Detection of selection signatures within candidate regions underlying trypanotolerance in outbred cattle populations

Breeding indigenous African taurine cattle tolerant to trypanosomosis is a straightforward approach to control costs generated by this disease. A recent study identified quantitative trait loci (QTL) underlying trypanotolerance traits in experimental crosses between tolerant N'Dama and susceptible Boran zebu cattle. As trypanotolerance is thought to result from local adaptation of indigenous cattle breeds, we propose an alternative and complementary approach to study the genetic architecture of this trait, based on the identification of selection signatures within QTL or candidate genes. A panel of 92 microsatellite markers was genotyped on 509 cattle belonging to four West African trypanotolerant taurine breeds and 10 trypanosusceptible European or African cattle breeds. Some of these markers were located within previously identified QTL regions or candidate genes, while others were chosen in regions assumed to be neutral. A detailed analysis of the genetic structure of these different breeds was carried out to confirm a priori grouping of populations based on previous data. Tests based on the comparison of the observed heterozygosities and variances in microsatellite allelic size among trypanotolerant and trypanosusceptible breeds led to the identification of two significantly less variable microsatellite markers. BM4440, one of these two outlier loci, is located within the confidence interval of a previously described QTL underlying a trypanotolerance-related trait. Detection of selection signatures appears to be a straightforward approach for unravelling the molecular determinism of trypanosomosis pathogenesis. We expect that a whole genome approach will help confirm these results and achieve a higher resolving power.

Identification of seven haplotypes of the caprine PrP gene at codons 127, 142, 154, 211, 222 and 240 in French Alpine and Saanen breeds and their association with classical scrapie

In sheep, susceptibility to scrapie is mainly influenced by polymorphisms of the PrP gene. In goats, there are to date few data related to scrapie susceptibility association with PrP gene polymorphisms. In this study, we first investigated PrP gene polymorphisms of the French Alpine and Saanen breeds. Based on PrP gene open reading frame sequencing of artificial insemination bucks (n=404), six encoding mutations were identified at codons 127, 142, 154, 211, 222 and 240. However, only seven haplotypes could be detected: four (GIH154RQS, GIRQ211QS, GIRRK222S and GIRRQP240) derived from the wild-type allele (G127I142R154R211Q222S240) by a single-codon mutation, and two (S127IRRQP240 and GM142RRQP240) by a double-codon mutation. A case–control study was then implemented in a highly affected Alpine and Saanen breed herd (90 cases/164 controls). Mutations at codon 142 (I/M), 154 (R/H), 211 (R/Q) and 222 (Q/K) were found to induce a significant degree of protection towards natural scrapie infection. Compared with the baseline homozygote wild-type genotype I142R154R211Q222/IRRQ goats, the odds of scrapie cases in IRQ211Q/IRRQ and IRRK222/IRRQ heterozygous animals were significantly lower [odds ratio (OR)=0.133, P<0.0001; and OR=0.048, P<0.0001, respectively]. The heterozygote M142RRQ/IRRQ genotype was only protective (OR=0.243, P=0.0186) in goats also PP240 homozygous at codon 240. However, mutated allele frequencies in French Alpine and Saanen breeds were low (0.5–18.5 %), which prevent us from assessing the influence of all the possible genotypes in natural exposure conditions.

Which PrP haplotypes in a French sheep population are the most susceptible to atypical scrapie?

A French sheep case control study has been organised to estimate the effects of the PrP haplotypes on resistance to atypical scrapie. The ALHQ and AFRQ haplotypes are significantly more susceptible than the others.

Differentiation of European cattle by AFLP fingerprinting

The Neolithic introduction of domestic cattle into Europe was followed by differential adaptation, selection, migration and genetic isolation, leading ultimately to the emergence of specialized breeds. We have studied the differentiation of European cattle by amplified fragment length polymorphism (AFLP) fingerprinting. Combining AFLP data sets from two laboratories yielded 81 biallelic polymorphic markers scored in 19-22 individual animals from 51 breeds. Model-based clustering differentiated Podolian cattle as well as French and Alpine breeds from other European cattle. AFLP genetic distances correlated well with microsatellite-based genetic distances calculated for the same breeds. However, the AFLP data emphasized the divergence of taurine and indicine cattle relative to the variation among European breeds and indicated an Eastern influence on Italian and Hungarian Podolian breeds. This probably reflects import from the East after the original introduction of domestic cattle into Europe. Our data suggest that Italian cattle breeds are relatively diverse at the DNA sequence level.

Genetic characterization of southwestern European bovine breeds: a historical and biogeographical reassessment with a set of 16 microsatellites

The origin of Iberian cattle has been suggested by some authors to be the product of European and north African cattle entrances during the last few thousands of years. However, these hypotheses were mainly based on morphological similarities. This study analyzed 889 unrelated individuals from 15 representative Iberian breeds and 3 French breeds for 16 microsatellite loci. Statistical tests were used to calculate interpopulation genetic distances (D(A)) and principal components analysis (PCA). To visualize the geographical distribution of the genetic differentiation between Iberian cattle breeds, data from the PCA analysis were used to construct synthetic maps. Genetic similarity among neighboring Iberian breeds is mainly caused by gene flow. However, recent demographic fluctuations and reproductive isolation in Alistana, Mirandesa, and Tudanca has increased genetic drift, which may be the main cause for the relatively high differentiation of these populations. The synthetic maps constructed with the first and second PCs revealed (1) a large differentiation between Northern Iberian breeds rather than between more geographically distant breeds, and (2) a clear east-west gradient that may be related with the model of demic diffusion of agriculture. Finally, we detected no strong evidence for an African genetic influence in the Iberian cattle breeds analyzed in this study.

Is a Multivariate Consensus Representation of Genetic Relationships Among Populations Always Meaningful?

To determine the relationships among closely related populations or species, two methods are commonly used in the literature: phylogenetic reconstruction or multivariate analysis. The aim of this article is to assess the reliability of multivariate analysis. We describe a method that is based on principal component analysis and Mantel correlations, using a two-step process: The first step consists of a single-marker analysis and the second step tests if each marker reveals the same typology concerning population differentiation. We conclude that if single markers are not congruent, the compromise structure is not meaningful. Our model is not based on any particular mutation process and it can be applied to most of the commonly used genetic markers. This method is also useful to determine the contribution of each marker to the typology of populations. We test whether our method is efficient with two real data sets based on microsatellite markers. Our analysis suggests that for closely related populations, it is not always possible to accept the hypothesis that an increase in the number of markers will increase the reliability of the typology analysis.

Genetic diversity measures of local European beef cattle breeds for conservation purposes

This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean F(st) = 0.07; P<0.01). Five different genetic distances were computed and compared with no correlation found to be significantly different from 0 between distances based on the effective size of the population and those which use the size of the alleles. The Weitzman recursive approach and a multivariate analysis were used to measure the contribution of the breeds diversity. The Weitzman approach suggests that the most important breeds to be preserved are those grouped into two clusters: the cluster formed by the Mirandesa and Alistana breeds and that of the Sayaguesa and Tudanca breeds. The hypothetical extinction of one of those clusters represents a 17% loss of diversity. A correspondence analysis not only distinguished four breed groups but also confirmed results of previous studies classifying the important breeds contributing to diversity. In addition, the variation between breeds was sufficiently high so as to allow individuals to be assigned to their breed of origin with a probability of 99% for simulated samples.

Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites

To guide genetic conservation programmes with objective criteria, general genetic variability has to be taken into account. This study was conducted to determine the genetic variation between 10 cattle breeds by using 17 microsatellite loci and 13 biochemical markers (11 blood groups, the transferrin and beta-casein loci). Microsatellite loci were amplified in 31-50 unrelated individuals from 10 cattle breeds: Charolais, Limousin, Breton Black Pied, Parthenais, Montbéliard, Vosgien, Maine-Anjou, Normande, Jersey and Holstein. Neighbor-joining trees were calculated from genetic distance estimates. The robustness of tree topology was obtained by bootstrap resampling of loci. A total of 210 alleles of the 17 microsatellites were detected in this study and average heterozygosities ranged from 0.53 in the Jersey breed to 0.66 in the Parthenais breed. In general, low bootstrap values were obtained: with the 17 microsatellites, the highest bootstrap values concerned the Holstein/Maine-Anjou grouping with an occurrence of 74%; with the biochemical markers, this node had an occurrence of 79% and the Charolais/Limousin grouping appeared with an occurrence of 74%; when microsatellites and biochemical polymorphism were analysed together, the occurrence of the Holstein/Maine-Anjou grouping was 90% and that of the Charolais/Limousin grouping was 42%. These results suggest that 30 microsatellites, a number currently considered as sufficient to distinguish closely related breeds is, in fact, probably insufficient.

Individual multilocus genotypes using microsatellite polymorphisms to permit the analysis of the genetic variability within and between Italian beef cattle breeds

We investigated the genetic variability within and between cattle breeds. The polymorphisms of 17 microsatellites were studied in 220 unrelated animals belonging to four Italian beef cattle breeds (Chianina, Marchigiana, Romagnola, and Piemontese). Variations of allelic frequencies were examined to characterize the breeds and their relationships. Wahlund coefficients, Polymorphism Information Content values, and Haldane exact test for Hardy-Weinberg proportions were calculated. The results show that the Hardy-Weinberg equilibrium is not always maintained. Moreover, in addition to the classical genetic distances, a new method, based on the consideration of a multilocus genotype of each animal, was set up to measure the genetic similarity between animals or within groups of animals. All the results showed that, whereas Chianina occupies an intermediate position and Piemontese is the most distinct of all four breeds, Marchigiana and Romagnola display the strongest similarity. The new method also provides evidence that average similarities are always higher within breeds than between breeds. By comparing pairwise the multilocus genotypes, it was also possible to discriminate the individuals with higher or lower genetic similarities so that each breed could be subdivided into two groups of animals in relation to their similarity to the average breed multilocus genotype. High similarities between breeds were detected, somewhat surprisingly, when the most homogeneous groups of each breed were compared. The microsatellite multilocus genotype is particularly efficient in evaluating the between- and within-breeds genetic similarities and for subgrouping genetically more homogeneous animals.

A set of 99 cattle microsatellites: characterization, synteny mapping, and polymorphism

Cattle microsatellite clones (136) were isolated from cosmid (10) and plasmid (126) libraries and sequenced. The dinucleotide repeats were studied in each of these sequences and compared with dinucleotide repeats found in other vertebrate species where information was available. The distribution in cattle was similar to that described for other mammals, such as rat, mouse, pig, or human. A major difference resides in the number of sequences present in the bovine genome, which seemed at best one-third as large as in other species. Oligonucleotide primers (117 pairs) were synthesized, and a PCR product of expected size was obtained for 88 microsatellite sequences (75%). Synteny or chromosome assignment was searched for each locus with PCR amplification on a panel of 36 hamster/bovine somatic cell hybrids. Of our bovine microsatellites, eighty-six could be assigned to synteny groups of chromosomes. In addition, 10 other microsatellites--HEL 5, 6, 9, 11, 12, 13 (Kaukinen and Varvio 1993), HEL 4, 7, 14, 15--as well as the microsatellite found in the kappa-casein gene (Fries et al. 1990) were mapped on the hybrids. Microsatellite polymorphism was checked on at least 30 unrelated animals of different breeds. Almost all the autosomal and X Chr microsatellites displayed polymorphism, with the number of alleles varying between two and 44. We assume that these microsatellites could be very helpful in the construction of a primary public linkage map of the bovine genome, with an aim of finding markers for Economic Trait Loci (ETL) in cattle.

Hormonal induction of c-fos and HSP68 mRNAs on an isolated coronary perfused adult rat heart

Transient growth signals which can be related to protein synthesis and cellular growth are of particular interest in the heart because of the incidence of cardiac hypertrophy in man. The isolated coronary perfused adult rat heart or the so-called Langendorff preparation, is an useful model in exploring not only protein synthesis but also c-fos/c-myc protooncogene and Heat Shock Protein (HSP) gene expression. Phenylephrine infusion in this preparation induces c-fos expression whether the heart is beating or reversibly or irreversibly arrested by solutions enriched in KCl. Norepinephrine has the same effect. Quantitative analysis with slot blots shows that in both cases the adrenergic effect has a dual origin since it is inhibited both by propranolol, a beta-adrenergic antagonist, and terazosine, a soluble alpha 1-adrenergic antagonist. We conclude that the isolated heart is a useful tool to explore the early changes in gene expression which occur in this tissue in response to various physiological stimuli.