GEO DataSets

(Submitter supplied) Here, we report on a novel chicken comb phenotype, designated Antler-comb. Using a 600K Axiom® Genome-Wide Chicken Genotyping Array, we separately genotyped 12 and 24 female Hetian Wildtype-comb and Antler-comb chickens, respectively. Meanwhile, we sequenced the genomes of 10 Hetian Antler-comb and 10 Wildtype-comb chickens to interrogate the GWAS results and explore the potential genetic variants underlying this phenotype. more...

Organism:

Gallus gallus

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL23815

36 Samples

Download data: CEL, XLSX

(Submitter supplied) Campylobacter jejuni is a common cause of diarrheal disease worldwide. Human infection typically occurs through the ingestion of contaminated poultry products. We previously demonstrated that an attenuated Escherichia coli live vaccine strain expressing the C. jejuni N-glycan on its surface reduces the Campylobacter load in more than 50% of vaccinated leghorn and broiler birds to undetectable levels (responder birds), whereas the remainder of the animals were still colonized (non-responders). more...

Organism:

Gallus gallus

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL23815

134 Samples

Download data: CEL, TXT

(Submitter supplied) The conservation and development of chicken has considerably affected human activities, but the admixture history of chicken breeds has so far been poorly demonstrated especially for Chinese indigenous breeds. Using genotypes from 580961 single nucleotide polymorphism markers scored in 1201 animals, we evaluate the genetic diversity (heterozygosity and proportion of polymorphic markers), Linkage disequilibrium (LD) decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance) and migration events (Treemix and f-statistics) of eight domesticated chicken breeds. more...

Organism:

Gallus gallus

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL23815

1193 Samples

Download data: CEL, TXT

(Submitter supplied) Dongxiang blue-shelled chicken, an indigenous chicken breed in China, has segregated significantly for the dermal hyperpigmentation phenotype. Two lines of the chicken have been divergently selected with respect to comb color for over 20 generations. The recent selection has also resulted in a significant difference in egg production. The red comb line (RCL) chicken produces significantly higher number of eggs than that by the dark comb line (DCL) chicken. more...

Organism:

Gallus gallus

Type:

SNP genotyping by SNP array

Platform:

GPL23815

178 Samples

Download data: CEL, TXT

(Submitter supplied) DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals. The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).

Organism:

Gallus gallus

Type:

Genome variation profiling by SNP array

Platform:

GPL23815

96 Samples

Download data: CEL, VCF

(Submitter supplied) The genetic foundation of chicken tail feather color is not very well studied to date, though that of body feather color is extensively explored. In the present study, we used a synthetic chicken dwarf line (DW), which was originated from the hybrids between a black tail chicken breed, Rhode Island Red (RIR) and a white tail breed, Dwarf Layer (DL), to understand the genetic rules of the white/black tail color. more...

Organism:

Gallus gallus

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL23815

176 Samples

Download data: CEL, TXT

(Submitter supplied) Beak deformities (BD) of different forms have been documented in many wild birds. The phenomenon is termed as “the largest epizootic of gross abnormalities ever recorded among wild bird populations.” Frequencies of 1% to 3% of BD (crossed beaks) were found in several indigenous chickens including Silkies, Qingyuan Partridge, Huxu, and the Beijing-You (BJY) chickens (studied here). Birds with deformed beaks have poor production performance and induce higher mortality. more...

Organism:

Gallus gallus

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL23815

96 Samples

Download data: CEL, TXT

(Submitter supplied) #%chip_type=Axiom_GW_GT_Chicken #%genome-species=Gallus gallus #%genome-version=galGal5 Protocol: see manufacturer's web site

Organism:

Gallus gallus

7 Series

1909 Samples

Download data: CSV