bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial diversity and the origin of Iberian sheep
Authors: Pedrosa Susana , Arranz Juan-José , Brito Nuno , Molina Antonio , San Primitivo Fermín , Bayón Yolanda
Published: June 2009

Mitochondrial DNA diversity was analysed in 19 Iberian and six foreign sheep breeds. Three mtDNA lineages (B, A and C) were found in the Iberian sheep, with type B clearly predominating over the others. The results were analysed for each of the morphologically determined breed groups in Iberian sheep: Merino, Entrefino, Churro and Iberian trunks. MtDNA lineage C was found only in the Iberian trunk composed of Montesina and Ojalada. These two populations had high mtDNA variability, and in the Iberian sheep only Merino Branco had more variation. The other three Merino types studied showed moderate variability, including the most authentic Merino, the Spanish Merino. These three Merinos clustered closely in a multidimensional scaling representation of distances, while the fourth breed (Merino Branco) showed a clear separation. As for the other two trunks, breeds from the Churro group showed greater maternal uniformity while results for populations included in the so-called Entrefino trunk seemed to have a more heterogeneous maternal origin. The results obtained are discussed with available data from nuclear markers and with morphological classifications, and all this information is analysed in relation to the origin of the different Iberian sheep breeds.
Random regression models for detection of gene by environment interaction
Authors: Lillehammer Marie , Ødegård Jørgen , Meuwissen Theo H.E.
Published: June 2009

Two random regression models, where the effect of a putative QTL was regressed on an environmental gradient, are described. The first model estimates the correlation between intercept and slope of the random regression, while the other model restricts this correlation to 1 or -1, which is expected under a bi-allelic QTL model. The random regression models were compared to a model assuming no gene by environment interactions. The comparison was done with regards to the models ability to detect QTL, to position them accurately and to detect possible QTL by environment interactions. A simulation study based on a granddaughter design was conducted, and QTL were assumed, either by assigning an effect independent of the environment or as a linear function of a simulated environmental gradient. It was concluded that the random regression models were suitable for detection of QTL effects, in the presence and absence of interactions with environmental gradients. Fixing the correlation between intercept and slope of the random regression had a positive effect on power when the QTL effects re-ranked between environments.
Haplotype kinship for three populations of the Goettingen minipig
Authors: Flury Christine , Weigend Steffen , Ding Xiangdong , Täubert Helge , Simianer Henner
Published: June 2009

To overcome limitations of diversity measures applied to livestock breeds marker based estimations of kinship within and between populations were proposed. This concept was extended from the single locus consideration to chromosomal segments of a given length in Morgan. Algorithms for the derivation of haplotype kinship were suggested and the behaviour of marker based haplotype kinship was investigated theoretically. In the present study the results of the first practical application of this concept are presented. Full sib pairs of three sub-populations of the Goettingen minipig were genotyped for six chromosome segments. After haplotype reconstruction the haplotypes were compared and mean haplotype kinships were estimated within and between populations. Based on haplotype kinships a distance measure is proposed which is approximatively linear with the number of generations since fission. The haplotype kinship distances, the respective standard errors and the pedigree-based expected values are presented and are shown to reflect the true population history better than distances based on single-locus kinships. However the marker estimated haplotype kinship reveals variable among segments. This leads to high standard errors of the respective distances. Possible reasons for this phenomenon are discussed and a pedigree-based approach to correct for identical haplotypes which are not identical by descent is proposed.
Non-additive genetic effects for fertility traits in Canadian Holstein cattle (Open Access publication )
Authors: Palucci Valentina , Schaeffer Lawrence R. , Miglior Filippo , Osborne Vern
Published: June 2009

The effects of additive, dominance, additive by dominance, additive by additive and dominance by dominance genetic effects on age at first service, non-return rates and interval from calving to first service were estimated. Practical considerations of computing additive and dominance relationships using the genomic relationship matrix are discussed. The final strategy utilized several groups of 1000 animals (heifers or cows) in which all animals had a non-zero dominance relationship with at least one other animal in the group. Direct inversion of relationship matrices was possible within the 1000 animal subsets. Estimates of variances were obtained using Bayesian methodology via Gibbs sampling. Estimated non-additive genetic variances were generally as large as or larger than the additive genetic variance in most cases, except for non-return rates and interval from calving to first service for cows. Non-additive genetic effects appear to be of sizeable magnitude for fertility traits and should be included in models intended for estimating additive genetic merit. However, computing additive and dominance relationships for all possible pairs of individuals is very time consuming in populations of more than 200 000 animals.
Association with litter size of new polymorphisms on ESR1 and ESR2 genes in a Chinese-European pig line
Authors: Muñoz Gloria , Ovilo Cristina , Estellé Jordi , Silió Luis , Fernández Almudena , Rodriguez Carmen
Published: June 2009

The objective of this study was to search for polymorphisms in the coding region of the estrogen receptors 1 and 2 (ESR1 and ESR2 )and to analyze the effects of these variants and the well known intronic ESR1 Pvu II polymorphism on litter size in a Chinese-European pig line. We identified five silent single nucleotide polymorphisms (SNP) in the ESR1 cDNA: c.669T > C (exon 3), c.1227C > T (exon 5), c.1452C > T (exon 7), c.1665T > C and c.1755A > G (exon 8). One pair of these SNP (c.1665T > C and c.1755A > G) co-segregated in the analyzed line, and the SNP c.669T > C showed the same segregation pattern as the Pvu II polymorphism. These polymorphisms were tested in this study, although the c.1452C > T SNP within exon 7 was not analyzed due to its low informativeness. In the ESR2 cDNA, one missense SNP was found within exon 5, which caused an amino acid substitution in the coded protein: "c.949G > A (p.Val317Met)" and was tested on sow litter size. Information on 1622 litter records from 408 genotyped sows was analyzed to determine whether these SNP influenced the total number of piglets born (TNB) or the number of born alive (NBA). The polymorphisms ESR1: [Pvu II; c.669T > C], ESR1: [c.1665T > C; c.1755A > G] and ESR2: c.949G > A showed no statistically significant association with litter size. However, the ESR1: c.1227T allele was significantly associated with TNB. The additive substitution effect was estimated to be 0.40 piglets born per litter (P < 0.03), and no dominance effects were observed. This SNP could be useful in assisted selection for litter size in some pig lines, as a new genetic marker in linkage disequilibrium with the causative mutation.
Late reproductive senescence in a rabbit line hyper selected for reproductive longevity, and its association with body reserves
Authors: Theilgaard Per , Sánchez Juan Pablo , Pascual Juan José , Berg Peer , Friggens Nic C. , Baselga Manuel
Published: June 2009

The aim of the present study was to investigate differences in reproductive and body traits during successive parities between two genetic lines. The LP line was constituted by means of selection of animals having an extremely high number of parities (at least 25) and an average reproductive performance compared to the V line selected for litter size at weaning during 31 generations. The two lines were found to have an equal reproductive performance in the first three parities, but the LP line had higher reproductive performance from the fourth parturition onwards. The low reproductive performance after the third parity in the V line was suggested to be caused by constrained environmental conditions in the test station. A line by parity interaction was also observed for body weight, since body weight declined going from the third to the fourth parity in the LP line but not the V line. Thus, it was concluded that hyper selection for reproductive longevity and average prolificacy successfully delayed reproductive senescence, and that this newly founded line showed less environmental sensitivity, which might have been mediated by a higher body reserve.
Empirical evaluation of selective DNA pooling to map QTL in dairy cattle using a half-sib design by comparison to individual genotyping and interval mapping
Authors: Mariasegaram Maxy , Robinson Nicholas Andrew , Goddard Michael Edward
Published: June 2009

This study represents the first attempt at an empirical evaluation of the DNA pooling methodology by comparing it to individual genotyping and interval mapping to detect QTL in a dairy half-sib design. The findings indicated that the use of peak heights from the pool electropherograms without correction for stutter (shadow) product and preferential amplification performed as well as corrected estimates of frequencies. However, errors were found to decrease the power of the experiment at every stage of the pooling and analysis. The main sources of errors include technical errors from DNA quantification, pool construction, inconsistent differential amplification, and from the prevalence of sire alleles in the dams. Additionally, interval mapping using individual genotyping gains information from phenotypic differences between individuals in the same pool and from neighbouring markers, which is lost in a DNA pooling design. These errors cause some differences between the markers detected as significant by pooling and those found significant by interval mapping based on individual selective genotyping. Therefore, it is recommended that pooled genotyping only be used as part of an initial screen with significant results to be confirmed by individual genotyping. Strategies for improving the efficiency of the DNA pooling design are also presented.
Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods
Authors: Uleberg Eivind , Meuwissen Theo H. E.
Published: June 2009

Two previously described QTL mapping methods, which combine linkage analysis (LA) and linkage disequilibrium analysis (LD), were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA) gave good results as long as the distance between the QTL was large (> 90 cM). When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA) gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM) the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.
Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L.
Authors: David Lior , Rosenberg Noah A. , Lavi Uri , Feldman Marcus W. , Hillel Jossi
Published: June 2009

Genetic relationships among eight populations of domesticated carp (Cyprinus carpio L.), a species with a partially duplicated genome, were studied using 12 microsatellites and 505 AFLP bands. The populations included three aquacultured carp strains and five ornamental carp (koi) variants. Grass carp (Ctenopharyngodon idella) was used as an outgroup. AFLP-based gene diversity varied from 5% (grass carp) to 32% (koi) and reflected the reasonably well understood histories and breeding practices of the populations. A large fraction of the molecular variance was due to differences between aquacultured and ornamental carps. Further analyses based on microsatellite data, including cluster analysis and neighbor-joining trees, supported the genetic distinctiveness of aquacultured and ornamental carps, despite the recent divergence of the two groups. In contrast to what was observed for AFLP-based diversity, the frequency of heterozygotes based on microsatellites was comparable among all populations. This discrepancy can potentially be explained by duplication of some loci in Cyprinus carpio L., and a model that shows how duplication can increase heterozygosity estimates for microsatellites but not for AFLP loci is discussed. Our analyses in carp can help in understanding the consequences of genotyping duplicated loci and in interpreting discrepancies between dominant and co-dominant markers in species with recent genome duplication.
Extensive intragenic recombination and patterns of linkage disequilibrium at the CSN3 locus in European rabbit
Authors: Carneiro Miguel , Ferrand Nuno
Published: June 2009

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.
A practical approach for minimising inbreeding and maximising genetic gain in dairy cattle
Authors: Haile-Mariam Mekonnen , Bowman Phil J , Goddard Mike E
Published: June 2009

A method that predicts the genetic composition and inbreeding (F) of the future dairy cow population using information on the current cow population, semen use and progeny test bulls is described. This is combined with information on genetic merit of bulls to compare bull selection methods that minimise F and maximise breeding value for profit (called APR in Australia). The genetic composition of the future cow population of Australian Holstein-Friesian (HF) and Jersey up to 6 years into the future was predicted. F in Australian HF and Jersey breeds is likely to increase by about 0.002 and 0.003 per year between 2002 and 2008, respectively. A comparison of bull selection methods showed that a method that selects the best bull from all available bulls for each current or future cow, based on its calf's APR minus F depression, is better than bull selection methods based on APR alone, APR adjusted for mean F of prospective progeny after random mating and mean APR adjusted for the relationship between the selected bulls. This method reduced F of prospective progeny by about a third to a half compared to the other methods when bulls are mated to current and future cows that will be available 5 to 6 years from now. The method also reduced the relationship between the bulls selected to nearly the same extent as the method that is aimed at maximising genetic gain adjusted for the relationship between bulls. The method achieves this because cows with different pedigree exist in the population and the method selects relatively unrelated bulls to mate to these different cows. Selecting the best bull for each current or future cow so that the calf's genetic merit minus F depression is maximised can slow the rate of increase in F in the population.
Genetic relationship of discrete-time survival with fertility and production in dairy cattle using bivariate models
Authors: González-Recio Oscar , Alenda Rafael
Published: June 2009

Bivariate analyses of functional longevity in dairy cattle measured as survival to next lactation (SURV) with milk yield and fertility traits were carried out. A sequential threshold-linear censored model was implemented for the analyses of SURV. Records on 96 642 lactations from 41 170 cows were used to estimate genetic parameters, using animal models, for longevity, 305 d-standardized milk production (MY305), days open (DO) and number of inseminations to conception (INS) in the Spanish Holstein population; 31% and 30% of lactations were censored for DO and INS, respectively. Heritability estimates for SURV and MY305 were 0.11 and 0.27 respectively; while heritability estimates for fertility traits were lower (0.07 for DO and 0.03 for INS). Antagonist genetic correlations were estimated between SURV and fertility (-0.78 and -0.54 for DO and INS, respectively) or production (-0.53 for MY305), suggesting reduced functional longevity with impaired fertility and increased milk production. Longer days open seems to affect survival more than increased INS. Also, high productive cows were more problematic, less functional and more liable to being culled. The results suggest that the sequential threshold model is a method that might be considered at evaluating genetic relationship between discrete-time survival and other traits, due to its flexibility.
Genetic and environmental effects on semen traits in Lacaune and Manech tête rousse AI rams (Open Access publication)
Authors: David Ingrid , Druart Xavier , Lagriffoul Gilles , Manfredi Eduardo , Robert-Granié Christèle , Bodin Loys
Published: June 2009

Data from 51 107 and 11 839 ejaculates collected on rams of the "Lacaune" and "Manech tête rousse" breeds, respectively, were analysed to determine environmental and genetic factors affecting semen production traits (ejaculate volume, semen concentration, number of spermatozoa and motility) in young (≤1 year) and adult (≥2 years) rams. Fixed effects and variance components were estimated using multiple trait animal models within each breed. For all traits, the main environmental effects identified were year, season, number of ejaculations, daily variation, interval from previous to current collection and age. Heritability estimates were moderate for volume, concentration and number of spermatozoa (0.12 to 0.33) and lower for motility (0.02 to 0.14). Genetic correlations between ages differed from 1 for all traits (0.14 to 0.90), indicating that semen characteristics corresponded to different traits in young and adult rams. Genetic and phenotypic correlations among traits within age category were globally similar for the different breeds and categories of animals.
Breeding salmonids for feed efficiency in current fishmeal and future plant-based diet environments
Authors: Quinton Cheryl D. , Kause Antti , Koskela Juha , Ritola Ossi
Published: June 2009

The aquaculture industry is increasingly replacing fishmeal in feeds for carnivorous fish with soybean meal (SBM). This diet change presents a potential for genotype-environment (G × E) interactions. We tested whether current salmonid breeding programmes that evaluate and select within fishmeal diets also improve growth and efficiency on potential future SBM diets. A total of 1680 European whitefish from 70 families were reared with either fishmeal- or SBM-based diets in a split-family design. Individual daily gain (DG), daily feed intake (DFI) and feed efficiency (FE) were recorded. Traits displayed only weak G × E interactions as variances and heritabilities did not differ substantially between the diets, and cross-diet genetic correlations were near unity. In both diets, DFI exhibited moderate heritability and had very high genetic correlation with DG whereas FE had low heritability. Predicted genetic responses demonstrated that selection to increase DG and FE on the fishmeal diet lead to favourable responses on the SBM diet. Selection for FE based on an index including DG and DFI achieved at least double FE gain versus selection on DG alone. Therefore, current breeding programmes are improving the biological ability of salmonids to use novel plant-based diets, and aiding the aquaculture industry to reduce fishmeal use.
A heuristic two-dimensional presentation of microsatellite-based data applied to dogs and wolves
Authors: Veit-Kensch Claudia E , Medugorac Ivica , Jedrzejewski Włodzimierz , Bunevich Aleksei N , Foerster Martin
Published: June 2009

Methods based on genetic distance matrices usually lose information during the process of tree-building by converting a multi-dimensional matrix into a phylogenetic tree. We applied a heuristic method of two-dimensional presentation to achieve a better resolution of the relationship between breeds and individuals investigated. Four hundred and nine individuals from nine German dog breed populations and one free-living wolf population were analysed with a marker set of 23 microsatellites. The result of the two-dimensional presentation was partly comparable with and complemented a model-based analysis that uses genotype patterns. The assignment test and the neighbour-joining tree based on allele sharing estimate allocated 99% and 97% of the individuals according to their breed, respectively. The application of the two-dimensional presentation to distances on the basis of the proportion of shared alleles resulted in comparable and further complementary insight into inferred population structure by multilocus genotype data. We expect that the inference of population structure in domesticated species with complex breeding histories can be strongly supported by the two-dimensional presentation based on the described heuristic method.
Consensus genetic structuring and typological value of markers using multiple co-inertia analysis
Authors: Laloë Denis , Jombart Thibaut , Dufour Anne-Béatrice , Moazami-Goudarzi Katayoun
Published: June 2009

Working with weakly congruent markers means that consensus genetic structuring of populations requires methods explicitly devoted to this purpose. The method, which is presented here, belongs to the multivariate analyses. This method consists of different steps. First, single-marker analyses were performed using a version of principal component analysis, which is designed for allelic frequencies (%PCA). Drawing confidence ellipses around the population positions enhances %PCA plots. Second, a multiple co-inertia analysis (MCOA) was performed, which reveals the common features of single-marker analyses, builds a reference structure and makes it possible to compare single-marker structures with this reference through graphical tools. Finally, a typological value is provided for each marker. The typological value measures the efficiency of a marker to structure populations in the same way as other markers. In this study, we evaluate the interest and the efficiency of this method applied to a European and African bovine microsatellite data set. The typological value differs among markers, indicating that some markers are more efficient in displaying a consensus typology than others. Moreover, efficient markers in one collection of populations do not remain efficient in others. The number of markers used in a study is not a sufficient criterion to judge its reliability. "Quantity is not quality".
Chromosomal control of pig populations in France: 2002–2006 survey
Authors: Ducos Alain , Berland Hélène-Marie , Bonnet Nathalie , Calgaro Anne , Billoux Sébastien , Mary Nicolas , Garnier-Bonnet Amélie , Darré Roland , Pinton Alain
Published: June 2009

The chromosomal control of pig populations has been widely developed in France over the last ten years. By December 31st, 2006, 13 765 individuals had been karyotyped in our laboratory, 62% of these since 2002. Ninety percent were young purebred boars controlled before service in artificial insemination centres, and 3% were hypoprolific boars. So far, 102 constitutional structural chromosomal rearrangements (67 since 2002) have been described. Fifty-six were reciprocal translocations and 8 peri- or paracentric inversions. For the first time since the beginning of the programme and after more than 11 000 pigs had been karyotyped, one Robertsonian translocation was identified in 2005 and two others in 2006. The estimated prevalence of balanced structural chromosomal rearrangements in a sample of more than 7700 young boars controlled before service was 0.47%. Twenty-one of the 67 rearrangements described since 2002 were identified in hypoprolific boars. All were reciprocal translocations. Twelve mosaics (XX/XY in 11 individuals, XY/XXY in one individual) were also diagnosed. Two corresponded to hypoprolific boars, and three to intersexed animals. The results presented in this communication would justify an intensification of the chromosomal control of French and, on a broader scale, European and North-American pig populations.
NNAT and DIRAS3 genes are paternally expressed in pigs
Authors: Cheng Huan-Chen , Zhang Feng-Wei , Deng Chang-Yan , Jiang Cao-De , Xiong Yuan-Zhu , Li Feng-E , Lei Ming-Gang
Published: June 2009

Although expression and epigenetic differences of imprinted genes have been extensively characterised in man and the mouse, little is known on livestock species. In this study, the polymorphism-based approach was used to detect the imprinting status of NNAT and DIRAS3 genes in five heterozygous pigs (based on SNP) of Large White and Meishan F1 hybrids. The results show that both genes were paternally expressed in all the tested tissues (heart, liver, spleen, lung, kidney, stomach, small intestine, skeletal muscle, fat, uterus, ovary and pituitary). In addition, the NNAT gene had two transcripts in all tested tissues, which is consistent with its counterpart in man and cattle.
A new view on dam lines in Polish Arabian horses based on mtDNA analysis
Authors: Głażewska Iwona , Wysocka Anna , Gralak Barbara , Prus Renata , Sell Jerzy
Published: June 2009

Polish Arabian horses are one of the oldest and the most important Arab populations in the world. The Polish Arabian Stud Book and the Genealogical Charts by Skorkowski are the main sources of information on the ancestors of Polish Arabs. Both publications were viewed as credible sources of information until the 1990s when the data regarding one of the dam lines was questioned. The aim of the current study was to check the accuracy of the pedigree data of Polish dam lines using mtDNA analysis. The analyses of a 458 bp mtDNA D-loop fragment from representatives of 15 Polish Arabian dam lines revealed 14 distinct haplotypes. The results were inconsistent with pedigree data in the case of two lines. A detailed analysis of the historical sources was performed to explain these discrepancies. Our study revealed that representatives of different lines shared the same haplotypes. We also noted a genetic identity between some lines founded by Polish mares of unknown origin and lines established by desert-bred mares.
The EADGENE Microarray Data Analysis Workshop (Open Access publication)
Authors: de Koning Dirk-Jan , Jaffrézic Florence , Lund Mogens Sandø , Watson Michael , Channing Caroline , Hulsegge Ina , Pool Marco H. , Buitenhuis Bart , Hedegaard Jakob , Hornshøj Henrik , Jiang Li , Sørensen Peter , Marot Guillemette , Delmas Céline , Cao Kim-Anh Lê , San Cristobal Magali , Baron Michael D. , Malinverni Roberto , Stella Alessandra , Brunner Ronald M. , Seyfert Hans-Martin , Jensen Kirsty , Mouzaki Daphne , Waddington David , Jiménez-Marín Ángeles , Pérez-Alegre Mónica , Pérez-Reinado Eva , Closset Rodrigue , Detilleux Johanne C , Dovč Peter , Lavrič Miha , Nie Haisheng , Janss Luc
Published: June 2009

Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses.
Predicting the consequences of selecting on PrP genotypes on PrP frequencies, performance and inbreeding in commercial meat sheep populations
Authors: Man Wing-Young N , Lewis Ronald M , Boulton Kay , Villanueva Beatriz
Published: June 2009

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 and metabolic aspects of androstenone and skatole deposition in pig adipose tissue: A review (Open Access publication)
Authors: Robic Annie , Larzul Catherine , Bonneau Michel
Published: June 2009

High levels of androstenone and skatole in fat tissues are considered the primary causes of boar taint, an unpleasant odour and flavour of the meat from non-castrated male pigs. The aim of this article is to review our current knowledge of the biology and genetic control of the accumulation of androstenone and skatole in fat tissue. Two QTL mapping studies have shown the complexity of the genetic control of these traits. During the last ten years, several authors have taken a more physiological approach to investigate the involvement of genes controlling the metabolism of androstenone and skatole. Although some authors have claimed the identification of candidate genes, it is more appropriate to talk about target genes. This suggests that genes affecting androstenone and skatole levels will have to be sought for among specific or non-specific transcription factors interacting with these target genes.
A rapid conditional enumeration haplotyping method in pedigrees
Authors: Gao Guimin , Hoeschele Ina
Published: June 2009

Haplotyping in pedigrees provides valuable information for genetic studies (e.g., linkage analysis and association study). In order to identify a set of haplotype configurations with the highest likelihoods for a large pedigree with a large number of linked loci, in our previous work, we proposed a conditional enumeration haplotyping method which sets a threshold for the conditional probabilities of the possible ordered genotypes at every unordered individual-marker to delete some ordered genotypes with low conditional probabilities and then eliminate some haplotype configurations with low likelihoods. In this article we present a rapid haplotyping algorithm based on a modification of our previous method by setting an additional threshold for the ratio of the conditional probability of a haplotype configuration to the largest conditional probability of all haplotype configurations in order to eliminate those configurations with relatively low conditional probabilities. The new algorithm is much more efficient than our previous method and the widely used software SimWalk2.
Detection of quantitative trait loci for reproduction and production traits in Large White and French Landrace pig populations (Open Access publication)
Authors: Tribout Thierry , Iannuccelli Nathalie , Druet Tom , Gilbert Hélène , Juliette Riquet , Ronan Gueblez , Mercat Marie-José , Bidanel Jean-Pierre , Milan Denis , Le Roy Pascale
Published: June 2009

A genome-wide scan was performed in Large White and French Landrace pig populations in order to identify QTL affecting reproduction and production traits. The experiment was based on a granddaughter design, including five Large White and three French Landrace half-sib families identified in the French porcine national database. A total of 239 animals (166 sons and 73 daughters of the eight male founders) distributed in eight families were genotyped for 144 microsatellite markers. The design included 51 262 animals recorded for production traits, and 53 205 litter size records were considered. Three production and three reproduction traits were analysed: average backfat thickness (US_M) and live weight (LWGT) at the end of the on-farm test, age of candidates adjusted at 100 kg live weight, total number of piglets born per litter, and numbers of stillborn (STILLp) and born alive (LIVp) piglets per litter. Ten QTL with medium to large effects were detected at a chromosome-wide significance level of 5% affecting traits US_M (on SSC2, SSC3 and SSC17), LWGT (on SSC4), STILLp (on SSC6, SSC11 and SSC14) and LIVp (on SSC7, SSC16 and SSC18). The number of heterozygous male founders varied from 1 to 3 depending on the QTL.
Measuring connectedness among herds in mixed linear models: From theory to practice in large-sized genetic evaluations
Authors: Fouilloux Marie-Noëlle , Clément Virginie , Laloë Denis
Published: June 2009

A procedure to measure connectedness among groups in large-sized genetic evaluations is presented. It consists of two steps: (a) computing coefficients of determination (CD) of comparisons among groups of animals; and (b) building sets of connected groups. The CD of comparisons were estimated using a sampling-based method that estimates empirical variances of true and predicted breeding values from a simulated n-sample. A clustering method that may handle a large number of comparisons and build compact clusters of connected groups was developed. An aggregation criterion (Caco) that reflects the level of connectedness of each herd was computed. This procedure was validated using a small beef data set. It was applied to the French genetic evaluation of the beef breed with most records and to the genetic evaluation of goats. Caco was more related to the type of service of sires used in the herds than to herd size. It was very sensitive to the percentage of missing sires. Disconnected herds were reliably identified by low values of Caco. In France, this procedure is the reference method for evaluating connectedness among the herds involved in on-farm genetic evaluation of beef cattle (IBOVAL) since 2002 and for genetic evaluation of goats from 2007 onwards.
A comparison of strategies for Markov chain Monte Carlo computation in quantitative genetics
Authors: Waagepetersen Rasmus , Ibánẽz-Escriche Noelia , Sorensen Daniel
Published: June 2009

In quantitative genetics, Markov chain Monte Carlo (MCMC) methods are indispensable for statistical inference in non-standard models like generalized linear models with genetic random effects or models with genetically structured variance heterogeneity. A particular challenge for MCMC applications in quantitative genetics is to obtain efficient updates of the high-dimensional vectors of genetic random effects and the associated covariance parameters. We discuss various strategies to approach this problem including reparameterization, Langevin-Hastings updates, and updates based on normal approximations. The methods are compared in applications to Bayesian inference for three data sets using a model with genetically structured variance heterogeneity.
Quantitative trait loci for fertility traits in Finnish Ayrshire cattle
Authors: Schulman Nina F. , Sahana Goutam , Lund Mogens S. , Viitala Sirja M. , Vilkki Johanna H.
Published: June 2009

A whole genome scan was carried out to detect quantitative trait loci (QTL) for fertility traits in Finnish Ayrshire cattle. The mapping population consisted of 12 bulls and 493 sons. Estimated breeding values for days open, fertility treatments, maternal calf mortality and paternal non-return rate were used as phenotypic data. In a granddaughter design, 171 markers were typed on all 29 bovine autosomes. Associations between markers and traits were analysed by multiple marker regression. Multi-trait analyses were carried out with a variance component based approach for the chromosomes and trait combinations, which were observed significant in the regression method. Twenty-two chromosome-wise significant QTL were detected. Several of the detected QTL areas were overlapping with milk production QTL previously identified in the same population. Multi-trait QTL analyses were carried out to test if these effects were due to a pleiotropic QTL affecting fertility and milk yield traits or to linked QTL causing the effects. This distinction could only be made with confidence on BTA1 where a QTL affecting milk yield is linked to a pleiotropic QTL affecting days open and fertility treatments.
Expression pattern and polymorphism of three microsatellite markers in the porcine CA3 gene
Authors: Wu Jian , Zhou Donghai , Deng Changyan , Xiong Yuanzhu , Lei Minggang , Li Fenge , Jiang Siwen , Zuo Bo , Zheng Rong
Published: June 2009

Carbonic anhydrase III (CA3) is an abundant muscle protein characteristic of adult type-1, slow-twitch, muscle fibres. In order to further understand the functions of the porcine CA3 protein in muscle, the temporal and spatial distributions of its gene product were analysed and the association between the presence of specific polymorphisms and carcass traits in the pig was also examined. Real-time PCR revealed that the CA3 mRNA expression showed no differences with age in skeletal muscles from Yorkshire pigs at postnatal day-1, month-2, and month-4. We provide the first evidence that CA3 is differentially expressed in the skeletal muscle of Yorkshire and Meishan pig breeds. In addition, the whole pig genomic DNA sequence of CA3 was investigated and shown to contain seven exons and six introns. Comparative sequencing of the gene from three pig breeds revealed the existence of microsatellite SJ 160 in intron 5 and microsatellite SJ 158 and a novel microsatellite marker that includes a tandem repeat of (TC)n in intron 4. We also determined the allele number and frequencies of the three loci in seven pig breeds and found that they are low polymorphic microsatellite markers. Statistical analysis showed that the CA3 microsatellite polymorphism was associated with dressing percentage, internal fat rate, carcass length, rib number and backfat thickness in the pig.
Simultaneous fine mapping of closely linked epistatic quantitative trait loci using combined linkage disequilibrium and linkage with a general pedigree
Authors: Lee Sang Hong , van der Werf Julius H.J.
Published: June 2009

Causal mutations and their intra- and inter-locus interactions play a critical role in complex trait variation. It is often not easy to detect epistatic quantitative trait loci (QTL) due to complicated population structure requirements for detecting epistatic effects in linkage analysis studies and due to main effects often being hidden by interaction effects. Mapping their positions is even harder when they are closely linked. The data structure requirement may be overcome when information on linkage disequilibrium is used. We present an approach using a mixed linear model nested in an empirical Bayesian approach, which simultaneously takes into account additive, dominance and epistatic effects due to multiple QTL. The covariance structure used in the mixed linear model is based on combined linkage disequilibrium and linkage information. In a simulation study where there are complex epistatic interactions between QTL, it is possible to simultaneously map interacting QTL into a small region using the proposed approach. The estimated variance components are accurate and less biased with the proposed approach compared with traditional models.
Genetic parameters related to environmental variability of weight traits in a selection experiment for weight gain in mice; signs of correlated canalised response
Authors: Ibáñez-Escriche Noelia , Moreno Almudena , Nieto Blanca , Piqueras Pepa , Salgado Concepción , Gutiérrez Juan Pablo
Published: June 2009

Data from an experimental mice population selected from 18 generations to increase weight gain were used to estimate the genetic parameters associated with environmental variability. The analysis involved three traits: weight at 21 days, weight at 42 days and weight gain between 21 and 42 days. A dataset of 5273 records for males was studied. Data were analysed using Bayesian procedures by comparing the Deviance Information Criterion (DIC) value of two different models: one assuming homogeneous environmental variances and another assuming them as heterogeneous. The model assuming heterogeneity was better in all cases and also showed higher additive genetic variances and lower common environmental variances. The heterogeneity of residual variance was associated with systematic and additive genetic effects thus making reduction by selection possible. Genetic correlations between the additive genetic effects on mean and environmental variance of the traits analysed were always negative, ranging from -0.19 to -0.38. An increase in the heritability of the traits was found when considering the genetic determination of the environmental variability. A suggested correlated canalised response was found in terms of coefficient of variation but it could be insufficient to compensate for the scale effect associated with an increase of the mean.
Data transformation for rank reduction in multi-trait MACE model for international bull comparison
Authors: Tarres Joaquim , Liu Zengting , Ducrocq Vincent , Reinhardt Friedrich , Reents Reinhard
Published: June 2009

Since many countries use multiple lactation random regression test day models in national evaluations for milk production traits, a random regression multiple across-country evaluation (MACE) model permitting a variable number of correlated traits per country should be used in international dairy evaluations. In order to reduce the number of within country traits for international comparison, three different MACE models were implemented based on German daughter yield deviation data and compared to the random regression MACE. The multiple lactation MACE model analysed daughter yield deviations on a lactation basis reducing the rank from nine random regression coefficients to three lactations. The lactation breeding values were very accurate for old bulls, but not for the youngest bulls with daughters with short lactations. The other two models applied principal component analysis as the dimension reduction technique: one based on eigenvalues of a genetic correlation matrix and the other on eigenvalues of a combined lactation matrix. The first one showed that German data can be transformed from nine traits to five eigenfunctions without losing much accuracy in any of the estimated random regression coefficients. The second one allowed performing rank reductions to three eigenfunctions without having the problem of young bulls with daughters with short lactations.
Exploration of cytoplasmic inheritance as a contributor to maternal effects in Welsh Mountain sheep
Authors: Pritchard Tracey , Cahalan Christine , Dewi Ioan Ap
Published: June 2009

Cytoplasmic effects were investigated using a dataset comprising three breeding groups of Welsh Mountain sheep. The influences of cytoplasmic effects were investigated by comparing animal models with and without a random term representing cytoplasmic effects. The models were applied to the eight-week weight, scan weight (mean 152 days) and ultrasonically scanned muscle and fat depth. The animal model included the random effects of animals and the maternal additive genetic, maternal permanent environmental and maternal common environmental effects. In total there were 24 569, 10 509, 8389, 8369 records for the eight-week weight, scan weight, muscle depth and fat depth respectively. Four subsets were further analysed containing maternal lines with at least five, ten, fifteen and twenty animals/line. There was no evidence of cytoplasmic effects on eight-week weight and muscle depth. Cytoplasmic effects contributed 1–2% of phenotypic variance for scan-weight and fat depth, but the effect was generally non-significant (P > 0.05). As the number of animals per maternal line increased, the magnitude of cytoplasmic effects also increased for these traits. Direct heritability estimates for the eight-week weight, scan weight, muscle depth and fat depth using the full dataset were 0.18, 0.25, 0.24, and 0.21 respectively.