影响藏猪与大约克夏猪肌肉品质的lncRNA的筛选及功能分析

Screening and Functional Analysis of lncRNA Affecting Muscle Quality in Tibetan and Yorkshire Pigs

旨在分析藏猪和大约克夏猪(180日龄)背最长肌组织中与猪肉质性状相关的长链非编码RNA(lncRNAs)和基因,探讨lncRNAs在猪肉品质中的分子调控作用,为猪肉质性状的改良提供理论依据。本研究根据先前公布的数据,以饲养在相同条件下的180日龄健康藏公猪(n=3)和大约克夏公猪(n=3)为研究对象,收集背最长肌肉品质表型数据,利用相同个体背最长肌转录组数据筛选差异表达lncRNAs和差异表达基因(DEGs)。根据差异表达lncRNAs和DEGs位置关系以及表达的相关性预测lncRNAs顺式作用(cis)和反式作用(trans)的靶DEGs,并对trans靶DEGs进行GO生物学过程和KEGG通路富集分析。进一步筛选潜在影响肌肉生长发育和脂肪沉积的候选差异表达lncRNAs和靶DEGs,构建lncRNAs-DEGs-生物学过程调控网络。最后将筛选的候选靶基因与藏猪和大约克夏猪的肉质性状(滴水损失、pH、肉色、大理石花纹、肌内脂肪含量、肌纤维横截面积、眼肌面积和维生素B_(1)含量)进行关联分析。结果显示,在藏猪和大约克夏猪背最长肌组织中共鉴定出1546个lncRNAs和20219个mRNAs,其中包括49个差异表达lncRNAs和154个DEGs,差异表达lncRNAs分别顺式和反式调控7个和138个靶DEGs。功能富集分析发现,大量靶DEGs显著富集到与肌肉生长发育和脂肪沉积相关的生物学过程,包括磷脂酰肌醇3-激酶信号的正调控、肌肉结构发育、脂肪细胞分化、JAK-STAT级联的正调控、MAPK级联的正调控等。调控网络显示,MSTRG.34836.10、MSTRG.151.1调控的靶DEGs最多,其次是MSTRG.21406.1、MSTRG.26709.1。关联分析发现,这些lncRNAs调控的候选靶DEGs有11个与肉质性状显著相关。综上表明,本研究鉴定的部分差异表达lncRNAs与肌肉生长发育和脂肪沉积有关,分析发现这些差异表达lncRNAs可能通过调控HES1、LEP、TGFB2和PER2等基因的表达影响猪肉品质,为进一步解析猪肉质性状的潜在分子机制奠定了基础。

This study aimed to identify the long non-coding RNAs(lncRNAs)and genes related to pork quality traits of the longissimus dorsi in Tibetan pigs and Yorkshire pigs(180 days old),and to further explore their molecular regulatory role,which could provide theoretical basis for the improvement breeding of pork quality traits.According to previously published data,180-day-old healthy Tibetan boars(n=3)and Yorkshire boars(n=3)raised under the same conditions were used as the research objects to collect phenotype data of the quality of the longissimus dorsi and the transcriptome data of the longissimus dorsi of the same individual were used to screen differentially expressed lncRNAs and differentially expressed genes(DEGs).Cis-and trans-target DEGs were predicted based on the positional relationship and expression correlation of differentially expressed lncRNAs and DEGs,then trans-target DEGs were enriched by GO biological processes and KEGG pathway analysis.Subsequently,lncRNAs-DEGs-biological process regulatory network related to muscle growth and fat deposition was constructed.Then,association events between candidate target genes and meat quality traits were analyzed,which comprised of drip loss,pH,meat color,marbling,intramuscular fat content,muscle fiber cross-sectional area,loin muscle area and vitamin B_(1) content.A total of 1546 lncRNAs and 20219 mRNAs were identified in the longissimus dorsi of Tibetan pigs and Yorkshire pigs,there were 49 differentially expressed lncRNAs and 154 DEGs of them based on statistical analysis.Of these,7 cis and 138 trans regulatory DEGs targeted by differentially expressed lncRNAs were predicted.Functional enrichment analysis showed that a large number of candidate DEGs were significantly enriched in biological processes of muscle growth and fat deposition,including positive regulation of phosphatidylinositol 3-kinase signaling,muscle structure development,fat cell differentiation,positive regulation of JAK-STAT cascade,and positive regulation of MAPK cascade,etc.Evidence from regulatory network showed that MSTRG.34836.10 and MSTRG.151.1 had the most target DEGs,followed by MSTRG.21406.1,MSTRG.26709.1.Association analysis indicated that 11 candidate target DEGs were significantly related to the meat quality traits.Taken together,some differentially expressed lncRNAs identified in this study were related to muscle growth and fat deposition.It was also suggested that these differentially expressed lncRNAs had an effect on pork quality by regulating the expression of HES1,LEP,TGFB2,and PER2.This study laid the foundation for further analysis of the potential molecular mechanism of pork quality traits.