Project description:During the long history of chicken domestication, eyelid color, like skin color and shank color, has been one of the unique physical traits of Chinese indigenous chickens that influence consumer behavior. In China, the Lindian chicken, which has colored feathers, is renowned for the appetizing flavor of its meat and eggs, and its eyelid colors varies from deep to light shades, including black, gray, red, and light yellow. To identify the genes controlling eyelid pigmentation, the expression profiles of black and light-yellow eyelids of Lindian chickens were analyzed with transcriptome sequencing. We detected 13,466 genes expressed in the eyelids, among which 14 were differentially expressed. A KEGG pathway analysis showed that tyrosine metabolism and melanogenesis genes were significantly enriched among these DEGs (corrected P < 0.05). Therefore, we infer that melanin metabolism is one of main factors affecting Lindian chicken eyelid pigmentation. In summary, we have identified the melanin genes responsible for eyelid pigmentation of the Lindian chicken, and also provide a valuable resource for the future study of the physical traits of chickens.

2018-10-25 | GSE101452 | GEO

Skin transcriptome profiles associated with skin color in chickens

Project description:This work was to study the transcriptome profiles in the skin of chickens with black versus white skin using high-throughput RNA deep-sequencing technology, to investigate the different expression profiles of the genes involved in skin pigmentation, then look for the main differences between black and white skin colors in Lueyang chickens. 16-week-old white and black female Lueyang chickens (5 birds per color) were selected for the sample collection. A piece of skin (8 mm in diameter) from the left back was collected . Total RNA was extracted from the sample using Trizol reagent . Three RNA samples from either the black or white skin samples were pooled following mRNA isolation. The sequencing of the library was performed using an Illumina HiSeq 2000 (LianChuan Sciences, Hangzhou, China). According the result of sequencing, some colored gene expressions were validated using Real time quantitative polymerase chain reaction (qPCR).

2015-05-20 | E-GEOD-68460 | biostudies-arrayexpress

Project description:Resequencing data for black-bone chicken

| PRJNA1021750 | ENA

Project description:transcriptome data for black-bone chicken

| PRJNA1056484 | ENA

Affymetrix SNP array data for Dwarf and Rhode Island Red chicken samples

Project description: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. The DW line still contain the individuals with black or white tails, even if the body feather are predominantly red, after more than ten generation of self-crossing and being selected for the body feather color. We firstly performed four crosses using the DW line chickens including black tail male to female, reciprocal crosses between the black and white, and white male to female to elucidate the inheritance pattern of the white/black tail. We found that (i) the white/black tail feather colors are independent of body feather color and (ii) the phenotype are autosomal simple trait and (iii) the white are dominant to the black in the DW lines. Furtherly, we performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color by using black tail chickens from the RIR and DW chickens and white individuals from DW lines.

2019-05-02 | GSE130568 | GEO

Gallus gallus isolate:China | breed:Xichuan black-bone chickens

Project description:Gallus gallus isolate:China | breed:Xichuan black-bone chickens Raw sequence reads

| PRJNA642410 | ENA