Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle

Identification and characterization of copy number variations in cattle

Copy number variations (CNVs) are an important source of genetic changes. They are defined as a gain or loss of genomic region ranging from 50 bp to several megabases. CNVs have been shown to be associated with many diseases and some phenotypic traits in several species, including cattle. We used Pindel, Delly, BreakDancer, and CNVnator to identify CNVs using whole-genome sequencing data of 200 animals from eight French dairy and beef cattle breeds. We selected only deletions and duplications predicted by at least two tools and present in at least two animals. We identified a total of 29,132 autosomal deletions and duplications which cover between 31 to 34% (784 to 865 Mb) of the autosomal genome, with an average of 6,000 events per animal. Among these deletions and duplications, 27,690 were present in at least two animals. Out of theses, 26,417 events were deletions, 674 were duplications and 599 regions were both (deletion and duplication within the same region). We defined a CNV as deletion and duplication in the same region, and we termed this region as CNV-Region (CNVR). The size of CNVRs ranged from 100 bp to 9.3 Mb with a median of 1.3 kb and a mean of 45 kb. From the identified deletions and duplications, 8,283 overlapped with 9,733 annotated genes including 290 CNVRs overlapping with 974 annotated genes, including some genes known to be implicated in some traits of economic importance. Our study provides an extensive view of the CNVRs in French dairy and beef breeds. CNVRs with an effect on some commercially interesting phenotypes could be used to improve genetic selection of these eight French breeds

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Associations between Nitric Oxide Synthase Genes and Exhaled NO-Related Phenotypes according to Asthma Status

International audienceBACKGROUND: The nitric oxide (NO) pathway is involved in asthma, and eosinophils participate in the regulation of the NO pool in pulmonary tissues. We investigated associations between single nucleotide polymorphisms (SNPs) of NO synthase genes (NOS) and biological NO-related phenotypes measured in two compartments (exhaled breath condensate and plasma) and blood eosinophil counts. METHODOLOGY: SNPs (N = 121) belonging to NOS1, NOS2 and NOS3 genes were genotyped in 1277 adults from the French Epidemiological study on the Genetics and Environment of Asthma (EGEA). Association analyses were conducted on four quantitative phenotypes: the exhaled fraction of NO (Fe(NO)), plasma and exhaled breath condensate (EBC) nitrite-nitrate levels (NO2-NO3) and blood eosinophils in asthmatics and non-asthmatics separately. Genetic heterogeneity of these phenotypes between asthmatics and non-asthmatics was also investigated. PRINCIPAL FINDINGS: In non-asthmatics, after correction for multiple comparisons, we found significant associations of Fe(NO) levels with three SNPs in NOS3 and NOS2 (P ≤ 0.002), and of EBC NO2-NO3 level with NOS2 (P = 0.002). In asthmatics, a single significant association was detected between Fe(NO) levels and one SNP in NOS3 (P = 0.004). Moreover, there was significant heterogeneity of NOS3 SNP effect on Fe(NO) between asthmatics and non-asthmatics (P = 0.0002 to 0.005). No significant association was found between any SNP and NO2-NO3 plasma levels or blood eosinophil counts. CONCLUSIONS: Variants in NO synthase genes influence Fe(NO) and EBC NO2-NO3 levels in adults. These genetic determinants differ according to asthma status. Significant associations were only detected for exhaled phenotypes, highlighting the critical relevance to have access to specific phenotypes measured in relevant biological fluid

Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes

<p>Abstract</p> <p>Background</p> <p>Rainbow trout (<it>Oncorhynchus mykiss</it>) are cultivated worldwide for aquaculture production and are widely used as a model species to gain knowledge of many aspects of fish biology. The common ancestor of the salmonids experienced a whole genome duplication event, making extant salmonids such as the rainbow trout an excellent model for studying the evolution of tetraploidization and re-diploidization in vertebrates. However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents.</p> <p>Results</p> <p>A total of 176,485 high quality BES, were generated, representing approximately 4% of the trout genome. BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. The fractions of the 97,846 non-repetitive trout BES reads that had significant BLASTN hits against the zebrafish, medaka and stickleback genome databases were 15%, 16.2% and 17.9%, respectively, while the fractions of the non-repetitive BES reads that had significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 10.7%, 9.5% and 9.5%, respectively. Comparative genomics using paired BAC-ends revealed several regions of conserved synteny across all the fish species analyzed in this study.</p> <p>Conclusions</p> <p>The characterization of BES provided insights on the rainbow trout genome. The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. The numerous microsatellites will facilitate integration of the linkage and physical maps and serve as valuable resource for fine mapping QTL and positional cloning of genes affecting aquaculture production traits. Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome.</p

Sequence-based GWAS meta-analyses for beef production traits

International audienceFive partners of the H2020 BovReg project have performed sequence-based GWAS for 28 beef production traits (4 growth, 9 morphology, and/or 15 carcass traits) using 54,782 animals from 15 different purebred or crossbred cattle populations. These results were herein combined to conduct 16 different meta-analyses (MA) with both the z-score and the fixed effects MA methods. We identified QTL in 15 MA on BTA2, 5, 6, 7, 10, 11, 13, 14, 15, 17, and 20, most of them being common to several MA. Overall, the fixed effects method outperformed the zscore method in terms of significance level and number of QTL detected. Compared to withinpopulation GWAS, MA found a higher number of QTL in which variants were more frequently located in genes (e.g. MSTN, LCORL, ARRDC3, PLAG1, COL3A1)

Development of mixers and Local Oscillators for THz Heterodyne Instruments at Observatoire de Paris - LERMA

This article presents current R&D activities at Observatoire de Paris – Laboratoire d'Etude du Rayonnement et de la Matière en Astrophysique in the fields of low noise mixers and local oscillators for heterodyne instruments dedicated to astrophysics, planetology and the sciences of the atmosphere

Sequence-based GWAS meta-analyses for beef production traits

When performed at the whole genome sequence level, the meta-analysis (MA) of within-population GWAS results can be powerful and accurate to identify causal variants for complex traits. An objective of the H2020 BovReg project is to perform MA at the sequence level for various dairy and beef cattle traits. For beef production, five partners from France, Switzerland, Germany, and Canada contributed with 54,782 animals from 15 purebred populations Charolais, Montbéliarde, Normande, Limousine, Blonde d’Aquitaine, Brown Swiss, Original Braunvieh or crossbred Charolais x Holstein, and Angus, Charolais and beef composite. Each partner conducted sequence-based within-population GWAS for 4 growth, 9 morphology, and/or 15 carcass traits. We combined these GWAS results to conduct 16 MA with both fixed effects and z-score methods.This study demonstrates the value of MA, in complement to within-population GWAS, in identifying a larger number of QTL, a lower number of variants in QTL and candidate variants located more frequently in genes. By applying here the most commonly MA methods used for GWAS, we confirm that the fixed effects method appears more powerful in detecting QTL, although MA combine substantially different traits in the present study. In several regions, MA directly pointed out variants in genes, including MSTN, LCORL, ARRDC3, and PLAG1, previously associated with morphology and carcass traits in various studies. For example, the Q204X mutation, ranked 1st in the QTL peaks at the proximal end of BTA2 and causing a premature stop codon in the gene encoding myostatin (MSTN), was reported as one of the polymorphisms responsible for the double-muscled phenotype in several cattle breeds. We also identified dozens of other variants located in genes having a function that may be related to meat production traits (e.g. COL3A1 collagen type III alpha 1 chain). By better identifying genes and candidate causative variants associated with beef production traits in cattle, MA appear to be of great interest to decipher the biological mechanisms underlying these traits.The BovReg project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 815668

Identification of genome regions and promising candidate genes linked to innate immune capacity on young Holstein calves

International audienceIn order to investigate the genomic control of innate immune response, the concentration levels of 14 cytokines produced naturally or in response to whole blood stimulation with three pattern recognition receptors agonists were determined in 623 Holstein calves enrolled in the Healthycalf project. The effect of the immunostimulants and the relationship among the cytokines produced were observed through a principal components analysis, and 50K GWAS were performed on all cytokine x condition traits. Results showed that most cytokines are oriented together following the first component that explained 70% of the variability and partially discriminated the agonistic conditions. Additionally, 40 genome regions were found in association with at least one trait with some regions being largely shared between conditions and cytokines. Seven positional candidate genes were considered as especially interesting due to their functional link to innate immune response reported from the literature