Faits marquants 2024 de l'unité GABI

Towards selecting dairy cows to reduce methane emissions

To combat climate change, it is essential to reduce greenhouse gas emissions, including methane produced by ruminants. As part of the Methabreed project funded by Apis-Gene, a cattle selection strategy has been implemented to reduce methane emissions. A key challenge was obtaining large-scale measurements, so the strategy was as follows: (a) development of methane prediction equations based on mid-infrared (MIR) spectra of milk: to this end, nearly 28,000 methane measurements were obtained by GreenFeeds on experimental farms and compared with 1,800 MIR spectra; (b) application of these equations to more than 28 million MIR spectra collected from French commercial farms participating in milk recording; (c) genetic analysis of this high-throughput data and implementation of a pilot genomic evaluation. This evaluation has been approved by breeding organisations and will be rolled out in 2025 for an initial selection of cattle that emit less methane..

Contact : Didier Boichard, Pauline Martin 

Reference:

• Fresco S., Boichard D., Lefebvre R., Barbey S., Gaborit M., Fritz S., Martin P. 2024. Short Communication: Correlation of methane production, intensity, and yield with residual feed intake throughout lactation in Holstein cows. Animal, 18, 101110. https://doi.org/10.1016/j.animal.2024.101110
• Fresco S., Vanlierde A., Boichard D., Lefebvre R., Gaborit M., Bore R., Fritz S., Gengler N., Martin P. 2024. Combining heterogeneous GreenFeed measurements to predict methane emissions from cow milk mid-infrared spectra and phenotypes. Animal, 18, 101200. https://doi.org/10.1016/j.animal.2024.101200
• Fresco S., Boichard D., Fritz S., Martin P. Genetic parameters for methane production, intensity, and yield predicted from milk mid-infrared spectra throughout lactation in Holstein dairy cows. J Dairy Sci, https://doi.org/10.3168/jds.2024-25231

Estimation of non-genetic parental effects in dairy cattle

Various early factors, such as the mode of reproduction or maternal and environmental factors during gestation, can affect embryonic or foetal development. This raises the question of whether these effects are long-lasting, particularly on the future career of the animals born. National cattle databases can provide some answers to these questions, as they contain a wide variety of phenotypic data recorded on animals from different breeding methods, with information on various maternal and environmental parameters during gestation, as well as the origin of the semen batch used for each insemination. Several studies have sought to quantify the effects of different paternal and maternal factors on the performance of Holstein and Montbéliarde dairy cattle daughters before or during their first lactation: (1) the method of reproduction used to conceive them (sexed semen, embryo transfer, in vitro fertilisation), (2) maternal factors during their mother's gestation (outside temperature, age, parity, health events), and finally (3) the batch of bull semen used. The traits analysed concerned milk production and composition, cow size, fertility and udder health. Overall, due to the large sample sizes analysed, most of the effects observed in adult females are statistically significant but modest in magnitude: most effects are less than 1% of the phenotypic mean. With regard to heat stress, its effect is greatest during the first month of gestation. For the industry, practical considerations are limited because these effects are small. In particular, for environmental temperature, the effects on the daughter born from gestation are much more limited than the direct effects on the cow herself.  

Contact : Didier Boichard,  Aurélie Vinet 

Reference:

• Fouéré C., Sanchez M.P., Boussaha M., Fritz S., Vinet A., Kiefer H., Boichard D., Hoze C. 2024. A large population study to assess the magnitude of prenatal programming in dairy cattle. J Dairy Sci., 107:5913–5923. https://doi.org/10.3168/jds.2023-24051
• Vinet A., Fouéré C., Cuyabano B.C.D, Mattalia S., Vallée R., Barbat A., Bertrand C., Hoze C., Boichard D. Long-lasting effects of in utero heat stress on subsequent performances of heifers and primiparous cows. J Dairy Sci., 107. https://doi.org/10.3168/jds.2024-25168
• Fouéré C., Hoze C., Besnard F., Boussaha M., Boichard D., Sanchez M.P. 2024. Investigating the impact of paternal age, paternal heat stress, and estimation of semen batch variance on dairy cow phenotype. Genet Sel Evol, 56, 46. https://doi.org/10.1186/s12711-024-00918-2

A resounding success for the 14th International Havemeyer Foundation Horse Genome Workshop organised by INRAE in Caen from 12 to 15 May 2024

The 14th Havemeyer Horse Genome Workshop was held from 12 to 15 May 2024 at the University of Caen and brought together an international community of 110 people (45% from the USA) to share the latest findings on horse genetics. Created in 1995, this event takes place every two years, alternating between the United States and another partner country. Historically, it has been largely funded by the Dorothy Havemeyer Foundation (NY, USA). This 14th edition was organised at the University of Caen by the Integrative Biology and Equine Genetics (BIGE) team of the GABI UMR131 unit, in local collaboration with the LABÉO laboratory and the CAGT laboratory (CNRS, Paul Sabatier University, Toulouse). The conference covered four main themes with guest lectures and workshops: 1) equine evolution, breed development and management; 2) functional genomics, epigenetics and reproduction; 3) performance and welfare genomics; 4) equine disease genomics. The guest speakers presented an overview of the prehistory and history of horse domestication (L. Orlando, CNRS, CAGT), the epigenetic transmission of fertility traits (H Kiefer, INRAE, Breed), and the fight against genetic doping in humans (N Leuenberger, Lausanne University Hospital).

The event was a great success, raising the international profile of INRAE, the GABI unit and local partners LABÉO, the city of Caen and the Normandy Region.

Contact : Eric Barrey 

Website: https://horse-genome.workshop.inrae.fr/ 

Integration of multi-omic data for the identification of biomarkers of bull fertility

Bull fertility is an important economic trait, and the use of subfertile semen for artificial insemination reduces the overall efficiency of the livestock sector. Male fertility is a multifactorial phenotype that depends on genetic, epigenetic, physiological and environmental factors. In this study, we combined -omic data (genotypes, sperm DNA methylation at the CpG level and small non-coding RNAs) and semen parameters measured on a large cohort of 98 Montbéliard bulls with contrasting fertility levels. Four methodologies were considered to identify predictive biomarkers related to bull fertility: logistic Lasso, random forests, gradient boosting and neural networks. The variables selected by these methods were annotated in terms of genes in order to perform functional enrichment analyses. The genes targeted by the most contributory CpGs, SNPs and miRNAs were all found to be involved in development. Interestingly, fragments derived from ribosomal RNAs were overrepresented, suggesting a role in male fertility. These markers could be used in the future to identify subfertile bulls in order to increase the overall efficiency of the breeding sector.

Contact : Florence Jaffrezic

Reference :

• V. Costes, E. Sellem, S. Marthey, C. Hoze, A. Allais-Bonnet, L. Schibler, H. Kiefer, F. Jaffrézic (2024). Multi-omics data integration for the identification of biomarkers for bull fertility. PLoS ONE, 19. 10.1371/journal.pone.0298623

Study of tissue regeneration by stem cells and progenitor cells from bovine mammary epithelium

Milk, the sole source of nutrients for young mammals at birth, is secreted by the epithelial cells of the mammary gland. Its development and the maintenance of mammary tissue in adults depend on the proliferation and differentiation of mammary stem and progenitor cells. These cells have been extensively studied in women and mice, but less frequently in farm animals. Their identification in cattle could make it possible to modulate mammary gland development or influence the persistence of lactation. Here, we studied the ability of bovine mammary epithelial cell populations to reconstruct such tissue after transplantation into the mammary adipose tissue of mice. Transplants of mammary tissue fragments from Holstein heifers developed according to the morphological model of the bovine mammary gland. In contrast, the transplantation of sorted mammary epithelial cells led to the development of growths that did not have the epithelial structures characteristic of the bovine mammary gland (ducts, alveoli, connective tissue). Similar results were obtained with the transplantation of mammary epithelial cells sorted according to the expression of stem cell markers, or basal lineage cells, which developed into clusters of cells surrounded by segments of connective tissue. Thus, the sorted cells did not express the ability to regenerate epithelial tissue. Further studies will be needed to identify mammary stem/progenitor cells with the ability to regenerate functional mammary tissue.

Contact : Fabienne Le Provost 

Reference:
L. Finot, C. Hue-Beauvais, E. Aujean, F. Le Provost, E. Chanat (2024) Sorted stem/progenitor epithelial cells of pubertal bovine mammary gland present limited potential to reconstitute an organised mammary epithelium after transplantation. PLOS ONE 19(10): e0296614. https://doi.org/10.1371/journal.pone.0296614

Characterisation of the vaginal and faecal microbiota of dairy cows and influence of host genetics on the faecal microbiota

The microbiota, which comprises all the microorganisms present in a given environment, plays a key role in animal health and productivity. In ruminants and cattle in particular, the relationship with the digestive microbiota is a special example of symbiosis between a host and its microbiota. However, the specific microbiota of dairy cows and their interactions with the host remain largely unexplored. A collaboration between GD Biotech - Gènes Diffusion and INRAE has made it possible to finely characterise the microorganisms in 1,171 vaginal swabs and 1,875 faecal samples from Holstein cows, revealing significant links between the composition of these microbiotes and the animals' production, fertility and health performance. This work also highlights the genetic influence of the host on the composition of the faecal microbiota, opening up prospects for optimised breeding and selection practices.

Contact : Marie-Pierre Sanchez, Jordi Estellé-Fabrellas

Reference

• Brulin L., Ducrocq S., Even G., Sanchez M.-P., Martel S., Merlin S., Audebert C., Croiseau P., Estelle J. Dairy traits are strongly associated with bovine fecal microbiota and its Bifidobacterium abundance. Animal, 18:101243. https://doi.org/10.1016/j.animal.2024.101243 
• Brulin L., Ducrocq S., Even G., Sanchez M.-P., Martel S., Merlin S., Audebert C., Croiseau P., Estelle J. 2024. Characterization of bovine vaginal microbiota and its relationship with host fertility, health and production. Scientific Reports, 14:19277. https://doi.org/10.1038/s41598-024-69715-7 
• Brulin L., Ducrocq S., Estelle J., Even G., Martel S., Merlin S., Audebert C., Croiseau P., Sanchez M.P. The fecal microbiota of Holstein cows is heritable and genetically correlated to dairy performances. Journal of Dairy Science, https://doi.org/10.3168/jds.2024-25003

Analysis of mitochondrial nuclear sequences in ruminants

Nuclear sequences of mitochondrial origin, known as NUMTs (nuclear mitochondrial DNA), have been identified in the nuclear genome of most species. These NUMT sequences can be a source of artefacts if they are not taken into account. In recent years, we have studied NUMTs in different species of ruminants. These studies are a prerequisite for analysing mitochondrial genetic diversity. To date, we have published results for three species, with the catalogue of NUMTs in domestic yaks due to be published in 2024.

Contact : Dominique Rocha

Reference:
[1] Tramontin Grau E., Charles M., Féménia M., Rebours E., Vaiman A., Rocha D. (2020) Survey of mitochondrial sequences integrated into the bovine nuclear genome. Scientific Reports 10(1):2077. doi: 10.1038/s41598-020-59155-4.
[2] Féménia M., Charles M., Boulling A., Rocha D. (2021). Identification and characterisation of mitochondrial sequences integrated into the ovine nuclear genome. Animal Genetics 52(4): 556-559. doi: 10.1111/age.13096.
[3] Poncet M., Féménia M., Pierre C., Charles M., Capitan A., Boulling A., Rocha D. (2024). Nuclear sequences of mitochondrial origin in domestic yak. Sci. Rep. 14(1):10217. doi: 10.1038/s41598-024-61147-7.