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Comparative transcriptome profiles of Lindian chicken eyelids identify melanin genes controlling eyelid pigmentation

ABSTRACT: 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.

ORGANISM(S): Gallus gallus

PROVIDER: GSE101452 | GEO | 2018/10/25

REPOSITORIES: GEO

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Project description:Ma-Huang chicken as a high-quality broiler is one of the most popular chickens in the frozen chicken market. However, some chicken may instead have white or lighter skin, which directly causes economic losses every year. To obtain better insight into the molecular mechanisms associated with the process of pigmentation of yellow-skinned broilers reared under intensive conditions, a total of six-hundred Ma-Huang chickens was randomly selected in a single slaughterhouse, the color measurements were carried out on both cloaca(alive) and five different part after slaughtering adopting the L* a* b* system and using a 3nh-NH310 colorimeter, color values from areas of the chicken skin pear each image automatically retrieved by MATLAB, production and slaughtering traits were also measured, comparative transcriptomic analysis of high yellowness(s_deep) versus low yellowness(s_light) skin was performed using the Illumina Hiseq 4000. Average values of the cloaca(alive), cloaca (hair removal), thigh, shank and abdominal fat were 8.98, 7.66, 2.62, 7.29 and 12.86, respectively. The better production and slaughtering traits were observed in higher skin yellowness chicken. Yellowness values of the cloaca(alive) and after slaughtering were significantly correlated (p < 0.05), suggesting that the color of after slaughtering evaluation may be carried out on cloaca(alive). A total of 19061 unigenes were assembled from the reads obtained from the skin of two groups, 882 unigenes were differentially expressed between s_deep and s_light (Fold change ≥ 2, Adjusted P <= 0.001), 612 that up-regulated and 270 that down-regulated genes in s_deep skin, as compared with s_light skin. Twelve promising candidate genes may play an important role in the pigmentation of chicken skin, i.e. GPR143, PMEL, TYR, CYP11A1, TECRL, ACACB, TLR2B, ALDH1A3, FHL2, TECRL, DUOX2, SMOC1 were included. Furthermore, some important functional pathways were revealed, such as the biological process, cellular component and molecular function, which appear to be much activity in skin pigmentation. Our data provide a valuable resource for identifying genes whose functions are critical to skin pigmentation, facilitate understanding the molecular mechanisms of the skin color variation on yellow-skinned broiler chickens under commercial conditions, accelerate the molecular selection of the specific strain on consistent skin colors which allow reduction in pigment use to achieve the skin acceptance by the consumer.

Dataset Information

Comparative transcriptome profiles of Lindian chicken eyelids identify melanin genes controlling eyelid pigmentation

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