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De novo mutations arising in the germline add to genetic variation. The number of de novo mutations occurring every generation, especially structural variants, has not been well studied in most species, including livestock. We used whole-genome sequencing from 46 pig trios from two commercial lines to identify de novo structural variants (dnSVs) present in the offspring. We characterised these dnSV by identifying their parent-of-origin, predicting their causal mechanisms, and identifying their functional annotations. We identified four dnSVs, including two clusters of mutations. One of these clusters contained a deletion, and three duplications, one of which was inverted. This cluster was the only dnSV that could be phased and was located in the paternal haplotype of the proband. All four identified dnSVs were located within the introns of genes. Our study is the first of its kind to identify and characterise dnSVs using whole genome shotgun sequence data in pigs.

Over the last decades major advances in the use of sequence data to improve pig breeding have been achieved. A key achievement was the publication of the pig reference genome and subsequent design of selection single-nucleotide polymorphism (SNP) chips to implement genomic selection. This chapter outlines major advances and future use of genome sequencing for improved pig breeding. It discusses that the breeding community will shift from the use of a single reference genome to a more comprehensive pig pangenome that better covers structural variation. In addition, the impact of deleterious variation and subsequent purging strategies is discussed. It is predicted that the functional genomic information published by the Functional Annotation of Animal Genomes (FAANG) consortium will aid in the discovery of functionally important (regulatory) variation. More specifically, regulatory variants can be discovered with large-scale gene expression data sets to discover expression quantitative trait loci (eQTLs). The annotation can be further improved by mapping regulatory regions in the genome by using-large scale epigenomic data sets that assess chromatin modifications and methylation states. The discovered functional variation can subsequently be used to improve pig breeding by adding functional markers to the selection chips, significantly improving prediction accuracies. Together, the chapter provides a comprehensive overview of the current status and future steps in the use of genome sequencing for pig breeding.

International audience; Los autores exponen las dificultades por las que hubo de pasar la respuesta a un artículo, publicado en Science en 2018, en el que se afirmaba que el Neandertal es el autor de ciertas pinturas de tres cuevas españolas, según dataciones obtenidas por el método del uranio-torio. En esa respuesta, se explicitaban las distintas fuentes de error que pueden conducir a fechas anormalmente envejecidas y se recapitulaban los argumentos arqueológicos que contradicen dataciones tan antiguas. Muchos de los evaluadores de las revistas americanas prefirieron confiar en la arqueometría más que en la Arqueología europea, para ellos desconocida. Así, el artículo circuló por las manos de numerosos revisores, transcurriendo un año y medio antes de que pudiera, por fin, salir en el Journal of Human Evolution. Este proceso ilustra la opacidad que subyace tras la aparente objetividad y neutralidad del procedimiento de evaluación científica de revisión por pares cuando se trata de contradecir a científicos de reconocido prestigio.

The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.Heredity advance online publication, 28 September 2016; doi:10.1038/hdy.2016.79.

The level of deleterious genetic variation in highly managed domestic populations is influenced by a variety of factors including mutation rate, effective population size, and artificial selection. Small populations enhance the risk of inbreeding depression, which negatively impacts individual fitness and population viability. Inbreeding depression has largely been attributed to the accumulation of recessive harmful mutations in the genome: inbreeding increases the probability of these mutations to become homozygous. Past population bottlenecks, including domestication, have been indicated as major driver of genetic load in populations. While lethal variants can quickly be purged from small populations, the frequency of slightly deleterious mutations is expected to rise due to less effective natural selection. Because of genetic hitch-hiking, mildly harmful mutations are thought to be over-represented in regions of the genome under selection. Recent advances in genome sequencing have opened exciting possibilities to actually measure the amount of harmful mutations in genomes. Using re-sequence data from 421 individuals, we provide an overview of the occurrence of deleterious mutations in individual pig genomes. An alternative approach to identify lethal variants in the genome, is offered by the vast amount of genotyped pedigreed individuals due to the widespread use of genomic selection in current breeding programs. This allows the identification of recessive deleterious variants by testing for statistical depletion, or even the absence, of specific haplotypes in homozygous state. We have used a combination of whole genome sequencing and 60K genotyping (23,800 individuals) to identify and characterize lethal variants segregating in three commercial pig breeding lines. Keywords: genome sequencing, lethal recessive, loss of function mutation, selective sweeps

This corrects the article DOI: 10.1038/hdy.2016.79.

This corrects the article DOI: 10.1038/hdy.2016.79.

Trabajo presentado al: 68th Annual Meeting of the European Federation of Animal Science (EAAP). (Tallin, Estonia. 28 agosto - 2 septiembre)., The increment of world population increases the need of improving feed efficiency traits of livestock. However, the molecular mechanisms behind different feed efficiency traits and their regulation by nutrition remain poorly understood. Nowadays, Next Generation Sequencing methods allow understanding differences in gene expression and identifying functional candidate genes and pathways that control target traits in order to design strategies to increase feed efficiency. The present study was designed to identify (RNA-seq) differentially expressed (DE) genes in the liver tissues of fattening merino lambs caused by milk restriction during the suckling period. Forty male lambs were assigned randomly to two intake levels (n=20 per group) during the suckling period, namely ad libitum (ADL) and restricted (RES) groups. When they reached 15 kg of live body weight (LBW), all the animals were offered the same complete pelleted diet at a restricted level (40 g/kg) to ensure no selection of ingredients and no differences in dry matter intake during the fattening period. All the lambs were slaughtered with 27 kg of LBW and four animals from each group were selected for RNA-seq. Thirty-eight DE annotated genes were identified, with 23 DE genes being down-regulated and 15 up-regulated in the RES relative to the ADL group. RES lambs showed over-expression of lipid and xenobiotic metabolism pathways. Moreover, those genes involved in protein synthesis or protease inhibitors were down-regulated in the RES group, whereas those related to proteolytic degradation were up-regulated, thus suggesting a higher catabolism of proteins in these lambs. In conclusion, a restricted milk intake level during the suckling period of merino lambs promoted long term effects on hepatic transcriptomic profile which might have modified fatty acids metabolism and increased catabolism of proteins and detoxification of xenobiotics during the fattening period.

Exercise-induced oxygen desaturation (EID) is associated with increased risk of mortality in chronic obstructive pulmonary disease (COPD). Several screening tests have been proposed to predict EID, including FEV1, DLCO and baseline-SpO2. We aimed to validate a proposed cut-off of baseline-SpO2 ≤95% as simple screening procedure to predict EID during six-minute walk test (6MWT). In addition, we studied the prevalence and characteristics of patients exhibited EID to SpO2nadir ≤88%.402 non-hypoxemic COPD patients performed 6MWT. Sensitivity and specificity of baseline SpO2 ≤95% as a cut-off to predict EID and determinants of EID were investigated.158 patients (39%) exhibited EID. The sensitivity of baseline-SpO2 ≤95% to predict EID was 81.0%, specificity 49.2%, positive and negative predictive values were 50.8% and 80.0%, respectively. In a multivariate model, DLCO

In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island South-East Asia (ISEA). A previous study revealed signatures of interspecific admixture between these Sus species (Genome biology, 14, 2013, R107). However, the timing, directionality and extent of this admixture remain unknown. Here, we use a likelihood-based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that interspecific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.

Genomics was tien jaar geleden topwetenschap die alleen bedreven werd in dure laboratoria van universiteiten en onderzoeksinstituten. Nu gebruiken fokbedrijven DNA-chips om al op jonge leeftijd te kunnen voorspellen welke stier het beste sperma levert, en om te zien of berengeur bij varkens door een slim fokprogramma kan worden voorkomen.

Genomics was tien jaar geleden topwetenschap die alleen bedreven werd in dure laboratoria van universiteiten en onderzoeksinstituten. Nu gebruiken fokbedrijven DNA-chips om al op jonge leeftijd te kunnen voorspellen welke stier het beste sperma levert, en om te zien of berengeur bij varkens door een slim fokprogramma kan worden voorkomen.

Initiatives to establish transboundary conservation areas have been expanding in Southern Africa, intending to allow free movements of wild species across the fences in order to restock previously depleted areas. Nevertheless, these initiatives are increasing disease transfer risks at the wildlife-livestock interface, which is likely to have a significant long lasting impact on conservation, economics and sanitation. Among wild species, the African buffalo (Syncerus caffer) is known to be one of the main species responsible for the maintenance and potential spread of diseases. To fully understand the buffalo population dynamics, we aimed to generate a library of SNPs with high accuracy in population screening, that would permit to determine dispersal rate and environmental barriers that can slow down or completely stop spread of diseases. 18.5 million sequences of 76bp were generated on an Illumina Genome Analyzer from DNA of 13 buffalos. We identifi ed 3,000 putative SNPs by aligning the reads with the cattle genome (Bos taurus). Out of this set, an assay of 384 SNPs was designed taking care of each SNP's quality scores, minor allele frequencies, design scores and position in the genome. The use of those markers is completely innovative, as most of the time, they have only been developed on human model or domestic organisms. They are one of the most powerful tools and are becoming the marker of choice in genetic analyses. (Texte intégral)

BACKGROUND: The widespread use of gastrointestinal endoscopy for diagnosis and treatment requires effective, standardised report systems. This need is further increased by the limited storage of images, and by the need for structured databases for surveillance and epidemiology. We therefore aimed for a report system which would be quick, easy to learn, and suitable for use in busy daily practice. METHODS: Endobase III is an endoscopy information system offering three different ways of report writing, i.e. standard reports, text blocks and Minimal Standard Terminology (MST). A working group of two university and four general hospitals worked as a reference group for the development of standard reports and text blocks. Guidelines from various gastrointestinal endoscopy societies were followed to compose the reports. RESULTS: Standard reports were based on a list of distinct diagnoses; text blocks were based on anatomic landmarks and individual procedures. As such, 316 standard reports were developed for upper and lower gastrointestinal endoscopy, and endoscopic retrograde cholangiopancreatography (ERCP). In this way selecting one diagnosis produces a complete report. A total of 1571 different text blocks were additionally developed for each part of the gastrointestinal tract and for procedures during endoscopy. This module allowed generation of a full report on the combination of text blocks. Reports could be composed and printed within two minutes for 90% of cases. CONCLUSION: Standard reports and text blocks are a quick, user-friendly way of report writing accepted and used by a number of gastroenterologists in the Netherlands

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Effects of genetic variation in porcine adipocyte and heart fatty acid-binding protein genes, A-FABP and H-FABP, respectively, on intramuscular fat (IMF) content and backfat thickness (BFT) were examined in F2 crossbreds of Meishan and Western pigs. The involvement of each FABP gene in IMF accretion was studied to confirm previous results for Duroc pigs. The F2 crossbred pigs were genotyped for various markers including microsatellite sequences situated within both FABP genes. Linkage analysis assigned the A-FABP and H-FABP genes to marker intervals S0001-S0217 (20 cM) on SSC4 and Sw316-S0003 (16.6 cM) on SSC6, respectively, refining previous chromosomal assignments. Next, the role of both chromosome regions/genes on genetic variation in IMF content and BFT was studied by 1) screening SSC4 and SSC6 for QTL affecting both traits by performing a line-cross analysis and 2) estimation of the effect of individual A-FABP and H-FABP alleles on both traits. In the first analysis, suggestive and chromosome-wise significant evidence for a QTL affecting IMF was detected on SSC6. The H-FABP gene is a candidate gene for this effect because it resides within the large region containing this putative QTL. The second analysis showed a considerable but nonsignificant effect of H-FABP microsatellite alleles on IMF content. Suggestive evidence for a QTL affecting BFT was found on SSC6, but H-FABP was excluded as a candidate gene. In conclusion, present and previous results support involvement of H-FABP gene polymorphisms in IMF accretion independently from BFT in pigs. Therefore, implementation of these polymorphisms in marker-assisted selection to control IMF content independently from BFT may be considered. In contrast to previous findings for Duroc pigs, no evidence was found for an effect of the A-FABP gene on IMF or BFT in this population.

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The invention relates to a gene located on chromosome 1 in chickens, which in birds is involved in so called autosomal dwarfism. The most likely candidate gene has a homolog in mice and men and is called HMGI-c. The sequence of the cDNA and genomic DNA of the gene is provided, as well as uses of said sequence or parts or derivatives thereof, as well as methods of using sequences from this gene or flanking sequences, or microsatellite markers in close vicinity to this gene in methods for selecting for one of the two alleles of this gene. Specifically provided are breeding methods using discrimination between dwarf fenotypes and non dwarf fenotypes, which are a result of the allele variation within this gene.

The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health.

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In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the “Fowls for Africa” program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource. The lines included the Black Australorp, Potchefstroom Koekoek, New Hampshire, Ovambo, Lebova- Venda and a Naked Neck line. Unbiased estimates for heterozygosity ranged from 50% in the Potchefstroom Koekoek to as high as 65% in the Naked Neck chickens. FIS values varied from as low as 0.16 for the Black Australorp line to as high as 0.35 for the Ovambo chickens. The FST values indicated moderate to high genetic differentiation between the Naked Neck and New Hampshire (0.11); Ovambo and Naked Neck lines (0.12), and Naked Neck and Lebowa- Venda (0.14). A total of 13% of the total genetic variation observed was between the chicken lines and 87% within the lines, supporting moderate genetic differentiation. Population structure was assessed using STRUCTURE where the Black Australorp was genetically best defined. Although six clusters for the different populations could be distinguished, the other lines were not as clearly defined, with individual birds tending to share more than one cluster. Results support a broad classification of these lines and further investigation of unique alleles is recommended for conservation of the lines within the program. Keywords: Native chicken, microsatellite markers, genetic variation, population structure, South Africa South African Journal of Animal Science Vol. 38 (4) 2008: pp. 271-281

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This paper suggests the introduction of a third stage in regresssion tree growing approach. To this aim, a statistical testing procedure based on the {\it F} statistics, is proposed. In particular, the testing procedure is applied to the CART sequence of pruned subtrees, resulting in a single final tree structured prediction rule, which is statistically reliable and might not coincide with any tree in the sequence itself.