Quantifizierung der Methanemissionen bei Rindern mit Hilfe des fäkalen Biomarkers Archaeol

Das im Verdauungstrakt von Wiederkauern produzierte Methan ist als Endprodukt anaerober Nahrungsumsetzung vom Tier nicht weiter verwertbar. Daher wird es ausgestoßen und stellt eine globale Belastung für das Klima dar. Aus diesen Gründen werden Versuche zur Senkung der Methanemission von Wiederkäuern mit unterschiedlichen Ansätzen verfolgt. Ziel des Projektes MethanA war die Untersuchung eines im Kot detektierbaren Markers für die Methanemission und im Rahmen dessen die Evaluierung und Bewertung von Archaeol als Hilfsmerkmal für die Zucht auf verminderte Methanproduktion beim Rind. In eigener Vorarbeit wurden bei zehn Kühen Gaswechselmessungen in Respirationskammern mittels zweier Durchgänge und Fütterung zweier verschiedener Rationen durchgeführt. Es zeigte sich ein signifikanter Einfluss des Versuchsdurchlaufs, welcher aus dem Effekt des Laktationsstadiums (100. vs. 130. ±3 Laktationstag) sowie aus dem Effekt der Ration (stärkereich vs. faserreich) bestand. Im ersten Respirationsversuch zum 100. Laktationstag wurde eine stärke- und fettreiche Ration verabreicht (178 g Stärke/kg Trockenmasse (TM), 44 g Fett/kg TM) und ad libitum gefüttert. Im zweiten Durchlauf zum 135. Laktationstag erhielten die Kühe eine stärke- und fettreduziertere Ration (99 g Stärke/kg TM, 27 g Fett/kg TM). Die Methanproduktion (l/d) wurde für 24 Stunden gemessen, wobei Kotproben für die Archaeol-Analyse um 06:30, 10:00 und 14:30 Uhr entnommen wurden. Die Laktationsnummer des Tieres hatte keinen signifikanten Effekt. Die Beziehung zwischen dem fäkalen Archaeolgehalt und der Methanproduktion zeigte sich relativ schwach linear und nur tendenziell signifikant (R2 = 0,16). Bei Bezug der Methanausscheidung auf Basis der Trockenmasseaufnahme verbesserte sich die Beziehung deutlich (R2 = 0,53). Bei Einzelbetrachtung der Kotproben konnten die um 10:00 Uhr gesammelte Proben die Variation der Methanproduktion am besten erklären (R2 = 0,23). Im anschließenden Praxisversuch wurde über die Phasen Transit, Laktation und Trockenstehen von 31 Kühen zu festgelegten Zeitpunkten Kotproben entnommen und auf den Archaeolgehalt hin analysiert. Es konnte eine starke Variation der Archaeolausscheidung zwischen aber auch innerhalb der Tiere im Produktionsverlauf beobachtet werden. Die geringste in der Praxis detektierte Konzentration von Archaeol im Kot betrug 12 μg und die höchste Konzentration lag bei 59,7 μg. In der 2. Laktation zeigte sich ein geringeres Konzentrationsniveau an Archaeol im Kot verglichen mit der 1. und 3. Laktation. Der Zeitpunkt der Probenahme in der Laktation bzw. zur Trockenstehphase hatte einen hoch signifikanten Einfluss auf den fäkalen Archaeolgehalt. Die Wiederholbarkeit für das Merkmal fäkale Archaeolkonzentration betrug für alle drei Produktionsphasen 32 %, die Heritabilität für das Merkmal fäkale Archaeolkonzentration ist somit maximal moderat

The repertoire of equine intestinal α-defensins

<p>Abstract</p> <p>Background</p> <p>Defensins represent an important class of antimicrobial peptides. These effector molecules of the innate immune system act as endogenous antibiotics to protect the organism against infections with pathogenic microorganisms. Mammalian defensins are classified into three distinct sub-families (α-, β- and θ-defensins) according to their specific intramolecular disulfide-bond pattern. The peptides exhibit an antimicrobial activity against a broad spectrum of microorganisms including bacteria and fungi. Alpha-Defensins are primarily synthesised in neutrophils and intestinal Paneth cells. They play a role in the pathogenesis of intestinal diseases and may regulate the flora of the intestinal tract. An equine intestinal α-defensin (DEFA1), the first characterised in the <it>Laurasiatheria</it>, shows a broad antimicrobial spectrum against human and equine pathogens. Here we report a first investigation of the repertoire of equine intestinal α-defensins. The equine genome was screened for putative α-defensin genes by using known α-defensin sequences as matrices. Based on the obtained sequence information, a set of oligonucleotides specific to the α-defensin gene-family was designed. The products generated by reverse-transcriptase PCR with cDNA from the small intestine as template were sub-cloned and numerous clones were sequenced.</p> <p>Results</p> <p>Thirty-eight equine intestinal α-defensin transcripts were determined. After translation it became evident that at least 20 of them may code for functional peptides. Ten transcripts lacked matching genomic sequences and for 14 α-defensin genes apparently present in the genome no appropriate transcript could be verified. In other cases the same genomic exons were found in different transcripts.</p> <p>Conclusions</p> <p>The large repertoire of equine α-defensins found in this study points to a particular importance of these peptides regarding animal health and protection from infectious diseases. Moreover, these findings make the horse an excellent species to study biological properties of α-defensins. Interestingly, the peptides were not found in other species of the <it>Laurasiatheria </it>to date. Comparison of the obtained transcripts with the genomic sequences in the current assembly of the horse (EquCab2.0) indicates that it is yet not complete and/or to some extent falsely assembled.</p

Coat Color Roan Shows Association with KIT Variants and No Evidence of Lethality in Icelandic Horses

Roan (Rn) horses show a typical seasonal change of color. Their body is covered with colored and white hair. We performed a descriptive statistical analysis of breeding records of Icelandic horses to challenge the hypothesis of roan being lethal in utero under homozygous condition. The roan to non-roan ratio of foals from roan × roan matings revealed homozygous roan Icelandic horses to be viable. Even though roan is known to be inherited in a dominant mode and epistatic to other coat colors, the causative mutation is still unknown. Nevertheless, an association between roan phenotype and the KIT gene was shown for different horse breeds. In the present study, we identified KIT variants by Sanger sequencing, and show that KIT is also associated with roan in the Icelandic horse breed

Structural variants and tandem repeats in the founder individuals of four F2 pig crosses and implications to F2 GWAS results

Background Structural variants and tandem repeats are relevant sources of genomic variation that are not routinely analyzed in genome wide association studies mainly due to challenging identification and genotyping. Here, we profiled these variants via state-of-the-art strategies in the founder animals of four F2 pig crosses using whole-genome sequence data (20x coverage). The variants were compared at a founder level with the commonly screened SNPs and small indels. At the F2 level, we carried out an association study using imputed structural variants and tandem repeats with four growth and carcass traits followed by a comparison with a previously conducted SNPs and small indels based association study. Results A total of 13,201 high confidence structural variants and 103,730 polymorphic tandem repeats (with a repeat length of 2-20 bp) were profiled in the founders. We observed a moderate to high (r from 0.48 to 0.57) level of co-localization between SNPs or small indels and structural variants or tandem repeats. In the association step 56.56% of the significant variants were not in high LD with significantly associated SNPs and small indels identified for the same traits in the earlier study and thus presumably not tagged in case of a standard association study. For the four growth and carcass traits investigated, many of the already proposed candidate genes in our previous studies were confirmed and additional ones were identified. [...] Conclusions The current study provides insights into the characteristics of structural variants and tandem repeats and their role in association studies. A systematic incorporation of these variants into genome wide association studies is advised. While not of immediate interest for genomic prediction purposes, this will be particularly beneficial for elucidating biological mechanisms driving the complex trait variation

Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe

Background Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful. Results Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility. This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible

Identification of candidate genes for congenital splay leg in piglets by alternative analysis of DNA microarray data

The congenital splay leg syndrome in piglets is characterized by a temporarily impaired functionality of the hind leg muscles immediately after birth. Etiology and pathogenetic mechanisms for the disease are still not well understood. We compared genome wide gene expression of three hind leg muscles (M. adductores, M. gracilis and M. sartorius) between affected piglets and their healthy littermates with the GeneChip® Porcine Genome Array (Affymetrix) in order to identify candidate genes for the disease. Data analysis with standard algorithms revealed no significant differences between both groups. By application of an alternative approach, we identified 63 transcripts with differences in two muscles and 5 genes differing between the groups in three muscles. The expression of six selected genes (SQSTM1, SSRP1, DDIT4, ENAH, MAF, and PDK4) was investigated with SYBRGreen RT - Real time PCR. The differences obtained with the microarray analysis could be confirmed and demonstrate the validity of the alternative approach to microarray data analysis. Four genes with different expression levels in at least two muscles (SQSTM1, SSRP1, DDIT4, and MAF) are assigned to transcriptional cascades related to cell death and may thus indicate pathways for further investigations on congenital splay leg in piglets

Dominance and parent-of-origin effects of coding and non-coding alleles at the acylCoA-diacylglycerol-acyltransferase (DGAT1) gene on milk production traits in German Holstein cows

<p>Abstract</p> <p>Background</p> <p>Substantial gene substitution effects on milk production traits have formerly been reported for alleles at the K232A and the promoter VNTR loci in the bovine acylCoA-diacylglycerol-acyltransferase 1 (<it>DGAT1</it>) gene by using data sets including sires with accumulated phenotypic observations of daughters (breeding values, daughter yield deviations). However, these data sets prevented analyses with respect to dominance or parent-of-origin effects, although an increasing number of reports in the literature outlined the relevance of non-additive gene effects on quantitative traits.</p> <p>Results</p> <p>Based on a data set comprising German Holstein cows with direct trait measurements, we first confirmed the previously reported association of <it>DGAT1 </it>promoter VNTR alleles with milk production traits. We detected a dominant mode of effects for the <it>DGAT1 </it>K232A and promoter VNTR alleles. Namely, the contrasts between the effects of heterozygous individuals at the <it>DGAT1 </it>loci differed significantly from the midpoint between the effects for the two homozygous genotypes for several milk production traits, thus indicating the presence of dominance. Furthermore, we identified differences in the magnitude of effects between paternally and maternally inherited <it>DGAT1 </it>promoter VNTR – K232A haplotypes indicating parent-of-origin effects on milk production traits.</p> <p>Conclusion</p> <p>Non-additive effects like those identified at the bovine <it>DGAT1 </it>locus have to be accounted for in more specific QTL detection models as well as in marker assisted selection schemes. The <it>DGAT1 </it>alleles in cattle will be a useful model for further investigations on the biological background of non-additive effects in mammals due to the magnitude and consistency of their effects on milk production traits.</p

Precision of genetic parameters and breeding values estimated in marker assisted BLUP genetic evaluation

In practical implementations of marker-assisted selection economic and logistic restrictions frequently lead to incomplete genotypic data for the animals of interest. This may result in bias and larger standard errors of the estimated parameters and, as a consequence, reduce the benefits of applying marker-assisted selection. Our study examines the impact of the following factors: phenotypic information, depth of pedigree, and missing genotypes in the application of marker-assisted selection. Stochastic simulations were conducted to generate a typical dairy cattle population. Genetic parameters and breeding values were estimated using a two-step approach. First, pre-corrected phenotypes (daughter yield deviations (DYD) for bulls, yield deviations (YD) for cows) were calculated in polygenic animal models for the entire population. These estimated phenotypes were then used in marker assisted BLUP (MA-BLUP) evaluations where only the genotyped animals and their close relatives were included

Are scurs in heterozygous polled (Pp) cattle a complex quantitative trait?

International audienceAbstractBackgroundBreeding genetically hornless, i.e. polled, cattle provides an animal welfare-friendly and non-invasive alternative to the dehorning of calves. However, the molecular regulation of the development of horns in cattle is still poorly understood. Studying genetic characters such as polledness and scurs, can provide valuable insights into this process. Scurs are hornlike formations that occur occasionally in a wide variety of sizes and forms as an unexpected phenotype when breeding polled cattle.MethodsWe present a unique dataset of 885 Holstein–Friesian cattle with polled parentage. The horn phenotype was carefully examined, and the phenotypic heterogeneity of the trait is described. Using a direct gene test for polledness, the polled genotype of the animals was determined. Subsequently, the existence of a putative scurs locus was investigated using high-density genotype data of a selected subset of 232 animals and two mapping approaches: mixed linear model-based association analyses and combined linkage disequilibrium and linkage analysis.ResultsThe results of an exploratory data analysis indicated that the expression of scurs depends on age at phenotyping, sex and polled genotype. Scurs were more prevalent in males than in females. Moreover, homozygous polled animals did not express any pronounced scurs and we found that the Friesian polled allele suppresses the development of scurs more efficiently than the Celtic polled allele. Combined linkage and linkage disequilibrium mapping revealed four genome-wide significant loci that affect the development of scurs, one on BTA5 and three on BTA12. Moreover, suggestive associations were detected on BTA16, 18 and 23. The mixed linear model-based association analysis supports the results of the combined linkage and linkage disequilibrium analysis. None of the mapping approaches provided convincing evidence for a monogenic inheritance of scurs.ConclusionsOur results contradict the initial and still broadly accepted model for the inheritance of horns and scurs. We hypothesise an oligogenetic model to explain the development of scurs and polledness

Quasi-classical path integral approach to supersymmetric quantum mechanics

{}From Feynman's path integral, we derive quasi-classical quantization rules in supersymmetric quantum mechanics (SUSY-QM). First, we derive a SUSY counterpart of Gutzwiller's formula, from which we obtain the quantization rule of Comtet, Bandrauk and Campbell when SUSY is good. When SUSY is broken, we arrive at a new quantization formula, which is found as good as and even sometime better than the WKB formula in evaluating energy spectra for certain one-dimensional bound state problems. The wave functions in the stationary phase approximation are also derived for SUSY and broken SUSY cases. Insofar as a broken SUSY case is concerned, there are strong indications that the new quasi-classical approximation formula always overestimates the energy eigenvalues while WKB always underestimates.Comment: 13 pages + 5 figures, complete paper submitted as postscript file, to appear in Phys. Rev.