Genomic diversity and signatures of selection in meat and fancy rabbit breeds based on high-density marker data

open6noThe study was funded by the PSRN (Programma di Sviluppo Rurale Nazionale) Cun-Fu and Cun-Fu 2 projects (co-funded by the European Agricultural Fund for Rural Development of the European Union and by the Italian Ministry of Agriculture, Food and Forestry—MiPAAF) and by the University of Bologna RFO 2019 programme.Background: Domestication of the rabbit (Oryctolagus cuniculus) has led to a multi-purpose species that includes many breeds and lines with a broad phenotypic diversity, mainly for external traits (e.g. coat colours and patterns, fur structure, and morphometric traits) that are valued by fancy rabbit breeders. As a consequence of this human-driven selection, distinct signatures are expected to be present in the rabbit genome, defined as signatures of selection or selective sweeps. Here, we investigated the genome of three Italian commercial meat rabbit breeds (Italian Silver, Italian Spotted and Italian White) and 12 fancy rabbit breeds (Belgian Hare, Burgundy Fawn, Champagne d’Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex, Rhinelander and Thuringian) by using high-density single nucleotide polymorphism data. Signatures of selection were identified based on the fixation index (FST) statistic with different approaches, including single-breed and group-based methods, the latter comparing breeds that are grouped based on external traits (different coat colours and body sizes) and types (i.e. meat vs. fancy breeds). Results: We identified 309 genomic regions that contained signatures of selection and that included genes that are known to affect coat colour (ASIP, MC1R and TYR), coat structure (LIPH), and body size (LCORL/NCAPG, COL11A1 and HOXD) in rabbits and that characterize the investigated breeds. Their identification proves the suitability of the applied methodologies for capturing recent selection events. Other regions included novel candidate genes that might contribute to the phenotypic variation among the analyzed breeds, including genes for pigmentation-related traits (EDNRA, EDNRB, MITF and OCA2) and body size, with a strong candidate for dwarfism in rabbit (COL2A1). Conclusions: We report a genome-wide view of genetic loci that underlie the main phenotypic differences in the analyzed rabbit breeds, which can be useful to understand the shift from the domestication process to the development of breeds in O. cuniculus. These results enhance our knowledge about the major genetic loci involved in rabbit external traits and add novel information to understand the complexity of the genetic architecture underlying body size in mammals.openBallan, Mohamad; Bovo, Samuele; Schiavo, Giuseppina; Schiavitto, Michele; Negrini, Riccardo; Fontanesi, LucaBallan, Mohamad; Bovo, Samuele; Schiavo, Giuseppina; Schiavitto, Michele; Negrini, Riccardo; Fontanesi, Luc

Comparative analysis of genomic inbreeding parameters and runs of homozygosity islands in several fancy and meat rabbit breeds

Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (~150) and the lowest in Italian Silver (~106). The average length of ROH ranged from 4.001 ± 0.556 Mb in Italian White to 6.268 ± 1.355 Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome

Effect of rearing system (free-range vs cage) on gut and muscle histomorphology and microbial loads of Italian White breed rabbits

Objective The growing consumers’ interest on animal welfare has raised the request of products obtained by alternative rearing systems. The present study was conducted to assess the influence of housing system on gut and muscle morphology and on microbial load in rabbits reared under free-range (FR) and cage system (CS). Methods A total of forty weaned (35 days of age) male Italian White breed rabbits were allotted according to the rearing system, and at 91 days of age were randomly selected and slaughtered for the morphological evaluation of tissue from duodenum and longissimus lumborum. Morphometric analysis of the villus height, villus width, crypt depth, villus height/crypt depth ratio, and villus surface was performed. The microbial loads on hind muscle was determined by total mesophilic aerobic count (TMAC), Escherichia coli and Enterobacteriaceae; whereas, total anaerobic bacteria count (TABC) and TMAC, E. coli and Enterobacteriaceae was determined on caecal content. Results Rearing system did not interfere with the duodenum and muscle histomorphology in both rabbit groups. Similarly, microbial load of caecal content showed no significant differences on the TABC and TMAC. Conversely, significant difference was found for E. coli strains in caecal content, with the lower counts in FR compared to CS rabbits (p<0.01). Microbiological assay of muscle revealed significant lower TMAC in FR vs CS rabbits (p< 0.05). All rabbit meat samples were negative for E. Coli and Enterobacteriaceae. Conclusion Free-range could be considered a possible alternative and sustainable rearing system in rabbits to preserve gut environment and muscle quality

Evaluating productive performance, meat quality and oxidation products of Italian White breed rabbits under free-range and cage rearing system

Objective: Free-range systems have been increasingly available to the consumer due to increased demand for more sustainable meat-products. In the current study, the effect of free-range (FR) and cage system (CS) was explored on growth performance, meat quality and oxidation products in Italian White breed rabbits during the growing-fattening phase (5 to 13 weeks of age). Methods: Forty rabbits were randomly allotted to two treatment groups according to the rearing system, and each treatment group was replicated five times with four subjects in each replicate (20 rabbits per treatment-group). All rabbits fed the same diet as pelleted, and under FR system, no additional feeds were available to animals. Results: Rearing system had significant effect on rabbit growth performance, where CS group resulted in higher final body weight (P&lt;0.045) and gain (P&lt;0.029) and better feed efficiency (P&lt;0.025) compared to FR rabbits. Most carcass traits were not affected by rearing system; however, a reduction of abdominal fat content (P &lt; 0.015) and meat lipids (P&lt;0.034) was observed in FR rabbits. Rearing system had no effects on meat fatty acid profile, whereas meat from FR rabbits resulted less susceptible to lipid and protein oxidation compared to caged animals. Conclusion: In overall, free-range system could be suggested as a substitute for conventional caged system because of free-range system preserved rabbit meat from oxidation

Improving the Rabbit Semen Cryopreservation Protocol: Comparison Between Two Extenders and Inseminating Doses

This study has been designed to optimize the semen freezing protocol in rabbits. In this regard we compared a Tris-citrate-glucose (If G) extender with a commercial one (Cortalap (R)), that to the best of our knowledge has never been used up to now on the in vitro freezability and fertilizing ability of cryopreserved rabbit semen. Two different inseminating semen (loses were considered. Five pooled semen samples were divided into two subsamples and each of them were diluted to a ratio 1:1 (v:v) with a freezing extender composed of TCG or Cortalap (R) containing 16% of di methylsulfoxide and 0.1 mol/L of sucrose. The extended semen was filled into 0.25 mL plastic straws and frozen above a liquid nitrogen surface. After thawing (50 degrees C/10 seconds) we determined sperm motility, viability, membrane functionality, acrosome and DNA integrity. Our results showed that the Cortalap (R) extender significantly improved the in vitro post-thaw sperm quality, in comparison to T(X:. When we compared the extenders in vivo, no significant differences in the reproductive performances were observed independently by inseminating doses used. In this study we demonstrated that Cortaliqt extender can be used as an alternative to TCG. Thus, the Cortalait being a ready to use extender, implies a reduce of time, mistakes and microbial contaminations during its preparation. This discovery is significant because it provides an important contribution to the creation of the first Italian semen cryobank of rabbit breeds and also for livestock rabbit farms based on artificial insemination (AI) program

Antimicrobial Efficacy of Phyto-L, Thiosulfonate from Allium spp. Containing Supplement, against Escherichia Coli Strains from Rabbits

Simple Summary The aim of this study was to evaluate the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of Phyto-L (Pro Tech s.r.l.), a commercial product containing organosulfur compounds (OSCs) such as propyl propane thiosulfonate (PTSO) from Allium spp., on 108 enteropathogenic E. coli (EPEC) strains responsible for colibacillosis in rabbits. Bacterial suspensions with a charge of 10(8) CFU/mL were tested with different concentrations (20, 10, 5, 2.5, 1.25, 0.6, 0.3, and 0.15 &amp; mu;L/mL) of Phyto-L. To evaluate MBC values, bacterial suspensions corresponding to the MIC and above the MIC were plated on Tryptic Soy agar (TSA) without Phyto-L. The MICs of the tested strains corresponded to 1.25 &amp; mu;L/mL (37/108-34.3%), 2.5 &amp; mu;L/mL (70/108-64.8%), and 5 &amp; mu;L/mL (1/108-0.9%). The MBCs were 1.25 &amp; mu;L/mL (15/108-13.9%), 2.5 &amp; mu;L/mL (46/108-42.6%), 5 &amp; mu;L/mL (9/108-8.3%), 10 &amp; mu;L/mL (20/108-18.5%), 20 &amp; mu;L/mL (8/108-7.4%), and higher than 20 &amp; mu;L/mL (10/108-9.3%). Based on the results obtained, Phyto-L has antibacterial activity on EPEC strains. Therefore, in field applications, Phyto-L should be useful in limiting the E. coli load in the rabbit gut, preventing the occurrence of colibacillosis. Moreover, considering that 10(4)-10(5) CFU/g of feces is the charge of E. coli normally present in the intestinal contents of rabbits under physiological conditions, it is possible that lower dosages than those found in this study may be effective in preventing the disease in rabbit farms. Colibacillosis, caused by enteropathogenic Escherichia coli (EPEC), is one of the most common diseases in rabbit farms, resulting in economic losses due to mortality and decrease in production. Until recently, antimicrobials were used to both treat and prevent disease on livestock farms, leading to the possible risk of antimicrobial resistance (AMR) and the selection of multidrug-resistant (MDR) bacteria. Therefore, interest in alternative control methods, such as the use of natural substances, has increased in the scientific community. The aim of this study was to evaluate the antimicrobial efficacy of Phyto-L (Pro Tech s.r.l.), a product containing organosulfur compounds (OSCs) such as propyl propane thiosulfonate (PTSO) from Allium spp., against 108 strains of E. coli isolated from rabbits with colibacillosis from 19 farms. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of Phyto-L were assessed. Bacterial suspensions with a charge of 10(8) CFU/mL, corresponding to those found in the rabbit gut under pathologic conditions, were tested with different concentrations from 20 to 0.15 &amp; mu;L/mL of Phyto-L. For each strain, the MIC and concentrations above the MIC were plated on Tryptic Soy agar (TSA) without Phyto-L to assess the MBCs. MIC and MBC values ranged from 1.25 to 5 &amp; mu;L/mL and 1.25 to 20 &amp; mu;L/mL, respectively, depending on the strain tested. The data showed an interesting antibacterial activity of Phyto-L against EPEC strains. Therefore, this product could be effective in preventing colibacillosis in field application, especially considering that 10(4)-10(5) CFU/g of feces is the amount of E. coli usually found in the gut contents of rabbits under physiological condition