Identification Of Genes Associated With Muscle Growth And Intramuscular Fat Deposition In Tianzhu White Yak

The yak(Bos grunniens)is mainly distributed in the Qinghai-Tibet Plateau and its adjacent high-altitude areas,and it is the main source of meat,milk and animal protein for local herdsmen.However,yak meat has the characteristics of coarser muscle fiber,low-fat content and poor tenderness when compared with that of B.taurus cattle,which seriously affects the eating quality.In order to better understand the genetic regulation mechanism of meat quality formation in yaks,the 6-,30-and 54-month-old Tianzhu white yak were selected,each group contains 3 yaks.RNA-Seq based transcriptome and TMT based proteome were used to explore the molecular mechanism of yak muscle growth and intramuscular fat deposition.It provides scientific basis and theoretical support for the selection of yak meat quality and molecular breeding.The main results are as follows:1.The yaks had a faster growth rate at 6-30 months of age,compared with 30-54 months of age.With the increase of age,the shear force,IMF content and muscle fiber diameter of yak increased significantly(P < 0.05 or P < 0.01).2.In total,1576,124,and 1407 differentially expressed genes(DEGs)were identified in M6 vs M30,M30 vs M54,and M6 vs M54 comparisons,respectively.A total of 2047 DEGs were screened for three stages.To determine the gene expression trajectories,STEM(Short Time-series Expression Miner)analysis clustered the DEGs significantly into four groups which could be divided into two classes(P-value < 0.05): class-up profiles had up-regulated patterns and class-down profiles featured down-regulated patterns.Based on that cluster analysis,GO enrichment analysis found that DEGs in class-up and class-down were significantly enriched in 393 and 86 GO terms,respectively,and multiple GO terms related to muscle growth and lipid metabolism were found.Furthermore,KEGG enrichment analysis showed that the DEGs in class-up and class-down profiles were significantly enriched in 64 and 16 signaling pathways respectively,and PI3 K Akt,FOXO,PPAR signaling pathways related to muscle development and lipid metabolism were found.Based on gene function and pathway analysis,seven growth-related genes(MSTN,IGF1,IGFBP5,IGFBP6,MYL1,MYL3 and TNNT1)and four lipid-related genes(ADIPOQ,FABP4,PLIN1 and LPL)were identified in class-up profiles;Seven growth-related genes(IGF2,IGF1 R,IGFBP1,IGFBP2,FoxO1,FoxO3 and FBXO32)and six lipid-related genes(ACSL4,STAT5 A,ACACB,LPIN1,PPARδ and ADIPOR1)were identified in class-down profiles.Finally,the expression levels of 14 DEGs were verified by reverse transcription-quantitative PCR(RT-qPCR)and the results were consistent with the Illumina transcriptome profile.3.A total of 17708 petides and 4770 proteins were obtained by TMT analysis.While 424,139 and 475 differentially expressed proteins(DEPs)were identified in M6 vs M30,M30 vs M54,and M6 vs M54 comparisons,respectively.Through DEPs cluster analysis,216 upregulated DEPs and 460 down-regulated DEPs were identified among the three groups.GO enrichment analysis found that DEPs in up-regulated and down-regulated patterns were significantly enriched in 153 and 330 GO terms,respectively,and multiple GO terms related to growth and lipid metabolism were found.KEGG enrichment analysis showed that up-and down-regulated DEPs were significantly enriched in 12 and 18 signaling pathways,and that the down-regulated DEPs were also enriched in the pathways related to growth and fatty acid metabolism,such as cardiac muscle contraction,ECM-receptor interaction,and fatty acid metabolism pathways.Based on the function and pathway analysis,11 growth-related proteins(MYL3,MYLK2,MYBP-C,MYBP-H,MYL9,MYH10,MYH13,TPM1,CFL1,CSRP1 and CSRP3),14 lipid deposition related proteins(HADHA,HADHB,HADH,ACADM,ACADVL,ACADSB,ACAD8,FASN,CD36,FABP3,HSPB1,HSPB6,HSPB7 and HSPB8)were identified,respectively.Protein-protein interaction network analysis showed that MYL3,MYL9,MYH10,MYLK2,TPM1 and CD36,HADH,HADHA,HADHB,ACADM,ACADVL and FABP3 were important nodes of protein network map related to muscle growth and fat deposition,respectively.It was speculated that they might be important proteins regulating muscle growth and IMF deposition of yaks.In this study,based on the clarification of the growth and the changes of meat quality traits of Tianzhu white yak.By the analysis of transcriptome and proteomics data,multiple signaling pathways related to muscle growth and fat deposition were identified,such as PI3K-Akt,cardiac muscle contraction,FoxO and PPAR signaling pathways,with 25 and 24 muscle growth and IMF deposition related genes and proteins of yak being obtained,respectively.The results provide basic data for elucidating the molecular mechanism of muscle growth and IMF deposition in Tianzhu white yak.