Staphylococcosis is one of the most important infectious diseases in rabbit medicine, especially in commercial farming. Previous studies revealed the existence of virulent variants adapted to rabbits. Typical and atypical, highly virulent as well as low virulent variants have been isolated and reported from industrial units in all major rabbit-meat-producing countries. Preceding the research focused on detecting defined nucleotide sequences, the genome of these organisms as a whole was rarely subjected to scientific investigations. The authors sequenced 51 Staphylococcus strains originating from industrial rabbit farms in Hungary. Another 12 draft genomes of rabbit isolates were constructed from read sequences available in digital repositories, and were compared based on whole-genome multilocus sequence typing. The clonal origin of highly virulent variants is confirmed, the strains from Hungary were closely related with the strains isolated in the UK, Italy, and Spain. Atypical highly virulent strains are the most prevalent in Hungary, they form a separate clonal cluster. The low virulent strains were genetically similar, but more heterogeneous than the highly virulent (HV) and aHV strains even by the traditional MLST typing scheme. Other “non-aureus” Staphylococcus species were also identified.

The European rabbit exists in the wild and has several highly bred domesticated forms. There are well-separated wild European rabbit populations, and intensive breeding has resulted in various forms and utilizations. In this work, we aimed to carry out an extended WGS-based population genomics study on several wild European rabbit populations and selected breeds. Utilizing multiple methods, we showed that although domestic and wild populations were clearly separated, there was evidence of admixture between them in France and Hungary. The populations showed various levels of inbreeding, with one of the Hungarian subpopulations having excess runs of homozygosity. We identified numerous variants fixed in either domestic or wild animals, two of which were found to be fixed at different alleles in the two populations. Some putatively selected regions did not overlap with any known genes in the rabbit genome, suggesting some importance to these intergenic sites. The enrichment of selected regions in certain types of transcription factor binding sites suggests a possible role for these regulatory elements during domestication. In addition, the new high-coverage rabbit whole-genome sequences may provide helpful material for further population genetics analyses.

A major problem of large-scale rabbit farming is digestive diseases. Relatively few data on parasitic diseases of industrial rabbit populations are available. The aim of the study was to evaluate the seasonaldependent incidence of Eimeria spp. and Passalurus ambiguus infections at large-scale rabbit farms. The survey was carried out between 2018 and 2022 at 29 Hungarian and 2 Slovakian rabbit farms. Altogether, 7612 faecal samples were examined. Eimeria oocysts and P. ambiguus eggs were detected on all rabbit farms examined, although only a relatively small portion of faecal samples was found positive. Eimeria oocysts and P. ambiguus eggs were found in 32 and 6% of the samples, respectively. Our findings for the seasonal-dependent evaluation of collected data showed that the highest proportion of Eimeria positive samples occurred during the summer (35.3%) and autumn (36.2%) periods. In winter, a significantly lower infection rate was found (29.5 %; P<0.05). The most favourable results were observed in spring (25.1%; P<0.05). As for P. ambiguus, the highest rate of infection was measured in spring (8.4%) and the lowest in summer (4.5%; P<0.01). The autumn and winter periods showed intermediate results (6.7 and 5.5 %, respectively).

Allele-specific expression (ASE) reflects the unequal expression of the parental alleles and can imply functional variants in cis-regulatory elements. The conventional ASE detection methods often depend on the presence of heterozygous variants in transcripts or sequencing a large number of individuals, both of which are often limited. In this study, we present a family-based strategy for detecting ASE and potential cis-regulatory elements utilizing both RNA-seq and whole-genome sequencing (WGS) from a pedigree. Using a rabbit family consisting of two divergent parents and their eight offspring, we identified 913 ASE genes by analyzing inheritance patterns of gene expression levels. Expression was classified into three levels—high, medium, and low—and used to define seven distinct expression groups across the family (e.g., H_L: high in the mother, low in the father, and intermediate in the offspring). Many ASE genes lacked heterozygous exonic variants, and inference was achieved via RNA read count patterns. We also pinpointed conserved transcription factor binding sites (TFBS) with sequence variants showing similar inherited genotypic patterns (e.g., AAxBB), suggesting their regulatory roles as eQTLs. Differential gene expression (DEG) analysis between the parents highlighted some candidate genes related to meat production and quality traits. Our findings show that the family-based method using RNA-seq and WGS data is promising for exploring ASE and mapping possible eQTLs.

The aim was to investigate the effect of dietary crude fibre (CF) content on Eimeria excretion and production in fattening rabbits. Weaned rabbits were divided into two groups: The control group (C) was fed a commercial pelleted diet (CF = 17%); the high-fibre group (HF) was fed a diet with a higher fibre content (CF = 24%). In Experiment 1, the production of 90 rabbits per group was compared and mortality data and faecal samples from 800 rabbits per group were analysed. In Experiment 2, the production of 90 growing rabbits and the faecal samples and mortality of 1050 animals per group were studied. Although feed consumption did not differ between groups, the HF group had lower weight gain than the C group (P < 0.001). The body weight of the HF group was lower at the end of fattening (P < 0.001). The HF group had a very unfavourable feed conversion ratio (4.07). Mortality was not different between the groups. In both groups, Eimeria oocysts were detected in faecal samples from 44-45 days of age until the end of fattening. A higher proportion of moderately pathogenic Eimeria species was detected in the C group compared to the HF group, and highly pathogenic oocysts were observed only in the C group.