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Series GSE110145 Query DataSets for GSE110145
Status Public on May 05, 2018
Title Genome-wide association study and transcriptome analysis provide new insights into the white/red earlobe color formation in chicken
Organism Gallus gallus
Experiment type Genome variation profiling by high throughput sequencing
Summary Background: Earlobe color is a typical external trait in chicken. There are some previous studies showing that the chicken white/red earlobe color is a polygenic and sex-linked trait in some breeds, but its molecular genetic and histological mechanisms still remain unclear. Methods: We herein utilized histological section, genome-wide association study (GWAS) and RNA-seq, further to investigate the potential histological and molecular genetic mechanisms of white/red earlobe formation in Qiangyuan Partridge chicken (QYP). Results: through histological section analysis, we found the dermal papillary layer of red earlobes had many more blood vessels than that of white earlobes. And we identified a total of 44 SNPs from Chromosome 1, 2, 3, 4, 9, 10, 11, 13, 19, 20, 23 and Z, that was significantly associated with the chicken white/red earlobe color from GWAS, along with 73 significantly associated genes obtained (e.g., PIK3CB, B4GALT1 and TP63), supporting the fact that the white/red earlobe color was also polygenic and sex-linked in QYP. Importantly, PIK3CB and B4GALT1 are both involved in the biological process of angiogenesis, which may directly give rise to the chicken white earlobe formation through regulating blood vessel density in chicken earlobe. Additionally, through contrast of RNA-seq profiles between white earlobe skins and red earlobe skins, we further identified TP63 and CDH1 differentially expressed. Combined with the existing knowledge of TP63 in epithelial development and tumor angiogenesis, we propose that down-regulated TP63 in white earlobes may play roles in thickening the skin and decreasing the vessel numbers in dermal papillary layer, thereby contributing to the white earlobe formation via paling the redness of the skin in QYP, but the specific mechanism remains further clarified. Conclusion: our findings advance the existing understanding of the white earlobe formation, as well as provide new clues to understand the molecular mechanism of chicken white/red earlobe color formation.
 
Overall design 100 QYPs with white earlobe and 100 QYPs with red earlobe were separately genotyped for GWAS. Genotyping strategy was based on Specific-Locus Amplified Fragment Sequencing. GWAS was based on Plink case-control model.
 
Contributor(s) Luo W, Xu J
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Submission date Feb 05, 2018
Last update date Nov 10, 2021
Contact name Wei Luo
E-mail(s) 799166371@qq.com
Phone 0086+13926427090
Organization name South China Agricultural University
Department The College of Animal Science
Lab Animal genetics and reproduction
Street address Wushan Road
City Guangzhou
State/province Guangdong
ZIP/Postal code 510642
Country China
 
Platforms (2)
GPL16133 Illumina HiSeq 2000 (Gallus gallus)
GPL23499 Illumina HiSeq 4000 (Gallus gallus)
Samples (200)
GSM2978514 1: white earlobe
GSM2978515 2: white earlobe
GSM2978516 3: white earlobe
Relations
BioProject PRJNA432949
SRA SRP132196

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE110145_ear_color_plink_p_value_out_replacement.txt.gz 1.3 Mb (ftp)(http) TXT
GSE110145_filter0.8.filter.snplist_replacement.txt.gz 14.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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