| The skin is an important external organ of animals,containing many physiological functions,and its growth and development are regulated by various genes.Chenghua pig is a unique local pig breed in southwestern China.As it ages,its facial skin exhibits a pattern of continuous thickening and deepening of wrinkling.In order to explore the gene function characteristics of Chenghua pig’s facial skin,this study selected four Chenghua pigs at different development stages,D3,90,D180 and Y3,as the test objects.Through the whole transcriptome sequencing,the expression characteristics of m RNA and three common non-coding RNA(miRNA,lnc RNA and circRNA)were excavated,and the following results were obtained:(1)The facial skin of Chenghua pigs has the characteristics of continuous thickening and deepening of wrinkles at different stages of development.(2)On the premise of qualified quality inspection of total RNA,the raw data(Raw data)of 120,118,117 and 118 Mb(Lnc RNA Seq library)and 36.5,35.4,36.4 and 35.7Mb(Small RNA seq library)were obtained at D3,D90,D180 and Y3 time points through full transcriptome sequencing,and then the high-quality data(Clean reads)of 117,116,114 and 114 Mb and 33.7,32.9,34.1 and 33.3 Mb were filtered,Then,these high-quality segments were compared to the reference genome,resulting in an average alignment rate of 88.35%.(3)In order to explore the characteristics of gene function changes at different growth stages,we screened the significantly different transcriptome at each time point for GO and KEGG enrichment analysis.The results showed that the differential transcript functions of m RNA,miRNA,lnc RNA and circRNA in the facial skin growth and development of Chenghua pigs were mainly enriched in five aspects: cell process,environmental information processing,organ system development,immune disease and metabolism.In addition,compared with the other three time points,the PPAR pathway related to skin proliferation and migration was significantly enriched in D180,suggesting that it may be a key node in development.(4)The analysis of the top10 transcriptome expression of four kinds of RNA at each time point found that the thickening of the facial skin of Chenghua pigs was related to COL3A1,COL1A2 and COL1A1 genes,which might also be associated with ssc-let-7a,ssc-let-7c,URS0000EF6A54,URS0001979623 and novel＿circ＿007090 and other nc RNA related.By constructing a protein interaction network,the two most complex overlapping genes CD80 and FCGR2 B related to immune diseases were screened.By limiting the expression patterns of differentially expressed genes at different stages,it was found that the deepening of facial skin wrinkling may be related to the continuous downregulation of ELN expression.(5)In order to explore the interaction between m RNA and non-coding RNA,gene targeting relationships between miRNA and m RNA,lnc RNA and circRNA that are significantly correlated in expression level were screened by integrating the transcripts obtained from actual sequencing and software prediction,and based on this,ssc-miR-542-5p,ssc-miR-133 b,ssc-miR-136-3p Five circRNA-miRNA-m RNA regulatory relationships related to skin function,with novel-ssc-miR1347-5p and ssc-miR-885-5p as core regulatory elements.In summary,there is a significant differential expression of m RNA,miRNA,lnc RNA,and circRNA during the development of facial skin in Chenghua pigs,which promotes the formation of unique facial skin traits.This study enriches the study of skin genetic characteristics of local breed resources in China,Chenghua pig,and provides theoretical basis for further conservation and development and utilization. |
