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Ma Y.,China Agricultural University | Ma Y.,University of Gottingen | Ding X.,China Agricultural University | Qanbari S.,University of Gottingen | And 3 more authors.
Heredity | Year: 2015

Identifying signatures of recent or ongoing selection is of high relevance in livestock population genomics. From a statistical perspective, determining a proper testing procedure and combining various test statistics is challenging. On the basis of extensive simulations in this study, we discuss the statistical properties of eight different established selection signature statistics. In the considered scenario, we show that a reasonable power to detect selection signatures is achieved with high marker density (>1 SNP/kb) as obtained from sequencing, while rather small sample sizes (~15 diploid individuals) appear to be sufficient. Most selection signature statistics such as composite likelihood ratio and cross population extended haplotype homozogysity have the highest power when fixation of the selected allele is reached, while integrated haplotype score has the highest power when selection is ongoing. We suggest a novel strategy, called de-correlated composite of multiple signals (DCMS) to combine different statistics for detecting selection signatures while accounting for the correlation between the different selection signature statistics. When examined with simulated data, DCMS consistently has a higher power than most of the single statistics and shows a reliable positional resolution. We illustrate the new statistic to the established selective sweep around the lactase gene in human HapMap data providing further evidence of the reliability of this new statistic. Then, we apply it to scan selection signatures in two chicken samples with diverse skin color. Our analysis suggests that a set of well-known genes such as BCO2, MC1R, ASIP and TYR were involved in the divergent selection for this trait. © 2015 Macmillan Publishers Limited All rights reserved. Source

Ni G.,University of Gottingen | Strom T.M.,Helmholtz Center Munich | Pausch H.,TU Munich | Reimer C.,University of Gottingen | And 4 more authors.
BMC Genomics | Year: 2015

Background: The technical progress in the last decade has made it possible to sequence millions of DNA reads in a relatively short time frame. Several variant callers based on different algorithms have emerged and have made it possible to extract single nucleotide polymorphisms (SNPs) out of the whole-genome sequence. Often, only a few individuals of a population are sequenced completely and imputation is used to obtain genotypes for all sequence-based SNP loci for other individuals, which have been genotyped for a subset of SNPs using a genotyping array. Methods: First, we compared the sets of variants detected with different variant callers, namely GATK, freebayes and SAMtools, and checked the quality of genotypes of the called variants in a set of 50 fully sequenced white and brown layers. Second, we assessed the imputation accuracy (measured as the correlation between imputed and true genotype per SNP and per individual, and genotype conflict between father-progeny pairs) when imputing from high density SNP array data to whole-genome sequence using data from around 1000 individuals from six different generations. Three different imputation programs (Minimac, FImpute and IMPUTE2) were checked in different validation scenarios. Results: There were 1,741,573 SNPs detected by all three callers on the studied chromosomes 3, 6, and 28, which was 71.6 % (81.6 %, 88.0 %) of SNPs detected by GATK (SAMtools, freebayes) in total. Genotype concordance (GC) defined as the proportion of individuals whose array-derived genotypes are the same as the sequence-derived genotypes over all non-missing SNPs on the array were 0.98 (GATK), 0.97 (freebayes) and 0.98 (SAMtools). Furthermore, the percentage of variants that had high values (>0.9) for another three measures (non-reference sensitivity, non-reference genotype concordance and precision) were 90 (88, 75) for GATK (SAMtools, freebayes). With all imputation programs, correlation between original and imputed genotypes was >0.95 on average with randomly masked 1000 SNPs from the SNP array and >0.85 for a leave-one-out cross-validation within sequenced individuals. Conclusions: Performance of all variant callers studied was very good in general, particularly for GATK and SAMtools. FImpute performed slightly worse than Minimac and IMPUTE2 in terms of genotype correlation, especially for SNPs with low minor allele frequency, while it had lowest numbers in Mendelian conflicts in available father-progeny pairs. Correlations of real and imputed genotypes remained constantly high even if individuals to be imputed were several generations away from the sequenced individuals. © 2015 Ni et al. Source

Cebrian-Serrano A.,Instituto Valenciano Of Investigaciones Agrarias | Cebrian-Serrano A.,BioTalentum Ltd | Silvestre M.A.,Instituto Valenciano Of Investigaciones Agrarias | Silvestre M.A.,University of Valencia | And 2 more authors.
Animal Science Papers and Reports | Year: 2013

A combination of sex-sorted sperm and ovum pick up (OPU) -in vitro fertilization (IVF) techniques could improve the overall efficiency of the process and develop the commercial opportunities for sexsorted sperm. Despite intrinsic differences which have been found between bovine oocytes collected post-mortem from slaughterhouse ovaries and those collected by OPU, only a few studies about IVF with sex-sorted sperm have used oocytes collected by OPU. In addition, to our knowledge, the effect of sex-sorted sperm on embryo development and quality using OPU-oocytes have been studied in buffalo (Bubalus bubalis) and in Bos indicus, but not in Bos taurus, therefore we aim to address this issue in this study. Oocytes were retrieved by OPU from mature dry cows and in vitro matured. In vitro fertilization was performed with sex-sorted or unsorted sperm, and afterwards presumptive zygotes were in vitro cultured for 9 days. Oocytes fertilized with sex-sorted sperm showed a lower cleavage rate (52.43 vs. 69.09%, respectively; P<0.05) but similar blastocyst rate compared to oocytes fertilized by unsorted sperm (29.63 vs. 31.58%, respectively). Moreover, the percentages of excellent or good blastocyst (87.50 vs. 85.71%) as well as the timing of the blastocyst formation at day 7 (10.53 vs. 5.56%) and day 8 (30.26 vs. 24.07%) post IVF was not different between sex-sorted and unsorted groups. In conclusion, sex-sorted sperm and OPU-IVF are efficient and valuable tools to produce bovine embryos of predetermined sex and from individual donors. Source

Bauersachs S.,Gene Center | Ulbrich S.E.,TU Munich | Reichenbach H.-D.,Institute for Animal Breeding | Reichenbach M.,Gene Center | And 8 more authors.
Biology of Reproduction | Year: 2012

Interferon tau (IFNT), a type I IFN similar to alpha IFNs (IFNA), is the pregnancy recognition signal produced by the ruminant conceptus. To elucidate specific effects of bovine IFNT and of other conceptus-derived factors, endometrial gene expression changes during early pregnancy were compared to gene expression changes after intrauterine application of human IFNA2. In experiment 1, endometrial tissue samples were obtained on Day (D) 12, D15, and D18 postmating from nonpregnant or pregnant heifers. In experiment 2, heifers were treated from D14 to D16 of the estrous cycle with an intrauterine device releasing IFNA2 or, as controls, placebo lipid extrudates or PBS only. Endometrial biopsies were performed after flushing the uterus. All samples from both experiments were analyzed with an Affymetrix Bovine Genome Array. Experiment 1 revealed differential gene expression between pregnant and nonpregnant endometria on D15 and D18. In experiment 2, IFNA2 treatment resulted in differential gene expression in the bovine endometrium. Comparison of the data sets from both studies identified genes that were differentially expressed in response to IFNA2 but not in response to pregnancy on D15 or D18. In addition, genes were found that were differentially expressed during pregnancy but not after IFNA2 treatment. In experiment 3, spatiotemporal alterations in expression of selected genes were determined in uteri from nonpregnant and early pregnant heifers using in situ hybridization. The overall findings of this study suggest differential effects of bovine IFNT compared to human IFNA2 and that some pregnancy-specific changes in the endometrium are elicited by conceptus-derived factors other than IFNT. © 2012 by the Society for the Study of Reproduction, Inc. Source

Weikard R.,Leibniz Institute for Farm Animal Biology | Widmann P.,Leibniz Institute for Farm Animal Biology | Buitkamp J.,Institute for Animal Breeding | Emmerling R.,Institute for Animal Breeding | Kuehn C.,Leibniz Institute for Farm Animal Biology
Animal Genetics | Year: 2012

A parallel association study was performed in two independent cattle populations based on 41 validated, targeted single nucleotide polymorphisms (SNPs) and four microsatellite markers to re-evaluate the multiple quantitative trait loci (QTL) architecture for milk performance on bovine chromosome 6 (BTA6). Two distinct QTL located in the vicinity of the middle region of BTA6, but differing unambiguously regarding their effects on milk composition and yield traits were validated in the German Holstein population. A highly significant association of the protein variant ABCG2 p.Tyr581Ser with milk composition traits reconfirmed the causative molecular relevance of the ABCG2 gene in QTL region 1, whereas in QTL region 2, significant and tentative associations between gene variants RW070 and RW023 (located in the promoter region and exon 9 of the PPARGC1A gene for milk yield traits) were detected. For the German Fleckvieh population, only RW023 showed a tentative association with milk yield traits, whereas those loci with significant effects in German Holsteins (ABCG2 p.Tyr581Ser, RW070) showed fixed alleles. Even though our new data highlight two variants in the PPARGC1A gene (RW023, RW070) in QTL region 2, based on the results of our study, currently no unequivocal conclusion about the causal background of this QTL affecting milk yield traits can be drawn. Notably, the German Holstein and Fleckvieh populations, known for their divergent degree of dairy type, differ substantially in their allele frequencies for the growth-associated NCAPG p.Ile442Met locus. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics. Source

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