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

Abstract

BackgroundColoration 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.ResultsIn 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.ConclusionCommon 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.

Combined Transcriptome and Proteome Leukocyte’s Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis

“…The study revealed co-differential expression of 170 genes/proteins, with 122 genes/proteins displaying the same expression trends in both transcriptome and proteome profiles. The low to moderate correlation could be attributed to a variety of factors, including translation efficiency, alternative splicing, mRNA stability, folding, assembly, transport and localization, secretion, and degradation (48)(49)(50). Since the present study utilized publicly available transcriptomics databases and proteomics results from the current assessment, this 122 codifferentially expressed genes/proteins might be considered as representative of altered biological processes.…”

Population Structure and Genetic Diversity Analysis of “Yufen 1” H Line Chickens Using Whole-Genome Resequencing

“…The matching line of the “Yufen 1” layer was authorized by the National Commission on Livestock and Poultry Genetic Resource in 2015. A closed breeding method was used to develop line H by crossing barred plumaged-original Gushi chicken (GS) with an egg-laying brown-shelled Babcock B-380 grandparent line C. As the progenitor, line H is characterized by early sexual maturity, a fast plumage line, a high egg production, and a Columbian feather pattern [ 12 ]. However, knowledge on the genomic structure of the “Yufen 1” H line chicken (YF) is still scant.…”

Functional Differentiation of BMP7 Genes in Zebrafish: bmp7a for Dorsal-Ventral Pattern and bmp7b for Melanin Synthesis and Eye Development

“…The Wnt signaling pathway plays a vital role via the microphthalmia-associated transcription factor ( Mitf ) in the development of melanophores ( Jin et al, 2001 ). Wnt7b is a direct target of canonical BMP signaling in hair follicle stem cells, and wnt7b expression reaches a peak during the development of black and white striped feather hair follicles in the neck of eight-week-old chicken ( Kandyba and Kobielak, 2014 ; Wang et al, 2019 ). In Ctenophorus decresii , wnt7b showed stronger expression in skin with a high melanin concentration ( Mclean et al, 2017 ).…”