Combined Transcriptomics and Proteomics Forecast Analysis for Potential Genes Regulating the Columbian Plumage Color in Chickens

Abstract

31Background 32 Coloration is one of the most recognizable characteristics in chickens, and clarifying 33 the coloration mechanisms will help us understand feather color formation. "Yufen I" 34 is an commercial egg-laying chicken breed in China, that was developed by a 35 three-line cross using lines H, N and D. Columbian plumage is a typical feather 36 character of the "Yufen I" H line. To elucidate the molecular mechanism underlying 37 pigmentation of Columbian plumage, this study utilizes the technology of 38 high-throughput sequencing to compare the transcriptome and proteome differences 39 in different feather follicular tissue, including the dorsal neck with black and white 40 striped feather follicles (Group A) and the ventral neck with white feather follicles 41 (Group B) in the "Yufen I" H line. 42 Results 43In this study, we identified a total of 21,306 genes and 5203 proteins in chicken 44 feather follicles. Among these, 209 genes and 382 proteins were differentially 45 expressed in two different locations, Group A and Group B, respectively. A total of 8 46 differentially expressed genes (DEGs) and 9 differentially expressed proteins (DEPs) 47 were found to be involved in the melanogenesis pathway. Besides, a specifically 48 expressed MED23 gene and a differential expressed GNAQ protein were involved in 49 melanin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis 50 mapped 190 DEGs and 322 DEPs, to 175 and 242 pathways, respectively, and there 51 were 166 pathways correlated with both DEGs and DEPs. 49 DEPs/DEGs overlapped 52 and were enriched for 12 pathways. Transcriptomic and proteomic analyses revealed 53 that the following pathways were activated: melanogenesis, cardiomycete adrenergic, 54 calcium and the cGMP-PKG. The expression of DEGs was validated by real-time 55quantitative polymerase chain reaction (qRT-PCR) that was similar to that of 56 RNA-seq. In addition, we found that MED23, FZD10, WNT7B and WNT11 genes 57 expression peaked at approximately 8 weeks in the "Yufen I" H line, which is 58 consistent with the molting cycle. As both the groups showed significant differences 59 in terms of expression of the genes studied, this study opens up avenues for study in 60 the future to assess their exact function in color of plumage. 61 Conclusion 62 These common DEGs and DEPs were enriched in the melanogenesis pathway. The 63 MED23 and GNAQ were also reported to have a crucial part synthesis of melanin. In 64 addition, this study is the first to reveal variations in gene and protein in the "Yufen I" 65 H line during Columbian feather color development, and discover principal genes and 66 proteins that would aid in the functional genomics studies in future. The results of the 67 present study provide a significant conceptual basis for the "Yufen I" H line future 68 breeding schemes and provide a basis for research on the mechanisms of feather 69 pigmentation. 70 71 Yufen I" is an egg-laying chicken breed in China, which was developed by a 106 three-line cross using line H as the ...

Transcriptome analysis of feather follicles reveals candidate genes and pathways associated with pheomelanin pigmentation in chickens

“…In previous studies, omics data were used to explore feather colour formation-related genes. The formation of Columbian plumage in chickens was related to changes in the expression of MED23 , FZD10 , WNT7B and WNT11 21 . DEGs between black and white feather colours in ducks were enriched in the pathways of melanogenesis ( c-Ki t/ TYR / TYRP1 ) and tyrosine metabolism ( TYR / TYRP1 ) 23 .…”

“…The formation of plumage colour is also influenced by the expression of various genes related to pigment formation in feather follicles during the growth period 16 . As the pivotal position for feather formation and melanogenesis, transcriptome profiling of the feather follicle has been performed to elucidate the process of morphogenesis and to identify candidate genes of diverse feather shapes and colours [17][18][19][20][21][22][23] .…”

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 – 50 ). Since the present study utilized publicly available transcriptomics databases and proteomics results from the current assessment, this 122 co-differentially expressed genes/proteins might be considered as representative of altered biological processes.…”

Transcriptome Comparison Reveals Key Components of Nuptial Plumage Coloration in Crested Ibis

“…Transcriptome profiling have shown that feathers from different parts of the body, characterized by different forms and serving different functions, undergo different genetic bases during generation at embryonic stages or regeneration thereafter [ 34 , 35 , 36 ], thus comparison between the black skin and other skin regions could help infer function of differentially expressed genes. Proteomic profiling could provide further evidences of the genetic differences underlying formation of different feathers [ 37 ]. On the other hand, the transcriptomic comparison of other skins between breeding and non-breeding season could reduce the difference caused by other physiological changes, instead of production of the black substance, which increase the causality of research results.…”