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Additional file 1: Fig. S1.. correlation clustering run on the methylation percentages at CpGs10 covered in at least 22 samples per group. Fig. S2: heatmap run on CpGs discriminant between sperm and somatic cells. Fig. S3: annotation of fertility-related DMRs relative to different genome features. Fig. S4: average DNA methylation at individual LINE and LTR repeats after alignment of the RRBS sequences on a Repbase artificial genome. Fig. S5: pyrosequencing validation of the upstream region of LBX1 gene. Fig. S6: fertility, semen functional parameters and semen sample characteristics in correctly classified and misclassified bulls. Fig. S7: PCA run on the methylation percentages at DMCs, with or without the imputation of missing values. Fig. S8: semen functional parameters before and after correction for the batch effect.

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Metabolomics has been increasingly used in animal and food sciences. Animal health is one of the most important factor that can also alter animal integrity and welfare. Some studies have already investigated the link between health and metabolic profile of dairy animals. These studies in metabolomics often consider a single type of sample using a single analytical platform (nuclear magnetic resonance or mass spectrometry). Only few studies with multi-platform approaches are also used with a single or a multi type of sample, but they mainly consider dairy cows’ metabolome although dairy goats present similar diseases, that it could be interesting to detect early to preserve animal health and milk production. This study aims to create a metabolic atlas of goat plasma, milk and feces, based on healthy animals. Our study describes a standard operating procedure for three goat matrices: blood plasma, milk, and feces using multiple platforms (NMR (1H), UHPLC (RP)-MS and UHPLC (HILIC)-MS) that follows a unique sample preparation procedure for each sample type to be analyzed on multi-platforms basis. Our method was evaluated for its robustness and allowed a better characterization of goat metabolic profile in healthy conditions.

International audience; Mycobacterium avium subsp. paratuberculosis is the etiological agent of Johne's disease in ruminants. Here, we report the annotated draft genome sequences of 142 M. avium subsp. paratuberculosis strains that were isolated from dairy cattle in France between 2014 and 2018. The genomes of these strains were sequenced using Illumina technology.

International audience; Introduction: Paratuberculosis is a chronic infection of the intestine, mainly the ileum, caused by Mycobacterium avium subsp. paratuberculosis (Map) in cattle and other ruminants. This enzootic disease is present worldwide and has a strong impact on the dairy cattle industry. For this species, the typing tools do not make it possible to investigate the genetic diversity of the strains. These limitations can be overcome by the application of Whole Genome Sequencing (WGS), particularly for clonal populations such as Map. WGS analyses can provide comprehensive genetic information, including information on genome evolution, discrimination of closely related strains and virulence determinants.The purpose of the present study was to undertake a whole-genome analysis of Map strains to identify accurate phylogenetic relationships between isolates and establish correlations between genomic traits and epidemiologicaldata within a population of well documented-strains.Materials and methods: A set of 200 animal field strains were selected based on a previous large-scale longitudinal study representative of the French Map population circulating in the West of France. Strains were isolated from bovine of breed Prim’Holstein or Normande naturally infected by Map. For each strain isolated, all information about the animal is available including: breed, herd prevalence, locations, serological status and excretion level. The genomic sequences of Map strains were obtained by Illumina MiSeq sequencing. Genomic sequences were assessed for potential contamination using Kraken2. Cleaned reads were aligned to the reference genome K-10 and SNP were called using FreeBayes. IQ-Tree was used to infer a SNP-based phylogeny.Results, discussion and conclusion: This study provided 200 new genomes of French strains isolates from naturally infected animals. Pangenome analysis of this panel confirmed the degree of Map clonality. SNP analyzes provided accurate phylogeny able to distinguish each strain divided into 4 clusters independently of the breed of the cattle. Interestingly, the phylogeny clearly distinct the two major MLVA profiles. A phylogeny was inferred with French Map isolates and with other Map isolates found across the world. Relations between genetic traits and epidemiological data will be investigated to better understand the transmission dynamics of the disease

International audience; Bovine paratuberculosis is a contagious and incurable disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), with adverse effects on animal welfare and serious economic consequences. In a previous GWAS conducted on 1644 Holstein cows with an accurately defined status for MAP (controls, non-clinical and clinical cases) and whole genome sequences (WGS) imputed using the 6th Run of the 1000 bull genomes (1kBG) project (multibreed population, UMD3.1 reference genome), we identified three genomic regions on chromosomes 12, 13, and 23. The objective of the present study was to conduct further investigations using the 7th Run of the 1kBG, which includes a larger Holstein population with WGS based on the recent ARS-UCD1.2 reference genome. 50K genotypes of the 1644 Holstein cows were imputed to the high-density (HD) level with FImpute and then up to WGS with Minimac using reference sets of 776 and 700 Holstein bulls, respectively. GWAS was carried out with GCTA, testing the individual effect of ~25M variant and accounting for the population structure through a HD-based genomic relationship matrix. After filtering variants for low imputation accuracy (R² < 0.3) or frequency (MAF < 0.001), 4815 variants had significant effects (6 ≤ -log(P) ≤ 34.5) on resistance to MAP. They were located in eight different genomic regions on chromosomes 6, 9, 12, 13 (2 regions), 14, 18, and 23. Two-thirds of these variants (3194) were located in genes, mainly in introns (2170), upstream or downstream regions (907), and exons (101 including 65 non-synonymous). In each region, the variants with the most significant effects were located in the TMPRSS11F, HS6T3, ABCC4, SNTA1, SNTB1, NOTCH4, NFKBTL1, ATP6V1G2, DDX39B, and ELOVL5 genes. This study confirms the three genomic regions we detected before and reveals five novel regions for resistance to MAP.

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Additional file 1: Figure S1. −log(P-value) plotted against the position of variants detected by GWAS (in grey) and conditional GWAS (GWAS_COJO; in blue).

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International audience; Spermatozoa have a remarkable epigenome in line with their degree of specialization, their unique nature and different requirements for successful fertilization. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine spermatozoa is still scarce. In the context of genomic selection, more information on the epigenetic features transferred to the embryo alongside the paternal genetic heritage is necessary, in order to improve semen quality control procedures and bull fertility. We characterized the bull sperm methylome relative to bovine fibroblasts and monocytes using reduced restriction bisulfite sequencing (RRBS). A wide majority of differentially methylated cytosines (DMCs) were less methylated in sperm than in somatic cells. Consistent with previous studies in other species, these hypomethylated DMCs were enriched for genes relevant to the germline differentiation program and sperm functions. The most remarkable observation was a dramatic enrichment for repeats and particularly for satellites, which may partly account for the lower global methylation we observed in bull sperm relative to sperm from other species (LUminometric Methylation Assay). We next investigated whether fertility biomarkers could be identified in the sperm methylome. Based on field fertility indicators, we compared fertile ejaculates, subfertile ejaculates and ejaculates from bulls with a disappointing career in contradiction with genomic predictions (Montbéliarde breed, n=10/group). The median age at production was consistent among groups and the phenotypic characterization revealed no significant differences except for the proportion of motile sperm, which was reduced in disappointing bulls. We identified 4823 DMCs targeting genes involved in signaling pathways, angiogenesis and the response to growth factors. Since DNA methylation is affected by the CpG content of the genome and its alteration by DNA polymorphism, an integrative approach was conducted to identify CpGs and SNPs in correlation, which revealed both direct and indirect interactions between the genome and the epigenome.

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