Showing papers in "Genetics Selection Evolution in 2003"
TL;DR: The distribution of population-specific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.
Abstract: In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of population-specific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.
279 citations
TL;DR: This project of QTL detection was carried out in the French Holstein, Normande, and Montbéliarde dairy cattle breeds and confirmed several already published QTL but most of them were original, particularly for non-production traits.
Abstract: A project of QTL detection was carried out in the French Holstein, Normande, and Montbeliarde dairy cattle breeds. This granddaughter design included 1 548 artificial insemination bulls distributed in 14 sire families and evaluated after a progeny-test for 24 traits (production, milk composition, persistency, type, fertility, mastitis resistance, and milking ease). These bulls were also genotyped for 169 genetic markers, mostly microsatellites. The QTL were analysed by within-sire linear regression of daughter yield deviations or deregressed proofs on the probability that the son receives one or the other paternal QTL allele, given the marker information. QTL were detected for all traits, including those with a low heritability. One hundred and twenty QTL with a chromosome-wise significance lower than 3% were tabulated. This threshold corresponded to a 15% false discovery rate. Amongst them, 32 were genome-wise significant. Estimates of their contribution to genetic variance ranged from 6 to 40%. Most substitution effects ranged from 0.6 to 1.0 genetic standard deviation. For a given QTL, only 1 to 5 families out of 14 were informative. The confidence intervals of the QTL locations were large and always greater than 20 cM. This experiment confirmed several already published QTL but most of them were original, particularly for non-production traits.
269 citations
TL;DR: The genetic structure of eight Spanish autochthonous populations (breeds) of beef cattle were studied from pedigree records, suggesting that a slight exchange of animals between herds will lead to a much more favourable evolution of inbreeding.
Abstract: The genetic structure of eight Spanish autochthonous populations (breeds) of beef cattle were studied from pedigree records. The populations studied were: Alistana and Sayaguesa (minority breeds), Avilena – Negra Iberica and Morucha ("dehesa" breeds, with a scarce incidence of artificial insemination), and mountain breeds, including Asturiana de los Valles, Asturiana de la Montana and Pirenaica, with extensive use of AI. The Bruna dels Pirineus breed possesses characteristics which make its classification into one of the former groups difficult. There was a large variation between breeds both in the census and the number of herds. Generation intervals ranged from 3.7 to 5.5 years, tending to be longer as the population size was larger. The effective numbers of herds suggest that a small number of herds behaves as a selection nucleus for the rest of the breed. The complete generation equivalent has also been greatly variable, although in general scarce, with the exception of the Pirenaica breed, with a mean of 3.8. Inbreeding effective population sizes were actually small (21 to 127), especially in the mountain-type breeds. However, the average relatedness computed for these breeds suggests that a slight exchange of animals between herds will lead to a much more favourable evolution of inbreeding. The effective number of founders and ancestors were also variable among breeds, although in general the breeds behaved as if they were founded by a small number of animals (25 to 163).
210 citations
TL;DR: Muscular hypertrophy (namely nt821(del11)) was mainly spread in different waves from northern Europe milk purpose populations in most breeds; however, other mutations arose in a single breed, were highly selected and have since scarcely evolved to other populations.
Abstract: A total of 678 individuals from 28 European bovine breeds were both phenotyped and analysed at the myostatin locus by the Single Strand Conformation Polymorphism (SSCP) method. Seven new mutations were identified which contribute to the high polymorphism (1 SNP every 100 bp) present in this small gene; twenty haplotypes were described and a genotyping method was set up using the Oligonucleotide Ligation Assay (OLA) method. Some haplotypes appeared to be exclusive to a particular breed; this was the case for 5 in the Charolaise (involving mutation Q204X) and 7 in the Maine-Anjou (involving mutation E226X). The relationships between the different haplotypes were studied, thus allowing to test the earlier hypothesis on the origin of muscular hypertrophy in Europe: muscular hypertrophy (namely nt821(del11)) was mainly spread in different waves from northern Europe milk purpose populations in most breeds; however, other mutations (mostly disruptive) arose in a single breed, were highly selected and have since scarcely evolved to other populations.
132 citations
TL;DR: The authors' data suggest that the causal mutation, a G to A transition, is localised in exon 2 of the MATP gene leading to an aspartic acid to asparagine substitution in the encoded protein.
Abstract: In horses, basic colours such as bay or chestnut may be partially diluted to buckskin and palomino, or extremely diluted to cream, a nearly white colour with pink skin and blue eyes. This dilution is expected to be controlled by one gene and we used both candidate gene and positional cloning strategies to identify the "cream mutation". A horse panel including reference colours was established and typed for different markers within or in the neighbourhood of two candidate genes. Our data suggest that the causal mutation, a G to A transition, is localised in exon 2 of the MATP gene leading to an aspartic acid to asparagine substitution in the encoded protein. This conserved mutation was also described in mice and humans, but not in medaka.
130 citations
TL;DR: As a consequence of selection, the selected animals were heavier than the C animals throughout the entire growth curve, and adult body weight was 7% higher in the selected line than in the control line.
Abstract: Gompertz growth curves were fitted to the data of 137 rabbits from control (C) and selected (S) lines. The animals came from a synthetic rabbit line selected for an increased growth rate. The embryos from generations 3 and 4 were frozen and thawed to be contemporary of rabbits born in generation 10. Group C was the offspring of generations 3 and 4, and group S was the contemporary offspring of generation 10. The animals were weighed individually twice a week during the first four weeks of life, and once a week thereafter, until 20 weeks of age. Subsequently, the males were weighed weekly until 40 weeks of age. The random samples of the posterior distributions of the growth curve parameters were drawn by using Markov Chain Monte Carlo (MCMC) methods. As a consequence of selection, the selected animals were heavier than the C animals throughout the entire growth curve. Adult body weight, estimated as a parameter of the Gompertz curve, was 7% higher in the selected line. The other parameters of the Gompertz curve were scarcely affected by selection. When selected and control growth curves are represented in a metabolic scale, all differences disappear.
113 citations
TL;DR: This extensive research on pig genetic diversity in China indicates that these 18 Chinese indigenous breeds may have one common ancestor, helps us to better understand the relative distinctiveness of pig genetic resources, and will assist in developing a national plan for the conservation and utilization of Chinese indigenous pig breeds.
Abstract: Chinese indigenous pig breeds are recognized as an invaluable component of the world's pig genetic resources and are divided traditionally into six types. Twenty-six microsatellite markers recommended by the FAO (Food and Agriculture Organization) and ISAG (International Society of Animal Genetics) were employed to analyze the genetic diversity of 18 Chinese indigenous pig breeds with 1001 individuals representing five types, and three commercial breeds with 184 individuals. The observed heterozygosity, unbiased expected heterozygosity and the observed and effective number of alleles were used to estimate the genetic variation of each indigenous breed. The unbiased expected heterozygosity ranged between 0.700 (Mashen) and 0.876 (Guanling), which implies that there is an abundant genetic variation stored in Chinese indigenous pig breeds. Breed differentiation was shown by fixation indices (FIT, FIS, and FST). The FST per locus varied from 0.019 (S0090) to 0.170 (SW951), and the average FST of all loci was 0.077, which means that most of the genetic variation was kept within breeds and only a little of the genetic variation exists between populations. The Neighbor-Joining tree was constructed based on the Nei DA (1978) distances and one large cluster with all local breeds but the Mashen breed, was obtained. Four smaller sub-clusters were also found, which included two to four breeds each. These results, however, did not completely agree with the traditional type of classification. A Neighbor-Joining dendrogram of individuals was established from the distance of -ln(proportions of shared alleles); 92.14% of the individuals were clustered with their own breeds, which implies that this method is useful for breed demarcation. This extensive research on pig genetic diversity in China indicates that these 18 Chinese indigenous breeds may have one common ancestor, helps us to better understand the relative distinctiveness of pig genetic resources, and will assist in developing a national plan for the conservation and utilization of Chinese indigenous pig breeds.
92 citations
TL;DR: The greatest similarity was found between G. gallus and the egg-type breeds of Mediterranean roots and/or true Bantams, which might testify that the indicated chicken groups occupied earlier stages in the evolution from the wild progenitor to the present biodiversity of chickens in the world.
Abstract: Published results were reassessed and original data are provided regarding the origin and relatedness of four postulated chicken breed lineages, egg-type, game, meat-type and Bantam, to each other and to the basic ancestral species of jungle fowls, Gallus gallus. A system approach was employed concerning the planning of the experiments. One element of the system approach is the choice of the breeds to be compared with G. gallus. These breeds were supposed to represent major evolutionary branches of chickens. Four experiments on genetic relationships were conducted using different estimation criteria including morphological discrete characters, body measurements, biochemical markers, and the activity of serum esterase-1. The greatest similarity was found between G. gallus and the egg-type breeds of Mediterranean roots and/or true Bantams. This fact might testify that the indicated chicken groups occupied earlier stages in the evolution from the wild progenitor to the present biodiversity of chickens in the world.
85 citations
TL;DR: A joint analysis of five paternal half-sib Holstein families that were part of two different granddaughter designs 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.
Abstract: 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.
80 citations
TL;DR: Body weight and breast yield were positively correlated with both initial and ultimate pH and negatively with the lightness of breast meat, both traits corresponding to PSE indicators.
Abstract: Genetic parameters for meat quality traits and their relationships with body weight and breast development were estimated for a total of 420 male turkeys using REML. The birds were slaughtered in a commercial plant and the traits measured included pH at 20 min (pH20) and 24 h post-mortem (pHu) and colour of the breast and thigh meat. The heritabilities of the rate and the extent of the pH fall in the breast muscle were estimated at h 2 D 0:21 0:04 and h 2 D 0:16 0:04, respectively. Heritabilities ranging from 0.10 to 0.32 were obtained for the colour indicators in the breast muscle. A marked negative genetic correlation (rg D 0:80 0:10) was found between pH20 and lightness (L ) of breast meat, both traits corresponding to PSE indicators. The pH20 in the thigh muscle had a moderate heritability (h 2 D 0:20 0:07) and was partially genetically related to pH 20 in the breast muscle (rgD 0:45 0:17). Body weight and breast yield were positively correlated with both initial and ultimate pH and negatively with the lightness of breast meat. turkey / meat quality / pH / colour / genetic parameters
68 citations
TL;DR: In this article, a fully Bayesian analysis using Gibbs sampling and data augmentation in a multivariate model of Gaussian, right censored, and grouped Gaussian traits is described.
Abstract: A fully Bayesian analysis using Gibbs sampling and data augmentation in a multivariate model of Gaussian, right censored, and grouped Gaussian traits is described. The grouped Gaussian traits are either ordered categorical traits (with more than two categories) or binary traits, where the grouping is determined via thresholds on the underlying Gaussian scale, the liability scale. Allowances are made for unequal models, unknown covariance matrices and missing data. Having outlined the theory, strategies for implementation are reviewed. These include joint sampling of location parameters; efficient sampling from the fully conditional posterior distribution of augmented data, a multivariate truncated normal distribution; and sampling from the conditional inverse Wishart distribution, the fully conditional posterior distribution of the residual covariance matrix. Finally, a simulated dataset was analysed to illustrate the methodology. This paper concentrates on a model where residuals associated with liabilities of the binary traits are assumed to be independent. A Bayesian analysis using Gibbs sampling is outlined for the model where this assumption is relaxed.
TL;DR: In this paper, a successful eugenic selection procedure for zebu Brahman cattle in Martinique (FWI) was developed, based on a genetic marker system targeting the highly polymorphic BoLA locus, eliminating only those individuals which are at the highest risk of contracting the disease.
Abstract: Bovine dermatophilosis is a severe skin infection of tropical ruminants inducing a severe loss in productivity and a 15% mortality rate. This disease is caused by the actinomycete bacterium Dermatophilus congolensis associated with the tick Amblyomma variegatum. Currently there are no prospects for a vaccine, and acaricide or antibiotic control is hampered by the development of chemoresistance. Animal breeders have observed that dermatophilosis susceptibility seems to be determined genetically, and we previously identified a BoLA-DRB3-DQB class II haplotype marker for high (R2 = 0.96) susceptibility to the disease. With this marker, we developed a successful eugenic selection procedure for zebu Brahman cattle in Martinique (FWI). Over a period of five years, a marked reduction in disease prevalence, from 0.76 to 0.02 was achieved, and this low level has been maintained over the last two years. The selection procedure, based on a genetic marker system targeting the highly polymorphic BoLA locus, eliminates only those individuals which are at the highest risk of contracting the disease. In the present work, we discuss the properties of this system, including the "heterozygote advantage" and the "frequency dependence" theories, and examine their involvement in the biological mechanisms at the host/pathogen interface. We speculate on the exact role of the MHC molecules in the control of the disease, how the natural selection pressure imposed by the pathogens selectively maintains MHC diversity, and how our results can be practically applied for integrated control of dermatophilosis in developing countries.
TL;DR: A bacterial artificial chromosome library was constructed by cloning Hind III-digested high molecular weight DNA from a gynogenetic channel catfish into the vector pBeloBAC11, demonstrating a 92% chance to find a unique sequence.
Abstract: A bacterial artificial chromosome (BAC) library was constructed by cloning Hind III-digested high molecular weight DNA from a gynogenetic channel catfish, Ictalurus punctatus, into the vector pBeloBAC11. Approximately 53 500 clones were arrayed in 384-well plates and stored at -80°C (CCBL1), while clones from a smaller insert size fraction were stored at -80°C without arraying (CCBL2). Pulsed-field gel electrophoresis of 100 clones after Not I digestion revealed an average insert size of 165 kb for CCBL1 and 113 kb for CCBL2. Further characterization of CCBL1 demonstrated that 10% of the clones did not contain an insert. CCBL1 provides a 7.2-fold coverage of the channel catfish haploid genome. PCR-based screening demonstrated that 68 out of 74 unique loci were present in the library. This represents a 92% chance to find a unique sequence. These libraries will be useful for physical mapping of the channel catfish genome, and identification of genes controlling major traits in this economically important species.
TL;DR: A comparison of power and accuracy of estimation of position and QTL effects of three multitrait methods and one single trait method for QTL detection was carried out on simulated data, taking into account the mixture of full and half-sib families.
Abstract: A comparison of power and accuracy of estimation of position and QTL effects of three multitrait methods and one single trait method for QTL detection was carried out on simulated data, taking into account the mixture of full and half-sib families. One multitrait method was based on a multivariate function as the penetrance function (MV). The two other multitrait methods were based on univariate analysis of linear combination(s) (LC) of the traits. One was obtained by a principal component analysis (PCA) performed on the phenotypic data. The second was based on a discriminate analysis (DA). It calculates a LC of the traits at each position, maximising the ratio between the genetic and the residual variabilities due to the putative QTL. Due to its number of parameters, MV was less powerful and accurate than the other methods. In general, DA better detected QTL, but it had lower accuracy for the QTL effect estimation when the detection power was low, due to higher bias than the other methods. In this case, PCA was better. Otherwise, PCA was slightly less powerful and accurate than DA. Compared to the single trait method, power can be improved by 30% to 100% with multitrait methods.
TL;DR: The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin and showing that ancestral populations are threatened by queen importations.
Abstract: The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain) was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca) and Pitiusas (Ibiza and Formentera), which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.
TL;DR: It is shown that no cow effect is needed in the lactation basis model because a censored record is not complete, a cow can appear as uncensored only once, and a cow cannot be censored after having been culled.
Abstract: An analysis of longevity in dairy cattle on a lactation basis is proposed. The approach allowed each lactation to have its own baseline hazard function, which gives a better description of the hazard than traditional analyses of the whole length of life. As a consequence, the overall fit of the model to the data was improved and fewer time-dependent variables were needed. Longevity on a lactation basis was defined from one calving to the next instead of from the first calving to culling. However, no new information was added and it was still the overall risk of being culled that was modelled. It is shown that no cow effect is needed in the lactation basis model because a censored record is not complete, a cow can appear as uncensored only once, and a cow cannot be censored after having been culled. Different subdivisions of the stage of lactation effect were tested and the first ten days of lactation were shown to correspond to an increased risk of being culled. There were no major differences in sire variance between the longevity analysed on a lactation basis and longevity based on the entire length of life.
TL;DR: Transmission is summarised by R0, the basic reproductive ratio of a pathogen, wherever possible a combination of genotypes should be used to minimise the invasion possibilities of pathogens that have mutated to overcome the effects of specific resistance alleles.
Abstract: This paper considers the use of disease resistance genes to control the transmission of infection through an animal population. Transmission is summarised by R0, the basic reproductive ratio of a pathogen. If R0 > 1.0 a major epidemic can occur, thus a disease control strategy should aim to reduce R0 below 1.0, e.g. by mixing resistant with susceptible wild-type animals. Suppose there is a resistance allele, such that transmission of infection through a population homozygous for this allele will be R02 1 and R02 1 the probability of a minor and major epidemics are 1/(R0 + 1) and (R0 - 1)/(R0 + 1). Wherever possible a combination of genotypes should be used to minimise the invasion possibilities of pathogens that have mutated to overcome the effects of specific resistance alleles.
TL;DR: This AFLP map of the Japanese quail already provides an efficient tool for quantitative trait loci (QTL) mapping and can be enriched with other marker types, especially mapped chicken genes that will enable to link the maps of both species and make use of the powerful comparative mapping approach.
Abstract: The quail is a valuable farm and laboratory animal. Yet molecular information about this species remains scarce. We present here the first genetic linkage map of the Japanese quail. This comprehensive map is based solely on amplified fragment length polymorphism (AFLP) markers. These markers were developed and genotyped in an F2 progeny from a cross between two lines of quail differing in stress reactivity. A total of 432 polymorphic AFLP markers were detected with 24 Taq I/Eco RI primer combinations. On average, 18 markers were produced per primer combination. Two hundred and fifty eight of the polymorphic markers were assigned to 39 autosomal linkage groups plus the ZW sex chromosome linkage groups. The linkage groups range from 2 to 28 markers and from 0.0 to 195.5 cM. The AFLP map covers a total length of 1516 cM, with an average genetic distance between two consecutive markers of 7.6 cM. This AFLP map can be enriched with other marker types, especially mapped chicken genes that will enable to link the maps of both species and make use of the powerful comparative mapping approach. This AFLP map of the Japanese quail already provides an efficient tool for quantitative trait loci (QTL) mapping.
TL;DR: This is the first reported study on the association of SNP in INOS, TRAIL, TGF-β2, T GF-β3, and IgL with the chicken response to SE.
Abstract: Several candidate genes were selected, based on their critical roles in the host's response to intracellular bacteria, to study the genetic control of the chicken response to Salmonella enteritidis (SE). The candidate genes were: inducible nitric oxide synthase (INOS), tumor necrosis factor related apoptosis inducing ligand (TRAIL), transforming growth factor β2 (TGF-β2), transforming growth factor β3 (TGF-β3), and immunoglobulin G light chain (IgL). Responses to pathogenic SE colonization or to SE vaccination were measured in the Iowa Salmonella response resource population (ISRRP). Outbred broiler sires and three diverse, highly inbred dam lines produced 508 F1 progeny, which were evaluated as young chicks for either bacterial load isolated from spleen or cecum contents after pathogenic SE inoculation, or the circulating antibody level after SE vaccination. Fragments of each gene were sequenced from the founder lines of the resource population to identify genomic sequence variation. Single nucleotide polymorphisms (SNP) were identified, then PCR-RFLP techniques were developed to genotype the F1 resource population. Linear mixed models were used for statistical analyses. Because the inbred dam lines always contributed one copy of the same allele, the heterozygous sire allele effects could be assessed in the F1 generation. Association analyses revealed significant effects of the sire allele of TRAIL-Sty I on the spleen (P < 0.07) and cecum (P < 0.0002) SE bacterial load. Significant effects (P < 0.04) were found on the cecum bacterial load for TGF-β3-Bsr I. Varied and moderate association was found for SE vaccine antibody response for all genes. This is the first reported study on the association of SNP in INOS, TRAIL, TGF-β2, TGF-β3, and IgL with the chicken response to SE. Identification of candidate genes to improve the immune response may be useful for marker-assisted selection to enhance disease resistance.
TL;DR: Under random mating, pedigree- inbreeding coefficients are clearly more closely related to true autozygosity than marker-inbreeding coefficients, and if mating is not random, the demands on the quality and quantity of pedigree records increase.
Abstract: There are several measures available to describe the genetic variability of populations. The average inbreeding coefficient of a population based on pedigree information is a frequently chosen option. Due to the developments in molecular genetics it is also possible to calculate inbreeding coefficients based on genetic marker information. A simulation study was carried out involving ten sires and 50 dams. The animals were mated over a period of 20 discrete generations. The population size was kept constant. Different situations with regard to the level of polymorphism and initial allele frequencies and mating scheme (random mating, avoidance of full sib mating, avoidance of full sib and half sib mating) were considered. Pedigree inbreeding coefficients of the last generation using full pedigree or 10, 5 and 2 generations of the pedigree were calculated. Marker inbreeding coefficients based on different sets of microsatellite loci were also investigated. Under random mating, pedigree-inbreeding coefficients are clearly more closely related to true autozygosity (i.e., the actual proportion of loci with alleles identical by descent) than marker-inbreeding coefficients. If mating is not random, the demands on the quality and quantity of pedigree records increase. Greater attention must be paid to the correct parentage of the animals.
TL;DR: The same mutation was found to be totally associated with the JEB phenotype in two French draft horse breeds, Trait Breton and Trait Comtois, providing breeders a molecular test to better manage their breeding strategies by genetic counselling.
Abstract: Epidermolysis bullosa (EB) is a heterogeneous group of inherited diseases characterised by skin blistering and fragility. In humans, one of the most severe forms of EB known as Herlitz-junctional EB (H-JEB), is caused by mutations in the laminin 5 genes. EB has been described in several species, like cattle, sheep, dogs, cats and horses where the mutation, a cytosine insertion in exon 10 of the LAMC2 gene, was very recently identified in Belgian horses as the mutation responsible for JEB. In this study, the same mutation was found to be totally associated with the JEB phenotype in two French draft horse breeds, Trait Breton and Trait Comtois. This result provides breeders a molecular test to better manage their breeding strategies by genetic counselling.
TL;DR: An immune response (IR) index to identify cows with high (H) and low (L) antibody-mediated immune responses (AMIR) had been previously devised but various antigen/adjuvant combinations were evaluated as inducers of DTH to be added to the IR-index.
Abstract: An immune response (IR) index to identify cows with high (H) and low (L) antibody-mediated immune responses (AMIR) had been previously devised. High AMIR associated with decreased mastitis and improved response to vaccination. Measurement of cell-mediated immune response (CMIR) was not included in the index; therefore various antigen/adjuvant combinations were evaluated as inducers of DTH to be added to the IR-index. The Bacillus Calmette Guerin (BCG)-induced/purified protein derivative (PPD)-elicited tuberculin skin test is a reliable measure of DTH; however, its use to identify livestock with high CMIR may be confounded due to previous exposure to Mycobacteria tuberculosis. DTH to BCG/PPD was therefore compared with that induced by Mycobacteria phlei (saprophyte) and its derivative phlein as the test antigen. Antibody to OVA was also evaluated. The results indicated that BCG/PPD and M. phlei/phlein induced similar DTH, but cross reaction to PPD was evident following induction of DTH using M. phlei making it a less than ideal alternative for testing livestock. Nonetheless, cows could be ranked for both AMIR and CMIR. RNA from two cows with the highest and lowest IR ranks was then used to probe a human 1.7 kD microarray to determine the ability of a human array to provide information on bovine genes associated with H and L.
TL;DR: This study presents a multivariate, variance component-based QTL mapping model implemented via restricted maximum likelihood (REML) and reports results on the statistical power to detect a QTL and on the precision of parameter estimates using univariate and bivariate approaches.
Abstract: This study presents a multivariate, variance component-based QTL mapping model implemented via restricted maximum likelihood (REML). The method was applied to investigate bivariate and univariate QTL mapping analyses, using simulated data. Specifically, we report results on the statistical power to detect a QTL and on the precision of parameter estimates using univariate and bivariate approaches. The model and methodology were also applied to study the effectiveness of partitioning the overall genetic correlation between two traits into a component due to many genes of small effect, and one due to the QTL. It is shown that when the QTL has a pleiotropic effect on two traits, a bivariate analysis leads to a higher statistical power of detecting the QTL and to a more precise estimate of the QTL's map position, in particular in the case when the QTL has a small effect on the trait. The increase in power is most marked in cases where the contributions of the QTL and of the polygenic components to the genetic correlation have opposite signs. The bivariate REML analysis can successfully partition the two components contributing to the genetic correlation between traits.
TL;DR: The main objectives of this work were to measure the extent and pattern of LD between a putative QTL and nearby markers in finite populations and investigate the usefulness of LD in fine mapping QTL in simulated populations using a dense map of multiallelic or bIALlelic marker loci.
Abstract: Recently, the use of linkage disequilibrium (LD) to locate genes which affect quantitative traits (QTL) has received an increasing interest, but the plausibility of fine mapping using linkage disequilibrium techniques for QTL has not been well studied. The main objectives of this work were to (1) measure the extent and pattern of LD between a putative QTL and nearby markers in finite populations and (2) investigate the usefulness of LD in fine mapping QTL in simulated populations using a dense map of multiallelic or biallelic marker loci. The test of association between a marker and QTL and the power of the test were calculated based on single-marker regression analysis. The results show the presence of substantial linkage disequilibrium with closely linked marker loci after 100 to 200 generations of random mating. Although the power to test the association with a frequent QTL of large effect was satisfactory, the power was low for the QTL with a small effect and/or low frequency. More powerful, multi-locus methods may be required to map low frequent QTL with small genetic effects, as well as combining both linkage and linkage disequilibrium information. The results also showed that multiallelic markers are more useful than biallelic markers to detect linkage disequilibrium and association at an equal distance.
TL;DR: The distribution of the expected genetic contribution of the founder animals was found to be unbalanced, especially in the BCH and LIM, and the need for a larger selection basis and more collective organisation in the CHA and RLH is outlined.
Abstract: Some demographic parameters, the genetic structure and the evolution of the genetic variability of six French meat sheep breeds were analysed in relation with their management. Four of these breeds are submitted to more or less intense selection: the Berrichon du Cher (BCH), Blanc du Massif Central (BMC), Charollais (CHA) and Limousin (LIM); the other two breeds are under conservation: the Roussin de La Hague (RLH) and Solognot (SOL). Genealogical data of the recorded animals born from 1970 to 2000 and of their known ancestors were used. The most balanced contributions of the different flocks to the sire-daughter path was found in the SOL. In the BCH, a single flock provided 43% of the sire-AI sire path, whereas the contributions of the flocks were more balanced in the BMC and LIM (the only other breeds where AI is used to a substantial amount). The distribution of the expected genetic contribution of the founder animals was found to be unbalanced, especially in the BCH and LIM. The effective numbers of ancestors (founders or not) for the ewes born from 1996 to 2000 were equal to 35 (BCH), 144 (BMC), 112 (CHA), 69 (LIM), 40 (RLH) and 49 (SOL). Inbreeding was not analysed in the BMC, due to incomplete pedigree information. From 1980 on, the rates of inbreeding, in percentage points per year, were +0.112 (BCH), +0.045 (CHA), +0.036 (LIM), +0.098 (RLH) and +0.062 (SOL). The implications of the observed trends on genetic variability are discussed in relation to the genetic management of each breed. The need for a larger selection basis in the BCH, the efficiency of the rules applied in the SOL to preserve the genetic variability and the need for a more collective organisation in the CHA and RLH are outlined.
TL;DR: In this study, a hierarchical threshold mixed model based on a cumulative t-link specification for the analysis of ordinal data or more, specifically, calving ease scores, was developed and decisively chosen as the better fitting model for this caling ease data using DIC and PBF.
Abstract: In this study, a hierarchical threshold mixed model based on a cumulative t-link specification for the analysis of ordinal data or more, specifically, calving ease scores, was developed. The validation of this model and the Markov chain Monte Carlo (MCMC) algorithm was carried out on simulated data from normally and t4 (i.e. a t-distribution with four degrees of freedom) distributed populations using the deviance information criterion (DIC) and a pseudo Bayes factor (PBF) measure to validate recently proposed model choice criteria. The simulation study indicated that although inference on the degrees of freedom parameter is possible, MCMC mixing was problematic. Nevertheless, the DIC and PBF were validated to be satisfactory measures of model fit to data. A sire and maternal grandsire cumulative t-link model was applied to a calving ease dataset from 8847 Italian Piemontese first parity dams. The cumulative t-link model was shown to lead to posterior means of direct and maternal heritabilities (0.40 ± 0.06, 0.11 ± 0.04) and a direct maternal genetic correlation (-0.58 ± 0.15) that were not different from the corresponding posterior means of the heritabilities (0.42 ± 0.07, 0.14 ± 0.04) and the genetic correlation (-0.55 ± 0.14) inferred under the conventional cumulative probit link threshold model. Furthermore, the correlation (> 0.99) between posterior means of sire progeny merit from the two models suggested no meaningful rerankings. Nevertheless, the cumulative t-link model was decisively chosen as the better fitting model for this calving ease data using DIC and PBF.
TL;DR: The results presented in this paper show the usefulness of the microdissection technique for characterising chromosomal rearrangements in species for which commercial probes are not available and confirmed that the main limiting factor of the technique is the quality of the chromosomal preparations, which does not allow the identification of target chromosomes or chromosome fragments in all cases.
Abstract: A pericentric inversion of chromosome 4 in a boar, as well as a case of (2q-;5p+) translocation mosaicism in a bull were analysed by chromosome painting using probes generated by conventional microdissection. For the porcine inversion, probes specific for p arms and q arms were produced and hybridised simultaneously on metaphases of a heterozygote carrier. In the case of the bovine translocation, two whole chromosome probes (chromosome 5, and derived chromosome 5) were elaborated and hybridised independently on chromosomal preparations of the bull who was a carrier of the mosaic translocation. The impossibility of differentiating chromosomes 2 and der(2) from other chromosomes of the metaphases did not allow the production of painting probes for these chromosomes. For all experiments, the quality of painting was comparable to that usually observed with probes obtained from flow-sorted chromosomes. The results obtained allowed confirmation of the interpretations proposed with G-banding karyotype analyses. In the bovine case, however, the reciprocity of the translocation could not be proven. The results presented in this paper show the usefulness of the microdissection technique for characterising chromosomal rearrangements in species for which commercial probes are not available. They also confirmed that the main limiting factor of the technique is the quality of the chromosomal preparations, which does not allow the identification of target chromosomes or chromosome fragments in all cases.
TL;DR: In this study the mRNA differential display method was applied to identify mastitis-associated expressed DNA sequences based on different expression patterns in mammary gland samples of non-infected and infected udder quarters of a cow.
Abstract: In this study the mRNA differential display method was applied to identify mastitis-associated expressed DNA sequences based on different expression patterns in mammary gland samples of non-infected and infected udder quarters of a cow. In total, 704 different cDNA bands were displayed in both udder samples. Five hundred-and-thirty two bands, (75.6%) were differentially displayed. Ninety prominent cDNA bands were isolated, re-amplified, cloned and sequenced resulting in 87 different sequences. Amongst the 19 expressed sequence tags showing a similarity with previously described genes, the majority of these sequences exhibited homology to protein kinase encoding genes (26.3%), to genes involved in the regulation of gene expression (26.3%), to growth and differentiation factor encoding genes (21.0%) and to immune response or inflammation marker encoding genes (21.0%). These sequences were shown to have mastitis-associated expression in the udder samples of animals with and without clinical mastitis by quantitative RT-PCR. They were mapped physically using a bovine-hamster somatic cell hybrid panel and a 5000 rad bovine whole genome radiation hybrid panel. According to their localization in QTL regions based on an established integrated marker/gene-map and their disease-associated expression, four genes (AHCY, PRKDC, HNRPU, OSTF1) were suggested as potentially involved in mastitis defense.
TL;DR: A hierarchical animal model developed for inference on genetic merit of livestock with uncertain paternity was compared to a model based on the Henderson average numerator relationship (ANRM) in a simulation study with 10 replicated datasets generated for each of two traits.
Abstract: A hierarchical animal model was developed for inference on genetic merit of livestock with uncertain paternity. Fully conditional posterior distributions for fixed and genetic effects, variance components, sire assignments and their probabilities are derived to facilitate a Bayesian inference strategy using MCMC methods. We compared this model to a model based on the Henderson average numerator relationship (ANRM) in a simulation study with 10 replicated datasets generated for each of two traits. Trait 1 had a medium heritability (h2) for each of direct and maternal genetic effects whereas Trait 2 had a high h2 attributable only to direct effects. The average posterior probabilities inferred on the true sire were between 1 and 10% larger than the corresponding priors (the inverse of the number of candidate sires in a mating pasture) for Trait 1 and between 4 and 13% larger than the corresponding priors for Trait 2. The predicted additive and maternal genetic effects were very similar using both models; however, model choice criteria (Pseudo Bayes Factor and Deviance Information Criterion) decisively favored the proposed hierarchical model over the ANRM model.
TL;DR: REML estimates of heritability were found to decline with generations of selection, suggesting a departure from the infinitesimal model, either because a limited number of genes was involved, or their frequencies were changed.
Abstract: In order to investigate the possibility of using the dwarf gene for egg production, two dwarf brown-egg laying lines were selected for 16 generations on average clutch length; one line (L1) was normally feathered and the other (L2) was homozygous for the naked neck gene NA. A control line from the same base population, dwarf and segregating for the NA gene, was maintained during the selection experiment under random mating. The average clutch length was normalized using a Box-Cox transformation. Genetic variability and selection response were estimated either with the mixed model methodology, or with the classical methods for calculating genetic gain, as the deviation from the control line, and the realized heritability, as the ratio of the selection response on cumulative selection differentials. Heritability of average clutch length was estimated to be 0.42 ± 0.02, with a multiple trait animal model, whereas the estimates of the realized heritability were lower, being 0.28 and 0.22 in lines L1 and L2, respectively. REML estimates of heritability were found to decline with generations of selection, suggesting a departure from the infinitesimal model, either because a limited number of genes was involved, or their frequencies were changed. The yearly genetic gains in average clutch length, after normalization, were estimated to be 0.37 ± 0.02 and 0.33 ± 0.04 with the classical methods, 0.46 ± 0.02 and 0.43 ± 0.01 with animal model methodology, for lines L1 and L2 respectively, which represented about 30% of the genetic standard deviation on the transformed scale. Selection response appeared to be faster in line L2, homozygous for the NA gene, but the final cumulated selection response for clutch length was not different between the L1 and L2 lines at generation 16.