Effective selection on the PrP gene has been implemented since October 2001 in all French sheep breeds.After four years, the ARR ''resistant'' allele frequency increased by about 35% in young males.The aim of this study was to evaluate the impact of this strong selection on genetic variability.It is focussed on four French sheep breeds and based on the comparison of two groups of 94 animals within each breed: the first group of animals was born before the selection began, and the second, 3-4 years later.Genetic variability was assessed using genealogical and molecular data (29 microsatellite markers).The expected loss of genetic variability on the PrP gene was confirmed.Moreover, among the five markers located in the PrP region, only the three closest ones were affected.The evolution of the number of alleles, heterozygote deficiency within population, expected heterozygosity and the Reynolds distances agreed with the criteria from pedigree and pointed out that neutral genetic variability was not much affected.This trend depended on breed, i.e. on their initial states (population size, PrP frequencies) and on the selection strategies for improving scrapie resistance while carrying out selection for production traits.genetic variability / scrapie resistance / molecular marker / pedigree / sheep

With the New Year comes the opportunity to make a quick assessment of the journal's production in the past year and to announce some changes for 2008.

In some situations, it is worthwhile to change not only the mean, but also the variability of traits by selection. Genetic variation in residual variance may be utilised to improve uniformity in livestock populations by selection. The objective was to investigate the effects of genetic parameters, breeding goal, number of progeny per sire and breeding scheme on selection responses in mean and variance when applying index selection. Genetic parameters were obtained from the literature. Economic values for the mean and variance were derived for some standard non-linear profit equations, e.g. for traits with an intermediate optimum. The economic value of variance was in most situations negative, indicating that selection for reduced variance increases profit. Predicted responses in residual variance after one generation of selection were large, in some cases when the number of progeny per sire was at least 50, by more than 10% of the current residual variance. Progeny testing schemes were more efficient than sib-testing schemes in decreasing residual variance. With optimum traits, selection pressure shifts gradually from the mean to the variance when approaching the optimum. Genetic improvement of uniformity is particularly interesting for traits where the current population mean is near an intermediate optimum.

Parameter expanded and standard expectation maximisation algorithms are described for reduced rank estimation of covariance matrices by restricted maximum likelihood, fitting the leading principal components only. Convergence behaviour of these algorithms is examined for several examples and contrasted to that of the average information algorithm, and implications for practical analyses are discussed. It is shown that expectation maximisation type algorithms are readily adapted to reduced rank estimation and converge reliably. However, as is well known for the full rank case, the convergence is linear and thus slow. Hence, these algorithms are most useful in combination with the quadratically convergent average information algorithm, in particular in the initial stages of an iterative solution scheme. restricted maximum likelihood / reduced rank estimation / algorithms / expectation maximisation / average information

Selection programmes based on prion protein (PrP) genotypes are being implemented for increasing resistance to scrapie. Commercial meat sheep populations participating in sire-referencing schemes were simulated to investigate the effect of selection on PrP genotypes on ARR and VRQ allele frequencies, inbreeding and genetic gain in a performance trait under selection. PrP selection strategies modelled included selection against the VRQ allele and in favour of the ARR allele. Assuming realistic initial PrP frequencies, selection against the VRQ allele had a minimal impact on performance and inbreeding. However, when selection was also in favour of the ARR allele and the frequency of this allele was relatively low, there was a loss of up to three to four years of genetic gain over the 15 years of selection. Most loss in gain occurred during the first five years. In general, the rate of inbreeding was reduced when applying PrP selection. Since animals were first selected on their PrP genotype before being selected on the performance trait, the intensity of selection on performance was weaker under PrP selection (compared with no PrP selection). Eradication of the VRQ allele or fixation of the ARR allele within 15 years of selection was possible only with PrP selection targeting all breeding animals.

Genetic analysis of disorder incidence in farmed animals is challenged by two factors. Disorders in different cohorts and environments could be caused by different factors, leading to changes in heritability and to less than unity genetic correlations across cohorts. Moreover, due to computational limitations, liability scale heritabilities at very low incidence may differ from those estimated at higher incidence. We tested whether these two dilemmas occur in skeletal deformations of farmed salmonids using multigeneration data from the Finnish rainbow trout breeding programme and previous salmonid studies. The results showed that heritability was close to zero in cohorts in which management practices maintained incidence at a low level. When there was a management failure and incidence was unusually high, heritability was elevated. This may be due to computational limitations at very low incidence and/or because deformations are induced by different factors in different cohorts. Most genetic correlations between deformations recorded in different generations were weakly to strongly positive. However, also negative correlations between generations were present, showing that high liability at one time can be genetically connected to low liability at another time. The results emphasise that genetic architecture of binary traits can be influenced by trait expression.

An F2 chicken population was established from a crossbreeding between a Xinghua line and a White Recessive Rock line. A total of 502 F2 chickens in 17 full-sib families from six hatches was obtained, and phenotypic data of 488 individuals were available for analysis. A total of 46 SNP on GGA1 was initially selected based on the average physical distance using the dbSNP database of NCBI. After the polymorphism levels in all F0 individuals (26 individuals) and part of the F1 individuals (22 individuals) were verified, 30 informative SNP were potentially available to genotype all F2 individuals. The linkage map was constructed using Cri-Map. Interval mapping QTL analyses were carried out. QTL for body weight (BW) of 35 d and 42 d, 49 d and 70 d were identified on GGA1 at 351–353 cM and 360 cM, respectively. QTL for abdominal fat weight was on GGA1 at 205 cM, and for abdominal fat rate at 221 cM. Two novel QTL for fat thickness under skin and fat width were detected at 265 cM and 72 cM, respectively.

Kappa-casein (CSN3) plays an important role in stabilising the Ca-sensitive caseins in the micelle. The European rabbit (Oryctolagus cuniculus) CSN3 has previously been shown to possess two alleles (A and B), which differ deeply in their intronic regions (indels of 100 and 1550 nucleotides in introns 1 and 4, respectively). Furthermore, a correlation between several reproductive performance traits and the different alleles was described. However, all these data were exclusively collected in rabbit domestic breeds, preventing a deeper understanding of the extensive polymorphism observed in the CSN3 gene. Additionally, the techniques available for the typing of both indel polymorphisms were until now not suitable for large-scale studies. In this report, we describe a simple, PCR-based typing method to distinguish rabbit CSN3 alleles. We analyse both ancient wild rabbit populations from the Iberian Peninsula and France, and the more recently derived English wild rabbits and domestic stocks. A new allele (C) showing another major indel (250 bp) in intron 1 was found, but exclusively detected in Iberian wild rabbits. In addition, our survey revealed the occurrence of new haplotypes in wild populations, suggesting that intragenic recombination is important in creating genetic diversity at this locus. This easy and low cost single-step PCR-based method results in an improvement over previous described techniques, can be easily set up in a routine molecular laboratory and would probably be a valuable tool in the management of rabbit domestic breeds.