Hervé Garreau

Direct and correlated responses to selection in two lines of rabbits selected for feed efficiency under ad libitum and restricted feeding: I. Production traits and gut microbiota characteristics

To get insights into selection criteria for feed efficiency, 2 rabbit lines have been created: the ConsoResidual line was selected for residual feed intake (RFI) with ad libitum feeding and the ADGrestrict line was selected for ADG under restricted feeding (-20% of voluntary intake). The first objective of this study was to evaluate, after 9 generations of selection, the direct and correlated responses to selection on production traits in the 2 lines for traits recorded during growth. Second, applying the 2 feeding conditions used for selection to both selected lines plus the control unselected line (generation 0, G0) in a 2 × 3 factorial trial, the line performances were compared and the gut microbiota of the lines was characterized. The correlated responses in feed conversion ratio (FCR) were remarkably equivalent in both selected lines (-2.74 genetic σ) but correlated responses in other traits were notably different. In the ConsoResidual line, selection for decreased RFI resulted in a small negative correlated response in BW at 63 d old (BW63) and in a null response in ADG. In the ADGrestrict line, on the contrary, the correlated response in BW63 was substantial (+1.59 σ). The 2 selected lines had a FCR reduced by 0.2 point compared with the G0 line, and the same difference was found in both feeding regimens ( < 0.001). Indeed, selection on ADG would lead to heavier animals with no significant reduction of feed costs, whereas selection on RFI leads to lower feed costs and no increase of animal BW under ad libitum feeding. Altogether, our results do not suggest any genotype × environment interaction in the response to feeding regimens. The intestinal microbial communities from efficient rabbits differed from their unselected counterparts in terms of fermentation end products and microbial phylotypes, suggesting a central role of these microbes in the better feed efficiency of the rabbits.

Genetic modeling of feed intake

With the development of automatic self-feeders and electronic identification, automated, repeated measurements of individual feed intake (FI) and BW are becoming available in more species. Consequently, genetic models for longitudinal data need to be applied to study FI or related traits. To handle this type of data, several flexible mixed-model approaches exist such as character process (CPr), structured antedependence (SAD), or random regression (RR) models. The objective of this study was to compare how these different approaches estimate both the covariance structure between successive measurements of FI and genetic parameters and their ability to predict future performances in 3 species (rabbits, ducks, and pigs). Results were consistent between species. It was found that the SAD and CPr models fit the data better than the RR models. Estimations of genetic and phenotypic correlation matrices were quite consistent between SAD and CPr models, whereas correlations estimated with the RR model were not. Structured antedependence and CPr models provided, as expected and in accordance with previous studies, a decrease of the correlations with the time interval between measurements. The changes in heritability with time showed the same trend for the SAD and RR models but not for the CPr model. Our results show that, in comparison with the CPr model, the SAD and RR models have the advantage of providing stable predictions of future phenotypes 1 wk forward whatever the number of observations used to estimate the parameters. Therefore, to study repeated measurements of FI, the SAD approach seems to be very appropriate in terms of genetic selection and real-time managements of animals.

Multiple-trait structured antedependence model to study the relationship between litter size and birth weight in pigs and rabbits.

BackgroundSome genetic studies need to take into account correlations between traits that are repeatedly measured over time. Multiple-trait random regression models are commonly used to analyze repeated traits but suffer from several major drawbacks. In the present study, we developed a multiple-trait extension of the structured antedependence model (SAD) to overcome this issue and validated its usefulness by modeling the association between litter size (LS) and average birth weight (ABW) over parities in pigs and rabbits.MethodsThe single-trait SAD model assumes that a random effect at time

Direct and correlated responses to selection in two lines of rabbits selected for feed efficiency under ad libitum and restricted feeding: II. Carcass and meat quality.

t_{j}

Direct and correlated responses to selection in two lines of rabbits selected for feed efficiency under ad libitum and restricted feeding: III. Digestion and excretion of nitrogen and minerals1

tj can be explained by the previous values of the random effect (i.e. at previous times). The proposed multiple-trait extension of the SAD model consists in adding a cross-antedependence parameter to the single-trait SAD model. This model can be easily fitted using ASReml and the OWN Fortran program that we have developed. In comparison with the random regression model, we used our multiple-trait SAD model to analyze the LS and ABW of 4345 litters from 1817 Large White sows and 8706 litters from 2286 L-1777 does over a maximum of five successive parities.ResultsFor both species, the multiple-trait SAD fitted the data better than the random regression model. The difference between AIC of the two models (AIC_random regression-AIC_SAD) were equal to 7 and 227 for pigs and rabbits, respectively. A similar pattern of heritability and correlation estimates was obtained for both species. Heritabilities were lower for LS (ranging from 0.09 to 0.29) than for ABW (ranging from 0.23 to 0.39). The general trend was a decrease of the genetic correlation for a given trait between more distant parities. Estimates of genetic correlations between LS and ABW were negative and ranged from −0.03 to −0.52 across parities. No correlation was observed between the permanent environmental effects, except between the permanent environmental effects of LS and ABW of the same parity, for which the estimate of the correlation was strongly negative (ranging from −0.57 to −0.67).ConclusionsWe demonstrated that application of our multiple-trait SAD model is feasible for studying several traits with repeated measurements and showed that it provided a better fit to the data than the random regression model.

Improving feed efficiency in rabbit production, a review on nutritional, technico-economical, genetic and environmental aspects☆

The dwarf phenotype characterizes the smallest of rabbit breeds and is governed largely by the effects of a single dwarfing allele with an incompletely dominant effect on growth. Dwarf rabbits typically weigh under 1 kg and have altered craniofacial morphology. The dwarf allele is recessive lethal and dwarf homozygotes die within a few days of birth. The dwarf phenotype is expressed in heterozygous individuals and rabbits from dwarf breeds homozygous for the wild-type allele are normal, although smaller when compared to other breeds. Here, we show that the dwarf allele constitutes a ∼12.1 kb deletion overlapping the promoter region and first three exons of the HMGA2 gene leading to inactivation of this gene. HMGA2 has been frequently associated with variation in body size across species. Homozygotes for null alleles are viable in mice but not in rabbits and probably not in humans. RNA-sequencing analysis of rabbit embryos showed that very few genes (4–29 genes) were differentially expressed among the three HMGA2/dwarf genotypes, suggesting that dwarfism and inviability in rabbits are caused by modest changes in gene expression. Our results show that HMGA2 is critical for normal expression of IGF2BP2, which encodes an RNA-binding protein. Finally, we report a catalog of regions of elevated genetic differentiation between dwarf and normal-size rabbits, including LCORL-NCAPG, STC2, HOXD cluster, and IGF2BP2. Levels and patterns of genetic diversity at the LCORL-NCAPG locus further suggest that small size in dwarf breeds was enhanced by crosses with wild rabbits. Overall, our results imply that small size in dwarf rabbits results from a large effect, loss-of-function (LOF) mutation in HMGA2 combined with polygenic selection.

Genetic parameters of resistance to non-specific diseases in rabbits in selection and challenging environments

To get insights into selection criteria for feed efficiency, 2 rabbit lines have been created: the ConsoResidual line was selected for residual feed intake (RFI) with ad libitum feeding and the ADGrestrict line was selected for ADG under restricted feeding. The aim of the present study was to evaluate the impact on carcass and meat quality of the genetic selections. This comparison was performed using 2 different feeding strategies corresponding to the selection design. Carcass and meat quality traits were recorded for the 3 lines (ConsoResidual, ADGrestrict, and an unselected control [generation 0 {G0}]) in the 2 feeding systems (ad libitum and restricted) for 163 animals. Concerning the line effect, the BW at 63 d old was higher for the ADGrestrict line compared with the G0 and ConsoResidual lines ( < 0.0001). There was no line effect on the gastrointestinal tract. The rabbits did not exhibit a different carcass yield but showed different carcass traits. Indeed, the ConsoResidual rabbits had a higher hind leg yield ( < 0.0001) but no difference in the meat-to-bone ratio of the hind leg. On the contrary, the ADGrestrict line had a higher proportion of forelegs plus thoracic cage ( = 0.03). We also found lower perirenal ( < 0.0001) and scapular fat yields ( < 0.0001) in ConsoResidual rabbits. The ADGrestrict line had an intermediate perirenal fat yield compared with the other 2 lines. The G0 line always exhibited higher fat yields. Concerning meat quality, the ConsoResidual rabbits showed a lower ultimate pH ( < 0.0001) and higher water loss (drip and cooking loss; < 0.002) compared with the G0 and ADGrestrict rabbits. The feeding level had a strong effect on the gastrointestinal tract ( = 0.0004) and the carcass yield ( = 0.001). The latter was decreased in restricted rabbits. The effects of feeding strategy on meat quality were detrimental in the case of restricted feeding. Even if the ultimate pH was slightly higher in restricted rabbits ( = 0.0002), the carcass chilling loss ( = 0.0005) and the drip loss during 6 d ( < 0.0001) were higher. The selection on ADG with restricted access to feed seems to be less adversely correlated with carcass traits and meat quality traits but it leads to an increase in the live weight of the rabbits. Adversely, the selection on RFI, without affecting growth rate, would not modify age at slaughter because growth rate is not affected, but it might induce detrimental effects on meat quality.

Estimation of Genetic Parameters of Pasteurellosis Resistance in Crossbred Rabbits

Selection for disease resistance is a powerful way to improve the health status of herds and to reduce the use of antibiotics. The objectives of this study were to estimate 1) the genetic parameters for simple visually assessed disease syndromes and for a composite trait of resistance to infectious disease including all syndromes and 2) their genetic correlations with production traits in a rabbit population. Disease symptoms were recorded in the selection herds of 2 commercial paternal rabbit lines during weighing at the end of the test (63 and 70 d of age, respectively). Causes of mortality occurring before these dates were also recorded. Seven disease traits were analyzed: 3 elementary traits visually assessed by technicians on farm (diarrhea, various digestive syndromes, and respiratory syndromes), 2 composite traits (all digestive syndromes and all infectious syndromes), and 2 mortality traits (digestive mortality and infectious mortality). Each animal was assigned only 1 disease trait, corresponding to the main syndrome ( = 153,400). Four production traits were also recorded: live weight the day before the end of test on most animals ( = 137,860) and cold carcass weight, carcass yield, and perirenal fat percentage of the carcass on a subset of slaughtered animals ( = 13,765). Records on both lines were analyzed simultaneously using bivariate linear animal models after validation of consistency with threshold models applied to logit-transformed traits. The heritabilities were low for disease traits, from 0.01 ± 0.002 for various digestive syndromes to 0.04 ± 0.004 for infectious mortality, and moderate to high for production traits. The genetic correlations between digestive syndromes were high and positive, whereas digestive and respiratory syndromes were slightly negatively correlated. The genetic correlations between the composite infectious disease trait and digestive or respiratory syndromes were moderate. Genetic correlations between disease and production traits were favorable. Our results indicate that it is possible to select rabbits using visually assessed disease syndromes without the need for a trade-off between health and production traits. Using a composite criterion that includes all infectious syndromes is easy to implement and heritable and is, therefore, a promising way to improve the general disease resistance in livestock species.