G. Erhardt

A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation

The detection of adaptive loci in the genome is essential as it gives the possibility of understanding what proportion of a genome or which genes are being shaped by natural selection. Several statistical methods have been developed which make use of molecular data to reveal genomic regions under selection. In this paper, we propose an approach to address this issue from the environmental angle, in order to complement results obtained by population genetics. We introduce a new method to detect signatures of natural selection based on the application of spatial analysis, with the contribution of geographical information systems (GIS), environmental variables and molecular data. Multiple univariate logistic regressions were carried out to test for association between allelic frequencies at marker loci and environmental variables. This spatial analysis method (SAM) is similar to current population genomics approaches since it is designed to scan hundreds of markers to assess a putative association with hundreds of environmental variables. Here, by application to studies of pine weevils and breeds of sheep we demonstrate a strong correspondence between SAM results and those obtained using population genetics approaches. Statistical signals were found that associate loci with environmental parameters, and these loci behave atypically in comparison with the theoretical distribution for neutral loci. The contribution of this new tool is not only to permit the identification of loci under selection but also to establish hypotheses about ecological factors that could exert the selection pressure responsible. In the future, such an approach may accelerate the process of hunting for functional genes at the population level.

A medium-density genetic linkage map of the bovine genome

A cattle genetic linkage map was constructed which covers more than 95 percent of the bovine genome at medium density. Seven hundred and forty six DNA polymorphisms were genotyped in cattle families which comprise 347 individuals in full sibling pedigrees. Seven hundred and three of the loci are linked to at least one other locus. All linkage groups are assigned to chromosomes, and all are orientated with regards to the centromere. There is little overall difference in the lengths of the bull and cow linkage maps although there are individual differences between maps of chromosomes. One hundred and sixty polymorphisms are in or near genes, and the resultant genome-wide comparative analyses indicate that while there is greater conservation of synteny between cattle and humans compared with mice, the conservation of gene order between cattle and humans is much less than would be expected from the conservation of synteny. This map provides a basis for high-resolution mapping of the bovine genome with physical resources such as Yeast and Bacterial Artificial Chromosomes as well as providing the underpinning for the interpolation of information from the Human Genome Project.USDA-MARC family and data for validating this family. P. Creighton, C. Skidmore, T. Holm, and A. Georgoudis provided some validation data for the BOVMAP families. R. Fries, S. Johnson, S. Solinas Toldo, and A. Mezzelani kindly made some of their FISH assignments available before publication. We wish to thank all those researchers who kindly sent us probes and DNA primers.

Gene-culture coevolution between cattle milk protein genes and human lactase genes

Milk from domestic cows has been a valuable food source for over 8,000 years, especially in lactose-tolerant human societies that exploit dairy breeds. We studied geographic patterns of variation in genes encoding the six most important milk proteins in 70 native European cattle breeds. We found substantial geographic coincidence between high diversity in cattle milk genes, locations of the European Neolithic cattle farming sites (>5,000 years ago) and present-day lactose tolerance in Europeans. This suggests a gene-culture coevolution between cattle and humans.

Transmitochondrial differences and varying levels of heteroplasmy in nuclear transfer cloned cattle.

To assess the extent of cytoplasmic genetic variability in cloned cattle produced by nuclear transplantation procedures, we investigated 29 individuals of seven male cattle clones (sizes 2–6) from two different commercial sources. Restriction enzyme and direct sequence analysis of mitochondrial DNA (mtDNA) detected a total of 12 different haplotypes. Transmitochondrial individuals (i.e., animals which share identical nuclei but have different mitochondrial DNA) were detected in all but one of the clones, demonstrating that mtDNA variation among cloned cattle is a very common phenomenon which prevents true genetic identity. The analyses also showed that the cytoplasmic genetic status of some investigated individuals and clones is further complicated by heteroplasmy (more than one mtDNA type in an individual). The relative proportions of different mtDNA‐types in two animals with mild heteroplasmy were estimated at 2:98% and 4:96% in DNA samples derived from blood. This is in agreement with values expected from karyoplast‐cytoplast volume ratios. In contrast, the mtDNA haplotype proportions observed in six other heteroplasmic animals of two different clones ranged from 21:79% to 57:43%, reflecting a marked increase in donor blastomere mtDNA contributions. These results suggest that mtDNA type of donor embryos and recipient oocytes used in nuclear transfer cattle cloning should be controlled to obtain true clones with identical nuclear and cytoplasmic genomes. Mol. Reprod. Dev. 54:24–31, 1999.

Classic scrapie in sheep with the ARR/ARR prion genotype in Germany and France

We report 2 natural scrapie cases in sheep carrying the ARR/ARR prion genotype, which is believed to confer resistance against classic scrapie and bovine spongiform encephalopathy.

Estimating genetic variability in temperamental traits in German Angus and Simmental cattle

Abstract Behavioural traits related to temperament were studied and the genetic variability estimated in German Angus (Aberdeen Angus×German dual purpose breeds) and Simmental cattle. Temperament was defined as the behavioural response of the animal to handling. Five progeny groups of both breeds (Simmental cattle, n =206; German Angus cattle, n =249) were tested in 2 consecutive years, 2 and 3 weeks after weaning. The animals were tested individually with a combination of a non-restrained and a restrained test. Each animal was separated from a group of 10 (separation yard, 100m 2 ) into a smaller area then confined in a corner of the restraint yard (25m 2 ). Behaviour was recorded and temperament scores were given by three different observers. The parameters of separation time, time spent running, number of escapes, aggression, vocalisation and time spent in the corner directed by the handler were recorded. Analysis of variance was performed with a model including breed, year, handler and sex as fixed effects. The model for estimating heritability included the sire as a random effect and sex, year and handler as fixed effects. In both models a regression on the age of the calf was included. The estimated heritability (±S.E.) for the different characteristics of temperament were between 0.0 and 0.61 (±0.17) for German Angus and, 0.0 and 0.59 (±0.41) for Simmental cattle with highest values for temperament scores. These were negatively correlated with daily weight gain. Simmental cattle were more difficult to handle than German Angus when considering the different parameters. The estimated heritability of some behavioural traits open a way of selection for temperament in German Angus and Simmental cattle assuming the high standard errors of the estimated values were caused primarily by the limited number of animals.

Prion protein allele A136H154Q171 is associated with high susceptibility to scrapie in purebred and crossbred German Merinoland sheep

Summary.Prion protein (PrP) genotypes were determined in eight sheep that have been tested positive for atypical scrapie from purebred or crossbred Merinoland sheep flocks in Germany and compared with the PrP genotypes of their flock mates. Two restriction fragment length polymorphism (RFLP) analyses were developed to determine all PRNP haplotypes occurring by variations at codons 136, 154 and 171. At least one copy of the A136H154Q171 (AHQ) allele was found in all scrapie-positive sheep while the frequency of AHQ varied from over 23% to less than 3% in the whole flocks. There was a significant association between PrP genotype and a positive scrapie diagnosis over all flocks, suggesting a high scrapie susceptibility of PrP genotypes including the AHQ allele, at least in sheep of Merinoland type. These results argue that sheep with the AHQ allele are not generally less susceptible to scrapie and support the hypothesis that the influence of this allele on scrapie susceptibility may vary from flock to flock depending on genetic and/or epidemiological factors. This has to be considered when strategies for the eradication of scrapie in sheep are based on PrP genotypes.

Combined analysis of data from two granddaughter designs: A simple strategy for QTL confirmation and increasing experimental power in dairy cattle

A joint analysis of five paternal half-sib Holstein families that were part of two different granddaughter designs (ADR- or Inra-design) was carried out for five milk production traits and somatic cell score in order to conduct a QTL confirmation study and to increase the experimental power. Data were exchanged in a coded and standardised form. The combined data set (JOINT-design) consisted of on average 231 sires per grandsire. Genetic maps were calculated for 133 markers distributed over nine chromosomes. QTL analyses were performed separately for each design and each trait. The results revealed QTL for milk production on chromosome 14, for milk yield on chromosome 5, and for fat content on chromosome 19 in both the ADR- and the Inra-design (confirmed within this study). Some QTL could only be mapped in either the ADR- or in the Inra-design (not confirmed within this study). Additional QTL previously undetected in the single designs were mapped in the JOINT-design for fat yield (chromosome 19 and 26), protein yield (chromosome 26), protein content (chromosome 5), and somatic cell score (chromosome 2 and 19) with genomewide significance. This study demonstrated the potential benefits of a combined analysis of data from different granddaughter designs.

Temperament traits of beef calves measured under field conditions and their relationships to performance.

A total of 3,050 German Angus (Aberdeen Angus x German dual-purpose breeds), Charolais, Hereford, Limousin, and German Simmental calves were used to examine temperament traits of beef cattle using 2 different test procedures. The chute test and the flight-speed test have been validated in terms of routine on-farm applicability. Behavior tests were performed in 2006 and 2007 on 24 commercial beef cattle farms located in the northern and eastern part of Germany. A single, trained observer assigned subjective scores to characterize the behavior of each animal during restraint in the head gate (calm, restless shifting, squirming, vigorous movement, violent struggling) and when leaving the chute (walk, trot, run, jumping out of the chute). Breed was a significant source of variation in chute scores and flight-speed scores (P < 0.001). Charolais and Limousin cattle had the greatest scores in both traits, whereas Herefords had the least (P < 0.001) chute scores. German Angus and Hereford calves had the least (P < 0.001) flight-speeds, indicating that these breeds have a more favorable temperament. Temperament scores differed significantly between male and female calves (P < 0.01), with females scoring better for both traits. Average daily BW gains of the calves were significantly influenced by effects of breed (P < 0.001) and sex (P < 0.001) of the calves. Heritabilities were estimated for chute- and flight-speed scores of beef cattle. They were least for chute score and flight-speed score of Limousin cattle with values of 0.11. In contrast, greatest heritabilities were 0.33 for chute score and 0.36 for flight-speed score of Hereford cattle. Genetic correlations were estimated among both temperament traits, with values between 0.57 and 0.98. Chute scores and visual flight-speed scores were negatively correlated with daily BW gain of the calves in most breeds. The results presented in this paper indicate that on-farm evaluation of beef cattle temperament is possible, either using the chute test or the flight-speed test. Genetic selection seems to be promising to improve temperament traits of beef cattle without decreasing production traits like ADG of the calves.

High Polymorphism in the K-Casein (CSN3) Gene from Wild and Domestic Caprine Species Revealed by DNA Sequencing

We assessed polymorphisms in exon IV of the kappa-casein gene (CSN3) in ten different breeds of domestic goat (Capra hircus) from three continents and in three related wild caprine taxa (Capra ibex, Capra sibirica and Capra aegagrus). Thirty-five DNA samples were sequenced within a 558 bp fragment of exon IV. Nine polymorphic sites were identified in domestic goat, including four new polymorphisms. In addition to four previously described polymorphic positions, a total of 13 polymorphisms allowed the identification of 13 DNA variants, corresponding to 10 protein variants. Because of conflicting nomenclature of these variants, we propose a standardized allele designation. CSN3*A, CSN3*B, and CSN3*D were found as widely distributed alleles in European goat breeds. Within Capra ibex we identified three variants and showed that the sequence of Capra aegagrus is identical to the most common Capra hircus variant, consistent with Capra aegagrus being the wild progenitor of domestic goats. A dendrogram was drawn to represent the molecular network between the caprine CSN3 variants.