J. M. Elsen

Early accumulation of PrPSc in gut-associated lymphoid and nervous tissues of susceptible sheep from a Romanov flock with natural scrapie

The immune system is known to be involved in the early phase of scrapie pathogenesis. However, the infection route of naturally occurring scrapie and its spread within the host are not entirely known. In this study, the pathogenesis of scrapie was investigated in sheep of three PrP genotypes, from 2 to 9 months of age, which were born and raised together in a naturally scrapie-affected Romanov flock. The kinetics of PrP(Sc) accumulation in sheep organs were determined by immunohistochemistry. PrP(Sc) was detected only in susceptible VRQ/VRQ sheep, from 2 months of age, with an apparent entry site at the ileal Peyers patch as well as its draining mesenteric lymph node. At the cellular level, PrP(Sc) deposits were associated with CD68-positive cells of the dome area and B follicles before being detected in follicular dendritic cells. In 3- to 6-month-old sheep, PrP(Sc) was detected in most of the gut-associated lymphoid tissues (GALT) and to a lesser extent in more systemic lymphoid formations such as the spleen or the mediastinal lymph node. All secondary lymphoid organs showed a similar intensity of PrP(Sc)-immunolabelling at 9 months of age. At this time-point, PrP(Sc) was also detected in the autonomic myenteric nervous plexus and in the nucleus parasympathicus nervi X of the brain stem. These data suggest that natural scrapie infection occurs by the oral route via infection of the Peyers patches followed by replication in the GALT. It may then spread to the central nervous system through the autonomic nervous fibres innervating the digestive tract.

Different allelic effects of the codons 136 and 171 of the prion protein gene in sheep with natural scrapie

Scrapie is a transmissible degenerative disease of the central nervous system occurring naturally in sheep. It belongs to the group of prion diseases also affecting man in which an abnormal isoform of the host-encoded prion protein (PrP) accumulating in the brain is responsible for neuronal death. Three main polymorphisms have been described in the sheep PrP gene, at positions 136, 154 and 171. A strong association between susceptibility/resistance to natural scrapie and a dimorphism at codon 136 of the ovine PrP gene has been reported in several breeds, including Romanov. This dimorphism, however, is not found in all scrapie-affected breeds. We have compared the PrP genotypes of Lacaune sheep obtained from enzootically affected flocks with those of apparently healthy sheep. A third variant at codon 171 was also evidenced. The results were compared with those obtained in a single experimental Romanov flock orally challenged with nematode parasites in which scrapie suddenly appeared and killed 80% of the sheep. We present evidence that, even in different epizootological circumstances, the major genetic factor controlling the susceptibility/resistance to natural scrapie in sheep, is represented by codon 171 genotype of the PrP gene. We also suggest that a modification of the allelic effects of codon 136 can occur in heavily infected animals.

Alternative models for QTL detection in livestock. I. General introduction

In a series of papers, alternative models for QTL detection in livestock are proposed and their properties evaluated using simulations. This first paper describes the basic model used, applied to independent half-sib families, with marker phenotypes measured for a two or three generation pedigree and quantitative trait phenotypes measured only for the last generation. Hypotheses are given and the formulae for calculating the likelihood are fully described. Different alternatives to this basic model were studied, including variation in the performance modelling and consideration of full-sib families. Their main features are discussed here and their influence on the result illustrated by means of a numerical example

Genetic mapping of the autosomal region involved in XX sex-reversal and horn development in goats.

Contrary to other genetic disorders, the genetic study of sex determination anomalies in humans stumbles over the difficulty in observing large pedigrees. In goats, abnormalities in sex determination are intimately linked to a dominant Mendelian gene coding for the “polled” (hornless) character, which could render this species an interesting animal model for the rare human cases of SRY-negative XX males. In this report, we describe genetic linkage between the polled/intersex synchome (PIS) and four microsatellite markers of the distal region of goat Chromosome 1 (CHI1), quite distinct from the bovine “polled” region. According to comparative mapping data, no sex-determining gene has been described so far in homologous regions in the human. This genetic localization constitutes a first step towards identifying a new autosomal sex-determining gene in mammals.

Accurate mapping of the “acid meat” RN gene on genetic and physical maps of pig Chromosome 15

It has been shown that a major gene, called RN, is responsible for the RTN technological yield, a meat quality porcine trait. Experimental families informative for the segregation of RN gene were constituted from animals belonging to the Laconie composite line. We have previously mapped the RN gene to Chromosome (Chr) 15 (Milan et al. Genet. Sel. Evol. 27, 195-199, 1995). A Chr 15 map was established with 16 markers. The RN gene was found to be located between markers Sw120 and Sw936, at 2 cM from Sw936 (LOD = 38.1). In addition, by localizing Sw936 at 15q21–22 using DISC-PCR, we also located RN on the physical map.

Genome-wide association studies for osteochondrosis in French trotter horses

A genome-wide association study for osteochondrosis (OC) in French Trotter horses was carried out to detect QTL using genotype data from the Illumina EquineSNP50 BeadChip assay. Analysis data came from 161 sire families of French Trotter horses with 525 progeny and family sizes ranging from 1 to 20. Genotypes were available for progeny (n = 525) and sires with at least 2 progeny (n = 98). Radiographic data were obtained from progeny using at least 10 views to reveal OC. All radiographic findings were described by at least 2 veterinary experts in equine orthopedics, and severity indices (scores) were assigned based on the size and location of the lesion. Traits used were a global score, the sum of all severity scores lesions (GM, quantitative measurement), and the presence or absence of OC on the fetlock (FM), hock (HM), and other sites (other). Data were analyzed using 2 mixed models including fixed effects, polygenic effects, and SNP or haplotype cluster effects. By combining results with both methods at moderate evidence of association threshold P < 5 × 10(-5), this genome-wide association study displayed 1 region for GM on the Equus caballus chromosome (ECA) 13, 2 for HM on ECA 3 and 14, and 1 for other on ECA 15. One region on ECA 3 for HM represented the most significant hit (P = 3 × 10(-6)). By comparing QTL between traits at a decreased threshold (P < 5 × 10(-4)), the 4 QTL detected for GM were associated to a QTL detected for FM or HM but never both. Another interesting result was that no QTL were found in common between HM and FM.

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.

Assessment of genetic variation explained by markers for wool traits in sheep via a segment mapping approach.

A first step towards the genetic dissection of quantitative traits is to perform a genome scan with DNA markers evenly spaced throughout the genome. However, and despite recent advancements in typing technology, a dense genome scan remains a lengthy and very expensive task. An alternative approach is to perform a preliminary typing with a reduced number of markers, not necessarily covering all chromosomes, in order to assess the fraction of total genetic variation explained by typed markers and to identify the most relevant chromosomes to pursue genotyping. The segment mapping strategy (Pe ́rez-Enciso and Varona 2000) is particularly well suited to this end, as it allows us to analyze simultaneously the whole genome. In short, the method consists of partitioning the genome into a series of segments, delimiting specific genome regions that we are interested in analyzing. The method allows us to model the segment as a fixed effect, as in crosses between inbred lines, as a random effect, e.g., in purebred analysis, or as a mixed model, which is useful in analyzing crosses between divergent breeds. The fraction of total genetic variance explained by each segment is subsequently estimated. In this approach, the most relevant question is the fraction of genetic variance explained by the whole segment; we are not interested so much in how many quantitative trait loci (QTLs) there are or in their exact position. We illustrate the proposed strategy in a halfsib design experiment in sheep for QTL detection in wool traits (Allain et al. 1998). The population analyzed came from the synthetic breed INRA401. This breed is a composite Romanov (prolific breed) and Berrichon du Cher (meat breed). It was created in France in 1980 (Ricordeau et al. 1992). The main selection objective is reproductive performance, and there is no selection on wool characteristics. The experimental resource population for the QTL study comprised 30 rams and 690 ewes, which produced 1109 lambs (694 males and 415 females). The number of offspring per sire ranged from 31 to 45. The number of ewes mated to a given ram also ranged from 31 to 45. Most of the ewes were mated to a single ram, but 78 of them were mated to two different rams. Thus, all individuals in the pedigree were indirectly related. Mid-side wool samples were taken from the offspring lambs at a fixed weight, 32 and 38 kg for females and males respectively (about 3 months of age). Staple length (SL) was measured. Then, after a washing treatment, wool samples were analyzed in a textile laboratory (ITF, France) by Optical Fiber Diameter Analysis for determining the mean (MFD) and the coefficient of variation (CVFD) of the fiber diameter. Fiber diameter was assessed according to the IWTO-4795 standard method. In total, 4000 fiber snippets per individual were measured. All sires, dams, and offspring were typed for the 40 microsatellites listed in Fig. 1, distributed among 20 out of the 26 ovine autosomes. The total length covered by all markers was about 600 cM, plus eight chromosomes where only one marker was available. The total length of the sheep genome is about 2500 cM. DNA was extracted from the blood, and PCR-amplified microsatellites were analyzed on a capillary electrophoresis equipment with fluorescent detection. Genetic distances between microsatellites within the same linkage group were estimated with the CRIMAP software. The linear model used to analyze the data was:

Connectedness in Genetic Evaluation

The problem of connectedness in genetic evaluation is part of the more general one of “adjusting” for nuisance parameters (e.g., herd x year x season) and of estimating genetic population means (group effects). After a review of approaches to the study of connectedness, its impact is discussed in relation to the type of model used (purely fixed or mixed; with or without genetic group) and to the properties sought from an estimator of genetic merit (unbiasedness vs. mean square error). Consideration of connectedness is especially important in the choice of alternative models. The degree of connectedness is likely to be a factor limiting the effectiveness of adjusting genetic evaluations for sources of bias. A coefficient to assess the degree of connectedness in practice is suggested. This coefficient involves pairs of levels of factors, and it varies between 0 (non-estimability) and 1 (balanced distribution according to the factors involved in disconnectedness). Small numerical examples are given to illustrate theoretical aspects of this problem. Practical applications based on the use of artificial insemination sires to connect herds over space and time are also presented.

The calculation of herbage intake of grazing sheep: A detailed comparison between models

Abstract This paper presents a review of the calculation of herbage intake by grazing sheep. A number of different simulation models and feeding recommendation sources are compared, both as to form and as to numerical results for a series of examples. In addition to the overall approach, the following aspects of the calculation of intake are considered; the effects of animal and plant characteristics on intake, the differences between lactating or gestating ewes and dry ewes, the treatment of intake from heterogeneous pastures, and herbage intake when milk, or supplements, are also available. The general conclusion is that the models presented are each likely to have only a limited range of applicability. The main use of this review, then, is to provide guidance in developing empirical models of intake for other situations, rather than to suggest a generally valid model.