Transcriptome Profiling Unveils Key Genes Regulating the Growth and Development of Yangzhou Goose Knob

Abstract

Goose is one of the most economically valuable poultry species and has a distinct appearance due to its possession of a knob. A knob is a hallmark of sexual maturity in goose (Anser cygnoides) and plays crucial roles in artificial selection, health status, social signaling, and body temperature regulation. However, the genetic mechanisms influencing the growth and development of goose knobs remain completely unclear. In this study, histomorphological and transcriptomic analyses of goose knobs in D70, D120, and D300 Yangzhou geese revealed differential changes in tissue morphology during the growth and development of goose knobs and the key core genes that regulate goose knob traits. Observation of tissue sections revealed that as age increased, the thickness of the knob epidermis, cuticle, and spinous cells gradually decreased. Additionally, fat cells in the dermis and subcutaneous connective tissue transitioned from loose to dense. Transcriptome sequencing results, analyzed through differential expression, Weighted Gene Co-expression Network Analysis (WGCNA), and pattern expression analysis methods, showed D70-vs.-D120 (up-regulated: 192; down-regulated: 423), D70-vs.-D300 (up-regulated: 1394; down-regulated: 1893), and D120-vs.-D300 (up-regulated: 1017; down-regulated: 1324). A total of 6243 differentially expressed genes (DEGs) were identified, indicating varied expression levels across the three groups in the knob tissues of D70, D120, and D300 Yangzhou geese. These DEGs are significantly enriched in biological processes (BP) such as skin morphogenesis, the regulation of keratinocyte proliferation, and epidermal cell differentiation. Furthermore, they demonstrate enrichment in pathways related to goose knob development, including ECM-receptor interaction, NF-kappa B, and PPAR signaling. Through pattern expression analysis, three gene expression clusters related to goose knob traits were identified. The joint analysis of candidate genes associated with goose knob development and WGCNA led to the identification of key core genes influencing goose knob development. These core genes comprise WNT4, WNT10A, TCF7L2, GATA3, ADRA2A, CASP3, SFN, KDF1, ERRFI1, SPRY1, and EVPL. In summary, this study provides a reference for understanding the molecular mechanisms of goose knob growth and development and provides effective ideas and methods for the genetic improvement of goose knob traits.

Keywords: DEGs; RNA-seq; WGCNA; Yangzhou goose; knob.

Figure 1

Comparison of histology of Yangzhou goose at different ages. Note: 70-day-old, 120-day-old, and 300-day-old Yangzhou goose knob skin tissues were collected and fixed and stained with HE. (A): 70-day-old, (B): 120-day-old, and (C): 300-day-old knob skin tissue. (A,B): 7.5×; (C): 5×. Between 70 and 120 days of age, the skin exhibited a notably thin structure, while by 300 days of age, it had developed a certain thickness. To accommodate this diversity in skin tissue thickness, we chose to employ two magnifications. The objective is to present the characteristics of the skin at different ages in a more intuitive manner, ensuring that observers can precisely comprehend and compare the structural variations and changes occurring in the skin during distinct periods. This strategic approach aims to offer more comprehensive and lucid image information, facilitating the observation and analysis of subtle changes throughout the process of skin development.

Figure 2

Principal component analysis and screening of DEGs for each sample. (A) Analysis of group principal component results. (B) The quantitative relationship of DEGs between each group. (C) Venn diagram of DEGs. (D) Clustering heatmap of DEGs.

Figure 3

Enrichment functional analysis of DEGs in each comparison group. (A) Top 20 GO terms (BP categories) during anserine knob development. (B) Top 20 enriched KEGG pathways during goose knob development.

Figure 4

(A) Gene network diagram of GO terms during goose knob morphogenesis. (B) Gene network map of the KEGG pathway during goose knob morphogenesis. (C) DEGs in Wnt, Th1, and Th2 cell differentiation, neuroactive ligand–receptor interaction, NF-kappa B, PI3K-Akt, and Rap1 signaling pathways during the morphogenesis of goose knob.

Figure 5

Time series expression analysis of DEGs. Selected clusters of DEGs correspond to biological processes (BPs), and candidate genes are shown next to each cluster. Note: profile#1: clusters1; profile#2: clusters2; profile#3: clusters3.

Figure 6

WGCNA analysis. (A) Division of gene modules and correlation between gene modules and sample information. The figure shows the clustering of genes, the division of gene modules, and the correlation between gene modules and module information, as well as the GO enrichment (top 3) analysis of modules. (B) KEGG functional analysis of key modules. Note: In Figure 6A group (D70, D120, D300), Length represents goose knob height, Width indicates goose knob width, and Height corresponds to goose knob height.

Figure 7

Visualization of pathways involved in goose knob development. This network involves a total of 17 signaling pathways and 167 pathway genes (Pearson correlation ≥ 0.9).

Figure 8

RT-PCR and RNA-seq. The mRNA expression of goose knob development-related genes and four DEGs.

Figure 9

Illustrative summary diagram depicting the regulation of pathways associated with the growth and development of goose knobs.