Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation of cattle genetic variants

ABSTRACT: An investigation into a sub set of cattle genetic variantion

PROVIDER: PRJEB75603 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Investigation of cattle genetic variants

Project description:An investigation into a sub set of cattle genetic variantion

2024-06-05 | PRJEB53221 | EVA

Investigation of genomic imprinting in cattle

Project description:Investigation of genomic imprinting in cattle

| PRJNA545948 | ENA

Next generation sequencing reveals the diversity and population-genetic properties of cattle CNVs

Project description:Structural and functional impacts of copy number variations (CNVs) on livestock genomes are not yet well understood. In this study, we have identified 1853 CNV regions (CNVRs) using population-scale sequencing data generated from 75 cattle of 8 breeds (Holstein, Angus, Jersey, Limousin, Romagnola, Brahman, Gir and Nelore). Individual genome sequence coverage ranged from 4 to 30 fold, with a mean of 11.8 fold. A total of 3.1% (87.5 Mb) of the cattle genome is predicted to be copy number variable, representing a substantial increase over the previous estimates (~2%). This dataset was highly correlated with array CGH data (r2 = 0.761) and was validated to be accurate with an estimated 12% false positive rate and a 19% false negative rate based on qPCR and array CGH, respectively. Hundreds of CNVs were found to be either breed specific or differentially variable across breeds, including the RICTOR gene in dairy breeds and the PNPLA3 gene in the beef breeds. In contrast, clusters of the PRP and PAG genes are duplicated in all sequenced animals, implicating that subfunctionalization, neofunctionalization or overdominance play a role in diversifying these fertility related genes. Further population-genetic analyses based on CNVs revealed the population structures of these taurine and indicine breeds and uncovered hundreds of positively selected CNV candidates near important functional genes. These CNV results provide a new glimpse of diverse selections during cattle speciation, domestication, breed formation, and recent genetic improvement.

2015-11-04 | GSE62990 | GEO

Investigation into the Genetic Control of Micronutrient Metabolism

Project description:Investigation into the Genetic Control of Micronutrient Metabolism

| PRJNA258427 | ENA

Investigation of genetic compensation in tdp1-/- zebrafish embryos

Project description:Investigation of genetic compensation in tdp1-/- zebrafish embryos

| PRJNA626551 | ENA

Genetic factors underlying immune response to tick infestation of resistant and susceptible cattle unrevealed by omics data integration

Project description:Genetic factors underlying immune response to tick infestation of resistant and susceptible cattle unrevealed by omics data integration

2023-12-01 | GSE224634 | GEO

Expression analysis of rumen epithelium of cattle during weaning

Project description:Investigation of whole genome gene expression level changes in rumen epithelium of dairy cattle at different stages of rumen development and on different diets.

2009-11-01 | GSE18382 | GEO

Investigation of barley genetic variants

Project description:An investigation into a sub set of barley genetic variantion

2023-01-20 | PRJEB59041 | EVA

Investigation of Duck genetic variants

Project description:An investigation into a sub set of duck genetic variantion

2023-03-18 | PRJEB43764 | EVA

Investigation of dugong genetic variants

Project description:An investigation into a sub set of dugong genetic variantion

2024-08-26 | PRJEB79357 | EVA