De Novo Transcriptome Sequencing Analysis of Goose (Anser anser) Embryonic Skin and the Identification of Genes Related to Feather Follicle Morphogenesis at Three Stages of Development

Abstract

The objective of this study was to evaluate the changes in the goose embryo transcriptome during feather development. RNA-Sequencing (RNA-Seq) was used to find the transcriptome profiles of feather follicles from three stages of embryonic dorsal skin at embryonic day 13, 18, and 28 (E13, E18, E28). The results showed that 3001, 6634, and 13,780 genes were differently expressed in three stages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially expressed genes (DEGs) in E13 vs. E18 were significantly mapped into the GO term of extracellular structure organization and the pathway of extracellular matrix (ECM)-receptor interaction. In E18 vs. E28, the top significantly mapped into GO term was the single-organism developmental process; the pathway was also the ECM-receptor interaction. DEGs in E13 vs. E28 were significantly mapped into the GO term of the multicellular organismal process and the pathway of cell adhesion molecules. Subsequently, the union of DEGs was categorized by succession cluster into eight profiles, which were then grouped into four ideal profiles. Lastly, the seven genes spatio-temporal expression pattern was confirmed by real-time PCR. Our findings advocate that interleukin 20 receptor subunit alpha (IL20RA), interleukin 6 receptor (IL6R), interleukin 1 receptor type 1 (IL-1R1), Wnt family member 3A (WNT3A), insulin-like growth factor binding protein 3 (IGFBP3), bone morphogenetic protein 7 (BMP7), and secreted-frizzled related protein 2 (SFRP2) might possibly play vital roles in skin and feather follicle development and growth processes.

Characterization of Embryonic Skin Transcriptome in Anser cygnoides at Three Feather Follicles Developmental Stages

“…In addition, the other one encoded cyclin-dependent kinase 2 (CDK2, Unigene0000009) and belonged to profile 0 which was identified as a down-regulated profile, suggesting that this gene might inhibit the development of the feather follicles in goose ( Figure 6). In addition, combining the results of GO and KEGG analysis, DEGs probably related to the skin and feather follicles development in Anser cygnoides were identified and compared with our previous studies in Anser anser (Liu et al 2018) by the values of RPKM and Count to show the expression of DEGs between the different species (Table S9).…”

“…Previous studies reported the formation, morphogenesis, differentiation, and maturation of the skin and feather follicles (Yu et al 2002;Lin et al 2006;Chen et al 2017). Recently, transcriptomic analysis have been conducted to identify candidate genes (gene expression patterns) involved in differentiation, growth regulation, survival, and morphogenesis of different types of feathers (in adults) and embryonic integuments of ducks, chicken and goose (Anser anser) (Ng and Li 2018;Liu et al 2018;Lowe et al 2015). Furthermore, Sello et al (2019) only reported a single time point during the embryonic skin development performance evaluation transcriptome between Anser anser and Anser cygnoides.…”

Identifying molecular pathways and candidate genes associated with knob traits by transcriptome analysis in the goose (Anser cygnoides)

“…Using the TRIzol ® Reagent (Animal RNA Purification Reagent for animal tissues; Invitrogen) following the manufacturer’s recommendations, and genomic DNA was removed using DNase I (TaKaRa). Total RNA purity,concentration and integrity of each samples were estimated by using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and only high-quality RNA samples were used to construct the sequencing library 20 .…”

Identifying Molecular Pathways and Candidate Genes Associated With Knob Traits by Transcriptome Analysis in the Goose (Anser Cygnoides)

“…Using the TRIzol ® Reagent (Animal RNA Puri cation Reagent for animal tissues; Invitrogen) following the manufacturer's recommendations., and genomic DNA was removed using DNase I (TaKaRa). Total RNA purity,concentration and integrity of each samples were estimated by using a Nanodrop 2000 instrument (Thermo Scienti c, Wilmington, DE, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and only high-quality RNA samples were used to construct the sequencing library 20 .…”