| As an important agricultural economic animal,pigs not only provide a large number of meat products for humans,but also can be used as a biomedical model for research.Due to the long-term manual selection of foreign pig breeds,their growth rate and lean meat rate have been greatly improved,but it has also caused the deterioration of meat quality and the decrease of intramuscular fat content.Although the local pig breeds in China far surpass the lean lean pig breeds abroad in terms of meat quality,adaptability and fertility,there are significant differences in traits such as lean meat rate and growth rate compared with foreign breeds.A large number of studies have shown that the formation of germplasm differences between Chinese and foreign pig breeds is related to the differential expression of genes,but the identification of differentially expressed linc RNAs(Long intergenic noncoding RNAs)and PASs(Polyadenylation sites)and their differences in skeletal muscle development The role in is unclear.Therefore,exploring the differential expression of linc RNAs and PASs related to skeletal muscle development of Chinese and foreign pigs from the transcriptome level is of great importance for the analysis of the molecular mechanism of muscle development differences between breeds.In this study,Dapulian pigs(Dapulian,D),which grow slowly but have good meat quality,and Landrace pigs(Landrace,L),which grow fast but have poor meat quality,and Landrace × Dapulian(LD)and Du Duroc × Landrace × Dapulian(DLD)was used as a test animal to identify differentially expressed linc RNAs and differential utilization PASs in skeletal muscles of different breeds of pigs using transcriptome data And analyze the function of differential linc RNAs and PASs.The main results of this study are as follows:1.Using 4 sets of 32 sample data as materials,using Hisat2,String Tie series software for linc RNAs identification and differential expression analysis.The results showed that a total of 381 linc RNAs were screened,of which 327 were known linc RNAs and 54 were newly identified linc RNAs.Using differential expression analysis to identify linc RNAs,a total of 167 differentially expressed linc RNAs were obtained,of which there were 150 known linc RNAs and 17 newly identified linc RNAs.2.Based on cis-regulation of linc RNA,a total of 87 differentially expressed genes within 100 k of upstream and downstream of differentially expressed linc RNAs with a correlation coefficient greater than 0.6 were screened.Gene Ontology(GO)analysis and KEGG(Kyoto encyclopedia of genes and genomes)were performed on these genes)Analysis and found that they are clustered in skeletal muscle fiber development and muscle contraction and other pathways.3.Using the expression data of differentially expressed m RNAs and differentially expressed linc RNAs as a matrix,a weighted gene co-expression network analysis(WGCNA)was used to construct a co-expression network,and a soft threshold of 12 was selected to divide the module from 12 Among the modules,4 modules significantly related to muscle development were identified,and finally 8 core linc RNAs were screened.Functional enrichment analysis showed that they may be involved in P13K-AKT pathway and AMPK signaling pathway,indirectly affecting muscle development.4.The location information is used to compare these differentially expressed linc RNAs to the QTL(Quantitative trait locus)database,and their functions are predicted based on the annotation information of the QTL database.The results showed that 161 differentially expressed linc RNAs fell on 362 QTLs related to muscle development,and most QTLs and DELs(Differentially expressed linc RNAs)were located on chromosomes 1 and 2.The statistical summary of these QTLs can be divided into 15 groups,of which muscle protein,lean percentage and muscle fiber related QTLs are the most.5.Screening using complete assembled RNA-seq data resulted in 4.18 million reads containing Poly(A)or Poly(T),and finally identified 12,490 PASs;annotation of PASs based on the pig reference genome revealed that 70% of the genes had There are more than 2 PASs,and most of the PASs are located in the 3’UTR(3’untranslated region),and a few PASs are located in the CDS(Coding sequence)region.6.The analysis of the number and utilization of PAS in skeletal muscle tissue found that PAS did not show a large number difference in the same tissue of different pig breeds,but the utilization of PASs was very different;and the number and utilization of PASs in genes Both are positively correlated with gene expression.The functional enrichment analysis of the differentially used PASs revealed that the genes corresponding to these PASs may be involved in muscle contraction,skeletal muscle tissue development,insulin pathway,etc.This indicates that the differential utilization of PASs between different varieties may be related to skeletal muscle development.In summary,this study systematically studied the differentially expressed genes of skeletal muscles of two breeds and hybrid pigs from the transcriptome level,screened and identified a group of new linc RNAs and PASs that may be related to skeletal muscle development,and compared transcriptions for the research pigs.Omics provides valuable genetic resources and helps to improve the understanding and understanding of the genetic structure of porcine transcriptomes. |
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