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


Autoři: Xinlei Wang aff001;  Donghua Li aff001;  Sufang Song aff002;  Yanhua Zhang aff001;  Yuanfang Li aff001;  Xiangnan Wang aff001;  Danli Liu aff001;  Chenxi Zhang aff001;  Yanfang Cao aff001;  Yawei Fu aff001;  Ruili Han aff001;  Wenting Li aff001;  Xiaojun Liu aff001;  Guirong Sun aff001;  Guoxi Li aff001;  Yadong Tian aff001;  Zhuanjian Li aff001;  Xiangtao Kang aff001
Působiště autorů: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China aff001;  College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China aff002
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0210850

Souhrn

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.

Klíčová slova:

Feathers – Gene expression – Gene regulation – Chickens – Melanin – Proteomes – RNA sequencing – Transcriptome analysis


Zdroje

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