Gilles Renand

Enteric methane emissions from cattle pose a significant environmental concern and represent a substantial energy loss for the animal, necessitating the development of effective mitigation strategies. The gastrointestinal microbiota plays a crucial role in determining both feed efficiency and methane production. Still, the specific microbial signatures that predict these traits across different production systems remain poorly understood. This study aimed to identify common predictive microbial biomarkers for feed efficiency and methane emissions using co-association network analysis across contrasting cattle production systems. Rumen liquid and faecal microbiota from 55 Charolais heifers (beef) and 56 Holstein cows (dairy) were analysed using 16S rRNA gene amplicon sequencing. Phenotypic data included feed efficiency, methane yield and acetate/propionate ratio. Co-association networks were constructed using Partial Correlation and Information Theory to identify amplicon sequence variants (ASVs) directly connected to phenotypes. Multiple regression analysis determined the minimal ASV sets required to achieve optimal predictive accuracy. Rumen microbiomes consistently showed superior predictive performance compared to faecal communities across all traits. Network-selected ASVs explained substantial phenotypic variance across traits and production systems ( R ²=0.45−0.84), consistently outperforming randomly selected ASVs by 0.13–0.44 R ² units. The ACET:PROP ratio showed the highest predictive accuracy ( R ²=0.84 in Charolais rumen, 0.77 in Holstein rumen), while minimal ASV sets achieved 93–97% of the full model's performance using 33–65% fewer ASVs (6–17 ASVs). Bacteroidaceae was consistently enriched across phenotypes in rumen networks, regardless of production system. Contrary to expectations, most associations were production system-specific, with notable exceptions including negative correlations between the ACET:PROP ratio and Prevotella / Ruminococcus genera and negative associations with members of the Succinivibrionaceae family for methane-related traits. The anatomical site-specific and production system-specific nature of most associations underscores the importance of context-specific approaches.

Dans un contexte économique et environnemental où l’élevage est de plus en plus questionné, la précocité, l’efficience alimentaire et la résilience sont devenus des points d’intérêt majeurs de par leur rôle potentiel pour améliorer l’efficience globale des élevages. Pour explorer ces caractères et les liens qui les unissent dans les systèmes allaitants, une expérimentation de grande envergure a été menée entre 2011 et 2021 sur 650 femelles charolaises. Cette expérimentation se découpait en trois périodes que les animaux effectuaient successivement : l’étude de la précocité sexuelle et de développement, l’étude de l’efficience alimentaire au travers de l’ingéré résiduel à deux ans, puis l’étude de la réponse à un challenge alimentaire (composé d’une phase de restriction et d’une phase de récupération) au cours de la lactation. Cet article regroupe l’ensemble des résultats obtenus. Si la précocité sexuelle définie par l’âge à la puberté est fortement liée à l’environnement (conduite, alimentation…) et notamment à la saison de naissance, l’héritabilité du caractère est néanmoins modérée (0,21 ± 0,08). Elle est également corrélée génétiquement avec un petit poids à la naissance et une forte croissance pré-sevrage. L’efficience alimentaire des animaux de deux ans est peu héritable (0,09 ± 0,08) mais corrélée favorablement avec la précocité. Face au challenge alimentaire, les vaches ont des réponses équilibrées entre perte de production laitière et mobilisation de réserves corporelles mais cette réponse moyenne de la race cache des disparités entre individus. Enfin, les génisses les plus efficientes présentaient des productions laitières amoindries une fois en lactation par rapport à leurs homologues inefficientes (jusqu’à − 0,7 kg de lait par jour en milieu de lactation soit environ 10 % de moins), ainsi que des retours en chaleurs plus long dans le cadre de la restriction alimentaire. Ces résultats promeuvent l’importance de considérer l’efficience sur le long terme en prenant en compte ses différentes composantes et de ne pas réaliser une sélection génétique sur une efficience alimentaire mesurée sur un moment court et unique pendant la phase de croissance.

Summary: Limousin, a renowned beef breed originating from central France, has been selectively bred over the last 100 years to improve economically important traits. We used whole‐genome sequencing data from 10 unrelated Limousin bull calves to detect polymorphisms and identify regions under selection. A total of 13 943 766 variants were identified. Moreover, 311 852 bi‐allelic SNPs and 92 229 indels located on autosomes were fixed for the alternative allele in all sequenced animals, including the previously reported missense deleterious F94L mutation in MSTN. We performed a whole‐genome screen to discover genomic regions with excess homozygosity, using the pooled heterozygosity score and identified 171 different candidate selective sweeps. In total, 68 candidate genes were found in only 57 of these regions, indicating that a large fraction of the genome under selection might lie in non‐coding regions and suggesting that a majority of adaptive mutations might be regulatory in nature. Many QTL were found within candidate selective sweep regions, including QTL associated with shear force or carcass weight. Among the putative selective sweeps, we located genes (MSTN, NCKAP5, RUNX2) that potentially contribute to important phenotypes in Limousin. Several candidate regions and genes under selection were also found in previous genome‐wide selection scans performed in Limousin. In addition, we were able to pinpoint candidate causative regulatory polymorphisms in GRIK3 and RUNX2 that might have been under selection. Our results will contribute to improved understanding of the mechanisms and targets of artificial selection and will facilitate the interpretation of GWASs performed in Limousin.

Residual energy intake (REI) on two successive diets (hay and maize based) and slaughter traits, including visceral organs, were phenotyped in 584 adult purebred Charolais cows. To investigate the relationships between these traits and their genetic determinism, we first estimated the genetic parameters, including correlations, using REML modeling under WOMBAT software. The animals were then genotyped on the BovineSNP50 SNPchip before being imputed to the 600K density and genome wide association study was performed with GCTA software. We found low heritability for REI (h² = 0.12 in each of the diet phases). Although the phenotypic correlation between the two diet phases was moderate (0.36), the genetic correlation was high (0.83), indicating a common genetic determinism for feed efficiency regardless of the diet. Correlations between REI and slaughter traits were negative regarding muscle-related traits and positive for fat-related traits, indicating that efficient animals generally had a more muscular carcass. It was also seen that feed efficiency was genetically and phenotypically correlated with smaller organs when expressed as a proportion of their empty body weight. From the GWAS analysis, seven QTLs were found to be associated with a trait at the genome-wide level of significance and 18 others at the chromosome-wide level. One important QTL was detected in BTA 2, reflecting the essential effect of the myostatin gene on both carcass composition and relative organ weight. Three QTLs were detected for REI during the maize diet phase on BTA 13, 19, and 28, the latter being significant at the genome-wide level. The QTLs on BTA 19 mapped into the TANC2 gene and the QTLs on BTA 28 into the KIF1BP gene, which are both known to interact with the same protein (KIF1A). However, no obvious functional link between these genes and feed efficiency could be made. Among the other QTLs detected, one association on BTA 4 with liver proportion mapped to the candidate gene WASL, which has previously been shown to be differentially expressed in liver cells and linked to feed restriction or cancer development. No QTLs were found to be common between feed efficiency and any slaughter traits.