GEO DataSets

(Submitter supplied) Lameness is an animal welfare issue that incurs substantial financial and environmental costs. This condition is commonly caused by digital dermatitis (DD), sole ulcers (SU), and white line disease (WLD). Susceptibility to these three foot disorders is due in part to genetics, indicating that genomic selection against these foot lesions can be used to reduce lameness prevalence. It is unclear whether selection against foot lesions will lead to increased susceptibility to other common diseases such as mastitis and metritis. more...

Organism:

Bos taurus

Type:

Genome variation profiling by SNP array

Platform:

GPL21267

417 Samples

Download data: IDAT, TXT

(Submitter supplied) The first mitotic division causes both parental genomes present in the zygote to segregate into two biparental diploid daughter cells. This fundamental tenet was challenged by the observation that blastomeres with different genome ploidy and distinct parental genotypes can coexist within individual embryos. We hypothesized that whole parental genomes can segregate into distinct blastomere lines during the multipolar division of the zygote, a phenomenon referred to as “heterogoneic” cell division. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL21267

184 Samples

Download data: IDAT, TXT

(Submitter supplied) Single-cell whole-genome haplotyping allows simultaneous detection of haplotypes associated with monogenic diseases, chromosome copy-numbering and subsequently, has revealed mosaicism in embryos and embryonic stem cells. Methods, such as karyomapping and haplarithmisis, were deployed as a generic and genome-wide approach for preimplantation genetic testing (PGT) and are replacing traditional PGT methods. more...

Organism:

Bos taurus

Type:

Genome variation profiling by array

Platform:

GPL21267

9 Samples

Download data: IDAT, TXT

(Submitter supplied) Sole ulcers (SU) and white line disease (WLD) are noninfectious claw lesions that arise due to compromised horn production and are common causes of lameness in dairy cattle, imposing welfare and profitability concerns. The low to moderate heritability estimates of SU and WLD susceptibility indicate that genetic selection could reduce their prevalence. To identify loci associated with SU and WLD susceptibility, generalized linear mixed model (GLMM) regression and random forest (RF) genome-wide association studies (GWAS) were performed. more...

Organism:

Bos taurus

Type:

Genome variation profiling by SNP array

Platform:

GPL21267

326 Samples

Download data: IDAT, TXT

(Submitter supplied) Digital dermatitis (DD) causes lameness in dairy cattle. To detect quantitative trait loci (QTL) associated with DD, genome-wide association studies (GWAS) were performed using high density single nucleotide polymorphism (SNP) genotypes and binary case/control, quantitative (average number of FW per hoof trimming record), and recurrent (cases with  2 DD episodes vs. controls) phenotypes from cows across four dairies (controls n = 129 vs. more...

Organism:

Bos taurus

Type:

Genome variation profiling by SNP array

Platform:

GPL21267

222 Samples

Download data: IDAT, TAB

(Submitter supplied) Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. more...

Organism:

Bos indicus; Bos grunniens; Bos taurus

Type:

Genome variation profiling by SNP array

Platform:

GPL21267

355 Samples

Download data: IDAT, TXT

(Submitter supplied) Using Illumina® BovineHD Genotyping BeadChip assay, we applied single sperms genotyping from one single Holstein bull to preliminarily describe its recombination map. We received 56 single sperms with qualified genotype information and totally detected 1,526 autosomal crossovers.

Organism:

Bos taurus

Type:

Other; Genome variation profiling by SNP array

Platform:

GPL21267

56 Samples

Download data: IDAT, TXT

(Submitter supplied) Chromosomal instability (CIN) occurs at high frequency during early in vitro embryogenesis and is known to be associated with early embryonic loss in humans. The chromosomal stability of in vivo-conceived cleavage stage embryos largely remains unknown. Here, we applied haplotyping and copy number profiling to investigate genomic architecture of 171 single bovine blastomeres and to compare the nature and frequency of CIN between in vivo embryos, in vitro embryos produced from ovum pick up with ovarian stimulation (OPU-IVF), and in vitro produced embryos from in vitro matured oocytes without ovarian stimulation (IVM-IVF). more...

Organism:

Bos taurus

Type:

SNP genotyping by SNP array

Platform:

GPL21267

236 Samples

Download data: IDAT

(Submitter supplied) Chimaerism and mixoploidy define the presence of cell lineages with different parental genomes or different ploidy states in a single individual. Our knowledge on their mechanistic origin results from indirect observations, often when the cell lineages have been subject to rigorous selective pressure during development. Here, we applied haplarithmisis to infer the haplotypes and the copy number of parental genomes in 116 single blastomeres comprising entire preimplantation stage bovine embryos (n=23) following in vitro fertilization. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL21267

192 Samples

Download data: TXT