Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bos taurus breed:Hereford

ABSTRACT: Mapping of transcription initiation in the bovine genome by RAMPAGE

PROVIDER: PRJNA630504 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11774000_1.fastq.gz	Fastqsanger.gz
	SRR11774000_2.fastq.gz	Fastqsanger.gz
	SRR11774001_1.fastq.gz	Fastqsanger.gz
	SRR11774001_2.fastq.gz	Fastqsanger.gz
	SRR11773902_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 362

Similar Datasets

A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford).

Project description:Ecoregional differences contribute to genetic environmental interactions and impact animal performance. These differences may become more important under climate change scenarios. Utilizing genetic diversity within a species to address such problems has not been fully explored. In this study Hereford cattle were genotyped with 50K Bead Chip or 770K Bovine Bead Chip to test the existence of genetic structure in five U.S. ecoregions characterized by precipitation, temperature and humidity and designated: cool arid (CA), cool humid (CH), transition zone (TZ), warm arid (WA), and warm humid (WH). SNP data were analyzed in three sequential analyses. Broad genetic structure was evaluated with STRUCTURE, and ADMIXTURE software using 14,312 SNPs after passing quality control variables. The second analysis was performed using principal coordinate analysis with 66 Tag SNPs associated in the literature with various aspects of environmental stressors (e.g., heat tolerance) or production (e.g., milk production). In the third analysis TreeSelect was used with the 66 SNPs to evaluate if ecoregional allelic frequencies deviated from a central frequency and by so doing are indicative of directional selection. The three analyses suggested subpopulation structures associated with ecoregions from where animals were derived. ADMIXTURE and PCA results illustrated the importance of temperature and humidity and confirm subpopulation assignments. Comparisons of allele frequencies with TreeSelect showed ecoregion differences, in particular the divergence between arid and humid regions. Patterns of genetic variability obtained by medium and high density SNP chips can be used to acclimatize a temperately derived breed to various ecoregions. As climate change becomes an important factor in cattle production, this study should be used as a proof of concept to review future breeding and conservation schemes aimed at adaptation to climatic events.

| S-EPMC5411102 | biostudies-literature

Sus scrofa breed:Yorkshire

Project description:Mapping of transcription initiation in the swine genome by RAMPAGE

| PRJNA672728 | ENA

Gallus gallus breed:White Leghorn

Project description:Mapping of transcription initiation in the chicken genome by RAMPAGE

| PRJNA672731 | ENA

Bos taurus breed:Hereford

Project description:Transcriptome of Gluteus

| PRJNA356090 | ENA

Bos taurus breed:Hereford

Project description:Transcriptome of Scapula muscle