Transcriptome sequencing analysis of the back skin tissues of different colors (black, white, and yellow) of Wannan cattle

This study used the back skin tissues of three different colors (black, white, and yellow) of Wannan cattle as research materials to conduct whole transcriptome sequencing analysis. The aim was to systematically analyze the expression characteristics and regulatory mechanisms of mRNA, lncRNA, circRNA, and miRNA in the skin tissues under different skin color phenotypes, providing data support for clarifying the molecular basis of skin pigmentation in Wannan cattle. The sequencing analysis covered multiple dimensions: for mRNA, not only the distribution patterns of reads in different regions and chromosomes were analyzed, but also SNP detection was conducted to identify genetic variation sites related to skin color, and alternative splicing analysis was carried out to explore the regulatory diversity of gene expression; for lncRNA, new lncRNA prediction was used to enrich the transcriptome information, and the potential regulatory targets were analyzed by combining target gene prediction. Meanwhile, differential expression analysis was performed to screen lncRNAs related to skin color, and comparisons were made between lncRNAs and mRNAs in terms of length, number of exons, ORF length, and expression levels to reveal the structural and expression differences between the two types of RNAs; in the circRNA study, circRNA prediction and type statistics were completed, and the distribution characteristics on chromosomes were analyzed. Through expression quantification and differential analysis, circRNAs related to skin color were obtained, and then GO/KEGG enrichment analysis was conducted on the host genes of the differential circRNAs to clarify the biological processes and signaling pathways they are involved in; for miRNA, base preference was analyzed to understand the molecular structure characteristics, and Rfam annotation and genome comparison were performed to determine the sequence attribution. Through target gene prediction and GO/KEGG enrichment analysis, the regulatory functions were explored, and known miRNA identification, new miRNA prediction, and miRNA family analysis were carried out to improve the miRNA regulatory network. The SRA data generated in this study comprehensively covered the whole transcriptome information of different skin color tissues of Wannan cattle, which can provide important raw data resources for subsequent research on the regulatory mechanisms of skin pigmentation in livestock and poultry, as well as the screening of genetic breeding molecular markers and other related fields, and has high scientific research application value and data sharing significance.