Transcriptome and Weighted Gene Co-Expression Network Analysis for Feather Follicle Density in a Chinese Indigenous Breed

Abstract

Feather follicle density plays an important role in appealing to consumers’ first impressions when making purchasing decisions. However, the molecular network that contributes to this trait remains largely unknown. The aim of this study was to perform transcriptome and weighted gene co-expression network analyses to determine the candidate genes relating to feather follicle density in Wannan male chickens. In total, five hundred one-day-old Wannan male chickens were kept in a conventional cage system. Feather follicle density was recorded for each bird at 12 weeks of age. At 12 weeks, fifteen skin tissue samples were selected for weighted gene co-expression network analysis, of which six skin tissue samples (three birds in the H group and three birds in the L group) were selected for transcriptome analysis. The results showed that, in total, 95 DEGs were identified, and 56 genes were upregulated and 39 genes were downregulated in the high-feather-follicle-density group when compared with the low-feather-follicle-density group. Thirteen co-expression gene modules were identified. The red module was highly significantly negatively correlated with feather follicle density (p < 0.01), with a significant negative correlation coefficient of −0.72. In total, 103 hub genes from the red module were screened. Upon comparing the 103 hub genes with differentially expressed genes (DEGs), it was observed that 13 genes were common to both sets, including MELK, GTSE1, CDK1, HMMR, and CENPE. From the red module, FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 were selected as the most important genes. These genes were enriched in the DNA binding pathway, the heterocyclic compound binding pathway, the cell cycle pathway, and the oocyte meiosis pathway. This study suggests that FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 may be involved in regulating the development of feather follicle density in Wannan male chickens. The results of this study reveal the genetic structure and molecular regulatory network of feather follicle density in Wannan male chickens, and provide a basis for further elucidating the genetic regulatory mechanism and identifying molecular markers with breeding value.

Identification of key modules and hub genes involved in regulating the feather follicle development of Wannan chickens using WGCNA

“…The samples were then stored at a temperature of -80°C. 15 male chicken samples of back skin tissue from 12 wk of age were obtained from our previous study ( Wang, et al, 2024a ).…”

“…Seven skin transcriptome data from 12 wk of age were obtained from our previous study ( Wang, et al, 2024a ). A total of 12 transcriptome datasets from 9 embryo skin tissues and three 12-wk-old Wannan chickens back skin tissues ( Wang, et al, 2024a ) were used for DEGs analyzed. Adapters and low-quality reads were removed using Cutadapt and Btrim with the parameters “-s -a 20 -q” ( Kong, 2011 ).…”

“…In total, 9 embryo skin tissues and seven 12-wk-old Wannan chickens back skin tissue RNA-seq datasets ( Wang, et al, 2024a ) were used for WGCNA analysis. The DESeq2 package (v 4.2.2) was used to normalize gene expression levels using the “varianceStabilizing Transformation” function ( Love, et al, 2014 ).…”