Abstract
BackgroundFur is an important genetically-determined characteristic of domestic rabbits; rabbit furs are of great economic value. We used the Solexa sequencing technology to assess gene expression in skin tissues from full-sib Rex rabbits of different phenotypes in order to explore the molecular mechanisms associated with fur determination.Methodology/Principal FindingsTranscriptome analysis included de novo assembly, gene function identification, and gene function classification and enrichment. We obtained 74,032,912 and 71,126,891 short reads of 100 nt, which were assembled into 377,618 unique sequences by Trinity strategy (N50=680 nt). Based on BLAST results with known proteins, 50,228 sequences were identified at a cut-off E-value ≥ 10-5. Using Blast to Gene Ontology (GO), Clusters of Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we obtained several genes with important protein functions. A total of 308 differentially expressed genes were obtained by transcriptome analysis of plaice and un-plaice phenotype animals; 209 additional differentially expressed genes were not found in any database. These genes included 49 that were only expressed in plaice skin rabbits. The novel genes may play important roles during skin growth and development. In addition, 99 known differentially expressed genes were assigned to PI3K-Akt signaling, focal adhesion, and ECM-receptor interactin, among others. Growth factors play a role in skin growth and development by regulating these signaling pathways. We confirmed the altered expression levels of seven target genes by qRT-PCR. And chosen a key gene for SNP to found the differentially between plaice and un-plaice phenotypes rabbit.Conclusions/SignificanceThe rabbit transcriptome profiling data provide new insights in understanding the molecular mechanisms underlying rabbit skin growth and development.
Highlights
Rex Rabbit furs are highly appreciated by consumers for their inherent beauty, lightness, softness, and good warmth retention properties
The raw data from Illumina deep-sequencing were deposited in the NCBI Short Read Archive (SRA) database with Accession number: PRJNA 271624
EGF was shown to induce more epithelial stem cells to line along the stratum basale and form clusters in the granular and spinous layers [25,26]. These findings suggested that EGF activation of stem cells occurs in the stratum basale and in other epidermal layers, and could quickly increase the number of epithelial cells and epidermis thickness to enhance protection and accelerate the epidermal renewal [26]
Summary
Rex Rabbit furs are highly appreciated by consumers for their inherent beauty, lightness, softness, and good warmth retention properties. Our team found that the quality of rabbit fur is affected by many factors, and its size is one of the significant standards for evaluation. This requires cultivation of large size populations in production. Some rex rabbits have shown wrinkles in abdomen and extremities during production; this phenotype is known as plaice. The skin size of wrinkle rabbits was found to be 15% larger than that of un-wrinkle animals, with the same quality fur. We used the Solexa sequencing technology to assess gene expression in skin tissues from full-sib Rex rabbits of different phenotypes in order to explore the molecular mechanisms associated with fur determination
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