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Les filières et systèmes d’élevage ont considérablement évolué au cours du XXe siècle. La recherche en génétique animale et la mise en place des programmes d’amélioration génétique ont joué un rôle important dans cette évolution. Aujourd’hui, le modèle dominant, caractérisé par une utilisation intensive d’intrants, une très grande spécialisation des systèmes et la recherche de coûts de production toujours plus bas, est remis en cause. Un objectif désormais largement partagé est de contribuer à l’émergence de systèmes alimentaires durables, équitables, sains et respectueux de l’environnement. L’agroécologie est un moyen pour atteindre cet objectif et guider la nécessaire transition des systèmes d’élevage, à laquelle la génétique animale doit contribuer. Des exemples de contributions passées, actuelles et potentielles sont présentés et positionnés selon cinq principes d’agroécologie proposés pour guider l’évolution des systèmes d’élevage. La plupart, telles que la sélection d’animaux résistants à différentes maladies infectieuses ou valorisant de façon plus efficace leur alimentation, correspondent à des niveaux de transition agroécologique faible, dans la mesure où elles ne remettent pas en cause les fondements, les composantes ou la conception générale des systèmes. De nouvelles contributions, visant une transition forte, fondée sur une reconception en profondeur des systèmes d’élevage, sont à développer à l’avenir.

Abstract Background In quail, two feather colour phenotypes i.e. fawn-2/beige and yellow are associated with the ASIP locus. The aim of our study was to characterize the structural modifications within this locus that explain the yellow mutation (large deletion) and the fawn-2/beige mutation (assumed to be caused by a different structural modification). Results For the yellow phenotype, we identified a complex mutation that involves a 141,162-bp long deletion. For the fawn-2/beige phenotype, we identified a 71-kb tandem duplication that comprises one unchanged copy of ASIP and one copy present in the ITCH-ASIP fusion gene, which leads to a transcript coding for a normal ASIP protein. Although this agrees with previous reports that reported an increased level of ASIP transcripts in the skin of mutant animals, we show that in the skin from fawn-2/beige embryos, this level is higher than expected with a simple duplication of the ASIP gene. Thus, we hypothesize that the 5′ region of the ITCH-ASIP fusion gene leads to a higher transcription level than the 5′ region of the ASIP gene. Conclusions We were able to conclude that the fawn-2 and beige phenotypes are caused by the same allele at the ASIP locus. Both of the associated mutations fawn-2/beige and yellow lead to the formation of a fusion gene, which encodes a transcript for the ASIP protein. In both cases, transcription of ASIP depends on the promoter of a different gene, which includes alternative up-regulating sequences. However, we cannot exclude the possibility that the loss of the 5′ region of the ASIP gene itself has additional impacts, especially for the fawn-2/beige mutation. In addition, in several other species including mammals, the existence of other dominant gain-of-function structural modifications that are localized upstream of the ASIP coding sequences has been reported, which supports our hypothesis that repressors in the 5′ region of ASIP are absent in the fawn-2/beige mutant.

Biomass allowance is a key feature in pasture-based rabbit production systems. It conditions not only the stock density (rabbits/m²) and/or the number of grazing days, it also influences the grazing behaviour of animals. When herbage restriction occurs, pelleted feed and/or cereal intake goes up. Inadequate pasture management may also impair the biomass quantity and quality if overgrazing occurs. To avoid the undesirable effects of overgrazing and better manage pellet and cereal intake, information on both biomass availability and rabbits’ grazing capacity are needed. Here, we present an adaptation of the rising plate meter method (developed for biomass intake measures for ruminants) for use in rabbit. To this end, we designed an experiment where two groups of 12 rabbits each were kept in two different fields: under an apple orchard (AO) or on fallow land (FL). We followed the animals for 5 consecutive weeks (from 45 to 80 d old). Rabbits lived in 25 m² movable paddocks, and every week a new paddock location (called paddock-spot) was made available for them. At each new paddock-spot, we measured the herbage height inside the paddocks and performed samplings of the available biomass (i.e. herbage cut after herbage height measurement) outside the paddocks. From this data we estimated the available biomass inside each paddock-spot by fitting linear regression equations of biomass to herbage height. Overall, rabbits in the AO and FL had access to 1328±65.7 and 1386±58.6 kg of dry matter (DM) per ha, respectively. In every field and paddock-spot, the biomass available was lower than the rabbits’ grazing capacity; overgrazing was the rule. Roughly, and under a restricted herbage allowance, rabbits in the AO ingested 45.2 g DM/d and rabbits in the FL 43.4 g DM/d. In the last week (64 to 80 d old), the biomass intake of rabbits in the AO and AL represented 26.4 and 23.5% of the total DM intake, respectively. These values, however, does not represent the real grazing capacity of growing rabbits. In this study, we provide some advice on the sampling method to obtain reliable biomass estimations and we mention two methods for handling influential observations in linear regression.

Abstract Background Ribosomal DNA (rDNA) repeats are situated in the nucleolus organizer regions (NOR) of chromosomes and transcribed into rRNA for ribosome biogenesis. Thus, they are an essential component of eukaryotic genomes. rDNA repeat units consist of rRNA gene clusters that are transcribed into single pre-rRNA molecules, each separated by intergenic spacers (IGS) that contain regulatory elements for rRNA gene cluster transcription. Because of their high repeat content, rDNA sequences are usually absent from genome assemblies. In this work, we used the long-read sequencing technology to describe the chicken IGS and fill the knowledge gap on rDNA sequences of one of the key domesticated animals. Methods We used the long-read PacBio RSII technique to sequence the BAC clone WAG137G04 (Wageningen BAC library) known to contain chicken NOR elements and the HGAP workflow software suit to assemble the PacBio RSII reads. Whole-genome sequence contigs homologous to the chicken rDNA repetitive unit were identified based on the Gallus_gallus-5.0 assembly with BLAST. We used the Geneious 9.0.5 and Mega software, maximum likelihood method and Chickspress project for sequence evolution analysis, phylogenetic tree construction and analysis of the raw transcriptome data. Results Three complete IGS sequences in the White Leghorn chicken genome and one IGS sequence in the red junglefowl contig AADN04001305.1 (Gallus_gallus-5.0) were detected. They had various lengths and contained three groups of tandem repeats (some of them being very GC rich) that form highly organized arrays. Initiation and termination sites of rDNA transcription were located within small and large unique regions (SUR and LUR), respectively. No functionally significant sites were detected within the tandem repeat sequences. Conclusions Due to the highly organized GC-rich repeats, the structure of the chicken IGS differs from that of IGS in human, apes, Xenopus or fish rDNA. However, the chicken IGS shares some molecular organization features with that of the turtles, which are other representatives of the Sauropsida clade that includes birds and reptiles. Our current results on the structure of chicken IGS together with the previously reported ribosomal gene cluster sequence provide sufficient data to consider that the complete chicken rDNA sequence is assembled with confidence in terms of molecular DNA organization.