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Half-sib Families (half-sib + family)
Kinds of Half-sib Families Selected AbstractsLymphocyte antigens in sheep: linkage to the MHC class II DRB1 geneINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 4 2001B. M. Jugo Summary In this work a typing battery of sera was developed to test lymphocyte antigens in sheep. Eight antigens were detected in a Latxa sheep sample. The serological determination of these antigens is described. As some of the detected antigens segregated in close linkage with class II DRB1 SSCP patterns in two half-sib families, we can conclude that they are coded by genes located in the MHC. Gene frequencies were very similar in Latxa Mutur Gorria and Latxa Mutur Beltza, the two varieties of the Latxa breed. Although few animals were typed in the comparison with other typing sera, it seems that two of our sera clusters detect the same antigens as those detected by other research groups working in other breeds with their own typing batteries. [source] Top down preselection using marker assisted estimates of breeding values in dairy cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2004Jörn Bennewitz Summary Top down preselection of young bulls before entering progeny testing has been proposed as a practicable form of marker-assisted selection (MAS), especially in dairy cattle populations with large male paternal half-sib families. Linkage phase between the superior (Q) and the inferior (q) QTL alleles of heterozygous sires (Qq at the QTL) with informative markers is established within each paternal half-sib family and may be used for selection among grand-progeny. If, additionally to sires, bulldams are also genotyped and data from consecutive generations are used, then a marker-assisted best linear unbiased prediction (MA-BLUP) model can be employed to connect the information of all generations and families of a top down design, and to select across all families. A customized ,augmented' sire model (with sires and dams of sires as random effects) is introduced for this purpose. Adapted formulae for the mixed model equations are given and their equivalence to a corresponding animal model and to a certain variant of previously proposed reduced animal models is shown. The application of the augmented sire model in MA-BLUP estimation from daughter-yield deviations and effective daughter contributions is presented. Zusammenfassung Die Top down Vorselektion von jungen Bullen vor der Nachkommenschaftsprüfung ist bekannt als eine praktikable Form der markergestützten Selektion in Milchrinderpopulationen. Die Kopplungsphasen zwischen dem günstigen (Q) und dem ungünstigen (q) Allel eines QTL heterozygoten Vaters (Qq am QTL) mit den Allelen gekoppelter genetischer Marker werden innerhalb Familien festgestellt und können zur Vorselektion von Enkeln genutzt werden. Wenn zusätzlich zu den Vätern die Mütter genotypisiert sind und Daten von mehreren Generationen vorliegen, können MA-BLUP Modelle genutzt werden, um Informationen von mehreren Familien und mehreren Generationen eines Top down Designs zusammenzuführen und um eine Vorselektion über Familien hinweg vorzunehmen. Hierfür wird ein geeignetes ,erweitertes' Vatermodell eingeführt, welches die Väter und zusätzlich die Mütter der Väter als zufällige Effekte enthält. Angepasste Formeln für die gemischten Modell Gleichungen werden beschrieben. Die Gleichheit dieses erweiterten Vatermodells mit einem entsprechenden Tiermodell und mit einer Variante des reduzierten Tiermodells wird gezeigt. Die Anwendung des erweiterten Vatermodells zur MA-BLUP Schätzung mit daughter yield deviations und effective daughter contributions ist beschrieben. [source] Comparison of estimated breeding values, daughter yield deviations and de-regressed proofs within a whole genome scan for QTLJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2001H. Thomsen An important issue in quantitative trait loci (QTL) detection is the use of phenotypic measurement as a dependent variable. Daughter yield deviations (DYDs) as the unit of choice are not available for all traits of interest. The use of de-regressed proofs (DRPFs) of estimated breeding values (EBVs) is an alternative to using daughter yield deviations. The objective of this study was to examine possible differences between DYDs and DRPFs within the use of QTL detection. The pedigree used was part of the granddaughter design of the German QTL effort. Consisting marker maps for livestock species were derived from all available data of 16 German Holstein paternal half-sib families with a total of 872 sires. The number of progeny ranged from 19 to 127. A whole genome scan was performed using weighted and unweighted multimarker regression with DYDs, DRPFs and EBVs as dependent variables for the traits milk, fat and protein yields. Results were compared with respect to the number of QTL detected. A similar number of QTL was detected with DRPFs and DYDs. Also, when dependent variables were weighted according to the variance of the trait, a higher number of QTL was detected at the desired level of significance as compared to using unweighted variables. Vergleich von Zuchtwerten, Daughter Yield Deviation und deregressierten Zuchtwerten bei der Genomanalyse zum Nachweis für QTL Ein bedeutender Einflussfaktor in der QTL-Analyse (QTL: Genorte für quantitativemarkmale) ist die Wahl der abhängigen Leistungsvariablen. Da Daughter Yield Deviations (DYDs) aber nicht für jedes Leistungsmerkmal zur Verfügung stehen, sollte untersucht werden, ob die De-regression von Zuchtwerten als alternative Variable in der QTL Analyse verwendet werden kann. Für die Untersuchung wurde ein Teil des Tiermaterials verwendet, das im Rahmen des Genomanalyseprojektes der Arbeitsgemeinschaft Deutscher Rinderzüchter untersucht wurde. Es standen 872 Bullen aus 16 väterlichen Halbgeschwisterfamilien der Rasse Deutsche Holsteins zur Verfügung. Die Zahl der Nachkommen pro Familie variierte von 19 bis 127. Unter Verwendung eines gewichteten als auch ungewichteten Multi-Marker Regressionsansatzes wurde ein Genomscan für die Leistungsmerkmale Milch-kg, Fett-kg und Eiweiss-kg durchgeführt, wobei als abhängige Variablen Zuchtwerte (EBV), Daughter Yield Deviations (DYD) und de-regressierte Zuchtwerte (DRPF) verwendet wurden. Die De-regression wurde auf der Basis der effektiven Töchterzahl, der Heritabilität des Merkmals und der additiv genetischen Verwandtschaftsmatrix durchgeführt. Alle Ergebnisse wurden in Hinblick auf die Anzahl der entdeckten QTL verglichen. Es zeigten sich dabei keine wesentlichen Unterschiede bei der Verwendung von DYDs und DRPFs. Die Rate der QTL Entdeckungen war bei beiden verwendeten Zuchtwerten annähernd gleich. Über den Vergleich unterschiedlicher Leistungsvariablen hinaus wurden die Ergebnisse der ungewichteten und gewichteten Analyse einander gegenübergestellt. Es konnte gezeigt werden, dass bei einer Gewichtung des Merkmals die Rate der QTL-Entdeckungen bei einem bestimmten Signifikanzniveau deutlich höher ist. [source] Determination of the inheritance pattern of hyperthelia in cattle by maximum likelihood analysis 1JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2000M. Brka Summary A previously published data-set with observations on supernumerary teats (hyperthelia) in dual-purpose Simmental was reanalysed by maximum-likelihood. The data comprised 537 unrelated animals and 614 members of 27 paternal half-sib families with known phenotype of each sire. The frequency of hyperthelia was 58% in unrelated animals, 51% in families with unaffected sire, and 73% in families with affected sires. Six different cases of single-gene inheritance were considered. The highest log-likelihood was obtained for additive inheritance and for a recessive pattern with 100% penetrance for recessive homozygotes and 32% for both other genotypes. Estimates for the gene frequency of the favourable allele were 0.34 and 0.29, respectively. Simple dominance or recessiveness with full or incomplete penetrance could be excluded. The possibility of finding paternal half-sib families with a heterozygous sire as a resource for a mapping experiment seem to be good in German Simmental. Zusammenfassung Untersuchung des Erbganges für Hyperthelie beim Rind mittels Maximum-Likelihood-Analyse Schon früher veröffentliche Daten mit Beobachtungen zum Auftreten überzähliger Zitzen (Hyperthelie) bei Fleckviehtieren wurden einer Maximum-Likelihood-Analyse unterzogen. Das Material bestand aus 537 unverwandten Tieren und 614 Tieren, die aus 27 verschiedenen väterlichen Halbgeschwistergruppen stammten, wobei der Phänotyp des Vaters jeweils bekannt war. Die relative Häufigkeit überzähliger Zitzen betrug 58% bei unverwandten Tieren, 51% bei Nachkommen von nicht betroffenen Vätern und 73% bei Nachkommen von Vätern, die selbst überzählige Zitzen aufwiesen. Sechs verschiedene Möglichkeiten monogener Vererbung wurden untersucht. Die höchsten Werte für die log-likelihood ergaben sich für einen additiven Erbgang sowie für eine Variante mit 100% Penetranz für die rezessiv Homozygoten und jeweils 32% Penetranz für die beiden anderen Genotypen. Für das erwünschte Allel wurde in beiden Varianten eine ähnliche Frequenz von 34% bzw. 29% geschätzt. Einfache dominante oder rezessive Erbgänge, auch mit unvollständiger Penetranz, konnten ausgeschlossen werden. Die Aussicht, für Kartierungsexperimente geeignete väterlichen Halbgeschwisterfamilien zu finden, scheint für die Rasse Fleckvieh günstig zu sein. [source] Genetic life history effects on juvenile survival in bluegillJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 2 2007B. D. NEFF Abstract Foraging behaviour under the risk of predation has important consequences on an individual's survivorship and fitness. In bluegill (Lepomis macrochirus), we have recently shown that offspring sired by males of alternative life histories differ in their foraging behaviour. Specifically, offspring sired by ,cuckolder' males take fewer risks during foraging than do offspring sired by ,parental' males. This behavioural difference can have important consequences on the fitness of the two life histories and thus the underlying evolutionary mechanism. Here, we examine the consequences of this behavioural variation on growth rate, condition and survivorship during early development of juveniles. We used split in vitro fertilization to generate maternal half-sibs that differed in sire life history. The resulting 18 455 larvae from 50 families were released into a microcosm with safe and risky foraging areas for approximately 2 months. A total of 262 juveniles (1.4%) survived of which parentage was unambiguously determined using microsatellite genetic markers for 254 (97%). Although we found significant dam effects, there was no difference in apparent growth rate or condition of juveniles sired by males of the two life histories. Of the 25 paired half-sib families, 15 had higher survivorship when sired by a cuckolder male, seven had higher survivorship when sired by a parental male and three had no surviving offspring from either sire. Thus, although growth was similar between the two offspring types, survivorship was not. Combining the differential survivorship estimate with paternity data from natural nests and the frequency of males adopting each life history, we calculated that the cuckolder life history has 1.87 times higher fitness than the parental life history. As such, the life histories likely are not governed by a genetic polymorphism. [source] Analysis of the incidence of infectious pancreatic necrosis mortality in pedigreed Atlantic salmon, Salmo salar L., populationsJOURNAL OF FISH DISEASES, Issue 11 2006D R Guy Abstract A total of 77 124 Atlantic salmon post-smolts, representing 197 full-sib families produced by 149 males and 197 females, experienced a field challenge from infectious pancreatic necrosis virus (IPNV), following transfer to three separate seawater sites. The first IPN mortality was observed 45 days after transfer, and the duration of the epidemic varied between 37 and 92 days among sites. Mortalities were traced to their parental families by PIT (Passive Integrated Transpondes) tag records and DNA genotyping. Full-sib family mean incidence of mortality was calculated for each family on each site. Heritabilities were estimated based on the heterogeneity of chi-square using incidence within half-sib families and the variance in incidence among full-sib families, both on the observed and underlying liability scale. The observed correlation among families across sites was used to estimate genetic correlations. The overall mortality rate was 10.8%, with only small differences between sites, ranging from 10.3% to 11.9%. Heritabilities on the liability scale were found to be moderate to strong, and ranged between 0.24 and 0.81, with a pooled estimate of 0.43, greater than is typically associated with disease traits. Genetic correlations among sites were all substantial, between 0.71 and 0.78, and indicated that a substantial component of the genetic variation displayed within sites was common to all. The results show that field challenges can yield very good genetic information on family differences in resistance, especially when replicated over sites, which may then be developed for use in selection for breeding strains of Atlantic salmon with greater resistance to IPN. [source] Contribution of direct and maternal genetic effects to life-history evolutionNEW PHYTOLOGIST, Issue 3 2009Laura F. Galloway Summary ,,Maternal effects are ubiquitous in nature. In plants, most work has focused on the effects of maternal environments on offspring trait expression. Less is known about the prevalence of genetic maternal effects and how they influence adaptive evolution. Here, we used multivariate genetic models to estimate the contributions of maternal and direct genetic (co)variance, the cross-generation direct-maternal covariance, and M, the matrix of maternal effect coefficients, for life-history traits in Campanulastrum americanum, a monocarpic herb. ,,Following a three-generation breeding design, we grew paternal half-sib families with full-sib relatives of each parent and measured juvenile and adult traits. ,,Seed size was influenced exclusively by maternal environmental effects, whereas maternal genetic effects influenced traits throughout the life cycle, including strong direct and maternal additive genetic correlations within and between generations for phenological and size traits. Examination of M suggested that both juvenile and adult traits in maternal plants influenced the expression of offspring traits. ,,This study reveals substantial potential for genetic maternal effects to contribute to adaptive evolution including cross-generation direct-maternal correlations that may slow selection response, maternal effects on phenology that reinforce genetic correlations, and within- and between-generation genetic correlations that may influence life-history polymorphism. [source] Validation of whole genome linkage-linkage disequilibrium and association results, and identification of markers to predict genetic merit for twinningANIMAL GENETICS, Issue 4 2010C. D. Bierman Summary A previous genome-wide search with a moderate density 10K marker set identified many marker associations with twinning rate, either through single-marker analysis or combined linkage-linkage disequilibrium (LLD; haplotype) analysis. The objective of the current study was to validate putative marker associations using an independent set of phenotypic data. Holstein bulls (n = 921) from 100 paternal half-sib families were genotyped. Twinning rate predicted transmitting abilities were calculated using calving records from 1994 to 1998 (Data I) and 1999 to 2006 (Data II), and the underlying liability scores from threshold model analysis were used as the trait in marker association analyses. The previous analysis used 201 bulls with daughter records in Data I. In the current analysis, this was increased to 434, providing a revised estimate of effect and significance. Bulls with daughter records in Data II totaled 851, and analysis of this data provided the validation of results from analysis of Data I. Single nucleotide polymorphisms (SNPs) were selected to validate previously significant single-marker associations and LLD results. Bulls were genotyped for a total of 306 markers. Nine of 13 LLD regions located on chromosomes 1, 2, 3, 6, 9, 22, 23(2) and 26 were validated, showing significant results for both Data I and II. Association analysis revealed 55 of 174 markers validated, equating to a single-marker validation rate of 31%. Stepwise backward elimination and cross-validation analyses identified 18 SNPs for use in a final reduced marker panel explaining 34% of the genetic variation, and to allow prediction of genetic merit for twinning rate. [source] The identification of QTL that affect the fatty acid composition of milk on sheep chromosome 11ANIMAL GENETICS, Issue 3 2010M. García-Fernández Summary In this work, we analysed 11 genetic markers localized on OAR11 in a commercial population of Spanish Churra sheep to detect QTL that underlie milk fatty acid (FA) composition traits. Following a daughter design, we analysed 799 ewes distributed in 15 half-sib families. Eight microsatellite markers and three novel SNPs identified in two genes related to fatty acid metabolism, acetyl-CoA carboxylase , (ACACA) and fatty acid synthase (FASN), were genotyped in the whole population under study. The phenotypic traits considered in the study included 22 measurements related to the FA composition of the milk and three other milk production traits (milk protein percentage, milk fat percentage and milk yield). Across-family regression analysis revealed four significant QTL at the 5% chromosome-wise level influencing contents of capric acid (C10:0), lauric acid (C12:0), linoleic conjugated acid (CLA) and polyunsaturated fatty acids (PUFA) respectively. The peaks of the QTL affecting C10:0 and PUFA contents in milk map close to the FASN gene, which has been evaluated as a putative positional candidate for these QTL. The QTL influencing C12:0 content reaches its maximum significance at 58 cM, close to the gene coding for the glucose-dependent insulinotropic polypeptide. We were not able to find any candidate genes related to fat metabolism at the QTL influencing CLA content, which is located at the proximal end of the chromosome. Further research efforts will be needed to confirm and refine the QTL locations reported here. [source] Confirmation and refinement of a QTL on BTA5 affecting milk production traits in the Fleckvieh dual purpose cattle breedANIMAL GENETICS, Issue 1 2010A. Awad Summary We analysed a QTL affecting milk yield (MY), milk protein yield (PY) and milk fat yield (FY) in the dual purpose cattle breed Fleckvieh on BTA5. Twenty-six microsatellite markers covering 135 cM were selected to analyse nine half-sib families containing 605 sons in a granddaughter design. We thereby assigned two new markers to the public linkage map using the CRI-MAP program. Phenotypic records were daughter yield deviations (DYD) originating from the routinely performed genetic evaluations of breeding animals. To determine the position of the QTL, three different approaches were applied: interval mapping (IM), linkage analysis by variance component analysis (LAVC), and combined linkage disequilibrium (LD) and linkage (LDL) analysis. All three methods mapped the QTL in the same marker interval (BM2830-ETH152) with the greatest test-statistic value at 118, 119.33 and 119.33 cM respectively. The positive QTL allele simultaneously increases DYD in the first lactation by 272 kg milk, 7.1 kg milk protein and 7.0 kg milk fat. Although the mapping accuracy and the significance of a QTL effect increased from IM over LAVC to LDL, the confidence interval was large (13, 20 and 24 cM for FY, MY and PY respectively) for the positional cloning of the causal gene. The estimated averages of pair wise marker LD with a distance <5 cM were low (0.107) and reflect the large effective population size of the Fleckvieh subpopulation analysed. This low level of LD suggests a need for increase in marker density in following fine mapping steps. [source] The variant red coat colour phenotype of Holstein cattle maps to BTA27ANIMAL GENETICS, Issue 1 2010D. L. Dreger Summary The variant red phenotype in Holstein cattle is indistinguishable from the traditional e/e recessive red phenotype caused by a mutation in melanocortin 1 receptor, but is inherited as a dominant trait in relation to black. Co-segregation analysis in four half-sib families segregating for variant red was conducted, excluding melanocortin 1 receptor, agouti signalling protein, attractin and melatonin receptor 1A as causative genes. However, variant red co-segregated with markers in a region of BTA27 that includes beta-defensin 103 (DEFB103). Two newly identified microsatellites and 5 SNPs 5, of DEFB103 were used for linkage mapping in four segregating families (LOD = 3.26). One haplotype was inherited in VR cattle in a 6-generation pedigree. [source] Quantitative trait loci with effects on feed efficiency traits in Hereford × composite double backcross populationsANIMAL GENETICS, Issue 6 2009G. C. Márquez Summary Two half-sib families of backcross progeny were produced by mating F1 Line 1 Hereford (L1) × composite gene combination (CGC) bulls with L1 and CGC cows. Feed intake and periodic weights were measured for 218 backcross progeny. These progenies were genotyped using 232 microsatellite markers that spanned the 29 BTA. Progeny from L1 and CGC females was analysed separately using composite interval mapping to find quantitative trait loci (QTL) affecting daily dry matter intake (DMI), average daily gain (ADG), feed conversion (FCR) and residual feed intake (RFI). Results from both backcrosses were pooled to find additional QTL. In the backcross to L1, QTL were detected for RFI and DMI on BTA11, FCR on BTA16, and ADG on BTA9. In the backcross to CGC, QTL were detected for RFI on BTA10, FCR on BTA12 and 16 and ADG on BTA15 and 17. After pooling, QTL were detected for RFI on BTA 2, 6, 7, 10, 11, 13 and 16; for FCR on BTA 9, 12, 16, 17 and 21; for ADG on BTA 9, 14, 15, 17; and for DMI on BTA 2, 5, 6, 9, 10, 11, 20 and 23. [source] Quantitative trait loci underlying milk production traits in sheepANIMAL GENETICS, Issue 4 2009B. Gutiérrez-Gil Summary Improvement of milk production traits in dairy sheep is required to increase the competitiveness of the industry and to maintain the production of high quality cheese in regions of Mediterranean countries with less favourable conditions. Additional improvement over classical selection could be reached if genes with significant effects on the relevant traits were specifically targeted by selection. However, so far, few studies have been undertaken to detect quantitative trait loci (QTL) in dairy sheep. In this study, we present a complete genome scan performed in a commercial population of Spanish Churra sheep to identify chromosomal regions associated with phenotypic variation observed in milk production traits. Eleven half-sib families, including a total of 1213 ewes, were analysed following a daughter design. Genome-wise multi-marker regression analysis revealed a genome-wise significant QTL for milk protein percentage on chromosome 3. Eight other regions, localized on chromosomes 1, 2, 20, 23 and 25, showed suggestive significant linkage associations with some of the analysed traits. To our knowledge, this study represents the first complete genome scan for milk production traits reported in dairy sheep. The experiment described here shows that analysis of commercial dairy sheep populations has the potential to increase our understanding of the genetic determinants of complex production-related traits. [source] Genetic mapping of quantitative trait loci for resistance to Haemonchus contortus in sheepANIMAL GENETICS, Issue 3 2009K. Marshall Summary This paper presents results from a mapping experiment to detect quantitative trait loci (QTL) for resistance to Haemonchus contortus infestation in merino sheep. The primary trait analysed was faecal worm egg count in response to artificial challenge at 6 months of age. In the first stage of the experiment, whole genome linkage analysis was used for broad-scale mapping. The animal resource used was a designed flock comprising 571 individuals from four half-sib families. The average marker spacing was about 20 cM. For the primary trait, 11 QTL (as chromosomal/family combinations) were significant at the 5% chromosome-wide level, with allelic substitution effects of between 0.19 and 0.38 phenotypic standard deviation units. In general, these QTL did not have a significant effect on faecal worm egg count recorded at 13 months of age. In the second stage of the experiment, three promising regions (located on chromosomes 1, 3 and 4) were fine-mapped. This involved typing more closely spaced markers on individuals from the designed flock as well as an additional 495 individuals selected from a related population with a deeper pedigree. Analysis was performed using a linkage disequilibrium,linkage approach, under additive, dominant and multiple QTL models. Of these, the multiple QTL model resulted in the most refined QTL positions, with resolutions of <10 cM achieved for two regions. Because of the moderate size of effect of the QTL, and the apparent age and/or immune status specificity of the QTL, it is suggested that a panel of QTL will be required for significant genetic gains to be achieved within industry via marker-assisted selection. [source] Age-dependent quantitative trait loci affecting growth traits in Scottish Blackface sheepANIMAL GENETICS, Issue 2 2009G. Hadjipavlou Summary To dissect age-dependent quantitative trait loci (QTL) associated with growth and to examine changes in QTL effects over time, the Gompertz growth model was fitted to longitudinal live weight data on 788 Scottish Blackface lambs from nine half-sib families. QTL were mapped for model parameters and weekly live weights and growth rates using microsatellite markers on chromosomes 1, 2, 3, 5, 14, 18, 20 and 21. QTL significance (using , = 0.05 chromosome-wide significance thresholds, unless otherwise stated) varied with age, and those for growth rate occurred earlier than equivalent QTL for live weight. A chromosome 20 QTL for growth rate was significant from 4 to 9 weeks (maximum significance at 6 weeks) and for maximum growth rate. For live weight, this QTL was significant from 8 to 16 weeks (maximum significance at 12 weeks). A nominally significant chromosome 14 QTL was detected for growth rates from birth to week 2 in the same families and location as an 8-week weight QTL. In addition, at the same position on chromosome 14, a QTL was significant for growth rate for 17,28 weeks (maximum significance at 24 weeks). A chromosome 3 QTL was significant for weights at early ages (birth to week 4) and a growth rate QTL on chromosome 18 was significant from 8 to 12 weeks. Fitting growth curves allowed the combination of information from multiple measurements into a few biologically meaningful variables, and the detection of growth QTL that were not observed from analyses of raw weight data. These QTL describe distinct parts of an animal's growth curve trajectory, possibly enabling manipulation of this trajectory. [source] Genetic mapping of the belt pattern in Brown Swiss cattle to BTA3ANIMAL GENETICS, Issue 2 2009C. Drögemüller Summary The white belt pattern of Brown Swiss cattle is characterized by a lack of melanocytes in a stretch of skin around the midsection. This pattern is of variable width and sometimes the belt does not fully circle the body. To identify the gene responsible for this colour variation, we performed linkage mapping of the belted locus using six segregating half-sib families including 104 informative meioses for the belted character. The pedigree confirmed a monogenic autosomal dominant inheritance of the belted phenotype in Brown Swiss cattle. We performed a genome scan using 186 microsatellite markers in a subset of 88 animals of the six families. Linkage with the belt phenotype was detected at the telomeric region of BTA3. Fine-mapping and haplotype analysis using 19 additional markers in this region refined the critical region of the belted locus to a 922-kb interval on BTA3. As the corresponding human and mouse chromosome segments contain no obvious candidate gene for this coat colour trait, the mutation causing the belt pattern in the Brown Swiss cattle might help to identify an unknown gene influencing skin pigmentation. [source] Two single nucleotide polymorphisms in the myostatin (GDF8) gene have significant association with muscle depth of commercial Charollais sheepANIMAL GENETICS, Issue 4 2008G. Hadjipavlou Summary To assess whether the same mutation(s) were responsible for similar phenotypes attributed to ovine chromosome 2 (OAR2) quantitative trait loci (QTL) in different sheep breeds, Suffolk, Texel and Charollais rams from British commercial flocks were genotyped for two single nucleotide polymorphisms (SNPs) located in the myostatin (GDF8) region of OAR2, previously detected in progeny of Belgian Texel rams exhibiting muscular hypertrophy. The first SNP (g.,2449G>C) was located upstream from the transcription start site and the second SNP (g.+6723G>A) in the 3, UTR of GDF8. The g.,2449C and g.+6723A alleles were absent in the Suffolk sires sampled, almost fixed in the Texel and segregating in the Charollais sires. Mixed model association analyses using SNP data on 338 Charollais lambs from 17 paternal half-sib families and phenotype and pedigree data on 56 500 lambs revealed that both SNPs had a significant association with muscle depth (P < 0.001). The SNPs were segregating at intermediate frequencies (p = 0.3) and exhibited strong linkage disequilibrium (r2 = 0.90). Animals with the g.+6723AA genotype had significantly greater muscle depth than those with either the g.+6723GG or the g.+6723AG genotypes (P < 0.002), with the g.+6723A allele, the likely causative mutation, having an additive effect of 1.20 (±0.30) mm and a dominance effect of ,0.73 (±0.36) mm. Based on estimated allelic effects and sample allele frequencies, the g.+6723G>A SNP explained 14% of the additive genetic variance of muscle depth. The maximum genetic variance for the trait (38%) attributed to the SNP would be attained at a g.+6723A allele frequency of 0.7. Our findings indicate that marker-assisted selection using these two GDF8 SNPs would be beneficial for the Charollais breed. [source] TYRP1 is associated with dun coat colour in Dexter cattle or how now brown cow?ANIMAL GENETICS, Issue 3 2003T. G. Berryere Summary Tyrosinase related protein 1 (TYRP1), which is involved in the coat colour pathway, was mapped to BTA8 between microsatellites BL1080 and BM4006, using a microsatellite in intron 5 of TYRP1. The complete coding sequence of bovine TYRP1 was determined from cDNA derived from skin biopsies of cattle with various colours. Sequence data from exons 2,8 from cattle with diluted phenotypes was compared with that from non-diluted phenotypes. In addition, full-sib families of beef cattle generated by embryo transfer and half-sib families from traditional matings in which coat colour was segregating were used to correlate TYRP1 sequence variants with dilute coat colours. Two non-conservative amino acid changes were detected in Simmental, Charolais and Galloway cattle but these polymorphisms were not associated with diluted shades of black or red, nor with the dun coat colour of Galloway cattle or the taupe brown colour of Braunvieh and Brown Swiss cattle. However, in Dexter cattle all 25 cattle with a dun brown coat colour were homozygous for a H424Y change. One Dexter that was also homozygous Y434 was red because of an ,E+/E+' genotype at MC1R which lead to the production of only phaeomelanin. None of the 70 remaining black or red Dexter cattle were homozygous for Y434. This tyrosine mutation was not found in any of the 121 cattle of other breeds that were examined. [source] Top down preselection using marker assisted estimates of breeding values in dairy cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2004Jörn Bennewitz Summary Top down preselection of young bulls before entering progeny testing has been proposed as a practicable form of marker-assisted selection (MAS), especially in dairy cattle populations with large male paternal half-sib families. Linkage phase between the superior (Q) and the inferior (q) QTL alleles of heterozygous sires (Qq at the QTL) with informative markers is established within each paternal half-sib family and may be used for selection among grand-progeny. If, additionally to sires, bulldams are also genotyped and data from consecutive generations are used, then a marker-assisted best linear unbiased prediction (MA-BLUP) model can be employed to connect the information of all generations and families of a top down design, and to select across all families. A customized ,augmented' sire model (with sires and dams of sires as random effects) is introduced for this purpose. Adapted formulae for the mixed model equations are given and their equivalence to a corresponding animal model and to a certain variant of previously proposed reduced animal models is shown. The application of the augmented sire model in MA-BLUP estimation from daughter-yield deviations and effective daughter contributions is presented. Zusammenfassung Die Top down Vorselektion von jungen Bullen vor der Nachkommenschaftsprüfung ist bekannt als eine praktikable Form der markergestützten Selektion in Milchrinderpopulationen. Die Kopplungsphasen zwischen dem günstigen (Q) und dem ungünstigen (q) Allel eines QTL heterozygoten Vaters (Qq am QTL) mit den Allelen gekoppelter genetischer Marker werden innerhalb Familien festgestellt und können zur Vorselektion von Enkeln genutzt werden. Wenn zusätzlich zu den Vätern die Mütter genotypisiert sind und Daten von mehreren Generationen vorliegen, können MA-BLUP Modelle genutzt werden, um Informationen von mehreren Familien und mehreren Generationen eines Top down Designs zusammenzuführen und um eine Vorselektion über Familien hinweg vorzunehmen. Hierfür wird ein geeignetes ,erweitertes' Vatermodell eingeführt, welches die Väter und zusätzlich die Mütter der Väter als zufällige Effekte enthält. Angepasste Formeln für die gemischten Modell Gleichungen werden beschrieben. Die Gleichheit dieses erweiterten Vatermodells mit einem entsprechenden Tiermodell und mit einer Variante des reduzierten Tiermodells wird gezeigt. Die Anwendung des erweiterten Vatermodells zur MA-BLUP Schätzung mit daughter yield deviations und effective daughter contributions ist beschrieben. [source] Identification of a 3.7-Mb region for a marbling QTL on bovine chromosome 4 by identical-by-descent and association analysisANIMAL GENETICS, Issue 6 2009K. Yokouchi Summary QTL mapping for growth and carcass traits was performed using a paternal half-sib family composed of 325 Japanese Black cattle offspring. Nine QTL were detected at the 1% chromosome-wise significance level at a false discovery rate of less than 0.1. These included two QTL for marbling on BTA 4 and 18, two QTL for carcass weight on BTA 14 and 24, two QTL for longissimus muscle area on BTA 1 and 4, two QTL for subcutaneous fat thickness on BTA 1 and 15 and one QTL for rib thickness on BTA 6. Although the marbling QTL on BTA 4 has been replicated with significant linkages in two Japanese Black cattle sires, the three Q (more marbling) haplotypes, each inherited maternally, were apparently different. To compare the three Q haplotypes in more detail, high-density microsatellite markers for the overlapping regions were developed within the 95% CIs (65 markers in 44,78 cM). A detailed haplotype comparison indicated that a small region (<3.7 Mb) around 46 cM was shared between the Qs of the two sires, whose dams were related. An association of this region with marbling was shown by a regression analysis using the local population, in which the two sires were produced and this was confirmed by an association study using a population collected throughout Japan. These results strongly suggest that the marbling QTL on BTA 4 is located in the 3.7-Mb region at around 46 cM. [source] | |||||||||||||