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Transcriptome analysis of feather follicles reveals candidate genes and pathways associated with pheomelanin pigmentation in chickens

ABSTRACT: In order to reveal the candidate genes related to yellow plumage in Chinese chicken, a hybrid population of Huiyang Bearded chicken and White Leghorn chicken, and transcriptome data were generated from the yellow and white feather follicle of F3 population in two periods (7 and 11weeks) respectively, using RNA-seq. 127 common different expressed genes were obtained(DEGs) between two periods, these DEGs were mainly enriched in the Gene Ontology classes ‘developmental pigmentation’, ‘melanin biosynthetic process’, ‘melanosome organization’, ‘melanosome membrane’ and ‘melanosome’all related to the pigmentation process. And involved genes were considered as pigment genes that play important roles in melanogenesis. The results reveal key functional genes and possible molecular mechanisms for the elucidation of yellow plumage formation in Chinese indigenous chickens.

ORGANISM(S): Gallus gallus

PROVIDER: GSE146956 | GEO | 2020/03/14

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.

Project description:Plumage color plays a prominent role in reproductive isolation and thus understanding the genetic basis of pigmentation patterns can provide critical insight into speciation. Subspecies of the dark-eyed junco (Junco hyemalis) show marked differences in melanic plumage coloration known to have evolved rapidly since the Last Glacial Maximum just 18,000 years ago. To understand this rapid radiation we studied the pigment composition and the genetic basis of coloration in two divergent subspecies, the slate-colored and Oregon juncos. We used HPLC and light microscopy to investigate pigment deposition patterns in feathers from four body areas. RNA-seq data generated under common garden experimental conditions were then used to compare the relative roles of differential gene expression in growing feathers and sequence divergence in loci expressed during feather development. Junco feathers were found to differ in eumelanin and pheomelanin content and distribution, producing a range of black, gray and brown colors. Transcriptomic data revealed marked regulatory differences among subspecies and among body-parts within subspecies in known melanin-pathway genes (including PMEL, TYR, TYRP1, OCA2, MLANA), but also in several novel or poorly known loci (EDAR, VPS33B, HPS1). Within subspecies, lighter feathers expressed less melanin synthesis genes, more ASIP, and showed differential expression of Wnt signaling genes. Feathers from different body regions also showed differential expression of Hox genes. The two subspecies differed in expression of ASIP and three other genes (MFSD12, KCNJ13, HAND2) previously associated with color development. Sequence variation in the expressed genes was not related to color differences between junco subspecies. Our findings suggest that differential expression of a few genes can account for marked differences in plumage color and pattern, a mechanism that can account for the rapid diversification of juncos. Several novel candidate pigmentation genes found in juncos may contribute to the expression of melanic coloration in other vertebrates.

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Transcriptome analysis of feather follicles reveals candidate genes and pathways associated with pheomelanin pigmentation in chickens

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