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Non‐genetic information (epigenetic, microbiota, behaviour) that results in different phenotypes in animals can be transmitted from one generation to the next and thus is potentially involved in the inheritance of traits. However, in livestock species, animals are selected based on genetic inheritance only. The objective of the present study was to determine whether non‐genetic inherited effects play a role in the inheritance of residual feed intake (RFI) in two species: pigs and rabbits. If so, the path coefficients of the information transmitted from sire and dam to offspring would differ from the expected transmission factor of 0.5 that occurs if inherited information is of genetic origin only. Two pigs (pig1, pig2) and two rabbits (rabbit1, rabbit2) datasets were used in this study (1,603, 3,901, 5,213 and 4,584 records, respectively). The test of the path coefficients to 0.5 was performed for each dataset using likelihood ratio tests (null model: transmissibility model with both path coefficients equal to 0.5, full model: unconstrained transmissibility model). The path coefficients differed significantly from 0.5 for one of the pig datasets (pig2). Although not significant, we observed, as a general trend, that sire path coefficients of transmission were lower than dam path coefficients in three of the datasets (0.46 vs 0.53 for pig1, 0.39 vs 0.44 for pig2 and 0.38 vs 0.50 for rabbit1). These results suggest that phenomena other than genetic sources of inheritance explain the phenotypic resemblance between relatives for RFI, with a higher transmission from the dam's side than from the sire's side.

Background Pasteurellosis (Pasteurella infection) is one of the most common bacterial infections in rabbits on commercial farms and in laboratory facilities. Curative treatments using antibiotics are only partly efficient, with frequent relapses. Breeding rabbits for improved genetic resistance to pasteurellosis is a sustainable alternative approach. In this study, we infected 964 crossbred rabbits from six sire lines experimentally with Pasteurella multocida. After post-mortem examination and bacteriological analyses, abscess, bacteria, and resistance scores were derived for each rabbit based on the extent of lesions and bacterial dissemination in the body. This is the first study to use such an experimental design and response traits to measure resistance to pasteurellosis in a rabbit population. We investigated the genetic variation of these traits in order to identify potential selection criteria. We also estimated genetic correlations of resistance to pasteurellosis in the experimental population with traits that are under selection in the breeding populations (number of kits born alive and weaning weight). Results Heritability estimates for the novel response traits, abscess, bacteria, and resistance scores, ranged from 0.08 (± 0.05) to 0.16 (± 0.06). The resistance score showed very strong negative genetic correlation estimates with abscess (− 0.99 ± 0.05) and bacteria scores (− 0.98 ± 0.07). A very high positive genetic correlation of 0.99 ± 0.16 was estimated between abscess and bacteria scores. Estimates of genetic correlations of the resistance score with average daily gain traits for the first and second week after inoculation were 0.98 (± 0.06) and 0.70 (± 0.14), respectively. Estimates of genetic correlations of the disease-related traits with average daily gain pre-inoculation were favorable but with high standard errors. Estimates of genetic and phenotypic correlations of the disease-related traits with commercial selection traits were not significantly different from zero. Conclusions Disease response traits are heritable and are highly correlated with each other, but do not show any significant genetic correlations with commercial selection traits. Thus, the prevalence of pasteurellosis could be decreased by selecting more resistant rabbits on any one of the disease response traits with a limited impact on the selection traits, which would allow implementation of a breeding program to improve resistance to pasteurellosis in rabbits.

Two rabbit lines have been created to result in better feed efficiency: the ConsoResidual line was selected for a lower residual feed intake under ad libitum feeding, and the ADGrestrict line was selected for higher ADG under restricted feeding (-20% of ad libitum). The present study aimed to analyze the digestion and excretion of N and minerals from 29 to 63 d of age of these 2 lines compared with an unselected control line (G0) under 2 feeding levels (ad libitum or restricted). The ADGrestrict line had greater digestibility compared with G0 (+1.3% for OM and N; < 0.05), and the ConsoResidual line had intermediate values. There was no genetic line effect on the digestibility of N and P and on minerals concentrations (P, Zn, and Cu) in the feces and in the urine. The N balance was improved for the 2 selected lines (+5%; < 0.05), leading to a reduced N output through the feces (0.06 g/d compared with G0; < 0.001) and the urine (-0.07 g/d; < 0.05) and to an improved N retention ratio (+3% compared with G0). Over the whole fattening period (d 29-63), significant differences were observed among lines only when fed ad libitum, with 13% greater DM fecal output and 5% greater N fecal output for G0. The N excretion in urine was 2 g less in the 2 selected lines, leading to a reduction of total N release of 4.4 g (compared with G0). The P excretion in feces (12 g) or urine (0.1 g) did not differ among the 3 lines. Over the whole fattening period and for ad libitum-fed rabbits, the 5% improvement in feed efficiency ( < 0.01) for the 2 selected lines corresponded to 400 g less feed intake (-8%) and to 20 g less N intake. The fecal excretion of the ADGrestrict and ConsoResidual lines were reduced by 200 g DM ( < 0.01), corresponding to 417 g fresh matter and 5 g of N. The excretion in minerals (P, Zn, and Cu) was not affected by the line. The feeding level strongly reduced the fecal and urine outputs (-50 and -60%, respectively; < 0.001). Higher digestibility coefficients ( < 0.001) were found in restricted-fed rabbits for OM (+6%), N (+8%), and P (+11%). The N balance was substantially improved by the restriction, with 40% less total (feces + urine) N excretion ( < 0.001). The P balance was improved by the restriction (0.469 vs. 0.360). Over the fattening period, the P fecal output was 37% less (-6 g) with 24% less feed intake and the Zn and Cu outputs were reduced by 27 (-130 mg) and 29% (-30 mg), respectively.

International audience; The aim of this experiment was to evaluate the significance of neonatal environment on feed efficiency. For that purpose, rabbits from a line selected for residual feed intake (RFI) during 10 generations (G10 kits) were cross-fostered with non-selected control does (i.e., G0 line), and reciprocally. In parallel, sibs were fostered by mothers from their original line. Nine hundred animals were raised in individual (N = 456) or collective (N = 320) cages. Traits analysed in this study were body weight at 32 days and at 63 days, average daily gain (ADG), feed intake between weaning and 63 days (FI), feed conversion ratio (FCR) and RFI. The maternal environment offered by does from the line selected for RFI deteriorated the FCR of the kits, independently of their line of origin, during fattening (+0.08 +/- 0.02) compared to FCR of kits nursed by G0 does. The line, the type of housing and the batch were significant effects for all the measured traits: G10 kits were lighter than their G0 counterparts at 32 days (-82.9 +/- 9 g, p < 0.0001) and at 63 days (-161 +/- 16 g, p < 0.0001). They also had a lower ADG (-2.36 +/- 0.36 g/day, p < 0.0001), RFI (-521 +/- 24 g/day, p < 0.0001) and a lower FI (-855 +/- 31 g, p < 0.0001), resulting in a more desirable feed efficiency (FCR: -0.35 +/- 0.02). There was no significant difference in the contrast of G10 and G0 performances between collective and individual/digestive cages (p > 0.22): -2.35 g/day versus 2.94 g/day for ADG, -0.39 versus -0.40 for FCR, -577 g versus -565 g for RFI and -879 g versus -859 g for FI, respectively). Thus, no genotype-by-environment (housing) interaction is expected at the commercial level, that is, no re-ranking of the animals due to collective housing.

This article reports draft genome sequences of 17 Pasteurella multocida strains isolated from naturally infected rabbits. The total lengths of the assembled contigs ranged between 2.21 and 2.48 Mb, and the total number of genes detected on the contigs ranged between 2,088 and 2,416.

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.

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.

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.

International audience; Cette synthèse fait le point sur les principales évolutions de l’amélioration génétique du porc en France depuis la loi sur l’élevage de 1966. Elle évoque rapidement les 20 premières années, qui ont fait l’objet d’une synthèse en 1986, puis décrit plus en détail les évolutions ultérieures. Les objectifs de sélection, initialement limités aux caractères de production, se sont complexifiés avec la prise en compte de la qualité de la viande, puis de la prolificité et enfin des aptitudes maternelles des truies. La mise en place d’une évaluation génétique utilisant la méthodologie du « BLUP - modèle animal » au milieu des années 1990 et le développement de l’insémination artificielle ont profondément changé le travail des sélectionneurs. Une nouvelle évolution majeure, la sélection génomique, a récemment été mise en place. La sélection a conduit à des améliorations importantes des performances pour les principaux caractères de l’objectif de sélection depuis 1970 : plus de 200 g de gain moyen quotidien, plus de 0,5 point d’indice de consommation, plus de 12 points de taux de viande maigre dans la carcasse, jusqu’à près de six porcelets nés vifs par portée supplémentaires. Ces évolutions favorables ont réduit l’empreinte environnementale de la production, mais ont également eu des effets défavorables : une augmentation la mortalité des porcelets avant sevrage et une plus grande hétérogénéité des performances. Les enjeux pour l’avenir en termes d’objectifs d’amélioration génétique (prise en compte de caractères liés au bien-être, à la robustesse et à l’adaptation…), de méthodes et d’outils sont ensuite discutés.

International audience; Genetic parameters for 21-d litter weight (LW21) and thigh muscle volume (TMV) were estimated, and based on these traits a two-trait selection index was created with the purpose of increasing the efficiency of the Pannon White rabbits' breeding programme. Litter weight at 21 d of age (LW21, n = 22,002) and thigh muscle volume (TMV, n=8124) measurements (based on computed tomography - CT) were analysed that were recorded between 1992 and 2016. The evaluated animals were reared in 4178 litters and the total number of rabbits involved in the pedigree file was 14,124. LW21 and TMV records were analysed jointly in a two-trait animal model. The estimated heritability for LW21 and TMV were 0.10 +/- 0.01 and 0.21 +/- 0.02, respectively, and the estimated genetic correlation between these traits was -0.24 +/- 0.07. The common environmental effect had the same magnitude (0.10 +/- 0.01) as the additive genetic effect. The created selection index constructed to have 50 and 50% contribution of the measured traits. Application possibility of the created index was tested on a given kindling batch. In this case, the first step of the selection procedure was performed either according to the current breeding programme (based on the LW21 breeding values) or based on the two trait selection index. The second step of selection was not changed (based on the TMV breeding values). The consequences of using index scores instead of the regular procedure were obtaining 27.8% higher average breeding value for TMV and 11.4% lower average breeding value for LW21. These results suggest that introduction of the index may improve economic efficiency.

International audience; AbstractBackgroundSome 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 tj\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$t_{j}$$\end{document} 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.

Despite substantial advances in animal production efficiency over the last 40 years, feed still represents the majority of production costs. The negative impacts of animal production on the environment must be reduced, which implies a reduction of nutrient losses to the environment associated with animal production. Feed efficiency, mostly expressed as feed conversion ratio (FCR), is a key indicator to judge the financial and environmental performance of a farming system. In intensive rabbit breeding, the average farm FCR (maternity + fattening units) in European farms improved from 3.8 to 3.4 during the past 15 years. This translates into a drop in nitrogen and phosphorus output of approximately 10%. This improvement can be attributed to progress in health control, nutritional factors and strategies, management and genetics. To optimize rabbit farm FCR, the reproducing stock as well as the fattening unit must be considered. This review summarizes the impact of different strategies to optimize FCR under intensive production conditions, where rabbits are exclusively fed a pelleted diet. High performing reproduction stock results in a lower FCR in maternity. The use of diets with nutrient levels to optimize digestive health, together with an appropriate feeding restriction after weaning, leads to minimal losses and has a large impact on the FCR. If the different fiber requirements are met, an increase of the dietary energy level, especially in the finishing stage, reduces the FCR by approximately 0.15 points, for an increase of 0.5 MJ DE. Future possibilities for genetic selection for feed efficiency are based on improvements to the residual feed intake. It seems possible to improve feed efficiency further by reducing feed intake without affecting weight gain. Such a genetic improvement would reduce both feed input (reducing costs) and output (reducing environmental impacts). An average farm FCR of 3.0, similar to that of pig breeding, can be reached in the next decade for rabbit meat production. (C) 2017 Elsevier B.V. All rights reserved.

The aim of this study was to compare the energy balance and dynamic of body reserves in rabbit females divergently selected for longevity. One hundred and twenty-nine females from a high longevity line (HL) and 131 females of a low longevity line (LL) were studied from the 1st to the 3rd kindling. Litter size and weight and female body weight were measured at kindling (1st, 2nd and 3rd), insemination (2nd and 3rd) and at weaning (1st and 2nd). The total body electric conductivity (TOBEC) method was used to estimate the body reserves in all females at artificial insemination and at weaning, and at kindling in females that achieved parturition. Energy balance between the 11th and the 21th d of lactation was also calculated for these females. No significant difference was found for fertility or for the number of offspring born alive and weaned. However, the total number of offspring born was higher in the LL line than in the HL line at the 2nd parturition (+1.12±0.46 g; Pnd artificial insemination (+107.0±29 g; P=0.049), leading to a similar weight between the lines at the 2nd artificial insemination. There was no significant difference between lines for estimated energy used for growth between the 11th and the 21th d of lactation, or for estimated milk production (2365±30 g in HL line vs. 2398±30 g in LL line), estimated using the weight gain of the kits between the 11th and 21st d of lactation, for feed intake measured during this period (351±5 g/d in HL line vs. 359±5 g/d in LL line) or for energy balance (–6.11±0.3 MJ in HL line vs. –6.30±0.3 MJ in LL line). However, body energy content was higher in HL females than in LL (+2.72±0.64 MJ; P=0.001). In conclusion, selection for higher functional longevity results in a better ability of females to use body reserves in their early reproductive life.

Rabbits softly swept to domestication When people domesticate animals, they select for tameness and tolerance of humans. What else do they look for? To identify the selective pressures that led to rabbit domestication, Carneiro et al. sequenced a domestic rabbit genome and compared it to that of its wild brethren (see the Perspective by Lohmueller). Domestication did not involve a single gene changing, but rather many gene alleles changing in frequency between tame and domestic rabbits, known as a soft selective sweep. Many of these alleles have changes that may affect brain development, supporting the idea that tameness involves changes at multiple loci. Science , this issue p. 1074 ; see also p. 1000

The objective of this study was to assess the feasibility of selecting for functional longevity in rabbits, defined as an ability to delay involuntary culling. Functional longevity was measured as the total number of AI performed after the first kindling. Breeding values were estimated using a discrete survival model. Male parents were selected on the basis of their progeny test results, and the efficiency of selection was estimated in the second generation, as was the correlated response on reproduction traits. A total of 48 males were progeny tested, based on the longevity of 10 daughters bred in 2 different farms. Based on their estimated genetic merit, 5 "high longevity" (HL) and 5 "low longevity" (LL) males were selected divergently and produced a new generation (5 bucks/sires and 10 daughters/bucks). A difference in longevity (+0.75 AI, i.e., 32 d) was observed between the 2 lines. In farm 1, the differences were mainly due to culling (26% in the LL line vs. 14% in the HL line) whereas mortality was similar in the 2 lines. In farm 2, mortality and culling were both higher in the LL line than in the HL line (33 vs. 15% and 19 vs. 7%, respectively). There was no difference between the 2 lines in terms of the reproduction traits recorded for each kindling. Nevertheless, because of the difference in the litter number between the 2 lines, the sum of young rabbits born alive per doe over her lifetime and the sum of young rabbits weaned per doe were higher in the HL line (+5 kits; P < 0.01). Selection for functional longevity using survival analysis is feasible for modifying lifetime reproduction traits.

Improvement of feed efficiency can be achieved by genetic selection directly on feed to BW gain ratio or for alternative traits. In the present study, 2 different traits were explored in the growing rabbit and their heritability and genetic correlations with traits recorded between weaning (30 d) and 63 d of age: i) residual feed intake (RFI), to select animals having low ad libitum feed intake independently from their production level, and ii) ADG under restricted feeding (ADGR; with a restriction level of 80% compared with ad libitum feeding of a control group), to select animals having high growth rate despite limited feed intake. To study these traits, 2 rabbit lines were established named i) ConsoResidual line and ii) ADGrestrict line. Under ad libitum or restricted feeding, it comes to select animals that waste less energy for maintenance, metabolism, or activity and retain more for tissue deposition. The selection process was similar in both lines. Data comprised records from generations 0 to 6 for about 1,800 rabbits per line measured for their BW at weaning and 63 d of age (BW63) and their individual feed consumption. Under ad libitum feeding, the heritability estimates were moderate for RFI (0.16 ± 0.05), ADG (0.19 ± 0.05), and feed conversion ratio (FCR; 0.22 ± 0.05). The high genetic correlation estimated between RFI and FCR (0.96 ± 0.03) was in accordance with the literature. The genetic correlation between RFI and ADG traits was not significant. Thus, selection for low RFI with ad libitum feeding was confirmed as a potential trait to improve FCR and reduce feed intake, with little effect on ADG. To our knowledge, there is no previous selection experiment on growing rabbits with restricted feeding. Our heritability estimates for ADGR and feed conversion ratio under restricted feeding (FCRR) were moderate (0.22 ± 0.06 and 0.23 ± 0.07, respectively) and had very high negative genetic correlation. Both selection criteria were found with high and favorable genetic correlations with feed efficiency recorded under each feeding regimen. However, their different genetic correlations with BW at weaning and at 63 d of age (BW63R; respectively, 0.85 and 0.17 for RFI and -0.25 and 0.81 for ADGR) suggested different impacts on major production traits that need further analyses to decipher the relative advantages of the 2 selection criteria, together with interactions between genotypes and feeding regimen.

International audience; Understanding the genetic structure of domestic species provides a window into the process of domestication and motivates the design of studies aimed at making links between genotype and phenotype. Rabbits exhibit exceptional phenotypic diversity, are of great commercial value, and serve as important animal models in biomedical research. Here, we provide the first comprehensive survey of nucleotide polymorphism and linkage disequilibrium (LD) within and among rabbit breeds. We resequenced 16 genomic regions in population samples of both wild and domestic rabbits and additional 35 fragments in 150 rabbits representing six commonly used breeds. Patterns of genetic variation suggest a single origin of domestication in wild populations from France, supporting historical records that place rabbit domestication in French monasteries. Levels of nucleotide diversity both within and among breeds were ;0.2%, but only 60% of the diversity present in wild populations from France was captured by domestic rabbits. Despite the recent origin of most breeds, levels of population differentiation were high (FST 5 17.9%), but the majority of polymorphisms were shared and thus transferable among breeds. Coalescent simulations suggest that domestication began with a small founding population of less than 1,200 individuals. Taking into account the complex demographic history of domestication with two successive bottlenecks, two loci showed deviations that were consistent with artificial selection, including GPC4, which is known to be associated with growth rates in humans. Levels of diversity were not significantly different between autosomal and X-linked loci, providing no evidence for differential contributions of males and females to the domesticated gene pool. The structure of LD differed substantially within and among breeds. Within breeds, LD extends over large genomic distances. Markers separated by 400 kb typically showed r2 higher than 0.2, and some LD extended up to 3,200 kb. Much less LD was found among breeds. This advantageous LD structure holds great promise for reducing the interval of association in future mapping studies.

L’évolution du contexte sanitaire, économique et social de la production de lapin de chair a conduit les chercheurs de l’INRA à étudier la sélection de nouveaux caractères pour mieux répondre aux attentes des professionnels mais également du citoyen-consommateur, en particulier dans le domaine de la santé et de la longévité des animaux. Ces études reposent principalement sur la mise en place d’expériences mais également sur l’analyse de données de sélectionneurs privés et donnent lieu, après validation, à des applications dans les schémas de sélection commerciaux. Pour réduire la mortalité des jeunes, les chercheurs privilégient l’amélioration des aptitudes maternelles: l’application d’un modèle à effets génétiques directs et maternels pour le poids au sevrage a ainsi permis d’améliorer les aptitudes maternelles pour ce caractère. Une expérience de sélection canalisante pour l’homogénéité des poids de naissance intra-portée a permis d’améliorer la survie périnatale du lapereau. L’amélioration de la longévité de la femelle en reproduction est rendue possible par la mise en œuvre des méthodes d’analyse de survie. La résistance génétique aux maladies, principalement l’entérocolite épizootique et la pasteurellose, est explorée pour réduire les pertes économiques mais également pour améliorer le bien-être des animaux et réduire les risques sanitaires liés à l’utilisation des antibiotiques. Pour améliorer l’efficacité alimentaire du jeune en engraissement et ainsi réduire les coûts alimentaires qui grèvent lourdement le revenu de l’éleveur, deux critères de sélection sont comparées: la consommation résiduelle et la vitesse de croissance en régime alimentaire rationné. Afin de diminuer l’utilisation des hormones pour l’induction de l’oestrus, de nouveaux programmes visent à étudier la variabilité génétique du comportement d’oestrus des lapines.

A divergent selection experiment on within-litter homogeneity of birth weight in rabbits was carried out at the INRA experimental farm at Auzeville. The two lines were created by selecting breeding does and bucks from the female strain AGP22 bred at the Grimaud Freres Selection Company. This involved a new model incorporating a genotypic value for the mean of individual birth weight and a genotypic value for the environmental variance. This new “trait” was modelled in the usual infinitesimal framework, giving estimated breeding values for environmental variability. There was a favourable selection response with a significant difference in within-litter standard deviation of birth weight between the lines selected for increasing (HOM) or decreasing (HET) homogeneity. At the end of the third generation, 31 females from the HOM line and 33 from the HET line were sacrificed to collect the uterine horns and measure their initial length (L1) and their length after elongation with a weight of 50 g (L2) and then 70 g (L3). The length in the homogeneous line was significantly greater, whatever the weight (L1: +1.3 cm, P=0.02; L2: +2.8 cm Pb0.001; L3: +4.2 cm, Pb0.001). The absolute and the relative elongations were significantly higher in the HOM line. There was no significant effect of the line on the number of ova shed, the weight of the ovary, or the weight of the uterine horns. It is concluded that the divergence between lines for the within-litter homogeneity of birth weight is at least partly due to the characteristics of the genital tract, i.e. the length and capacity for elongation of the uterine horn.

Obtaining unbiased estimates of the direct-maternal genetic correlation proves far from straightforward for several reasons. Consequently, the use of such over- or underestimated correlations may introduce errors in genetic evaluation models. The objective of our study was to evaluate how the value of the direct-maternal genetic correlation affects EBV. Direct, maternal, and total breeding values were predicted for the ADG or weight at weaning for 3 different species (sheep, rabbits, and pigs) using models that differ depending on the fixed value of the direct-maternal genetic correlation (ranging from -0.9 to 0.9) as well as a model in which the correlation was estimated. The results were consistent between species. The direct-maternal genetic correlation had a greater impact on the estimated maternal genetic effects than on direct effects. The lowest correlations between maternal breeding values obtained with different models were -0.20, -0.01, and -0.72 in pigs, sheep, and rabbits, respectively, whereas for the direct breeding value, the lowest correlations were 0.45, 0.90, and 0.95 in pigs, sheep, and rabbits, respectively. The total EBV, calculated as the unweighted sum of direct and maternal genetic effects, did not differ greatly between the models, the lowest correlations between total breeding values being 0.93, 0.98, and 0.97 for pigs, sheep, and rabbits, respectively. Given the uncertainty associated with estimating the direct-maternal genetic correlation, setting its value to 0 in genetic evaluation models appears to be a good compromise.

International audience; Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the FST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies.

The objective of the study was to analyze the reproductive longevity of 2 selected lines of rabbits. The first one was the Prat line, a line selected in Spain on litter size at weaning, and raised in overlapping generations. The second one was a French line, the A1077 line, selected on litter size at birth and individual weight at 63 d of age, managed in batches, and artificially inseminated with discrete generations. Reproductive longevity was measured beginning at the first successful mating, assessed by a pregnancy diagnosis in the Prat line, and at the first kindling in the A1077 line. In the A1077 line, culling for infertility occurred after 3 unsuccessful artificial inseminations. The trait analyzed, defined as the doe length of productive life (LPL), was the time in days between date of the first positive pregnancy diagnosis and date of culling or death in the Prat line. In the A1077 line, the trait was the number of AI after the first kindling. Effects included in the model were year-season, litter size at birth, reproductive cycle or physiological status x cycle interaction, age at first mating, batch (only for the A1077 line), and additive genetic value of the animal as a random effect. Survival analyses were carried out with a Cox model for the Prat line and a discrete model for the A1077 line. The estimated heritability values for LPL were around 0.16 in the Prat and A1077 lines with a model including physiological status x cycle interaction effect. Removing this effect from the model led to an increase in estimated genetic variance with h 2 = 0.24 and 0.19 in the Prat and A1077 lines, respectively. Including the traits LPL and number of AI from first fertile mating or AI in selection programs could increase reproductive longevity and decrease the replacement rate.

In Saccharomyces cerevisiae the cAMP-dependent protein kinase A pathway antagonizes the cellular response to stress. It is shown here that the cellular content of Cdc25p, the upstream activator of Ras and adenylyl cyclase, decays upon various stresses such as heat shock and oxidative and ethanol shocks, whereas its phosphorylation level and its localization are unaffected. In parallel with the reduction of Cdc25p, the maximal capacity of the cell to accumulate cAMP decreases when its feedback regulation is abolished. A deletion of CDC25 prevents this decrease. Paradoxically, in wild-type cells, with normal feedback regulation, the level of cAMP, which is much lower, is not reduced but is rather increased upon stress. These observations are consistent with a role of Cdc25p in sensing and transducing stress to downstream targets, either through a cAMP-independent pathway or by large fluctuations in the cAMP content of the cell.

In the yeast Saccharomyces cerevisiae, the zinc finger transcription factor Msn2p is a central component of the general stress response. It is activated in response to a wide variety of environmental changes, including physicochemical stresses as well as nutritional starvation, and induces the expression of a large set of genes required for cellular adaptation. The transcriptional activity of Msn2p in response to stresses is transient, and must therefore be strictly controlled. It is mainly regulated by reversible translocation from the cytoplasm to the nucleus upon the onset of stress, under the control of the cAMP-APK and the TOR pathways. In this report, we describe a new level of control: heat shock-induced degradation of Msn2p by the 26S proteasome. This degradation occurs in the nucleus and is further enhanced when Msn2p is fully active. Moreover, we show that the cyclin-dependent protein kinase Srb10p, a component of the transcription machinery, plays a role in the enhanced degradation of Msn2p upon heat shock. These findings provide new insights into the mechanisms by which Msn2p is transiently activated in response to stress.

We have found that the guanine nucleotide exchange factor for ras, Cdc25p, interacts with Ssa1p in Saccharomyces cerevisiae. This interaction was observed with GST-fused Cdc25p polypeptides and confirmed by coimmunoprecipitation with the endogenous Cdc25p. Hsp82 appeared also to be co-immunoprecipitated with Cdc25p, albeit to a lower level than Hsp70. In a strain deleted for SSA1 and SSA2, we observed a reduced cellular content of Cdc25p. Consistent with a reduced activity of the cAMP-dependent PKA pathway, the rate of accumulation of both trehalose and glycogen was stimulated in the ssa-deleted strain. Expression of SSA1 reversed these effects, whereas co-expression of SSA1 and PDE2 restored high accumulation. The expression of genes repressed by cAMP, GAC1 and TPS1, fused to beta-galactosidase, was also stimulated by deletion of SSA genes. The effect of ssa deletion on glycogen accumulation was lost in a strain deleted for CDC25 rescued by the RAS2ile152 allele. Altogether, these results lead to the conclusion that Ssa1p positively controls the cAMP pathway through Cdc25p. We propose that this connection plays a critical role in the adaptation of cells to stress conditions.

A divergent selection experiment based on the homogeneity of birth weight in rabbit was carried out at the INRA experimental farm of Auzeville. The two lines were created by selecting breeding does and bucks from the female strain AGP22 bred at the Grimaud Freres Selection company for environmental variability of birth weight. This involved a new model incorporating a genotypic value for the mean and a genotypic value for the environmental variance. There was a selection response with a significant difference in the within-litter standard deviation of birth weight between the lines after four generations of selection (6.93 g vs. 8.13 g). The mortality of kits at birth and from birth to weaning was lower in the “homogeneous” line than in the “heterogeneous” line (16.6% vs. 18.6% and 17.7% vs. 32.7%, respectively). The litter size at weaning was higher in the “homogeneous” line (7.22 vs. 5.39). The selection on the homogeneity of birth weight had no significant influence on the other traits. It was concluded that selection for reduced environmental variance of birth weight improved young rabbit survival without reducing the mean of birth weight.

International audience; Abstract: Incidence of visual signs of bacterial infection and mortality, from causes related to bacterial infection, were recorded on a weekly basis in growing meat rabbits from 5 to 10 weeks of age. Heritability of Weekly Incidence of disease was highest in weeks 9 and 10 (0.05 +/- 0.02 and 0.06 +/- 0.02, respectively with linear model, and 0.10 +/- 0.06 and 0.12 +/- 0.05, respectively with a threshold model). Common litter effects accounted for 5-20% of the variance of disease incidence, while maternal genetic variance was small (0-3 /0). Individuals from small litters at weaning had higher disease incidence, and disease incidence reduced as litter parity of the doe increased (P

Msn2p is a transcription factor that mediates a transient cellular response to multiple stresses and to changes in the nutritional environment. It was previously shown that the C-terminal half of Msn2p contains the DNA binding domain, a nuclear localization signal and nuclear export determinants which are activated by stress. In this report, we demonstrate that the N-terminal half of Msn2p contains the transcriptional activation domain(s). In addition, we present evidence that this region of Msn2p is able to mediate both the activation of transcription and export of the protein from the nucleus in response to stress. Interestingly, while the stress response integrated by the components of the C-terminal half that are involved in nucleocytoplasmic localization is reversed by elevated levels of cAMP, the effects of stress on the transcriptional activation domain and the localization determinants present in the N-terminal half of Msn2p are insensitive to variations in the intracellular cAMP concentrations.

In response to various stresses, as well as during the diauxic transition, the Msn2p and Msn4p transcription factors of Saccharomyces cerevisiae are activated and induce a large set of genes. This activation is inhibited by the Ras/cAMP/PKA (cAMP-dependent protein kinase) pathway. Here we show by immunoblotting experiments that Msn2p and Msn4p are phosphorylated in vivo during growth on glucose, and become hyperphosphorylated at the diauxic transition and upon heat shock. This hyperphosphorylation is correlated with activation of Msn2/4p-dependent transcription. An increased level of cAMP prevents and reverses these hyperphosphorylations, indicating that kinases other than PKA are involved. These results suggest that PKA and stress-activated kinases control Msn2/4p activity by antagonistic phosphorylation. It was also noted that Msn4p is transiently increased at the diauxic transition. Msn2p and Msn4p present different hyperphosphorylation patterns in response to different stresses.

The oligomerization state of Cdc25p, the guanine nucleotide exchange factor for ras from yeast, was analyzed using different complementary approaches. The two-hybrid system showed that the C-terminal part of Cdc25p (Cdc25-Ct) can interact with itself but also with Sdc25p-Ct, the corresponding part of Sdc25p, the other guanine exchange factor from yeast. The homotropic interaction of Cdc25p-Ct has been confirmed in yeast using immunoprecipitation experiments with epitope-tagged and beta-galactosidase-fused polypeptides. No other component was required for this interaction, since dimerization was shown to occur with material synthesized in vitro. The size of Cdc25-Ct produced in Escherichia coli has been directly measured on gel filtration columns and corresponds to a dimer. The dimerization domain is localized in the same part of the molecule as the catalytic domain and the portion responsible for membrane localization. The biological relevance of dimerization is still an open question, however by allowing heterodimerization with Sdc25p it could permit a more complex combinatorial regulation of ras in yeast.

The CDC25 gene product from Saccharomyces cerevisiae, the prototype of the family of ras guanine nucleotide exchange factors, is expressed as a 180-kDa polypeptide, tightly bound to a membrane fraction. The ability to complement a cdc25 defect is located in the 3' part of the gene (codons 877-1589). Sequence analysis reveals only a short hydrophobic domain (residues 1459-1471) and no consensus sequence for post-translational acylation. The SH3 domain present in the N-terminal part of Cdc25p is not involved nor required for membrane localization, since the N-terminal part of Cdc25p did not fractionate with a membrane pellet. In contrast, the C-terminal part was attached to a 18000 g pellet after subcellular fractionation and immunoblotting. This subcellular localization was conserved in a ras1 ras2 double disruption mutant and in a ira2 disruption mutant. Immunofluorescence analysis showed a patchy staining, mainly at the periphery of the cells. These patches were quite distinct from actin patches by double immunolabeling. By analysing a set of truncated derivatives, the elements required for a particulate localization were restricted to residues 1441-1552.

Pyruvate kinase (ATP: pyruvate 2-O-phosphotransferase, EC 2.7.1.40) from human liver and red cells has been purified to homogeneity; its subunit structure and some of its kinetic characteristics have been studied. The influence of a partial proteolysis by trypsin on the subunit structure, the isozymic pattern and the kinetic characteristics of red cell and liver enzyme have been investigated. From the results of this study we may conclude that: 1. Liver (L-type) pyruvate kinase is composed of 4 identical L subunits while the major form of erythrocyte enzyme (PK-R2) is a heterotetramer designated as L2L2', the molecular weight of L' being slightly higher than that of L subunits (63 000 and 58 000 respectively). Pyruvate kinase PK-R1, predominant in the erythroblasts and the young red cells, is composed of four identical L' subunits. 2. A mild tryptic attack is able to transform PK-R1 into PK-R2, then PK-R2 into pyruvate kinase L (PK-L). The same proteolytic treatment transforms the L' subunits into L ones. 3. Consequently L-type pyruvate kinase seems to be initially synthesized in the erythroid precursors as an L4' enzyme secondarily partially proteolysed into L2L2'. In liver a very active proteolytic system would be responsible for the total transformation into L4 pyruvate kinase. 4. L4' enzyme exhibits Michaelis-Menten kinetic behaviour with an apparent Michaelis constant of 3.8 mM whereas L4 enzyme shows both positive and negative homotropic interactions towards phosphoenolpyruvate and has [S] 0.5 of 1.2 mM. The characteristics of L2L2' are roughly intermediate between those of L4' and of L4. Fructose 1,6-biphosphate decreases [S]0.5 for these three pyruvate kinase forms without suppressing the differences in the apparent affinity for phosphoenolpyruvate of these enzymes. 5. L4 pyruvate kinase is more inhibited by Mg-ATP than L4', with L2L2' in the intermediate range. 6. Tryptic treatment of each enzyme form studied transforms its kinetic behaviour into that observed for L4.

Two isozymes of fructose-6-phosphate kinase and two isozymes of pyruvate kinase have been detected in Escherichia coli under a wide variety of growth conditions. Their kinetic behavior has been characteriized with respect to different effectors and substrates. The conclusions reached on one hand by Malcovati and Kornberg (Biochim. Biophys. Acta (1969) 178, 420-423), on the other hand by Fraenkel, Kotlarz and Buc (J. Biol. Chem. (1973) 248, 4865-4866) have been found to be true in aerobiosis as well as in anaerobiosis. The biosynthesis of the four proteins is sensitive to the nature of the carbon sources as well as to the shift from aerobic to anaerobic conditions. Kinetics of depression after a shift to anaerobiosis have been followed and found to be of the order of the doubling time.

We have identified a mutation called rcal (for rescue by cAMP) which allows adenylate cyclase-deficient mutants to divide in the presence of cAMP. We took advantage of this rcal mutation to study the effect of externally added cAMP on the onset of the resting state when cells are starved for ammonium. We measured the resistance of the cells to zymolyase treatment as a parameter of the resting state. We observed that the onset of the resting state is reversibly blocked by cAMP. This inhibitory effect of cAMP is discussed together with the cAMP control of the start. This leads us to propose a model in which the cAMP level, controlled by the availability of nutrients, should trigger the choice between the entry of the cell into the resting state and the initiation of a new division cycle.

In mammalian cells, the adenylate cyclase is regulated by extracellular signaling molecules, hormones and neurotransmitters. This regulation involves specific transmembrane receptors and transducers which are heterotrimer G-proteins. In response to the liganded receptor the G-protein is activated by dissociation of the GTP-bound a subunit which can then activate the adenylate cyclase. Although this complex system which also involves negative regulatory circuit, has been extensively studied, the details of its functioning have not yet been completely elucidated.

A Dictyostelium discoideum DNA fragment that complements the ura3 and the ura5 mutants of Saccharomyces cerevisiae has been sequenced. It contains an open reading frame of 478 codons capable of encoding a polypeptide of molecular weight 52475. This gene, named DdPYR5-6, encodes a bifunctional protein composed of the orotate phosphoribosyl transferase (OPRTase) and the orotidine-5′-phosphate decarboxylase (OMPdecase) domains described for UMP synthase in mammals. The existence of separate domains for the two activities was suspected because deletion of the N-terminal coding segment of the gene eliminated the ura5 but not the ura3 complementing activity. We have now confirmed that the two parts of the open reading frame share homology with known OPRTase and OMPdecase sequences. Several blocks of sequence are conserved among OPRTase from bacteria, fungi and slime mold and one of them corresponds to the consensus sequence for phosphoribosylbinding sites. The OMPdecase domain shows extensive similarity with the yeast and Neurospora crassa enzymes, suggesting that they have evolved from an ancestral gene which was fused to the OPRTase gene in D. discoideum. It is less related to the bacterial enzyme but all these sequences present conserved blocks of homology which could identify the active site. The codon usage is strongly biased in a manner similar to that found for other D. discoideum genes. The flanking DNA contains homopolymers of A and T and alternating sequences that are characteristic of the gene organization in D. discoideum.

In Saccharomyces cerevisiae , the product of the CDC25 gene is required for progression in the cell division cycle. It is necessary for cAMP production. It has been suggested that the CDC25 gene product acts through Ras proteins. We report the cloning of a DNA fragment from a new gene able to suppress the thermosensitive phenotype of the cdc 25−5 mutation. It is unable to suppress the defect of a mutant of the adenylate cyclase gene or of the ras1 , ras2 ts double mutant. This DNA fragment prevents the drop in cAMP level in cdc 25-5 mutant cells shifted to restrictive temperature. The complementing part of this fragment contains a truncated open reading frame (ORF) corresponding to the 3' end of a gene we named SCD25 . The 584-amino acid sequence deduced from this ORF shares 45% identity with the 592-aa C-terminal part of the CDC25 ORF which is sufficient for complementation of cdc25 mutations. Some of the common sequences between these two genes are also partially homologous with the amino acid sequence of LTE1 , another gene of S. cerevisiae . The capacity of the SCD25 fragment to suppress a cdc25 mutation and its homology to the C-terminal part of the CDC25 led us to propose that the CDC25 and the SCD25 C-terminal fragments each encode a protein domain which is capable in itself to support a similar biochemical function.