The chromosomes are separated with alternating colours. The grey and blue bars indicate the fraction of phenotypic variance attributed to a particular chromosome and QTL region, respectively. Extensive variant detection in the Fleckvieh population by low-coverage re-sequencing. The vertical axis is truncated for P values below -log10 However, strong linkage of potentially functional adjacent SNPs often precludes to finally proof the causality of individual variants [35]. Effect of the most significantly associated markers on the estimated breeding value EBV for paternal calving ease pCE in the Fleckvieh breed. Number of animals for each of the three datasets after quality control Dataset 54Kv1 54Kv2 K 54Kv1 2, – 54Kv2 – K Numbers along the diagonal represent the final number of animals for the two medium-density 54Kv1, 54Kv2 and for the high-density K dataset, respectively.

The resulting haplotypes were analyzed for association in a multilinear regression model implemented in R see above. It is well known, that distinct signalling pathways are essential for the development of specific mammary placodes [29]. Rees JL Genetics of hair and skin color. Genotypes were available for , SNPs. Orange dots represent significantly associated SNPs on a chromosome-wide level, red dots represent significantly associated SNPs on a genome-wide level. The allele frequency was the major determinant for imputation accuracy Figure S2.

Using high-density SNP panels for the identification of mendelian traits in cattle Besides the genome-wide analysis of complex traits and concomitant genomic evaluation of populations, high-density SNP panels offer an invaluable tool for the identification of mendelian pauzch in livestock species [49],[50].

Fries R, Pausch H Individual genome sequencing of livestock animals – En route to dissertaion selection 2. Several QTL have been identified for teat number and teat malformations in swine [78],[79]. Hubert Pausch has a forward-looking vision of customized livestock breeding.


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Red numbers indicate chromosomes with identified QTL. Training Course in Research Pasch Large. LEF1 mediated Wnt signalling is required for the morphogenesis of the mammary gland during embryogenesis [22], while DKK2 acts as an inhibitor of the canonical Wnt signalling [23].

dissertation hubert pausch

An increased activity of the Wnt signalling pathway results in the formation of ectopic placode-like structures [39]. This model yielded autosomal SNPs exceeding the significance threshold and a genome-wide inflation factor of 4.

In order to identify genomic regions predisposing to the development of supernumerary teats in cattle, a GWAS was performed using a PCA based and a mixed model based approach, respectively. Furthermore, causal variants affecting regulatory elements may be dissettation very distantly from the regulated gene, complicating theirs identification considerably [1]. Reducing the incidence of SNTs might thus increase the reproductive performance hhbert cattle, however additional investigations are necessary to confirm this hypothesis.

Proceedings of the National Academy of Sciences Another widely used approach to account for sample structure, albeit rather in human than in livestock GWAS, is accounting for the top axes of variation as inferred by principal components analysis PCA [73].

However, genotyping of cattle populations is mostly performed with a medium-dense genotyping array interrogating 54, SNPs only. ACOP considerably reduces the incidence of serious eye diseases in areas where animals are exposed to increased solar UV radiation [80],[81],[82]. Eye-area pigmentation is routinely recorded during the examination of first-crop daughters of test bulls as a categorical trait.

While traditional breeding schemes relied on progeny phenotyping and subsequent sire evaluation, the genetic value of individuals can now be accurately inferred based on genotype information only i. Comparison of the marker with the pedigree relationship revealed several inconsistencies, most likely resulting from mislabeling of DNA samples and false relationships. It is well known, that distinct signalling pathways are essential for the development of specific mammary placodes [29].


Qianqian Zhang: Towards Cattle Precision Breeding Using Next Generation Sequencing

DYDs for UC were available for animals. Thus, the two QTL might primarily affect fetal growth. Annals of the New York Academy of Sciences Allele substitution effects were estimated for each significant marker in a linear regression model implemented in R www. The identified regions often contain numerous functional candidate genes, rendering the identification of the underlying variant s a difficult task. N e is the major determinant for the number of existing independent chromosome segments [23], implying that denser SNP panels are necessary to capture the genetic variation for populations with large Ne.

Breeds with white heads, e. Incorporating Medical and Surgical Dermatology 8: Breeding value estimation was based on best linear unbiased prediction BLUP animal model.

Qianqian Zhang: Towards Cattle Precision Breeding Using Next Generation Sequencing

Thus, the current assembly must still be considered as a draft version. Journal of Animal Breeding and Genetics The heritability of calving traits, i. Brka M, Reinsch N, Kalm E Determination of the inheritance dissegtation of hyperthelia in cattle by maximum likelihood analysis 1.

dissertation hubert pausch

Prototypical for such traits is human height. TBX3 is regulated as downstream target of Wnt signalling [24].