Integration Analysis of Transcriptome and Proteome Reveal the Mechanisms of Goat Wool Bending

Abstract

Zhongwei goat is a unique Chinese native goat breed for excellent lamb fur. The pattern of flower spikes of the lamb fur was significantly reduced due to the reduction of the bending of the hair strands with growth. In order to explore the molecular mechanism underlying hair bending with growth, we performed the comprehensive analysis of transcriptome and proteome of skins from 45-days, 108-days and 365-days goat based on TMT-based quantitative proteomics and RNA-seq methods. In the three comparison groups, 356, 592 and 282 differentially expressed proteins (DEPs) were screened, respectively. KEGG pathway analysis indicated that DEPs were significantly enriched in a set of signaling pathways related to wool growth and bending, such as ECM-receptor interaction, PI3K-Akt signaling pathway, PPAR signaling pathway, protein digestion and absorption, and metabolic pathways. In addition, 20 DEPs abundance of goat skin at three development stages were examined by PRM method, which validated the reliability of proteomic data. Among them, KRT and collagen alpha family may play an important role in the development of goat hair follicle and wool bending. COL6A1, COL6A2, CRNN, TNC and LOC102178129 were identified as candidate genes based on combined analysis of transcriptome and proteome data and PRM quantification. Our results identify the differential expressed proteins as well as pathways related to the wool bending of Zhongwei goats and provide a theoretical basis for further revealing the molecular mechanism underlying wool bending of goats.

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

“…Among these DMG, KRT71 and CD44 were highly methylated in one-month-old lambs, whereas ROR2 and ZDHHC13 were highly methylated in 48-month-old sheep. Interestingly, a similar phenotype of curly fibers was also found in goats [138][139][140][141]. Further information on the curly fleece phenotype in sheep is provided in Additional file 2: Table S11.…”

Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differential isoform in skin tissues of different hair length Yak

“…Functional enrichment analysis of DEIs revealed significant enrichment in pathways related to hair follicle and skin development. For example, the extracellular matrix-mediated crosstalk of multiple signaling pathways has been shown to regulate the density of hair follicles in sheep and wool bending in goats [37,39]. It has been reported that enhanced focal adhesion can decrease cell migration in focal adhesion kinase-deficient mice [40], and the transition stage from telogen to anagen is associated with focal adhesion [41].…”

Comprehensive transcriptomic analysis unveils the interplay of mRNA and LncRNA expression in shaping collagen organization and skin development in Dezhou donkeys

“…Of these, Protein digestion and absorption, Metabolic pathways, PI3K-Akt signaling pathway, ECMreceptor interaction, and Relaxin signaling showed their pivotal roles in orchestrating collagen deposition within the dermal matrix, skin development, extracellular matrix and collagen fibril organization of Dezhou donkey skin (Table 2). Interestingly, a recent study found several important signaling pathways related to wool growth and bending, such as ECM-receptor interaction, PI3K-Akt signaling pathway, Relaxin signaling pathway, protein digestion and absorption, and metabolic pathways in Zhongwei goats (He et al, 2020;Liu et al, 2022). In addition, a recent experimental trial has shown that PI3K-Akt signaling pathway, Protein digestion and absorption and ECM−receptor interaction signaling pathways were associated with regulation of actin filament-based process, regulation of actin cytoskeleton organization, cell-matrix adhesion and collagen fibril Collagen Alpha family genes regulate protein digestion and absorption signaling pathway.…”