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Cytogenetic and Genome Research 02/2005; 109(4):533. · 1.53 Impact Factor
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J Bennewitz,
N Reinsch,
S Paul, C Looft,
B Kaupe,
C Weimann,
G Erhardt,
G Thaller,
Ch Kühn,
M Schwerin,
H Thomsen,
F Reinhardt,
R Reents,
E Kalm
[show abstract]
[hide abstract]
ABSTRACT: The gene, acyl-CoA:diacylglycerol acyltransferase1 (DGAT1), was recently identified as the one underlying the quantitative trait locus (QTL) for milk production traits in the centromeric region of the bovine chromosome 14. Until now, 2 alleles, the lysine variant (increasing fat yield, fat and protein percentage) and the alanine variant (increasing protein and milk yield), were postulated at DGAT1. This study investigated whether the diallelic DGAT1 polymorphism is responsible for all the genetic variation at the centromeric region of this chromosome for milk, fat, and protein yield and fat and protein percentage. A statistical model was applied to a granddaughter design to analyze 16 German Holstein families. The model included the diallelic DGAT1 effect and the QTL transition probability estimated for each chromosomal position by a multiple marker approach. Because the regression coefficient of this probability was corrected for the diallelic DGAT1 polymorphism, it represented a putative conditional QTL effect. The effect of the DGAT1 gene was always highly significant. The conditional QTL effect was significant genomewise for fat percentage at the proximal end of the chromosome and for protein percentage at a more distal chromosomal region. Additional chromosomewise significance was found for fat and protein yield. Our results suggest an additional source of genetic variance on this chromosome for these traits; either one or more additional alleles segregating at DGAT1 that were not previously detected, a second quantitative trait locus affecting these traits, or both.
Journal of Dairy Science 03/2004; 87(2):431-42. · 2.56 Impact Factor
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Cytogenetic and Genome Research 02/2004; 106(1):142. · 1.53 Impact Factor
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Manfred Schwerin,
Ch Kühn,
R Brunner,
T Goldammer,
J Bennewitz,
N Reinsch,
N Xu,
H Thomsen, C Looft,
C Weimann, [......],
G Erhardt,
I Medjugorac,
M Förster,
B Brenig,
F Reinhardt,
R Reents,
I Russ,
G Averdunk,
J Blümel,
E Kalm
Animal Science Papers and Reports Institute of Genetics and Animal Breeding. 01/2004; 22:95-100.
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Ch Kühn,
J Bennewitz,
N Reinsch,
N Xu,
H Thomsen, C Looft,
G A Brockmann,
M Schwerin,
C Weimann,
S Hiendleder,
G Erhardt,
I Medjugorac,
M Förster,
B Brenig,
F Reinhardt,
R Reents,
I Russ,
G Averdunk,
J Blümel,
E Kalm
[show abstract]
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ABSTRACT: A whole-genome scan to detect quantitative trait loci (QTL) for functional traits was performed in the German Holstein cattle population. For this purpose, 263 genetic markers across all autosomes and the pseudoautosomal region of the sex chromosomes were genotyped in 16 granddaughter-design families with 872 sons. The traits investigated were deregressed breedingvalues for maternal and direct effects on dystocia (DYSm, DYSd) and stillbirth (STIm, STId) as well as maternal and paternal effects on nonreturn rates of 90 d (NR90m, NR90p). Furthermore, deregressed breeding values for functional herd life (FHL) and daughter yield deviation for somatic cell count (SCC) were investigated. Weighted multimarker regression analyses across families and permutation tests were applied for the detection of QTL and the calculation of statistical significance. A ten percent genomewise significant QTL was localized for DYSm on chromosome 8 and for SCC on chromosome 18. A further 24 putative QTL exceeding the 5% chromosomewise threshold were detected. On chromosomes 7, 8, 10, 18, and X/Yps, coincidence of QTL for several traits was observed. Our results suggest that loci with influence on udder health may also contribute to genetic variance of longevity. Prior to implementation of these QTL in marker assisted selection programs for functional traits, information about direct and correlated effects of these QTL as well as fine mapping of their chromosomal positions is required.
Journal of Dairy Science 02/2003; 86(1):360-8. · 2.56 Impact Factor
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H Thomsen,
N Reinsch,
N Xu, C Looft,
S Grupe,
C Kühn,
G A Brockmann,
M Schwerin,
B Leyhe-Horn,
S Hiendleder,
G Erhardt,
I Medjugorac,
I Russ,
M Förster,
B Brenig,
F Reinhardt,
R Reents,
J Blümel,
G Averdunk,
E Kalm
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ABSTRACT: Genes determining the bovine erythrocyte antigens were mapped by linkage analysis. In total 9591 genotypes of 20 grandsire families with 1074 sires from a grand-daughter design were elucidated for the genes determining the erythrocyte antigens EAA, EAB, EAC, EAF, EAJ, EAL, EAM, EAN', EAR', EAS, EAT', and EAZ according to standard paternity testing procedures in the blood typing laboratories. Linkage analyses were performed with 248 microsatellite markers, eight SSCP markers and four polymorphic proteins and enzymes covering the 29 autosomes and the pseudoautosomal region of the sex chromosomes. The number of informative meioses for the blood group systems ranged from 76 to 947. Blood group systems EAM and EAT' were non-informative. Most of the erythrocyte antigen loci showed significant linkage to a single chromosome and were mapped unequivocally. The genes determining erythrocyte antigen EAA, EAB, EAC, EAL, and EAS were mapped to chromosomes 15, 12, 18, 3, and 21, respectively. Lod-score values ranged from 11.43 to 107.83. Moreover, the EAF system could be mapped to chromosome 17. However, the EAN' system previously known as part of the EAF system could be mapped to chromosome 5. In addition, the blood group systems EAJ, the new EAN', EAR', and EAZ, showed significant linkage to microsatellite markers on various chromosomes and also to other blood groups. The appearance of a single blood group system might be therefore either dependent on the existence of other blood group systems or because of an interaction between different loci on various chromosomes as is known in humans and in pigs.
Animal Genetics 05/2002; 33(2):107-17. · 2.40 Impact Factor
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H. Thomsen,
N. Reinsch,
N. Xu, C. Looft,
S. Grupe,
C. Kühn,
G. A. Brockmann,
M. Schwerin,
B. Leyhe-Horn,
S. Hiendleder,
G. Erhardt,
I. Medjugorac,
I. Russ,
M. Förster,
B. Brenig,
F. Reinhardt,
R. Reents,
J. Blümel,
G. Averdunk,
E. Kalm
[show abstract]
[hide abstract]
ABSTRACT: Genes determining the bovine erythrocyte antigens were mapped by linkage analysis. In total 9591 genotypes of 20 grandsire families with 1074 sires from a grand-daughter design were elucidated for the genes determining the erythrocyte antigens EAA, EAB, EAC, EAF, EAJ, EAL, EAM, EAN′, EAR′, EAS, EAT′, and EAZ according to standard paternity testing procedures in the blood typing laboratories. Linkage analyses were performed with 248 microsatellite markers, eight SSCP markers and four polymorphic proteins and enzymes covering the 29 autosomes and the pseudoautosomal region of the sex chromosomes. The number of informative meioses for the blood group systems ranged from 76 to 947. Blood group systems EAM and EAT′ were non-informative. Most of the erythrocyte antigen loci showed significant linkage to a single chromosome and were mapped unequivocally. The genes determining erythrocyte antigen EAA, EAB, EAC, EAL, and EAS were mapped to chromosomes 15, 12, 18, 3, and 21, respectively. Lod-score values ranged from 11.43 to 107.83. Moreover, the EAF system could be mapped to chromosome 17. However, the EAN′ system previously known as part of the EAF system could be mapped to chromosome 5. In addition, the blood group systems EAJ, the new EAN′, EAR′, and EAZ, showed significant linkage to microsatellite markers on various chromosomes and also to other blood groups. The appearance of a single blood group system might be therefore either dependent on the existence of other blood group systems or because of an interaction between different loci on various chromosomes as is known in humans and in pigs.
Animal Genetics 03/2002; 33(2):107 - 117. · 2.40 Impact Factor
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H. Thomsen,
N. Reinsch,
N. Xu, C. Looft,
S. Grupe,
C. Kühn,
G. A. Brockmann,
M. Schwerin,
B. Leyhe-Horn,
S. Hiendleder,
G. Erhardt,
I. Medjugorac,
I. Russ,
M. Förster,
B. Brenig,
F. Reinhardt,
R. Reents,
J. Blümel,
G. Averdunk,
E. Kalm
[show abstract]
[hide abstract]
ABSTRACT: The aim of this paper is to present the construction of a male genetic linkage map as a result of the bovine genome mapping project, which is a common effort of the German cattle breeding federation (ADR), four animal breeding institutes, three blood group laboratories and two animal data and breeding value evaluation centres. In total 20 grandsires with 1074 sires were provided from the German cattle population as reference families, 16 of these paternal half-sib groups are German Holstein families (DH), three are German Simmental (ST) families, and one is a Brown Swiss family (BS). Of 265 markers included in the linkage map, 248 were microsatellite markers, five were bovine blood group systems, eight SSCP markers and four proteins and enzymes. More than 239 000 genotypes resulted from typing the offspring for the respective markers and these were used for the construction of the map. On average 478 informative meioses were provided from each marker of the map. The summarized map length over all chromosomes was 3135.1 cM with an average interval size of 13.34 cM. About 17, 35.7 and 79.1% of the map intervals showed a maximum genetic distance between the adjacent markers of 5, 10 and 20 cM, respectively. The number of loci ranged from two (pseudoautosomal region of the sex chromosome, BTAY) to 15 (BTA23) with an average of 8.8 markers per chromosome. Comparing the length of the chromosomes shows variation from 49.6 cM for BTA26 to 190.5 cM for BTA1 with a mean of 107.7 cM for all autosomes of the genetic linkage map. It was possible to identify chromosomal discrepancies in locus order and map intervals by comparison with other published maps. The map provided sufficient marker density to serve as a useful tool for a scan of segregating quantitative trait loci.ZusammenfassungIm vorliegenden Artikel wird die Erstellung der genetischen Markerkarten für das Rindergenom im Rahmen des Genomanalyseprojektes der Arbeitsgemeinschaft Deutscher Rinderzüchter (ADR) vorgestellt. Auf der Basis des ,Granddaughter Designs' wurde ein Familienmaterial bestehend aus 20 väterlichen Halbgeschwistergruppen mit 1074 Söhnen für die Typisierung mit genetischen Markern bereitgestellt. Insgesamt 16 dieser paternalen Halbgeschwisterfamilien lassen sich der Rasse Deutsche Holsteins zuordnen, drei Familien entstammen der Rasse Deutsches Fleckvieh, und eine Familie gehört der Rasse Deutsches Braunvieh an. Dabei variiert die Anzahl der Söhne von 19–128 pro Vater. Für die Typisierung wurden 248 Mikrosatellitenmarker aus bereits publizierten Karten ausgewählt. Zusätzlich konnten 8 SSCP-und RFLP Marker, 5 Blutgruppensysteme und 4 Proteinmarker zur Entwicklung der genetischen Karte herangezogen werden. Die Anzahl der Marker variierte von 2 (pseudoautosomaler Bereich des Geschlechtschromosoms) bis 15 (Chromosom 23), wobei durchschnittlich 8.8 genetische Marker pro Chromosom typisiert wurden. Im Durchschnitt lieferten die genetischen Marker 478 informative Meiosen pro Marker. Alle Typisierungsergebnisse wurden in die Kieler Markerdatenbank übertragen und auf etwaige Fehler geprüft. Als Ergebnis konnten die genetischen Karten für alle 29 Autosomen und den pseudoautosomalen Bereich des Geschlechtschromosoms erstellt werden. Dabei wurde ein Bereich von 3135.1 cM des Rindergenoms abgedeckt, wobei die Länge des durchschnittlichen Markerintervalls 13.34 cM beträgt. Die Längen der Chromosomen zeigten eine Variation von 49.6 cM für Chromosom 26 bis zu 190.5 cM für Chromosom 1. Aufgrund der Anzahl informativer Meiosen und der Markerdichte bildet diese genetische Markerkarte in gutes Instrument für eine genomweite Suche nach segregierenden Genorten, die für die Variation von quantitativen Merkmalen verantwortlich sind.
Journal of Animal Breeding and Genetics 12/2001; 117(5):289 - 306. · 1.46 Impact Factor
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H. Thomsen,
N. Reinsch,
N. Xu, C. Looft,
S. Grupe,
C. Kühn,
G. A. Brockmann,
M. Schwerin,
B. Leyhe-Horn,
S. Hiendleder,
G. Erhardt,
I. Medjugorac,
I. Russ,
M. Förster,
B. Brenig,
F. Reinhardt,
R. Reents,
J. Blümel,
G. Averdunk,
E. Kalm
[show abstract]
[hide abstract]
ABSTRACT: 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 QTLEin 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.
Journal of Animal Breeding and Genetics 11/2001; 118(6):357 - 370. · 1.46 Impact Factor
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ABSTRACT: As part of a genome scan, ESTs derived from mammary gland tissue of a lactating cow were used as candidate genes for quantitative trait loci (QTL), affecting milk production traits. Resource families were genotyped with 247 microsatellite markers and 4 polymorphic ESTs. It was shown by linkage analysis that one of these ESTs, KIEL_E8, mapped to the centromeric region of bovine Chromosome (Chr) 14. Regression analysis revealed the presence of a QTL, with significant effect on milk production, in this chromosome region, and analysis of variance showed no significant interaction of marker genotype and family. The estimated significant differences between homozygous marker genotypes were 140 kg milk, -5.02 kg fat yield, and 2.58 kg protein yield for the first 100 days of lactation. Thus, there was strong evidence for a complete or nearly complete linkage disequilibrium between KIEL_E8 and the QTL. To identify the biological function of KIEL_E8, we extended the sequence for 869 bp by 5'-RACE. A 560-bp fragment of this shows a 90.9% similarity to a gene encoding a cysteine- and histidine-rich cytoplasmic protein in mouse. Although such a protein may have a regulatory function for lactation and a linkage disequilibrium between the EST marker and the QTL has been observed, it remains to be elucidated whether they are identical or not. Nevertheless, KIEL_E8 will be an efficient marker to perform marker-assisted selection in the Holstein-Friesian population.
Mammalian Genome 09/2001; 12(8):646-50. · 2.89 Impact Factor
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ABSTRACT: This article describes the construction of a high-resolution radiation hybrid map of Hsap 2q35 by using the TNG RH panel generated by irradiation with 50,000 rads. We were able to build a framework map of 1300 cR(50,000) including 34 markers ordered with odds higher than 1000:1. The comprehensive map includes 77 loci and describes a region of 3 Mb around the SLC11A1 gene. Because of the very small size of the fragments retained and a reduced retention frequency, it was difficult to build a high-resolution multi-point map of this region by using the TNG RH panel. Nevertheless, this study confirmed the very high potential of this RH panel for constructing a human, high-resolution physical map (2.3 kb/cR(50,000)). Moreover, human ESTs from Hsap 2q35 were hybridized with porcine BAC contigs to establish a porcine transcript map of the homologous region Sscr 15q25 (greater than 2.5 Mb). We identified 17 new genes in this porcine chromosomal region. We were able to compare the location of 26 genes mapped in both species. The gene order was similar except for two possible minor discrepancies in the Desmin sub-region, suggesting the existence of a porcine micro-region between TNP1 and IL8RB with an unknown origin.
Mammalian Genome 06/2001; 12(5):380-6. · 2.89 Impact Factor
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ABSTRACT: The poorly developed transcript maps and the limited resources for genome analysis hamper positional cloning of trait loci in farm animals. This study demonstrates that this will now be easier by the combined use of BAC contigs and the import of the near complete human transcript map. The conclusion was obtained by a comparative analysis of a 2.4-Mb BAC contig of the RN region in pigs. The contig was constructed as part of a successful positional cloning project, which identified PRKAG3 as the causative gene for the RN phenotype. A comparative map including the corresponding regions on human chromosome 2q35 and mouse chromosome 1 (region 36-44 cM) is reported. Sixteen coding sequences were mapped on the BAC contig. The majority of these were identified by BLAST searches of BAC end sequences and BAC shotgun sequences generated during the positional cloning project. Map data for the orthologues in humans were available for 12 of the 16 coding sequences, and all 12 have been assigned to 2q35. Furthermore, no evidence for any rearrangement in gene order was obtained. The extensive linkage conservation indicates that the near complete human transcript map will be an invaluable resource for positional cloning projects in pigs and other domestic animals.
Genomics 04/2001; 72(3):297-303. · 3.02 Impact Factor
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D Milan,
J T Jeon, C Looft,
V Amarger,
A Robic,
M Thelander,
C Rogel-Gaillard,
S Paul,
N Iannuccelli,
L Rask,
H Ronne,
K Lundström,
N Reinsch,
J Gellin,
E Kalm,
P L Roy,
P Chardon,
L Andersson
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ABSTRACT: A high proportion of purebred Hampshire pigs carries the dominant RN- mutation, which causes high glycogen content in skeletal muscle. The mutation has beneficial effects on meat content but detrimental effects on processing yield. Here, it is shown that the mutation is a nonconservative substitution (R200Q) in the PRKAG3 gene, which encodes a muscle-specific isoform of the regulatory gamma subunit of adenosine monophosphate-activated protein kinase (AMPK). Loss-of-function mutations in the homologous gene in yeast (SNF4) cause defects in glucose metabolism, including glycogen storage. Further analysis of the PRKAG3 signaling pathway may provide insights into muscle physiology as well as the pathogenesis of noninsulin-dependent diabetes mellitus in humans, a metabolic disorder associated with impaired glycogen synthesis.
Science 06/2000; 288(5469):1248-51. · 31.20 Impact Factor
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ABSTRACT: A bovine mammary gland cDNA-library was used to characterize and map genes expressed during lactation. Fifty cDNA clones selected by differential hybridization were sequenced from both ends, and sequences were examined for similarities with database sequences. For 34 of the transcripts, the sequences showed more than 80% similarity to previously characterized genes or expressed sequence tags (ESTs). Twenty cDNAs that could be of interest as candidate genes for milk production are selected for genetic or chromosomal mapping. Twenty-three out of the 39 designed primer pairs representing 16 cDNA clones amplified the expected fragments and were used for subsequent fluorescent single-strand conformation polymorphism analysis (F-SSCP) in the International Bovine Reference Panel families (IBRP). Ten polymorphic loci could be identified and used to genotype the IBRP animals, and nine of them were subsequently genetically mapped on nine chromosomes. In addition, eight loci from the 16 cDNA clones could be mapped by somatic cell hybrids, bringing the total number of mapped genes to 16, one of which was mapped genetically as well as physically. The mapped mammary gland ESTs are potentially useful for cloning economic trait loci by a positional candidate gene cloning approach.
Mammalian Genome 05/2000; 11(4):320-5. · 2.89 Impact Factor
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Cytogenetics and cell genetics 02/2000; 89(3-4):154-5.
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ABSTRACT: A total of 1,130 bulls belonging to 20 half-sib families of German dairy cattle were genotyped for 229 microsatellite markers on 30 chromosomes. The data were used in an attempt to map quantitative trait loci applying regression as multiple-marker regression. For association analysis with a granddaughter design, the estimated breeding values for 3 milk traits were used: milk production, fat production and protein production. The empirical values of significance thresholds were determined by using a permutation test on the experimental data. Several significant QTLs were found on some chromosomes, especially on the chromosome 14. The results give a strong support for the experiments of Coppieters et al. and Ron et al.
Acta Genetica Sinica 02/2000; 27(9):772-6.
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D. Milan,
L. Andersson, C. Looft,
V. Amarger,
A. Robic,
C. Rogel-Gaillard,
N. Iannucelli,
J. C. Caritez,
M. Yerle,
J. Gellin,
J. M. Elsen,
P. Chardon,
P. Le Roy
Journées Recherche Porcines en France. 01/2000; 32:357-360.
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Animal Genetics 07/1999; 30(3):234. · 2.40 Impact Factor
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Journal of Animal Science 06/1997; 75(5):1425. · 2.10 Impact Factor
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Animal Genetics 03/1997; 28(1):66. · 2.40 Impact Factor
