Fig 3 - available via license: Creative Commons Attribution 4.0 International
Content may be subject to copyright.
A heat-map exploring the differences in gene expression between WS and BS. Different colors represent different expression levels; a darker color represents higher expression and a greater log2 (RPKM) value.
Source publication
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 hav...
Citations
... The black-bone chicken is a highly prized breed in China due to its medicinal attributes, and it is often utilized in traditional Chinese medicinal dishes to promote health of body (Geng et al., 2010;Zhu et al., 2014;Zhang et al., 2015). Numerous studies have substantiated the medicinal qualities of black-bone chicken, attributing them to the abundant melanin content within the meat. ...
The blackness traits, considered an important economic factor in the black-bone chicken industry, still exhibits a common phenomenon of significant difference in blackness of breast muscle. To improve this phenomenon, this study compared growth traits, blackness traits, and transcriptome of breast muscles between the High Blackness Group (H group) and Low Blackness Group (L group) in the Xuefeng black-bone chickens. The results are as follows: 1) There was no significant difference in growth traits between the H group and the L group (P > 0.05). 2) The skin/breast muscle L values in the H group were significantly lower than those in the L group, while the breast muscle melanin content exhibited the opposite trend (P < 0.05). 3) A significant negative correlation was observed between breast muscle melanin content and skin/breast muscle L value (P < 0.05), and skin L value exhibiting a significant positive correlation with breast muscle L value (P < 0.05). 4) The breast muscle transcriptome comparison between the H group and L group revealed 831 and 405 DEGs in female and male chickens, respectively. This included 37 shared DEGs significantly enriched in melanosome, pigment granule, and the melanogenesis pathway. Seven candidate genes (DCT, PMEL, MLANA, TYRP1, OCA2, EDNRB2, and CALML4) may play a crucial role in the melanin production of breast muscle in Xuefeng black-bone chicken. The findings could accelerate the breeding process for achieving desired levels of breast muscle blackness and contribute to the exploration of the mechanisms underlying melanin production in black-bone chickens.
... With the development of next-generation sequencing technology, RNA sequencing (RNA-seq) technology has been widely used to reveal the genetic mechanisms underlying normal chicken skin color, as well as the development of embryonic and adult feathers [13][14][15]. However, few researchers have focused on feather and hair follicle changes during IM. ...
... The series test of cluster analysis was performed for all target differential genes in the 20 models obtained ( Figure 6A). Statistically significant color modules, namely modules 19,17,16,13,14,4,12, and 11 (p < 0.05), were identified. Module 19, consisting of 366 DEGs, exhibited an increasing trend, as shown in Figure 6B. ...
Simple Summary
Feather replacement is one of the most typical features of fasting-induced physiological remodeling, but the specific mechanism is unknown. By observing the changes in feathers and hair follicles throughout the process, this study reveals that molting can increase the market value of culled laying hens and improve the carcass appearance of chilled chickens. In addition, combined with transcriptome sequencing, candidate genes related to hair follicle development were found, namely DSP, CDH1, PKP1, etc., and a specific pathway elucidating how thyroid hormone affects feathering was proposed. These data provide a valuable resource for the analysis of the molecular mechanisms underlying the cyclical growth of hair follicles in the skin during induced molting.
Abstract
Induced molting is a common method to obtain a new life in laying hens, in which periodic changes in feathers are the prominent feature. Nevertheless, its precise molecular mechanism remains unclear. In this study, feather and hair follicle samples were collected during fasting-induced physiological remodeling for hematoxylin–eosin staining, hormone changes and follicle traits, and transcriptome sequencing. Feather shedding was observed in F13 to R25, while newborns were observed in R3 to R32. Triiodothyronine and tetraiodothyronine were significantly elevated during feather shedding. The calcium content was significantly higher, and the ash content was significantly lower after the changeover. The determination of hair follicle traits revealed an increasing trend in pore density and a decrease in pore diameter after the resumption of feeding. According to RNA-seq results, several core genes were identified, including DSP, CDH1, PKP1, and PPCKB, which may have an impact on hair follicle growth. The focus was to discover that starvation may trigger changes in thyroid hormones, which in turn regulate feather molting through thyroid hormone synthesis, calcium signaling, and thyroid hormone signaling pathways. These data provide a valuable resource for the analysis of the molecular mechanisms underlying the cyclical growth of hair follicles in the skin during induced molting.
... Differential gene expression analysis of our study also identified several melanin-related genes in both comparison groups (TH-1245 vs. BY-1245 and TH-1245 vs. YG-1245) that have been reported by numerous studies, such as TYRP1 (Yu et al., 2018a(Yu et al., ,b, 2023, HOXC9 (Zhang et al., 2015), PMEL (Yu et al., 2018b;Zheng et al., 2020), SLC6A9 (Zheng et al., 2020), and MLANA (Yu et al., 2018b). In a skin transcriptome profile analysis associated with the skin color of Lueyang blackboned chicken, a total of 649 differentially expressed genes (|log2 (FC)| > 1, P value ≤0.05) were identified between black and white skin chickens (BS vs. WS), including 314 upregulated genes and 335 downregulated genes. ...
The large amount of melanin deposited in Taihe black-boned silky fowl and other black-boned chicken breeds is a highly valued trait due to its desirable nutritional and functional properties, such as antiaging, immune-enhancing, and antifatigue properties. To identify the candidate genes and pathways potentially responsible for melanogenesis in Taihe black-boned silky fowl, digital gene expression tag (DGE-tag)-based transcriptome analyses were performed for 2 groups: wild-type Taihe black-boned silky fowl (TH-1245) vs. mutated Taihe black-boned silky fowl (BY-1245) and TH-1245 vs. wild-type Yugan black-boned chicken (YG-1245). In total, 430 and 765 differentially expressed genes (DEGs) were identified and 13 DEGs displaying different gene expression patterns between the 2 groups were considered valuable for further investigation, such as ANKRD1, MYOZ2, and MYOD1. Furthermore, 6 functionally grouped networks composed of 36 significant GO terms, mainly involved in muscle-related and signaling-related biological processes, were screened by functional enrichment network analysis. In addition, protein–protein interaction (PPI) network analysis identifies 2 top clusters containing 20 hub genes for 2 comparison groups. MYL1 and RPS14 were considered the most potential candidate genes among all hub genes. The Gene Set Enrichment Analysis (GSEA) results showed that the terms and pathways, such as muscle system process, arachidonic acid metabolism, melanogenesis, and tyrosine metabolism, may play important roles in the melanogenesis and further investigations were needed to clarify the relationships between these pathways and melanin. Overall, these results are helpful for furthering our understanding of melanogenesis in breast muscle of Taihe black-boned silky fowl and Yugan black-boned chicken.
... In recent years, several key genes involved in melanin deposition have been identified. These include MLPH, TYR, KIT, PMEL, MITF, agouti signaling (ASIP), melanocortin 1 receptor (MC1R), and endothelin 3 (EDN3) [32]. However, there has been little research on the association of pigmentation on chicken feathers. ...
As an essential genetic and economic trait, chicken feather color has long been an important research topic. To further understand the mechanism of melanin deposition associated with coloration in chicken feathers, we selected feather follicle tissues from the neck and wings of chickens with differently colored feathers (yellow, sub-Columbian, and silver) for transcriptome analysis. We focused on genes that were expressed in both the wings and neck and were expressed with the same trends in breeds with two different plumage colors, specifically, SLC45A2, GPNMB, MLPH, TYR, KIT, WNT11, and FZD1. GO and KEGG enrichment analyses showed the DEGs were enriched in melanin-related pathways, such as tyrosine metabolic pathway and melanogenesis, and PPI analysis highlighted the genes SLC45A2 and GPNMB as associated with melanin deposition. Verification experiments in chicken melanocytes demonstrated that these two genes promote melanocyte melanin deposition. These data enrich our knowledge of the mechanisms that regulate chicken feather color.
... Dou et al. [8] used transcriptome analysis to identify 25 differentially expressed genes and 11 transcription factors in the melanogenesis pathway and found that TFAP2B, TFAP2A, TCF21, and ELF3 genes may be the key genes regulating tyrosine metabolism and melanogenesis in chicken muscle. Zhang et al. [9] identified 649 differentially expressed genes on the black and white skin of Xianyang chickens and found KIT, ASIP, TYR, and OCA2 genes to be the main regulatory genes for melanin deposition in the skin of Xianyang chickens. Zhang et al. [10] revealed through high throughput sequencing that lncRNA LMEP on the regulatory mechanism of melanin deposition in the skin of Xichuan chickens. ...
... In this study, we did not find significant differences in the expression of the MITF gene in the skin of black and white meat chickens. Our findings are in agreement with those of Dou et al. [8] and Zhang et al. [9]. Yuan et al. [35] studied the eyelids of Lindian chickens and also found that the expression of the DCT gene was higher in black eyelids than in yellow eyelids. ...
Simple Summary
Chicken meat with high melanin content in black-boned chickens is considered a highly nutritious food with potential medicinal value. Tengchong Snow chicken is one of the valuable poultry resources in Yunnan Province, and this chicken is usually dominated by dark meat. However, during the rearing process, we found that a small number of white meat traits still existed in this chicken population. The purpose of this study was to investigate the deposition pattern and molecular mechanism of melanin formation in Tengchong Snow chickens. We selected Tengchong Snow black meat chicken (Bc) and white meat chicken (Wc) as the study subjects to determine differences in the luminance value (L value) and melanin content in their skin tissues at 1, 42 and 90 days; the L value and melanin content of the skin were measured using color chromatography, ELISA kits, and enzyme markers. We found that age had an effect on skin L values and melanin content. The L value gradually increased with age, while melanin content showed the opposite trend. Moreover, the L value of the skin tissue was negatively correlated with melanin content. Finally, we identified the TYR, DCT and EDNRB2 genes as being the possible main effector genes affecting skin pigmentation using transcriptome profiling; the expression of the TYR, DCT, MC1R, EDNRB2, GPR143, MITF, and TYRP1 genes also gradually decreased with increasing day age. In conclusion, this study describes and reveals the differences in L values and melanin content in chicken skin tissues. The results of the study provide a valuable theoretical basis for future breeding programs of Tengchong Snow chickens, as well as a foundation for studies on skin tone deposition and a theoretical reference for the future conservation and utilization of black-boned chickens.
Abstract
Tengchong Snow chickens are one of the most precious, black-boned chickens in Yunnan province and usually produce black meat. However, we found a small number of white meat traits in the chicken population during feeding. In order to determine the pattern of melanin deposition and the molecular mechanism of formation in the Tengchong Snow chicken, we measured the luminance value (L value) and melanin content in the skin of black meat chickens (Bc) and white meat chickens (Wc) using a color colorimeter, ELISA kit, and enzyme marker. The results showed that the L value of skin tissues in black meat chickens was significantly lower than that of white meat chickens, and the L value of skin tissues gradually increased with an increase in age. The melanin content of skin tissues in black meat chickens was higher than that of white meat chickens, and melanin content in the skin tissues gradually decreased with an increase in age, but this difference was not significant (p > 0.05); the L value of skin tissues in black meat chickens was negatively correlated with melanin content, and the correlation coefficient was mostly above −0.6. In addition, based on the phenotypic results, we chose to perform the comparative transcriptome profiling of skin tissues at 90 days of age. We screened a total of 44 differential genes, of which 32 were upregulated and 12 were downregulated. These DEGs were mainly involved in melanogenesis, tyrosine metabolism and RNA transport. We identified TYR, DCT, and EDNRB2 as possible master effector genes for skin pigmentation in Tengchong Snow black meat chickens through DEGs analysis. Finally, we measured the mRNA of TYR, DCT, MC1R, EDNRB2, GPR143, MITF, and TYRP1 genes through a quantitative real-time polymerase chain reaction (qPCR) and found that the mRNA of all the above seven genes decreased with increasing age. In conclusion, our study initially constructed an evaluation system for the black-boned traits of Tengchong Snow chickens and found key candidate genes regulating melanin deposition, which could provide an important theoretical basis for the selection and breeding of black-boned chickens.
... The black color difference in Cemani chickens is caused by the semi-dominant Fibromelanosis gene (Shinomiya et al. 2012). Gene mutations control color expression in chickens (Zhang et al. 2015). In addition, a recent study discovered that the different genotypes in the Cemani population, i.e. homozygous Fm/Fm and heterozygous Fm/fm + , have differing levels of blackness (Dharmayanthi et al. 2017;Dharmayanthi et al. 2022). ...
Cemani chicken is an Indonesian native chicken with black hyperpigmentation on feathers, skin, beak, comb, and flesh. Hyperpigmentation in chickens is called Fibromelanosis. Fibromelanosis in Cemani chickens is semi–dominant, producing two genotypes: homozygous (Fm/Fm) and heterozygous (Fm/fm+). Cemani chicken meat’s black color may indicate a higher mineral content than regular chicken meat. The study’s is aims are to detect genotype homozygous (Fm/Fm) and heterozygous (Fm/fm+) mutations and to determine the mineral content of Cemani chickens with homozygous (Fm/Fm) and heterozygous (Fm/fm+) genotypes. In the Cemani chicken population (n = 32), the Fm–specific allele genotype was detected using a Polymerase Chain Reaction–Restriction Fragment Length Polymorphism (PCR–RFLP) and the MluI restriction enzyme. The mineral contents of Cemani chicken tested were Fe, Zn, Mn, and Se. The results showed that homozygous Cemani chickens (Fm/Fm) had higher Fe and Zn mineral content. However, the homozygous (Fm/Fm) and heterozygous (Fm/fm+) Cemani chicken were not different in mineral content of Se and Mn. This study found that different genotypes of Cemani chicken had different mineral compositions. In the future, this analysis supports the selection of chicken strains with high antioxidant levels.
... In Botia superciliaris, the overexpression of miR-217-5p can inhibit pheomelanin formation by targeting Gsta2 (Zgc) [23]. Although transcriptomic investigations of variations in skin colour have been conducted in common carp [24], chicken (Gallus gallus) [25], red tilapia (Oreochromis mossambicus) [26], red crucian carp (Carassius auratus, red var.) [27], and Japanese flounder (Paralichthys olivaceus) [28], few studies have checked into this topic in reptiles to date. ...
Background
Aquatic animals show diverse body coloration, and the formation of animal body colour is a complicated process. Increasing evidence has shown that microRNAs (miRNAs) play important regulatory roles in many life processes. The role of miRNAs in pigmentation has been investigated in some species. However, the regulatory patterns of miRNAs in reptile pigmentation remain to be elucidated. In this study, we performed an integrated analysis of miRNA and mRNA expression profiles to explore corresponding regulatory patterns in embryonic body colour formation in the soft-shelled turtle Pelodiscus sinensis .
Results
We identified 8 866 novel genes and 9 061 mature miRNAs in the skin of Chinese soft-shelled turtles in three embryonic stages (initial period: IP, middle period: MP, final period: FP). A total of 16 563 target genes of the miRNAs were identified. Furthermore, we identified 2 867, 1 840 and 4 290 different expression genes (DEGs) and 227, 158 and 678 different expression miRNAs (DEMs) in IP vs. MP, MP vs. FP, and IP vs. FP, respectively. Among which 72 genes and 25 miRNAs may be related to turtle pigmentation in embryonic development. Further analysis of the novel miRNA families revealed that some novel miRNAs related to pigmentation belong to the miR-7386, miR-138, miR-19 and miR-129 families. Novel_miR_2622 and novel_miR_2173 belong to the miR-19 family and target Kit and Gpnmb , respectively. The quantification of novel_miR_2622 and Kit revealed negative regulation, indicating that novel_miR_2622 may participate in embryonic pigmentation in P. sinensis by negatively regulating the expression of Kit .
Conclusions
miRNA act as master regulators of biological processes by controlling the expression of mRNAs. Considering their importance, the identified miRNAs and their target genes in Chinese soft-shelled turtle might be useful for investigating the molecular processes involved in pigmentation. All the results of this study may aid in the improvement of P. sinensis breeding traits for aquaculture.
... It is the largest indigenous black-bone chicken breed in China and has Silkie-like dermal hyper-pigmentation, where the whole body is black, including the feathers, wingtips, beak, comb, skin, bones, legs, and paws [3]. In oriental countries, black-bone chickens are considered to contain nutritional and medicinal properties, and are an important component of medicinal diets [4]. ...
The quality of poultry products depends on genotype, rearing system, and environment. The aim of this study was to investigate the effects of different rearing systems on meat quality, amino acid composition, and breast muscle transcriptome from Lueyang black-bone chickens. Lueyang black-bone chickens (n = 900) were randomly divided into three groups (cage, flat-net, and free-range groups), with three replicates per group (100 chickens per replicate). At 16 weeks, a total of 36 healthy chickens (six males and six females per group) were collected, and their breast muscles were sampled to detect meat quality parameters, amino acid composition, and fatty acid contents. Furthermore, breast muscles from six random hens in each group were used for RNA-seq analysis. The results revealed that the values of pH, shear force, inosine monophosphate (IMP), palmitic acid, and linoleic acid in the free-range group were significantly higher than those in the caged group (p < 0.05). Fat content in the free-range group was significantly lower than in the caged and flat-net groups (p < 0.05). Glutamate (Glu) levels, the amino acid crucial for the umami taste, was significantly higher in the free-range group than in the caged group (p < 0.05). Meanwhile, there was no significant difference between the free-range and flat-net groups (p > 0.05). The breast muscle transcriptome results showed that there were 291, 131, and 387 differently expressed genes (DEGs) among the three comparison groups (caged vs. free-range, flat-net vs. caged, and flat-net vs. free-range, respectively) that were mainly related to muscle development and amino acid metabolism pathways. To validate the accuracy of the transcriptome data, eight genes (GOS2, ASNS, NMRK2, GADL1, SMTNL2, SLC7A5, AMPD1, and GLUL) which relate to fat deposition, skeletal muscle function, and flavor formation were selected for Real-time Quantitative PCR (RT-qPCR) verification. In conclusion, these results suggested that rearing systems significantly influenced the meat quality and gene expression of Lueyang black-bone chickens. All the data proved that free-range and flat-net systems may provide better flavor to consumers by affecting the deposition of flavor substances and the expression of related genes. These findings will provide a valuable theoretical basis for the rearing system selection in the poultry industry.
... When considering the carcass characteristics (Table 4), we focused on L*, which showed the melatonin content index. Zhang et al. [47] reported that skin color is important in blackbone chicken because the color of the meat and skin of the black chicken was used to determine the market price. The black color of the meat caused by the accumulation of melanoproteins and the pigment melanin in mammals and poultry is controlled by the genetics [48]. ...
The purpose of this study was to determine the combining abilities and heterosis for the growth performance and carcass characteristics in crosses between Hmong black-bone (HB), Chinese black-bone (CB), and Thai native (TN) chickens using a mating system diallel crossing. Nine crossbred chickens including HB × HB, CB × CB, TN × TN, HB × TN, TN × HB, CB × HB, HB × CB, TN × CB, and CB × TN, were tested. The total data were 699 recorded at the beginning of the experiment to 595 recorded in weeks 14 of age. Body weight (BW), average daily gain (ADG), feed conversion ratio (FCR), and survival rate (SUR) were recorded. Heterosis and combining ability regarding general combining ability (GCA), specific combining ability (SCA), and reciprocal combining ability (RCA) were estimated. The study found that CB had the greatest BW and ADG at all weeks (p < 0.05) except for hatch, while those of HB were the lowest. The highest GCA was found in CB; meanwhile, GCA was significantly negative in HB of all ages. Crossing between TN × CB had the greatest BW from 8 weeks of age, which was related to positive SCA and RCA values. However, the RCA value of TN × CB was lower than the SCA value of CB × TN. The yield percentages of the carcass in CB (87.00%) were higher than those in TN (85.05%) and HB (82.91%) (p < 0.05). The highest breast and thigh meat lightness (L*) values were obtained in TN (p < 0.05), while those of CB and HB were not different (p > 0.05). In the crossbreed, the yield percentage of the carcass was highest in TN × CB (89.65%) and CB × TN (88.55%) (p > 0.05) and was lowest in TN × HB (71.91%) (p < 0.05). The meat and skin color of the breast and thigh parts in the crossbreed had the lowest lightness in HB × CB (27.91 to 38.23) (p < 0.05), while those of TN × CB and CB × TN were insignificant (p > 0.05). In conclusion, crossing between the TN sires and CB dams has the preferable potential to develop crossbred Thai native chickens for commercial use based on their high growth performance.
... The diversiform coat color phenotypes segregating in Duroc hybrid pigs demonstrated that KIT is responsible for the complex variation (Wu et al., 2019). In addition, the coat color phenotypes of several species showed an indispensable association with the KIT gene (Zhang et al., 2015;Anello et al., 2019;Voß et al., 2020;Wen et al., 2021). The KITLG gene encodes the KIT ligand protein, which has a vital function in the pigment formation process (Yang et al., 2018). ...
The diversity of livestock coat color results from human positive selection and is an indispensable part of breed registration. As an important biodiversity resource, Asiatic wild ass has many special characteristics, including the most visualized feature, its yellowish-brown coat color, and excellent adaptation. To explore the genetic mechanisms of phenotypic characteristics in Asiatic wild ass and its hybrids, we resequenced the whole genome of one Mongolian Kulan (a subspecies of Asiatic wild ass) and 29 Kulan hybrids (Mongolian Kulan ♂×Xinjiang♀), and the ancestor composition indicated the true lineage of the hybrids. XP-EHH (Cross Population Extended Haplotype Homozygosity), θπ-ratio (Nucleotide Diversity Ratio), CLR (Composite Likelihood Ratio) and θπ (Nucleotide Diversity) methods were used to detect the candidate regions of positive selection in Asiatic wild ass and its hybrids. Several immune genes (DEFA1, DEFA5, DEFA7, GIMAP4, GIMAP1, IGLC1, IGLL5, GZMB and HLA) were observed by the CLR and θπ methods. XP-EHH and θπ-ratio revealed that these genes are potentially responsible for coat color (KITLG) and meat quality traits (PDE1B and MYLK2). Furthermore, the heatmap was able to show the clear difference in the haplotype of the KITLG gene between the Kulan hybrids and Asiatic wild ass group and the Guanzhong black donkey group, which is a powerful demonstration of the key role of KITLG in donkey color. Therefore, our study may provide new insights into the genetic basis of coat color, meat quality traits and immunity of Asiatic wild ass and its hybrids.
