs carrying the alternative haplotype at the homozygous state. In conclusion, the genetic variability of the CD4 gene is associated with immune response-related phenotypes in MeLiM minipigs

Rapid Discovery of De Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species

Abstract In humans, the clinical and molecular characterization of sporadic syndromes is often hindered by the small number of patients and the difficulty in developing animal models for severe dominant conditions. Here we show that the availability of large data sets of whole-genome sequences, high-density SNP chip genotypes and extensive recording of phenotype offers an unprecedented opportunity to quickly dissect the genetic architecture of severe dominant conditions in livestock. We report on the identification of seven dominant de novo mutations in CHD7, COL1A1, COL2A1, COPA, and MITF and exploit the structure of cattle populations to describe their clinical consequences and map modifier loci. Moreover, we demonstrate that the emergence of recessive genetic defects can be monitored by detecting de novo deleterious mutations in the genome of bulls used for artificial insemination. These results demonstrate the attractiveness of cattle as a model species in the post genomic era, particularly to confirm the genetic aetiology of isolated clinical case reports in humans