Dominique François

Universal DNA-Based Methods for Assessing the Diet of Grazing Livestock and Wildlife from Feces

Because of the demand for controlling livestock diets, two methods that characterize the DNA of plants present in feces were developed. After DNA extraction from fecal samples, a short fragment of the chloroplastic trnL intron was amplified by PCR using a universal primer pair for plants. The first method generates a signature that is the electrophoretic migration pattern of the PCR product. The second method consists of sequencing several hundred DNA fragments from the PCR product through pyrosequencing. These methods were validated with a blind analysis of feces from concentrate- and pasture-fed lambs. The signature method allowed differentiation of the two diets and confirmed the presence of concentrate in one of them. The pyrosequencing method allowed the identification of up to 25 taxa in a diet. These methods are complementary to the chemical methods already used. They could be applied to the control of diets and the study of food preferences.

Immune response to Haemonchus contortus infection in susceptible (INRA 401) and resistant (Barbados Black Belly) breeds of lambs.

The immune responses to Haemonchus contortus were compared in studies in resistant Barbados Black Belly (BBB) and susceptible INRA 401 (INRA) breeds of lambs. The cytokine patterns indicated a Th2‐biased response in both breeds. A more persistent and elevated Th2 cytokine mRNA transcription and blood eosinophilia were noted in the BBB lambs. However, at days 4 and 30 post‐infection, abomasal recruitment of eosinophils and mast cells were similar between the two breeds. Following primary infections, the BBB demonstrated a substantially lower faecal egg count compared to the INRA lambs. Furthermore, worm counts at 4 and 30 days post‐infection, and adult female worm size and in utero egg counts 30 days after the first infection were significantly lower in the BBB than in the INRA breed. In the INRA breed, re‐infection caused a significant reduction in most parasitological parameters compared with those observed after the primary infection. A similar response was not observed in the BBB sheep. In conclusion, while the major driving force in the response to H. contortus infection is a Th2‐biased immunity in which the BBB showed its maximal performance during the primary infection, the INRA breed performed better after re‐infection compared to its response to first exposure.

A genome scan for QTL affecting resistance to Haemonchus contortus in sheep.

Gastrointestinal nematodes are one of the main health issues in sheep breeding. To identify loci affecting the resistance to Haemonchus contortus, a genome scan was carried out using 1,275 Romane × Martinik Black Belly backcross lambs. The entire population was challenged with Haemonchus contortus in 2 consecutive experimental infections, and fecal egg counts (FEC) and packed cell volumes were measured. A subgroup of 332 lambs with extreme FEC was necropsied to determine the total worm burden, length of female worms, sex ratio in the worm population, abomasal pH, and serum and mucosal G immunoglobulins (IgG) responses. Pepsinogen concentration was measured in another subset of 229 lambs. For QTL detection, 160 microsatellite markers were used as well as the Illumina OvineSNP50 BeadChip that provided 42,469 SNP markers after quality control. Linkage, association, and joint linkage and association analyses were performed with the QTLMAP software. Linkage disequilibrium (LD) was estimated within each pure breed, and association analyses were carried out either considering or not the breed origin of the haplotypes. Four QTL regions on sheep chromosomes (OAR)5, 12, 13, and 21 were identified as key players among many other QTL with small to moderate effects. A QTL on OAR21 affecting pepsinogen concentration exactly matched the pepsinogen (PGA5) locus. A 10-Mbp region affecting FEC after the 1st and 2nd infections was found on OAR12. The SNP markers outperformed microsatellites in the linkage analysis. Taking advantage of the LD helped to refine the locations of the QTL mapped on OAR5 and 13.

Pedigree analysis of seven small French sheep populations and implications for the management of rare breeds.

Pedigree information was analyzed in 7 small populations of sheep raised in France (Bleu du Maine, Charmoise, Cotentin, on-farm Romanov, Romanov ex situ in vivo, Roussin de la Hague, Solognote) to estimate their genetic variability. The pedigree information for each breed, estimated by the number of equivalent generations traced, ranged from rather poor (4.6) to very good (10.5) when compared with other studies. On the basis of probabilities of gene origin, the effective number of ancestors ranged from 17 (on-farm Romanov breed) to 59 (Bleu du Maine). On the basis of the rate of inbreeding, the realized effective size was found to range from 65 (Romanov breed ex situ) to 231 (Bleu du Maine). The average kinship coefficients between rams from which semen doses are available in the French National Cryobank and the active ram and ewe populations were also computed. Results found in each breed were analyzed by taking into consideration the demographic evolution of the breeds, their management practices, and the use of cryopreservation as a way to preserve genetic variability. It appeared quite clear that, in populations in which AI with frozen semen is seldom used, factors that mainly affect the genetic variability are the female-to-male ratio, which should be as small as possible, and the number of reproducing female offspring by males, which should be as balanced as possible. Finally, our work showed that all populations under study have fairly good genetic variability in comparison with other species, despite their scarce numbers.

Genetic parameters for resistance to the Salmonella abortusovis vaccinal strain Rv6 in sheep

An experimental population (1216 lambs from 30 sires) of the Inra401 sheep was created in an Inra flock to allow QTL detection for susceptibility to Salmonella infection, wool and carcass traits. The Inra401 is a sheep composite line developed from two breeds: Berrichon du Cher and Romanov. At 113 days of age on average, the lambs were inoculated intravenously with 108Salmonella abortusovis Rv6 (vaccinal strain). They were slaughtered 10 days after the inoculation. Several traits were measured at inoculation and/or slaughtering to estimate the genetic resistance of the lambs to Salmonella infection: specific IgM and IgG1 antibody titres, body weight loss, spleen and pre-scapular node weights and counts of viable Salmonella persisting in these organs. This paper presents a quantitative analysis of the genetic variability of the traits related to salmonellosis susceptibility. The heritabilities of the traits varied between 0.10 and 0.64 (significantly different from zero). Thus, in sheep as well as in other species, the determinism of resistance to Salmonella infection is under genetic control. Moreover, the correlations between the traits are in agreement with the known immune mechanisms. The genetic variability observed should help QTL detection.

Quantitative trait loci linked to PRNP gene controlling health and production traits in INRA 401 sheep

In this study, the potential association of PrP genotypes with health and productive traits was investigated. Data were recorded on animals of the INRA 401 breed from the Bourges-La Sapinière INRA experimental farm. The population consisted of 30 rams and 852 ewes, which produced 1310 lambs. The animals were categorized into three PrP genotype classes: ARR homozygous, ARR heterozygous, and animals without any ARR allele. Two analyses differing in the approach considered were carried out. Firstly, the potential association of the PrP genotype with disease (Salmonella resistance) and production (wool and carcass) traits was studied. The data used included 1042, 1043 and 1013 genotyped animals for the Salmonella resistance, wool and carcass traits, respectively. The different traits were analyzed using an animal model, where the PrP genotype effect was included as a fixed effect. Association analyses do not indicate any evidence of an effect of PrP genotypes on traits studied in this breed. Secondly, a quantitative trait loci (QTL) detection approach using the PRNP gene as a marker was applied on ovine chromosome 13. Interval mapping was used. Evidence for one QTL affecting mean fiber diameter was found at 25 cM from the PRNP gene. However, a linkage between PRNP and this QTL does not imply unfavorable linkage disequilibrium for PRNP selection purposes.

Genetic parameter estimates for carcass traits in the inra401 composite sheep strain

Abstract An experimental population (1216 lambs from 30 sires) of INRA401 sheep was created to detect QTL controlling salmonellosis resistance, carcass traits and wool traits. INRA401 is a composite line developed from crosses between Berrichon du Cher and Romanov breeds. This paper describes a quantitative analysis of the genetic variability for carcass traits. Controlled traits included body and carcass weights, conformation score, carcass dimension, fat and skeleton measurements, surface area of longissimus dorsi. Using appropriate, fixed effect adjustments, genetic correlations and heritabilities were estimated from classical animal models. Heritabilities were found to be high in comparison to previous studies, indicating both a good standardisation of the environment and a high genetic variability in this newly created breed. On the whole the study shows that the data collected are promising in terms of QTL detection.

Importance of birthcoat for lamb survival and growth in the Romane sheep breed extensively managed on rangelands

The Romane sheep breed proved to be adapted to harsh conditions with high prolificacy and lamb survival in outdoor farming, even under bad climate conditions. This breed shows large variability in its fleece type at birth and it has been suggested that lamb survival could be related to birthcoat type. The aim of the present study was to: i) characterize the coat of the lamb at birth and quantify lamb survival in relation to the birthcoat type and its protective properties concerning heat loss in the Romane breed raised under permanent exposure outdoors from birth, and ii) estimate genetic parameters of birthcoat type in relation to lamb survival and live body weight. A total of 7,880 lambs from 104 sires and 1,664 dams were used in a 14-yr experiment. The pedigree file included 9,625 individuals over 15 generations. Birthcoat type, coat surface temperature, coat depth, lamb survival, and growth were measured from birth to weaning. Weather data (temperature, wind speed, relative humidity, and precipitation) were recorded daily during lambing time. Two types of coats were observed at birth: hairy coat (62.9% of lambs) with a long coat depth (average 23.3 mm) or woolly 1 (37.1% of lambs) with a short coat depth (average 8.3 mm). Birthcoat type was an important factor affecting lamb survival and growth from birth in the Romane breed. Total mortality rate was significantly less in hairy-bearing coat lambs than in short-woolly coat ones: 7.0% vs. 9.6%, 11.6 % vs. 14.8%, and 15.7 % vs. 20.1 % at 2, 10, and 50 d, respectively, and the relative risks of death increased by 37%, 67%, and 46 % at 2, 10, and 50 d of age, respectively, in short-woolly lambs. At birth, a significant lower coat surface temperature, indicating less heat loss, was observed in long-hairy coat lambs compared with others (21.1°C vs. 26.1°C). Heavier body weights and better growth performances up to the age of 50 d were observed in long-hairy-bearing coat lambs. Lamb survival was positively correlated to weather conditions at lambing time in short-woolly lambs, whereas no relation was observed in hairy-coat lambs. Heritability estimate of birthcoat type (hairy or woolly) is high (0.88). Genetic correlations between birthcoat type, lamb survival, and live body weight at birth were positive and moderate, suggesting that it would be beneficial to take birthcoat into account as an adaptive trait in any genetic strategies for sheep production in harsh conditions on rangelands.

Heterogeneity of variance components for preweaning growth in Romane sheep due to the number of lambs reared.

BackgroundThe pre-weaning growth rate of lambs, an important component of meat market production, is affected by maternal and direct genetic effects. The French genetic evaluation model takes into account the number of lambs suckled by applying a multiplicative factor (1 for a lamb reared as a single, 0.7 for twin-reared lambs) to the maternal genetic effect, in addition to including the birth*rearing type combination as a fixed effect, which acts on the mean. However, little evidence has been provided to justify the use of this multiplicative model. The two main objectives of the present study were to determine, by comparing models of analysis, 1) whether pre-weaning growth is the same trait in single- and twin-reared lambs and 2) whether the multiplicative coefficient represents a good approach for taking this possible difference into account.MethodsData on the pre-weaning growth rate, defined as the average daily gain from birth to 45 days of age on 29,612 Romane lambs born between 1987 and 2009 at the experimental farm of La Sapinière (INRA-France) were used to compare eight models that account for the number of lambs per dam reared in various ways. Models were compared using the Akaike information criteria.ResultsThe model that best fitted the data assumed that 1) direct (maternal) effects correspond to the same trait regardless of the number of lambs reared, 2) the permanent environmental effects and variances associated with the dam depend on the number of lambs reared and 3) the residual variance depends on the number of lambs reared. Even though this model fitted the data better than a model that included a multiplicative coefficient, little difference was found between EBV from the different models (the correlation between EBV varied from 0.979 to 0.999).ConclusionsBased on experimental data, the current genetic evaluation model can be improved to better take into account the number of lambs reared. Thus, it would be of interest to evaluate this model on field data and update the genetic evaluation model based on the results obtained.

Genetic variability of fleece shedding in the Martinik hair, Romane sheep breeds and their crossbreds

From the ancestral pelage of the domestic sheep which looks like the protective double coat of the wild sheep, changes following domestication and the development of textile industry resulted in the development of the modern woolled sheep with a large decrease in the tendency to moult and extension of wool fibre at the expense of coarse hair leading to a single coat where all fibres are similar in dimension and grow permanently. Wool production is still the main purpose of sheep farming in the southern hemisphere, but in Europe wool production is often unprofitable and there is an interest in the use of breeds that have no wool or shed their wool due to the relative value of meat and wool, and increasing shearing costs. In the present paper investigations were made to evaluate genetic variability of moulting or fleece shedding including QTL detection in the French Romane, the Martinik Hair, a hairy sheep without wool close to Barbados-Black- Belly and a Martinik Hair-Romane backcross population. In the Romane breed, 43.2% of adult ewes shed at least part of their fleece once a year during spring. Heritability estimate of moulting aptitude is high (0.46) but prevalence of total fleece shedding is low (1.5% of ewes shed all their fleece). In the Martinik Hair-Romane backcross population 72% of animals shed their fleece. It was proposed to introgress gene pool from the Martinik Hair in the Romane breed through an experimental design combining QTL detection and introgression of QTL for fleece shedding in the Romane breed.