Inbreeding depression on growth and prolificacy traits in two lines of rabbit.

Inbreeding depression in closed populations impairs animal fitness, health, and productivity. However, not all inbreeding is expected to be equally damaging. Recent inbreeding is thought to be more harmful than ancient inbreeding because selection decreases the frequency of unfavourable alleles with time. Accordingly, selection efficiency is improved by inbreeding in a process called purging. This research aimed to quantify inbreeding depression on growth and prolificacy traits in two lines of rabbits selected for just one growth (Caldes line) or prolificacy (Prat line) trait, and also to find some evidence of purging of deleterious alleles by selection. Caldes line comprised 51 generations and 124,371 animals in the pedigree. Prat line comprised 34 generations and 161,039 animals in the pedigree. The effects of old, intermediate, and new inbreeding (Fold, Fint, and Fnew), as well as total cumulated classical inbreeding (F) and 3 measurements of ancestral inbreeding (AHC, Fa.K, and Fa.B) were estimated for average daily gain (ADG), slaughter weight (SW), weaning weight (WW), born alive (BA), the total number of kits (NT), and the number of weaned kits (NW). There was a clear inbreeding depression for all growth and prolificacy traits in the Caldes line (-7.19 g/d, -0.45 kg, -0.25 kg, -6 kits, -4 kits, and -4 kits per unit of increase in F for ADG, SW, WW, BA, NT, and NW, respectively) and also in Prat line (-7.48 g/d, -0.31 kg, -0.11 kg, -4 kits, -5 kits, and -4 kits per unit of increase in F for ADG, SW, WW, BA, NT, and NW, respectively). The inbreeding partition appears to be a reliable alternative for assessing inbreeding depression and purging. Thus, for example, in the Caldes line and for ADG the regression coefficients were -7.61, -5.41, and 7.76 g/d per unit of increase in Fnew, Fint, and Fold, respectively. In addition, AHC and Fa.B may provide more accurate evidence of purging than Fa.K. This study confirms the existence of inbreeding depression for growth and prolificacy traits in both lines of rabbits and shows evidence of purging of deleterious recessive alleles involved both in growth and prolificacy, independently of the selection criteria established in the line.

A Co-Association Network Analysis Reveals Putative Regulators for Health-Related Traits in Pigs.

In recent years, the increase in awareness of antimicrobial resistance together with the societal demand of healthier meat products have driven attention to health-related traits in livestock production. Previous studies have reported medium to high heritabilities for these traits and described genomic regions associated with them. Despite its genetic component, health- and immunity-related traits are complex and its study by association analysis with genomic markers may be missing some information. To analyse multiple phenotypes and gene-by-gene interactions, systems biology approaches, such as the association weight matrix (AWM), allows combining genome wide association study results with network inference algorithms. The present study aimed to identify gene networks, key regulators and candidate genes associated to immunocompetence in pigs by integrating multiple health-related traits, enriched for innate immune phenotypes, using the AWM approach. The co-association network analysis unveiled a network comprised of 3,636 nodes (genes) and 451,407 edges (interactions), including a total of 246 regulators. From these, five genes (ARNT2, BRMS1L, MED12L, SUPT3H and TRIM25) were selected as key regulators as they were associated with the maximum number of genes with the minimum overlapping (1,827 genes in total). The five regulators were involved in pathways related to immunity such as lymphocyte differentiation and activation, platelet activation and degranulation, megakaryocyte differentiation, FcγR-mediated phagocytosis and response to nitric oxide, among others, but also in immunometabolism. Furthermore, we identified genes co-associated with the key regulators previously reported as candidate genes (e.g., ANGPT1, CD4, CD36, DOCK1, PDE4B, PRKCE, PTPRC and SH2B3) for immunity traits in humans and pigs, but also new candidate ones (e.g., ACSL3, CXADR, HBB, MMP12, PTPN6, WLS) that were not previously described. The co-association analysis revealed new regulators associated with health-related traits in pigs. This approach also identified gene-by-gene interactions and candidate genes involved in pathways related to cell fate and metabolic and immune functions. Our results shed new light in the regulatory mechanisms involved in pig immunity and reinforce the use of the pig as biomedical model.

Genetic parameters and associated genomic regions for global immunocompetence and other health-related traits in pigs.

The inclusion of health-related traits, or functionally associated genetic markers, in pig breeding programs could contribute to produce more robust and disease resistant animals. The aim of the present work was to study the genetic determinism and genomic regions associated to global immunocompetence and health in a Duroc pig population. For this purpose, a set of 30 health-related traits covering immune (mainly innate), haematological, and stress parameters were measured in 432 healthy Duroc piglets aged 8 weeks. Moderate to high heritabilities were obtained for most traits and significant genetic correlations among them were observed. A genome wide association study pointed out 31 significantly associated SNPs at whole-genome level, located in six chromosomal regions on pig chromosomes SSC4, SSC6, SSC17 and SSCX, for IgG, γδ T-cells, C-reactive protein, lymphocytes phagocytic capacity, total number of lymphocytes, mean corpuscular volume and mean corpuscular haemoglobin. A total of 16 promising functionally-related candidate genes, including CRP, NFATC2, PRDX1, SLA, ST3GAL1, and VPS4A, have been proposed to explain the variation of immune and haematological traits. Our results enhance the knowledge of the genetic control of traits related with immunity and support the possibility of applying effective selection programs to improve immunocompetence in pigs.

Characterization of the Maternally Derived Antibody Immunity against Rhdv-2 after Administration in Breeding Does of an Inactivated Vaccine.

Inactivated strain-specific vaccines have been successfully used to control rabbit haemorrhagic disease (RHD) caused by RHDV-2 in the rabbit industry. It is unknown whether and how vaccination of breeding does contributed to protect the population of young susceptible rabbit kits. The present study investigates whether the immunity against RHDV-2 produced by vaccination of breeding does is transmitted to their progeny and its dynamic once inherited by kits. For this purpose, New Zealand female rabbits of 8-9 weeks of age were allocated into 2 groups of 40 subjects each and bred during 6 reproductive cycles. The first experimental group was vaccinated with a commercially available inactivated vaccine against RHDV-2 whereas the second group was inoculated with PBS. Moreover, the present study was also meant to identify the mechanisms of transmission of that maternal immunity. For this reason, rabbit kits of vaccinated and non-vaccinated breeding does were cross-fostered before milk uptake. The RHDV-2 antibody response was monitored in the blood serum of breeding does and of their kits by competition ELISA (cELISA) and solid-phase ELISA (spELISA). Since it has been clearly demonstrated that cELISA positive rabbits are protected from RHD, we avoided the resorting of the challenge of the kits with RHDV-2. Results showed that RHDV-2 antibodies were inherited by kits up to one year from vaccination of breeding does. Once inherited, the maternally derived antibody response against RHDV-2 lasted at least until 28 days of life. Finally, the study also elucidated that the major contribution to the maternal derived immunity against RHDV-2 in kits was provided during gestation and probably transmitted through transplacental mechanisms although lactation provided a little contribution to it. The present study contributed to elucidate the characteristics of the maternal antibody immunity produced by vaccination and its mechanisms of transmission.

Role of AMPK signalling pathway during compensatory growth in pigs.

BACKGROUND: The molecular basis of compensatory growth in monogastric animals has not yet been fully explored. Herewith, in this study we aim to determine changes in the pig skeletal muscle transcriptome profile during compensatory growth following a feed restriction period. A RNA-Seq experiment was performed with a total of 24 females belonging to a Duroc commercial line. Half of the animals received either a restricted (RE) or ad libitum (AL) diet during the first fattening period (60-125 d of age). After that, all gilts were fed ad libitum for a further ~30 d until the age of ~155 d, when animals were slaughtered and samples of gluteus medius muscle were harvested to perform RNA-Seq analyses and intramuscular fat content determination. RESULTS: During the period following food restriction, RE animals re-fed ad libitum displayed compensatory growth, showed better feed conversion rate and tended to deposit more subcutaneous fat than AL fed animals. Animals were slaughtered in the phase of accelerated growth, when RE animals had not completely compensated the performance of AL group, showing lower live and carcass weights. At intramuscular level, RE gilts showed a higher content of polyunsaturated fatty acids during the compensatory growth phase. The comparison of RE and AL expression profiles allowed the identification of 86 (ǀlog2Fold-Changeǀ > 1, padj < 0.05) differentially expressed (DE) genes. A functional categorization of these DE genes identified AMPK Signaling as the most significantly enriched canonical pathway. This kinase plays a key role in the maintenance of energy homeostasis as well as in the activation of autophagy. Among the DE genes identified as components of AMPK Signaling pathway, five out of six genes were downregulated in RE pigs. CONCLUSIONS: Animals re-fed after a restriction period exhibited a less oxidative metabolic profile and catabolic processes in muscle than animals fed ad libitum. The downregulation of autophagy observed in the skeletal muscle of pigs undergoing compensatory growth may constitute a mechanism to increase muscle mass thus ensuring an accelerated growth rate. These results reveal that the downregulation of AMPK Signaling plays an important role in compensatory growth in pigs.

Interaction of direct and social genetic effects with feeding regime in growing rabbits.

BACKGROUND: Most rabbit production farms apply feed restriction at fattening because of its protective effect against digestive diseases that affect growing rabbits. However, it leads to competitive behaviour between cage mates, which is not observed when animals are fed ad libitum. Our aim was to estimate the contribution of direct ([Formula: see text]) and social ([Formula: see text]) genetic effects (also known as indirect genetic effects) to total heritable variance of average daily gain ([Formula: see text]) in rabbits on different feeding regimens (FR), and the magnitude of the interaction between genotype and FR (G × FR). METHODS: A total of 6264 contemporary kits were housed in cages of eight individuals and raised on full ([Formula: see text]) or restricted ([Formula: see text]) feeding to 75% of the ad libitum intake. A Bayesian analysis of weekly records of [Formula: see text] (from 32 to 60 days of age) in rabbits on [Formula: see text] and [Formula: see text] was performed with a two-trait model including [Formula: see text] and [Formula: see text]. RESULTS: The ratio between total heritable variance and phenotypic variance ([Formula: see text]) was low (<0.10) and did not differ significantly between FR. However, the ratio between [Formula: see text] (i.e. variance of [Formula: see text] relative to phenotypic variance) and [Formula: see text] was ~0.52 and 0.86 for animals on [Formula: see text] and [Formula: see text], respectively, thus [Formula: see text] contributed more to the heritable variance of animals on [Formula: see text] than on [Formula: see text]. Feeding regimen also affected the sign and magnitude of the correlation between [Formula: see text] and [Formula: see text], i.e. -0.5 and ~0 for animals on [Formula: see text] and [Formula: see text], respectively. The posterior mean (posterior sd) of the correlation between estimated total breeding values (ETBV) of animals on [Formula: see text] and [Formula: see text] was 0.26 (0.20), indicating very strong G × FR interactions. The correlations between [Formula: see text] and [Formula: see text] in rabbits on [Formula: see text] and [Formula: see text] ranged from -0.47 ([Formula: see text] on [Formula: see text] and [Formula: see text] on [Formula: see text]) to 0.64. CONCLUSIONS: Our results suggest that selection of rabbits for [Formula: see text] under [Formula: see text] may completely fail to improve [Formula: see text] in rabbits on [Formula: see text]. Social genetic effects contribute substantially to ETBV of rabbits on [Formula: see text] but not on [Formula: see text]. Selection for [Formula: see text] should be performed under production conditions regarding the FR, by accounting for [Formula: see text] if the amount of food is limited.

Modeling production functions and economic weights in intensive meat production of guinea pigs.

A profit function for a typical commercial farm of intensive guinea pig production was designed. The simulated farm contained 86 cages with a ratio of 7:1 females/males, with continuous mating. Kits were weaned at 15 days of age and slaughtered for meat production at 90 days of age. The absolute (EW) and relative economic weights of the main traits were calculated. The highest EW were kits produced per kindling (US$25), kits weaned per kindling (US$22), kits born alive per kindling (US$20), and the number of kindlings per female and year (US$12). Profit, returns, and costs per female and year were US$15, 68, and 53, respectively. Returns came from the production of young guinea pigs and discarded reproductive adults for meat production, 90 and 10% of the total returns. The highest costs were feeding and labor, 44 and 23% of the total cost. The EW and profit did not substantially change when simulating variations of ±20% in the prices of kilograms of fattening feed and kilograms of live weight of guinea pig, showing their robustness to future variations in market prices or to variations in prices between countries. The results obtained highlight the importance of the feeding costs in the guinea pig meat production.

Effect of feeding diets containing barley, wheat and corn distillers dried grains with solubles on carcass traits and meat quality in growing rabbits.

The effect of dietary inclusion of distillers dried grains with solubles (DDGS) on carcass and meat quality of longissimus muscle was studied in 100 growing rabbits from 28 to 59days old. Diets with no DDGS (C), barley (Db20), wheat (Dw20) and corn (Dc20) DDGS at 20% and corn (Dc40) DDGS at 40% were formulated. No effects on most of the carcass traits, texture and water holding capacity were found. Barley and corn DDGS led to a higher dissectible fat percentage. Meat redness was higher with Dw20 and pH was higher with Dw20 and Db20 than with Dc20. Protein and saturated fatty acids concentration declined as corn DDGS level increased. Dc40 led to the lowest saturated/unsaturated fatty acid ratio, atherogenic index and thrombogenic index. In conclusion, dietary inclusion of these DDGS at 20% did not affect most of the carcass and meat quality traits in rabbits.

Effect of selection for growth rate on the ageing of myofibrils, meat texture properties and the muscle proteolytic potential of m. longissimus in rabbits.

The effect of selection for growth rate on the degradation of the myofibrillar proteins and on meat texture properties of rabbit longissimus muscle at two ageing times (1 and 7 days) was studied as well as its effect on the proteolytic potential of the muscle. Two groups of contemporary animals (20 rabbits per group), one selected for growth rate (S) for 14 generations and the other unselected control group (C) were compared. The control group was formed from the offspring of the embryos belonging to the 7th generation and was compared with selected animals belonging to 21st generation. Myofibrillar protein degradation was studied by SDS-PAGE electrophoresis (12.5% and 4-15% polyacrylamide gels) followed by densitometric analysis of the pherograms. Texture properties were evaluated by Warner-Bratzler (WB) test and Texture profile analysis (TPA). The activities of proteolytic enzymes calpains and cathepsins and of their inhibitors were determined in the muscle at 24h. Densitometric analysis of the pherograms of samples aged 7 days showed an extra 30kDa band and the disappearance of a band with higher molecular weight than the myosin heavy chain with respect to samples aged 24h in both groups of rabbits. TPA results showed that cohesiveness was significantly lower in meat at 7 days than at 24h (P<0.0001), whereas springiness and chewiness presented a clear tendency to be lower at 7 days than at 24h (P=0.0646 and P=0.0764, respectively). Regarding the genetic type, S animals presented higher hardness and chewiness than C rabbits. Shear firmness (WB test) was significantly (P<0.0001) higher for S group, whereas no significant differences in shear force and area were found. No significant effect (P>0.05) of ageing time was detected using WB test. Selection for growth rate did not affect the activities of proteolytic enzymes or their inhibitors.

Effect of selection for growth rate on biochemical, quality and texture characteristics of meat from rabbits.

Biochemical characteristics, including myosin heavy chain I (MHC-I) percentage, isocitrate dehydrogenase and aldolase activities, meat quality traits and instrumental texture properties of rabbits selected for different growth rates were studied. The animals of the control (C) group (7th generation; n=60) were raised in parallel with those of selection (S) group (21st generation; n=60). Carcass weights (1230.1±19.8 and 1348.3±20.1 g, for C and S, respectively) and perirenal and scapular fat content differed significantly (P<0.01) between the two groups. Water holding capacity was expressed as the percentage of pressure released water and was significantly different (P<0.05) between groups C and S (33.29% and 35.57%). MHC-I percentage and aldolase activity also differed significantly (P<0.05) between groups, group C showing higher oxidative traits than group S (MHC-I: 12.5% and 9.8%; aldolase: 597.11 and 636.83 UI/g muscle). Texture properties from the Warner-Bratzler test showed higher (P<0.001) shear firmness for loin in the S group (1.69 kg/s cm(2)) than in the C group (1.34 kg/s cm(2)). In addition, the texture profile analysis indicated that chewiness, gumminess and hardness were also higher in the S group (P<0.01). In conclusion, the results confirmed a positive effect of the selection on productive traits and a negative effect on instrumental texture properties and on the water holding capacity of the meat.