Identification Of Novel LncRNA Related To The Growth Of Pig Skeletal Muscle And Screening Of Functional SNPs

Skeletal muscle tissue accounts for 35%-65% of the total body weight of animals.Its growth and development have an important impact on the meat production characteristics of livestock and poultry.Long non-coding RNA(LncRNA)is a kind of RNA with a length of more than 200 nt,which has no coding ability or can only encode short peptides.Studies have shown that LncRNA plays an important regulatory role in the growth and development of skeletal muscle.SNP can affect the function of LncRNA through a variety of mechanisms,thus regulating the growth and development of skeletal muscle.This study systematically identified and annotated LncRNA in the pig genome by integrating porcine multi tissue RNA-Seq sequencing data,and analyzed the expression patterns of LncRNA in different tissues by calculating relative expression scores in different tissue.Finally,the functions of SNPs and QTLs located in the LncRNA genomic region were predicted.The main research results are as follows:(1)Integrating RNA-Seq data from a total of 1505 samples of porcine multiple tissues in the NCBI database,47404 novel LncRNA transcripts from 23431 loci were identified through the construction of identification process.(2)Conservative analysis of LncRNA between pig and mouse species was conducted.Through location and sequence conservation analysis,995 LncRNAs in pig genome were identified as highly homologous to mouse LncRNA,13166 LncRNAs in pig genome were identified as position conservative,and 385 LncRNAs were identified as sequence and position conservative between pig and mouse species.(3)By analyzing the RNA-Seq data of 10 different tissues of pigs,the relative expression scores of LncRNA and m RNA in 10 different tissues were calculated.4617 LncRNAs and 3217 m RNA which relatively high expressed in muscle tissue were screened.The results of GO enrichment analysis confirmed that these genes may play an important role in the regulation of muscle growth and development.(4)Based on the analysis of RNA-Seq data from 27 different developmental stages of porcine skeletal muscle,the spatiotemporal expression profile of LncRNA and m RNA in skeletal muscle tissue was constructed.And 4061 LncRNAs were screened,which differentially expressed in different developmental stages of skeletal muscle tissue and relatively highly expressed in muscle.(5)The LncRNAs and m RNAs screened were divided into modules through WGCNA,and functional analysis was performed on each module.Finally,it was determined that 1034 m RNA and 1931 LncRNA in Turquoise module might have the function of regulating muscle growth and development.And 30 core m RNA of Turquoise module might play a core regulatory role in the module,including Myo D1,Myh3,Myh7 and other genes that play a key regulatory role in muscle development.(6)The 52901 SNP reported in the pig GWAS study and the pig SNP data from the db SNP database were collated and mapped to the genomic locations of LncRNA related to muscle development.The study found 1683104 SNPs located in the genomic region of myogenic LncRNA.And 476 SNPs and 484 QTLs that are significantly related to traits are located in the genome region of myogenic LncRNAs.Further functional analysis revealed that these SNPs and QTLs may regulate LncRNA function by influencing the binding of multiple transcription factors such as STAT5 a.In summary,this study has systematically identified the LncRNA in the pig genome,screened the LncRNA that has a regulatory role in myogenesis,and correlated the GWAS analysis results with LncRNA,providing new data for the identification of important LncRNA and functional SNPs in pig muscle growth and development traits.