基于WGCNA方法识别影响猪肉质性状的关键模块和基因

Identification of Key Gene Co-expression Modules and Genes Associated with Pork Quality Based on WGCNA Method

【目的】发掘和识别猪肉质性状相关的基因共表达模块和关键基因。【方法】采用加权基因共表达网络分析(weighted gene co-expression network analysis,WGCNA)、基因互作关系网络以及中心性方法,对来自NCBI基因表达数据库的大蒲莲猪和长白猪各8头个体的背最长肌基因表达数据集GSE119368进行关键基因共表达模块和基因挖掘,以3头撒坝猪和3头大白猪为素材对肉质性状部分关键基因进行qPCR验证。【结果】共鉴定出蓝色和红色2个与猪肉质性状显著相关的基因共表达模块(r值分别为0.89和0.91,P值分别为5E−6和7E−7);蓝色模块基因主要与快慢肌纤维转换及细胞外基质等相关,其中的10个基因COL3A1、COL5A1、COL1A2、COL14A1、CRTAP、COL5A3、LEPREL1、DEPTOR、COL4A2和COL6A2为肉质性状关键基因;红色模块基因主要与骨骼肌细胞及脂肪细胞分化等有关,其中的11个基因FBXL4、RNF115、FBXO40、ASB4、ASB15、UBE2L6、RNF41、ASB5、HERC5、SOCS1和ASB11为肉质性状关键基因;蓝色模块的前3个关键基因在撒坝猪和大白猪背最长肌中表达差异极显著(P<0.01),红色模块的前3个基因表达差异不显著(P>0.05)。【结论】研究结果初步鉴定了不同肉质类型猪种间肉质相关的基因共表达模块和关键基因,但相同肉质类型猪种的肉质性状关键基因及其效应可能存在明显差异。

[Purpose]To explore and identify the key gene co-expression modules and genes associated with meat quality trait in pigs.[Methods]The key gene co-expression modules and genes were investigated using gene expression data GSE119368 of longissimus dorsi muscles including eight Dapulian and eight Landrace pigs from NCBI GEO database by weighted gene co-expression network analysis(WGCNA),gene interaction network and centrality methods.Some key genes asso-ciated with pork quality trait were identified by qPCR on three Saba and three Large White pigs.[Results]Two gene co-expression modules including the blue and the red modules related to pork quality trait were identified,which the r values were 0.89(P=5E−6)and 0.91(P=7E−7),respectively.The genes in the blue module were mainly associated with transition between fast and slow fiber and extracellular matrix and so on.Among the identified genes,10 genes were identified as the key genes associated with pork quality,including COL3A1,COL5A1,COL1A2,COL14A1,CRTAP,COL5A3,LEPREL1,DEPTOR,COL4A2 and COL6A2.The genes in the red module were mainly related to skeletal muscle and fat cell differentiation.Among these genes,11 genes were identified as the key genes associated with pork quality,including FBXL4,RNF115,FBXO40,ASB4,ASB15,UBE2L6,RNF41,ASB5,HERC5,SOCS1 and ASB11.The expression levels of the top three genes in the blue module had extremely significant differences in longissimus dorsi muscles between Saba and Large white pig breeds(P<0.01),while the top three genes in the red module had no significant differences(P>0.05).[Conclusion]The results preliminarily identified the co-expression modules and key genes of meat quality between different types of pig breeds,but the key genes associated with meat quality trait and their effects between the pig breeds with the same meat type may be significantly dif-ferent.