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Les conditions pédoclimatiques du projet Herby® : contexte du réseau de paddocks en suivi
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Utilisation d’une puce très basse densité (1 100 SNP) pour la sélection génomique chez 3 races porcines françaises
No full textTo reduce genotyping costs for genomic selection, a Low-Density SNP (LD) chip, designed in 2016, is now used routinely. This panel is composed of approximately 1100 equidistant SNPs. The relevance of this chip has been studied in French populations of the Landrace, Large White and Pietrainpig breeds. The quality of imputation was estimated by the correlation between actual and imputed genotypes and error rates. The impact of imputation on the genomic evaluations was estimatedby the correlation between the genomic values obtained for the candidates with imputed genotypes, and those obtained with the high-densitygenotypes. Average error rates of imputation estimated on all the chromosomes were 0.03, 0.11 and 0.14for Landrace, Large White and Pietrain, respectively. The estimated correlations between actual and imputed genotypes were relativelyhigh at 0.93, 0.92 and 0.88forLandrace, Large White and Pietrain populations,respectively. Correlations between genomicbreedingvalues predicted with high-density genomicdata or imputed genomic data from the LD SNP panel rangedfrom0.89-0.97 for Large White and Landrace populations for reproductivetraits. They were higher than those obtained for the Pietrain population (0.80and 0.97for production traits, respectively). In conclusion, despite the limited number of SNPs on the low-density panel used in this study, the imputation accuracyis sufficient to use the imputed genotypes in the genomic evaluations. In practice, genotyping candidates with aLD chip is a solution for selecting future breeding pigsat lower cost
Life cycle assessment of iberian traditional pig production system in Spain
No full textTraditional Iberian pig production is characterized by outdoor systems that produce animals fed with natural resources. The aim of this study was to assess the environmental impacts of such systems through Life Cycle Assessment. Environmental impacts were analysed per kilogram of live weight at farm gate. Iberian pig production in montanera had the lowest impacts for climate change (CC), acidification (AC), eutrophication (EU) and cumulative energy demand (CED), being 3.4 kg CO2 eq, 0.091 molc H+ eq, 0.046 kg PO4 3- eq, and 20.7 MJ, respectively, due to the strict use of natural resources (acorns and grass) during the fattening period. As Iberian farms had a greater dependence on compound feed in cebo campo, environmental impacts on CC, AC, EU and CED were 22, 17, 95 and 28% higher, respectively, than with montanera. For land occupation (LO), however, cebo campo had a lower impact (31.6 m2/year) than montanera (43.0 m2/year) system. Traditional Iberian pig production systems have environmental impacts higher than conventional systems studied in literature but are similar to other traditional systems. Based on the present assessment, it is necessary to account for the contribution of emissions resulting from the consumption of natural resources to avoid the underestimation of environmental impacts
Neuromodulatory and possible anxiolytic-like effects of a spice functional food ingredient in a pig model of psychosocial chronic stress
No full textPsychological chronic stress is associated with the development of mood disorders, and spices have shown protective properties in this context. This research investigated the effects of a supplementation with a functional food ingredient containing spice extracts in a pig model of psychosocial chronic stress. Its impact on behavior, neurophysiology, immune system and gastrointestinal tract were evaluated. Almost no significant results were found at the gut and immune levels. An increased expression of 5-HT1AR and BDNF in the hippocampus and prefrontal cortex, respectively, and blood perfusion changes in several brain regions including the olfactory bulb, hippocampus, dorsolateral prefrontal cortex and dorsal anterior cingulate cortex were observed. Also, slight anxiolytic-like effects were observed in the Open-field and Novelty-Suppressed Feeding tests. These modulations of brain regions associated with the regulation of emotions and cognition as well as the potential effects on anxiety might come from the repeated stimulation of the olfactory system
Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows
No full textMitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. In this study, the rumen microbiome from Holstein cows was characterized through a combination of 16S rRNA gene and shotgun metagenomic sequencing. Methane production (CH4 ) and dry matter intake (DMI) were individually measured over 4-6 weeks to calculate the CH4 yield (CH4 y = CH4 /DMI) per cow. We implemented a combination of clustering, multivariate and mixed model analyses to identify a set of operational taxonomic unit (OTU) jointly associated with CH4 y and the structure of ruminal microbial communities. Three ruminotype clusters (R1, R2 and R3) were identified, and R2 was associated with higher CH4 y. The taxonomic composition on R2 had lower abundance of Succinivibrionaceae and Methanosphaera, and higher abundance of Ruminococcaceae, Christensenellaceae and Lachnospiraceae. Metagenomic data confirmed the lower abundance of Succinivibrionaceae and Methanosphaera in R2 and identified genera (Fibrobacter and unclassified Bacteroidales) not highlighted by metataxonomic analysis. In addition, the functional metagenomic analysis revealed that samples classified in cluster R2 were overrepresented by genes coding for KEGG modules associated with methanogenesis, including a significant relative abundance of the methyl-coenzyme M reductase enzyme. Based on the cluster assignment, we applied a sparse partial least-squares discriminant analysis at the taxonomic and functional levels. In addition, we implemented a sPLS regression model using the phenotypic variation of CH4 y. By combining these two approaches, we identified 86 discriminant bacterial OTUs, notably including families linked to CH4 emission such as Succinivibrionaceae, Ruminococcaceae, Christensenellaceae, Lachnospiraceae and Rikenellaceae. These selected OTUs explained 24% of the CH4 y phenotypic variance, whereas the host genome contribution was ~14%. In summary, we identified rumen microbial biomarkers associated with the methane production of dairy cows; these biomarkers could be used for targeted methane-reduction selection programmes in the dairy cattle industry provided they are heritable
Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding.
No full textIn this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability
Metabolomics to Exploit the Primed Immune System of Tomato Fruit.
No full textTargeted and untargeted metabolomics were used to investigate the metabolic regulations that underpin the priming of tomato fruit against pathogenic microbes that present different infection strategies. Metabolomic analyses revealed major changes after BABA treatment and after inoculation. Remarkably, primed responses seemed specific to the type of infection, rather than showing a common fingerprint of BABA-induced priming. Furthermore, top-down modelling from the detected metabolic markers allowed for the accurate prediction of the measured resistance to fruit pathogens and demonstrated that soluble sugars are essential to predict resistance to fruit pathogens. Altogether, our results demonstrate that metabolomics is particularly insightful for a better understanding of defence priming in fruit. Further experiments are underway in order to identify key metabolites that mediate broad-spectrum BABA-induced priming in tomato fruit
Contribution à la production d’un document technique synthétisant les données sur les pathologies parasitaires des animaux d’élevage
No full textEn Guadeloupe, les parasites occasionnent des pertes de productivité considérables en élevage avec un impact économique très important. A l’Unité de Recherches Zootechniques du centre INRAE Antilles-Guyane, des recherches sont réalisées pour mettre au point des stratégies limitant les pathologies parasitaires, dans une démarche agroécologique (gestion de pâturage, association d’espèces pâturant sur la même parcelle, utilisation de plantes alicamentaires…). Les résultats de ces recherches sont diffusés aux professionnels agricoles via des documents techniques publiés par l’unité.
Les travaux réalisés pendant le stage, contribueront à la réalisation d’un document technique sur les pathologies des animaux d’élevage, liées à la tique sénégalaise, Amblyomma variegatum. Ces travaux consistent en une recherche bibliographique sur ce parasite, ciblée sur trois sujets :
- La détermination des zones de présence
- Les pathologies liées chez les animaux et adaptation
- Les résistances aux traitements
La liste des documents répertoriés est analysée selon leur nature (thèse, article…) et selon les sujets traités, via les mots clés