# Transcriptional and Metabolic Networks Underlying Melanin Deposition in Silkie Chicken Muscle: A Multi-Omics Insights

## TL;DR

This study explores how Silkie chickens develop dark muscle pigmentation through combined analysis of gene activity and metabolite levels, revealing key genes and metabolic pathways involved in melanin production.

## Contribution

The study integrates transcriptomics and metabolomics to identify novel regulators and metabolic trade-offs in melanin deposition in chicken muscle.

## Key findings

- 488 differentially expressed genes and seven conserved melanogenesis genes are upregulated in Silkie chickens.
- Metabolomics shows depletion of L-tyrosine and its derivatives, indicating active melanin synthesis.
- Integrated analysis links tyrosine metabolism and redox balance to melanin deposition, with novel inhibitors identified.

## Abstract

Silkie chickens exhibit ectopic muscle melanin, with transcriptomics identifying 488 differentially expressed genes and seven conserved melanogenesis genes upregulated. Key pathways include melanogenesis and WNT signaling pathways; SOX10 is a hub regulator. Metabolomics revealed depleted L-tyrosine and derivatives, indicating active pigment synthesis. Integrated analysis linked tyrosine metabolism and redox balance, with metabolites like glutathione and p-coumaric acid negatively correlated, and ADP-ribose and pyridoxal positively associated. Novel inhibitors PNMT and HIBADH may modulate melanin deposition. Findings highlight a trade-off between pigmentation and redox homeostasis, offering molecular insights for trait improvement.

Silkie (SK) chickens, valued for dark meat, serve as a model to study melanin deposition in muscle. Integrated transcriptomics and metabolomics of SK vs. Arbor Acres (AA) broiler pectoralis were used to identify key molecular drivers of meat color. All birds were cage-raised under standardized temperature and light conditions with free access to feed and water. Pectoralis muscle samples were collected from 24-day-old healthy SK and AA chickens (n = 6). Transcriptome profiling identified 488 differentially expressed genes in SK chickens, with seven conserved melanogenesis genes (TYRP1, MLANA, TYR, MLPH, EDNRB2, PMEL, GPNMB) consistently upregulated across dark-pectoralis breeds, and melanogenesis and WNT pathways were activated. Co-expression network analysis highlighted SOX10 as a key hub regulator. Metabolomics quantified 129 differentially abundant metabolites. A critical finding was the significant depletion of L-tyrosine and its derivatives in SK muscle, despite upregulated melanogenesis genes. It indicates intense metabolic flux toward pigment synthesis. Integrated analyses converged on tyrosine metabolism and redox pathways: oxidized glutathione and p-coumaric acid correlated negatively with pigment deposition, while ADP-ribose and pyridoxal correlated positively. Additionally, novel inhibitors PNMT and HIBADH may modulate melanin deposition. These findings reveal a trade-off between pigment deposition and redox balance, providing molecular markers for poultry melanin-related trait improvement.