Michel Naves

Footprints of selection in the ancestral admixture of a New World Creole cattle breed

Admixed populations represent attractive biological models to study adaptive selection. Originating from several waves of recent introduction from European (EUT), African (AFT) and zebus (ZEB) cattle, New World Creole cattle allow investigating the response to tropical environmental challenges of these three ancestries. We here provide a detailed assessment of their genetic contributions to the Creole breed from Guadeloupe (CGU). We subsequently look for footprints of selection by combining results from tests based on the extent of haplotype homozygosity and the identification of excess/deficiency of local ancestry. To tackle these issues, 140 CGU individuals and 25 Brahman zebus from Martinique were genotyped at 44 057 SNPs. These data were combined to those available on 23 populations representative of EUT, AFT or ZEB. We found average proportions of 26.1%, 36.0% and 37.9% of EUT, AFT and ZEB ancestries in the CGU genome indicating a higher level of African and zebu ancestries than suggested by historical records. We further identified 23 genomic regions displaying strong signal of selection, most of them being characterized by an excess of ZEB local ancestry. Among the candidate gene underlying these regions, several are associated with reproductive functions (RXFP2, PMEPA1, IGFBP3, KDR, PPP1R8, TBXA2R and SLC7A5) and metabolism (PDE1B and CYP46A1). Finally, two genes (CENTD3 and SAMD12) are involved in cellular signalization of immune response. This study illustrates the relevance of admixed populations to identify footprints of selection by combining several tests straightforward to implement on large data sets.

Genetic Resistance of Creole Goats to Cowdriosis in Guadeloupe Status in 1995

A genetic predisposition to resistance (R)/susceptibility (S) has been demonstrated for cowdriosis in certain goal lines. In order to identify genetic markers of R/S and to follow their transmission to the offspring, 4 groups of sires and dams were crossbred in 1991, 1992, and 1993: Rr, RS, SR, and SS. The offspring were challenged at the age of six months with subsequent challenge of the S parent. From 28 presumed S dams, 7 turned out R and from 2 presumed S sires, 1 was R and the other undefinable. The resistance rate was 76% for 21 RR kids and 45% for 20 RS kids. The R character seems to be better transmitted by dams than the S one. No difference was observed between R and S goats in terms of incubation period and body temperature level after challenge. There was no statistical effect found of sex, litter size, or birth mass on the R/S character; only a slight effect on daily mass gain was observed. Sperm has been collected from 4 S sires (died after challenge) and 5 R sires, and stored in liquid nitrogen in order to conceive additional SR and SS progeny. Several caprine leucocyte antigens seem to be genetic markers of R (Be 1, CLY) and of S (Be 9, Be 22, Be 23). Further powerful tools like microsatellites and probes defining other interesting loci possibly involved in disease pathogenesis are now at hand and will be included in future experiments.

Incidence of Toxocara vitulorum in creole Calves of Guadeloupe.

The 247 calves from 112 Creole cows of Guadeloupe were monitored for Toxocara vitulorum infection from year 2002 to 2005. The cows were in good body condition and the calf growth rate was 880g/d on average. The overall prevalence of infection was estimated to 0.77 [0.72; 0.83]. The faecal egg count peaked 49 days after calf birth, and then decreased. No clinical symptom related to T. vitulorum infection was observed, and no effect on the calf growth rate was shown. It was concluded that, despite the high prevalence of T. vitulorum, the production loss remains under the level of detection, and no drenching is needed for well-fed animals.

Economic values of body weight, reproduction and parasite resistance traits for a Creole goat breeding goal

A specific breeding goal definition was developed for Creole goats in Guadeloupe. This local breed is used for meat production. To ensure a balanced selection outcome, the breeding objective included two production traits, live weight (BW11) and dressing percentage (DP) at 11 months (the mating or selling age), one reproduction trait, fertility (FER), and two traits to assess animal response to parasite infection: packed cell volume (PCV), a resilience trait, and faecal worm eggs count (FEC), a resistance trait. A deterministic bio-economic model was developed to calculate the economic values based on the description of the profit of a Guadeloupean goat farm. The farm income came from the sale of animals for meat or as reproducers. The main costs were feeding and treatments against gastro-intestinal parasites. The economic values were 7.69€ per kg for BW11, 1.38€ per % for FER, 3.53€ per % for DP and 3 × 10(-4)€ per % for PCV. The economic value for FEC was derived by comparing the expected profit and average FEC in a normal situation and in an extreme situation where parasites had developed resistance to anthelmintics. This method yielded a maximum weighting for FEC, which was -18.85€ per log(eggs per gram). Alternative scenarios were tested to assess the robustness of the economic values to variations in the economic and environmental context. The economic values of PCV and DP were the most stable. Issues involved in paving the way for selective breeding on resistance or resilience to parasites are discussed.

Production systems of Creole goat and their implications for a breeding programme.

The Creole goat is a local meat breed well adapted to the tropical environment of Guadeloupe, a French island in the Caribbean. A survey of 47 goat farmers was conducted in May 2008 to describe the Guadeloupean goat farming systems. It was the preliminary step for the implementation of a breeding programme for Creole goats. Farmers had 31 does on average. A small number (4%) kept only Creole goats. Most of them (62%) had a mixed herd of Creole and crossbreds. One-third of them (34%) reared only crossbred goats. Farmers appreciate the rusticity and resistance of the Creole goat but consider its growth as too slow. The most desired traits for goat selection were conformation and growth for males (77% of the answers). These traits were also important for females (30% of the answers). Maternal qualities were also frequently cited (maternal behaviour 23%, reproduction 20% and milk production 17%). Disease resistance was not seen as an important trait (10% and 7% of the answers for bucks and does, respectively). A typology constituted of five groups of farmers was also created. Farmers of three groups were retained to participate at a selection programme. They kept Creole goats and have expressed a strong willingness to join a selection programme. The results of the survey suggest that a breeding programme should mostly focus on the Creole goat as a maternal breed. Real consideration should be given to disease resistance. The Creole goat has indeed a key role to play in the sustainability of local farming systems.

Effects of feeding system and slaughter age on the growth and carcass characteristics of tropical-breed steers1

This study aimed to compare the growth performances and carcass characteristics of tropical-breed steers reared in 2 contrasted feeding systems (indoor vs. pasture) and slaughtered at different ages (early vs. late). A total of 309 Creole steers (growing at an initial BW of 173 ± 3 kg and an initial age of 252 ± 4 d) were used over a continuous 12-yr study. Indoor steers were housed in a cattle shed, fed fresh-cut grass plus concentrate, and slaughtered at 14.5 or 17.1 ± 0.1 mo of age. Pasture steers were pasture grazed without supplemental feed, and slaughtered at 17.6 and 21.2 ± 0.1 mo of age. Indoor-fed steers had a greater ADG (786 vs. 517 ± 29 g•d(-1); P < 0.0001) and more carcass fat (164 vs. 145 ± 4.5 g•kg(-1); P = 0.001) than pasture-fed steers. Late-slaughtered steers had decreased ADG (630 vs. 673 ± 27 g•d(-1); P = 0.001) but greater dressing percentages (hot dressing percentage = 55.7 vs. 54.7 ± 0.34%; chilled dressing percentage = 54.5 vs. 53.4 ± 0.34%; P < 0.0001) than early-slaughtered steers. The interaction between feeding system and slaughter age was significant for carcass tissue composition. Whole-carcass muscle content was greater in late-slaughtered steers than early-slaughtered steers, especially in pasture-fed steers (720 vs. 698 ± 6.0 g•kg(-1); P < 0.0001), but less so in indoor-fed steers (707 vs. 700 ± 5.9 g•kg(-1); P = 0.046). Furthermore, increasing slaughter age had no effect on carcass fat in indoor-fed steers (162 vs. 166 ± 4.8 g•kg(-1); P = 0.342), but decreased carcass fat in pasture-fed steers (150 vs. 140 ± 5.0 g•kg(-1); P = 0.014). The results showed that slaughter age and feeding system are 2 major factors that independently affect most of the growth and carcass traits of tropical-breed steers but jointly influence tissue deposition. Our study found that in tropical-breed steers that are grazing, late slaughtering grazing steers increased carcass muscle content without extra fat, thus yielding a carcass quality better suited to consumer choices.

Attractivity of cattle infested by Amblyomma variegatum (Acari: Ixodidae) for conspecific adult ticks from the field in Guadeloupe

Four field experiments were conducted with creole cattle in Guadeloupe to study the attractivity for adult ticks of animals previously infested with males of Amblyomma variegatum producing aggregation attachment pheromones (AAPs). In each experiment, two groups of cattle were used; the first group was infested with adult A. variegatum and the second group was kept free of ticks and pheromones by acaricidal treatment and by washing the hair and skin of previously infested sites. Both groups were then exposed to natural infestation by ticks present in the environment or by ticks bred in the laboratory and released on the pasture. The number of additional ticks infesting animals were compared between the treated and control groups. There were no significant differences between both groups in the numbers of new male ticks infesting the animals during the first days following the beginning of the experiment. Thereafter, comparison of the slopes of infestation indicated that infested cattle were no more attractive for male ticks than uninfested hosts. Uninfested cattle were spontaneously and rapidly infested by male ticks. It is concluded that carbon dioxide or another host component was a major attractant for A. variegatum males. Female ticks attached on predilection sites exclusively in the presence of AAP-producing males, i.e. 5–10 days after the attachment of the first males. Based on these results we postulate that slow-release devices impregnated with pheromones have no additional attractive effect on A. variegatum males under Caribbean conditions. However, they may be useful in inducing the attachment of females, but only in the first days preceding the arrival of pioneer AAP-producing males.

Assessing the risk status of livestock breeds: a multi-indicator method applied to 178 French local breeds belonging to ten species

espanolLa clasificacion de las razas animales segun su nivel de peligro en cuanto a su desaparicion es un elemento de base para un sistema nacional de alerta y de monitoreo de los recursos geneticos. Un enfoque multicriterio ha sido desarrollado para establecer el nivel de peligro de una poblacion animal domestica. En total, se mantuvieron seis criterios: (i) el numero total de hembras reproductoras, (ii) la evolucion de este numero en los cincos ultimos anos, o las cincos generaciones, segun la especie; (iii) la proporcion de cruzamientos; (iv) el tamano efectivo de la poblacion, (v) la organizacion de los criadores y el apoyo tecnico; (vi) el contexto socio-economico. Con el proposito de facilitar la combinacion de estos criterios de tipo diferente, los valores observados fueron convertidos en una escala de 0 (ausencia de amenaza) a 5 (amenaza maxima), la correspondencia entre valores observados y notas siendo especifica por cada criterio. Para cada raza, las notas estan presentadas de forma grafica y una nota de sintesis esta calculada como la media de las seis notas. Este metodo ha sido aplicado a 178 razas locales francesas perteneciendo a diez diferentes especies: ganado, ovino, caprino, cerdo, caballo, asno, gallina, pavo, oca, pato comun. Asi se demostro que la mayoria de las razas locales francesas se pueden considerar como en peligro: todas las razas locales de equido y de cerdo, casi la totalidad de las razas locales de aves de corral, alrededor de 80% de las razas locales de ganado o caprinos y la mitad de razas locales de ovinos. Se discute el interes de este metodo para la definicion de estrategias de conservacion et la elaboracion de politicas publicas. EnglishBreed risk status assessment methods are key components of country-based early warning and response systems. In this study, a multiindicator method was developed to assess the risk status of livestock populations. Six indicators were used: (i) the current number of breeding females; (ii) the change in the number of breeding females over the last 5 years or generations (depending on the species); (iii) percentage of cross-breeding; (iv) effective population size; (v) breeders organization and technical support; and (vi) socio-economic context. To make these indicators comparable, observed values were converted into scores on a six-point scale (from 0 = no threat to 5 = maximum threat); a specific conversion method was used for each indicator. For each breed, the different scores were analysed graphically and an overall score was calculated by averaging the six separate indicator scores. This approach was applied to 178 French local breeds, belonging to ten different species: horse, donkey, goat, pig, chicken, turkey, goose and Pekin duck. A large percentage of local breeds were found to be at risk to be lost for farming, although the results were species dependent. All local equine and pig breeds, as well as almost all local poultry breeds appeared to be endangered. About 80 percent of local goat and cattle breeds, and half local sheep breeds were also found to be at risk. The usefulness of this method with regards to conservation strategies and public policy is discussed francaisLa classification des races animales selon leur statut vis-a-vis d’un risque de disparition est un element-clef d’un systeme national d’alerte et de suivi des ressources genetiques. Une approche multi-indicateurs a ete developpee pour etablir le degre de menace d’une population animale domestique. Au total, six indicateurs ont ete retenus : (i) le nombre total de femelles reproductrices, (ii) l’evolution de ce nombre dans les cinq dernieres annees, ou generations, selon l’espece ; (iii) la proportion de croisement ; (iv) la taille efficace de la population ; (v) l’organisation des eleveurs et l’appui technique ; (vi) le contexte socio-economique. Afin de faciliter la combinaison de ces indicateurs de nature differente, les valeurs observees sont converties sur une echelle de 0 (absence de menace) a 5 (menace maximale), la correspondance entre valeurs observees et notes etant specifique de chaque indicateur. Pour chaque race, les notes sont representees de facon graphique et une note de synthese est attribuee en calculant la simple moyenne des six notes. Cette methode a ete appliquee a 178 races locales francaises appartenant a dix especes differentes : cheval, âne, bovins, ovins, caprins, porc, poule, dinde, oie, canard commun. Il a ete ainsi montre que la plupart des races locales francaises peuvent etre considerees comme menacees : toutes les races locales d’equides et de porc, la quasi-totalite des races locales de volailles, environ 80% des races locales bovines ou caprines, et la moitie des races locales ovines. L’interet de cette methode pour la definition de strategies de conservation et l’elaboration de politiques publiques est discute.

Comparison of tick resistance of crossbred Senepol × Limousin to purebred Limousin cattle

The comparison of resistance to natural tick infestation by Rhipicephalus microplus (Canestrini, 1887) of crossbred Senepol × Limousin and purebred Limousin cattle was investigated. The Senepol breed, originated from St Croix Island in the Caribbean is considered as a Bos taurus breed adapted to tropical conditions. Despite its B. taurus genetic background, it is believed to have a good tick resistance, but this resistance has never been assessed previously. Tick counts under natural infestation were carried out to investigate the difference of susceptibility between crossbred Senepol × Limousin and purebred Limousin cattle. Mixed-effect models were used to assess the effect of the breed on the number of ticks. Results show that Senepol × Limousin are five times less infested by ticks than purebred Limousin. These results underline the opportunity to use Senepol cattle for crossing with susceptible B. taurus breeds in tick infested areas, to combine tick resistance with beef production abilities.

Influence of trough versus pasture feeding on average daily gain and carcass characteristics in ruminants: a meta-analysis.

Quantitative meta-analysis was run on 108 publications featuring 116 experiments and 399 treatments dealing with the effect of trough or pasture feeding environment (FE) on ruminant performances. The objective was to compare the effect of trough or pasture FE on ADG, diet OM digestibility (OMD), various carcass characteristics, and the interaction between FE and complementation modalities. Live weight was adjusted to compare results between species. Results showed that trough-fed animals had higher ADG (+17.89%; P < 0.001), hot carcass yield (HYield; + 2.47%; P < 0.001) and carcass fat content (+ 24.87%; P < 0.001) than pasture-fed animals but lower carcass muscle and bone percentages (-1.60% [P = 0.010] and -7.63% [P = 0.003], respectively). Feeding environment had no effect on diet OMD (P = 0.818), but the number of observations was low. After considering the addition or not of concentrate in the diet (addiCO), FE effect persisted on ADG (P = 0.024) and carcass fat content (P = 0.027) but not on HYield (P = 0.078) or muscle and bone percentages (P = 0.119 and P = 0.581, respectively). After considering the nature of the concentrate (natCO), FE effect persisted on ADG (P < 0.001) and HYield (P = 0.004). Considering the percentage of concentrate in the diet (PCO) erased FE effect on ADG (P = 0.891) and HYield (P = 0.128). In contrast, considering the quantity of concentrate(QCO) erased FE effect on ADG (P = 0.084) but not on HYield (P = 0.006) or on carcass fat and muscle contents (P = 0.040 and P = 0.040, respectively) although the FE effect on carcass bone content persisted (P = 0.550). Animal species and physiological stage had no effect on any of the variables studied (P > 0.05) but experiment did (P ≤ 0.001). The increase in ADG was positively correlated to HYield in cattle (P = 0.002) and small ruminants (P = 0.003) and positively linked to carcass fat content (P = 0.007) but not carcass muscle content, which actually decreased (P = 0.001). Overall, this meta-analysis confirmed previous reports of FE effects and revealed how the differences generally reported result from a confounding effect of FE and nature of the diet. Indeed, in most of the studies used, trough-fed animals were supplemented with concentrate whereas pasture-fed animals were not. This research also highlighted the fact that pasture-fed animals have the potential to achieve the same performances as trough-fed animals when fed a similar diet.