Feather follicles transcriptome profiles in Bashang long-tailed chickens with different plumage colors

Expression and Mutation of SLC45A2 Affects Iris Color in Quail

Iris color is a prominent phenotypic feature of quail. To understand the mechanism of melanin deposition related to quail iris color, iris tissues were selected from Beijing white and Chinese yellow quail for transcriptome analysis. Differentially expressed genes (DEGs) associated with pigmentation were identified using RNA sequencing and validated by quantitative real-time polymerase chain reaction (RT-qPCR). The identified single nucleotide polymorphisms were studied using bioinformatics and iris color correlation analyses. A total of 485 DEGs were obtained, with 223 upregulated and 262 downregulated. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. Thirty-two genes were annotated using the GO database. Three important pigment synthesis pathways (Notch signaling, melanogenesis, and tyrosine metabolism) were identified in quail iris tissue (P < 0.05). The expression levels of solute carrier family 45 member 2 (SLC45A2), tyrosinase-related protein 1, vitamin D receptor, opsin 5, and docking protein 5 were significantly different between Beijing white and Chinese yellow quail, as verified by RT-qPCR. The c.1061C>T mutation in SLC45A2, which caused a single amino acid change at position 354 (threonine to methionine), was significantly associated with iris color in Beijing white and Chinese yellow quail, and might be the main reason for the different iris colors between these two quail species.

Molecular Regulatory Mechanisms in Chicken Feather Follicle Morphogenesis

In China, the sale of freshly slaughtered chickens is becoming increasingly popular in comparison with that of live chickens, and due to this emerging trend, the skin and feather follicle traits of yellow-feathered broilers have attracted a great deal of research attention. The feather follicle originates from the interaction between the epidermis and dermis in the early embryonic stage. Feather follicle morphogenesis is regulated by the Wnt, ectodysplasin (Eda), epidermal growth factor (EGF), fibroblast growth factor (FGF), bone morphogenetic protein (BMP), sonic hedgehog (Shh), Notch, and other signaling pathways that exist in epithelial and mesenchymal cells. The Wnt pathway is essential for feather follicle and feather morphogenesis. Eda interacts with Wnt to induce FGF expression, which attracts mesenchymal cell movement and aggregates to form feather follicle primordia. BMP acts as an inhibitor of the above signaling pathways to limit the size of the feather tract and distance between neighboring feather primordia in a dose-dependent manner. The Notch/Delta pathway can interact with the FGF pathway to promote feather bud formation. While not a part of the early morphogenesis of feather follicles, Shh and BMP signaling are involved in late feather branching. This review summarizes the roles of miRNAs/lncRNA in the regulation of feather follicle and feather growth and development and suggests topics that need to be solved in a future study. This review focuses on the regulatory mechanisms involved in feather follicle morphogenesis and analyzes the impact of SNP sites on feather follicle traits in poultry. This work may help us to understand the molecular regulatory networks influencing feather follicle growth and provide basic data for poultry carcass quality.

Transcriptome Profile Analysis Identifies Candidate Genes for the Melanin Pigmentation of Skin in Tengchong Snow Chickens

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.

A genome-wide association study for eumelanin pigmentation in chicken plumage using a computer vision approach

Chicken plumage colouration is an important trait related to productivity in poultry industry. Therefore, the genetic basis for pigmentation in chicken plumage is an area of great interest. However, the colour trait is generally regarded as a qualitative trait and representing colour variations is difficult. In this study, we developed a method to quantify and classify colour using an F₂ population crossed from two pure lines: White Leghorn and the Korean indigenous breed Yeonsan Ogye. Using red, green, and blue values in the cropped body region, we identified significant genomic regions on chromosomes 33:3 160 480-7 447 197 and Z:78 748 287-79 173 793. Furthermore, we identified two potential candidate genes (PMEL and MTAP) that might have significant effects on melanin-based plumage pigmentation. Our study presents a new phenotyping method using a computer vision approach and provides new insights into the genetic basis of melanin-based feather colouration in chickens.

Whole Genome Analyses Reveal Novel Genes Associated with Chicken Adaptation to Tropical and Frigid Environments

INTRODUCTION

Investigating the genetic footprints of historical temperature selection can get insights to the local adaptation and feasible influences of climate change on long-term population dynamics.

OBJECT

Chicken is a significative species to study genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties. Yet, few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments.

METHOD

Here, we generated whole genome resequencing of 119 domesticated chickens in China including the following breeds which are in order of breeding environmental temperature from more tropical to more frigid: Wenchang chicken (WCC), green-shell chicken (GSC), Tibetan chicken (TBC), and Lindian chicken (LDC).

RESULTS

Our results showed WCC branched off earlier than LDC with an evident genetic admixture between WCC and LDC, suggesting their closer genetic relationship. Further comparative genomic analyses solute carrier family 33 member 1 (SLC33A1) and thyroid stimulating hormone receptor (TSHR) genes exhibited stronger signatures for positive selection in the genome of the more tropical WCC. Furthermore, genotype data from about 3,000 African local ecotypes confirmed that allele frequencies of single nucleotide polymorphisms (SNPs) in these 2 genes appeared strongly associated with tropical environment adaptation. In addition, the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) gene exhibited a strong signature for positive selection in the LDC genome, and SNPs with marked allele frequency differences indicated a significant relationship with frigid environment adaptation.

CONCLUSION

Our findings partially clarify how selection footprints from environmental temperature stress can lead to advantageous genomic adaptions to tropical and frigid environments in poultry and provide a valuable resource for selective breeding of chickens.

Genome-Wide Analysis Identifies Candidate Genes Encoding Feather Color in Ducks

Comparative population genomics and genome-wide association studies (GWAS) offer opportunities to discover human-driven detectable signatures within the genome. From the point of view of evolutionary biology, the identification of genes associated with the domestication of traits is of interest for the elucidation of the selection of these traits. To this end, an F2 population of ducks, consisting of 275 ducks, was genotyped using a whole genome re-sequence containing 12.6 Mb single nucleotide polymorphisms (SNPs) and four plumage colors. GWAS was used to identify the candidate and potential SNPs of four plumage colors in ducks (white, spot, grey, and black plumage). In addition, FST and genetic diversity (π ratio) were used to screen signals of the selective sweep, which relate to the four plumage colors. Major genomic regions associated with white, spotted, and black feathers overlapped with their candidate selection regions, whereas no such overlap was observed with grey plumage. In addition, MITF and EDNRB2 are functional candidate genes that contribute to white and black plumage due to their indirect involvement in the melanogenesis pathway. This study provides new insights into the genetic factors that may influence the diversity of plumage color.

Transcriptome analysis of genes potentially associated with white and black plumage formation in Chinese indigenous ducks (Anas platyrhynchos)

1. Plumage colour is an important recognisable characteristic of duck (Anas platyrhynchos), but the coloration mechanisms remain largely unknown. To elucidate the molecular mechanisms underlying the formation of black and white plumage, the following study applied RNA sequencing (RNA-Seq) to catalogue the global gene expression profiles in the duck feather bulbs of black and white colours.2. Black feather bulbs were collected from Putian Black ducks (B-PTB) and black Longsheng Jade-green ducks (B-LS), while white feather bulbs were collected from Putian White ducks (W-PTW), Putian Black ducks (W-PTB) and Longsheng Jade-green ducks (W-LS). Sixteen cDNA libraries were constructed and sequenced for transcriptional analysis. Three comparison groups were employed to analyse differentially expressed genes (DEGs), including W-PTB versus B-PTB, W-PTW versus B-PTB and W-LS versus B-LS.3. The results showed 180 DEGs between W-PTB and B-PTB, 303 DEGs between W-PTW and B-PTB, and 108 DEGs between W-LS and B-LS. Further analysis showed that 18 DEGs were directly involved in the pigmentation process and melanogenesis signalling pathway. Additionally, the distribution of DEGs varied amongst groups whereby ASIP appeared only in the W-LS versus B-LS group, GNAI1 and ZEB2 appeared only in the W-PTW versus B-PTB group, and KITLG, EDN3 and FZD4 appeared only in W-PTB versus B-PTB.4. The findings suggested that the mechanism of feather albinism may differ between duck breeds. This study provided new information for discovering genes that are important for feather pigmentation and helps elucidate molecular mechanisms involved in black and white plumage in ducks.

Combined transcriptomics and proteomics forecast analysis for potential genes regulating the Columbian plumage color in chickens

BACKGROUND

Coloration is one of the most recognizable characteristics in chickens, and clarifying the coloration mechanisms will help us understand feather color formation. "Yufen I" is a commercial egg-laying chicken breed in China that was developed by a three-line cross using lines H, N and D. Columbian plumage is a typical feather character of the "Yufen I" H line. To elucidate the molecular mechanism underlying the pigmentation of Columbian plumage, this study utilizes high-throughput sequencing technology to compare the transcriptome and proteome differences in the follicular tissue of different feathers, including the dorsal neck with black and white striped feather follicles (Group A) and the ventral neck with white feather follicles (Group B) in the "Yufen I" H line.

RESULTS

In this study, we identified a total of 21,306 genes and 5,203 proteins in chicken feather follicles. Among these, 209 genes and 382 proteins were differentially expressed in two locations, Group A and Group B, respectively. A total of 8 differentially expressed genes (DEGs) and 9 differentially expressed proteins (DEPs) were found to be involved in the melanogenesis pathway. Additionally, a specifically expressed MED23 gene and a differentially expressed GNAQ protein were involved in melanin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis mapped 190 DEGs and 322 DEPs to 175 and 242 pathways, respectively, and there were 166 pathways correlated with both DEGs and DEPs. 49 DEPs/DEGs overlapped and were enriched for 12 pathways. Transcriptomic and proteomic analyses revealed that the following pathways were activated: melanogenesis, cardiomyocyte adrenergic, calcium and cGMP-PKG. The expression of DEGs was validated by real-time quantitative polymerase chain reaction (qRT-PCR) that produced results similar to those from RNA-seq. In addition, we found that the expression of the MED23, FZD10, WNT7B and WNT11 genes peaked at approximately 8 weeks in the "Yufen I" H line, which is consistent with the molting cycle. As both groups showed significant differences in terms of the expression of the studied genes, this work opens up avenues for research in the future to assess their exact function in determining plumage color.

CONCLUSION

Common DEGs and DEPs were enriched in the melanogenesis pathway. MED23 and GNAQ were also reported to play a crucial role in melanin synthesis. In addition, this study is the first to reveal gene and protein variations in in the "Yufen I" H line during Columbian feather color development and to discover principal genes and proteins that will aid in functional genomics studies in the future. The results of the present study provide a significant conceptual basis for the future breeding schemes with the "Yufen I" H line and provide a basis for research on the mechanisms of feather pigmentation.