Skin Transcriptome Profiles Associated with Skin Color in Chickens

Abstract

Nutritional and medicinal benefits have been attributed to the consumption of tissues from the black-boned chickens in oriental countries. Lueyang black-boned chicken is one of the native chicken breeds. However, some birds may instead have white or lighter skin, which directly causes economic losses every year. Previous studies of pigmentation have focused on a number of genes that may play important roles in coat color regulation. Illumina2000 sequencing technology was used to catalog the global gene expression profiles in the skin of the Lueyang chicken with white versus black skin. A total of 18,608 unigenes were assembled from the reads obtained from the skin of the white and black chickens. A total of 649 known genes were differentially expressed in the black versus white chickens, with 314 genes that were up regulated and 335 genes that were down-regulated, and a total of 162 novel genes were differentially expressed in the black versus white chickens, consisting of 73 genes that were up-regulated (including 4 highly expressed genes that were expressed exclusively in the skin of the black chickens) and 89 genes that were down-regulated. There were also a total of 8 known coat-color genes expressed in previous studies (ASIP, TYR, KIT, TYRP1, OCA2, KITLG, MITF and MC1R). In this study, 4 of which showed greater expression in the black chickens, and several were up-regulated, such as KIT, ASIP, TYR and OCA2. To our surprise, KITLG, MITF and MC1R showed no significant difference in expression between the black- and white-skinned chickens, and the expression of TYRP1 was not detected in either skin color. The expression of ASIP, TYR, KIT, TYRP1, OCA2, KITLG, MITF and MC1R was validated by real-time quantitative polymerase chain reaction (qPCR), and the results of the qPCR were consistent with the RNA-seq. This study provides several candidate genes that may be associated with the development of black versus white skin. More importantly, the fact that the MC1R gene showed no significant difference in expression between the black and white chickens is of particular interest for future studies that aim to elucidate its functional role in the regulation of skin color.

Illumina-sequencing based transcriptome study of coat color phenotypes in domestic goats

“…The genes with a red frame are upregulated and the genes with a green frame are down-regulated in the three comparison groups sheep, horse, pig, dog and donkey (Abitbol et al 2015;Ciampolini et al 2013;Drogemuller et al 2006;Han et al 2015;Norris and Whan 2008;Rieder et al 2001). Our finding that ASIP was detected only in the white skin and not in the dark skin is in contrast to an earlier finding in chickens that showed significantly greater ASIP expression in birds with black skin (Zhang et al 2015). MC1R is downstream of ASIP, but still fairly upstream in the melanogenesis pathway.…”

“…Like ASIP, MC1R mutations are associated with coat color variation in many domesticated species (e.g., cattle, sheep, pig, horse, rabbit, chicken, dog, cat, Japanese quail) (Fontanesi et al 2006;Joerg et al 1996;Kijas et al 1998;Marklund et al 1996;Nadeau et al 2006;Newton et al 2000;Schmutz et al 2003;Vage et al 1999). However, previous studies showed no significant differences in MC1R expression between the white skin and black spots in sheep and in black and white-skinned Lueyang chickens (Penagaricano et al 2012;Zhang et al 2015). Similarly, we observed no significant differences in MC1R expression between the goat skins with three different coat colors used in this study.…”

Transcriptome Profile Analysis of Mechanisms of Black and White Plumage Determination in Black-Bone Chicken

“…To compare DEGs in melanin pigmentation between skin and plumage, eight well known melanogenesis-related genes (MITF, TYR, KIT, OCA2, ASIP, MCIR, KITLG, and TYRP1 [56, 57]) from previous researches in chickens were checked in black and white feather bulbs using RNA-seq and quantitative real-time polymerase chain reaction (qRT-PCR). RNA-seq analysis showed that except for TYR and MITF (P < 0.05), no significant difference in expression was detected between black and white chicken feather bulbs (P> 0.05).…”

Comparative transcriptome analysis by deep RNA sequencing at early stage of skin pigmentation in goats (Capra hircus)

“…Although transcriptomic investigations on variations in skin color have been conducted in the common carp (Jiang and Bikle 2014b; Wang et al 2014), red tilapia (Zhu et al 2016), and chickens (Zhang et al 2015), few studies have investigated this topic in mammals to date. We first characterized the skin transcriptome in two breeds of fetal goats that feature different skin colors using deep RNA-seq methods.…”

“…In addition, few studies have characterized the global gene expression profile of skin pigmentation and development. Although investigations of the skin transcriptome have recently been conducted on coat color (Fan et al 2013) and hair follicles (Xu et al 2013a; Xu et al 2013b; Wang et al 2015; Yue et al 2015; Gao et al 2016) in sheep and goats, and skin color in the common carp (Jiang and Bikle 2014b; Wang et al 2014), red tilapia (Zhu et al 2016), and chickens (Zhang et al 2015), the genetic basis for skin pigmentation is not well understood compared to that of hair or coat color.…”