Fig 1.
“Yufen I” H line chicken and the feather bulbs used in this study.
(A). “Yufen I” H line chicken, (B). black and white striped-feathers in the dorsal neck, (C). white feathers in the ventral neck.
Table 1.
Gene expression and clean reads analyses in “Yufen I” H line feather follicles.
Fig 2.
Verification of DEGs via qRT-PCR.
The 2-ΔΔCT method was used for data analysis, and the housekeeping gene was GAPDH. Data shown on the vertical-axis represents the relative expression. Significant differences between two groups were determined by applying the unpaired Student’s t-test. * 0.01 < p < 0.05, ** p < 0.01. All dataare presented as means ± standard error (SE).
Fig 3.
qRT-PCR validation of DEGs involved in the feather cycle.
Changes in DEGs in feather follicles from the dorsal neck of the chicken at 0, 2, 4, 6, 8, 10 and 12 weeks.
Fig 4.
(A) GO functional annotation histogram of the DEGs. The vertical axis represents the three GO categories, the horizontal axis represents the gene number, and the number of genes is considered the difference in the proportion of the total. The GO annotations are classified in three basic categories, including cellular component, biological processes, and molecular function. (B) The degree of enrichment of the first 20 entries in the pathway. The pathway names are represented on the vertical axis, and the horizontal axis represents the pathways corresponding to the rich factor. The ratio of the number of DEGs and all annotated genes in the pathway is defined as the rich factor.
Table 2.
Information on identified proteins in chicken feather follicles.
Fig 5.
DEP analysis in terms of GOG, GO and KEGG.
(A) The horizontal axis represents the COG term, and the vertical axis represents the corresponding protein count illustrating the protein number of different function. (B) GO functional annotation histogram of the DEPs. The three GO categories are presented on the vertical axis under the GO term, the horizontal axis represents the gene number, and the number of genes is accounted for by differences in the proportion of the total. The GO annotations are classified in three basic categories including cellular component, biological processes, and molecular function. (C) The name of the pathway is mentioned on the vertical axis, and the pathway matching the rich factor are mentioned on the horizontal axis. The rich factor is the ratio of the number of DEPs in the pathway to the number of all annotated proteins in the pathway. After testing multiple hypotheses, Q values were completed with corrected P value in the range of 0–0.05. The enrichment was considered significant if the P-value was closer to zero.
Fig 6.
Correlations between the expression of proteins and genes.
The vertical-axis represents the protein expression level, and the horizontal-axis represents the genes expression level. (A) Scatter plots of the correlation between data sets of genes evaluated in both the proteomic and gene transcript analyses. (B) Scatter plots and coefficients of DEPs and DEGs correlation.
Fig 7.
Correlation of KEGG enrichment between transcriptome and proteome.
(A) Number of KEGG enrichment correlations between transcriptome and proteome. (B) The overview scatter diagram of KEGG enrichment correlations between the transcript levels and protein levels of genes.
Fig 8.
Differentially expressed feather color genes and proteins identified in the analyzed chicken feather follicles and their involvement in the melanogenesis pathway.
DEGs have a blue frame, and the DEPs have a red frame.