Transcriptome Study On The Molecular Mechanism Of The Different Marbling Phenotype In Beef Cattle

Inramuscular fat (IMF) deposition is a complex quantitative traits, it is little effect on IMF deposition (marbling) with studying one gene affecting quantitative traits. Therefore, two groups of FLW cattle with high and low marbling levels were selected with the same genetic background and management as the research object, selecting difference expression genes, single nucleotide variations (SNVs) and new transcripts related with IMF deposition using second-generation sequencing technology, and analyze polymorphism in UnCoupling Protein3(UCP3) and Thyroid Hormone Responsive Spot14Protein, THRSP) introns gene and their relationship with marbling related traits in crossbreed of Fuzhou Yellow cattle×Limousine×Wagyu (FLW) cattle, the aim of this sudy is to provide a theoretical basis to elucidate the molecular mechanism of the IMF deposition and further screening of effectively IMF deposition molecules marker.In RNA-Seq, total749differentially expressed genes (DEGs) in the two groups were identified (FC>2, P<0.05), in which there were366and383genes high and low-express in high marbling group (Y2).696of749DEGs were annotated in David database using GO analysis, enriched in956category, according to the category functions,145clusters were copolymerizated, in which293DEGs were not clustered, and8clusters related with fat and fatty acid digestion、absorptionx transport and other related process, after the removal of duplicated genes8clusters including48genes. Two pathways related to fat metabolism were found in KEGG enrichment analysis, they are MAPK signaling pathway and PPAR signaling pathway. The RT-qPCR results showed that the expression of8genes were corresponding to the trend in RNA-Seq, which indicated that the results of deep-sequencing were reliable.Further in-depth analysis of DEGs,2i DEGs associated with fat metabolism, PPARGC1A and PPARGCIB genes and SLC27A1and SLC27A6genes associated with PPAR signaling pathways high expression in Y2. Other series of genes (SCD, ABHD5, PRKAG2, GADD45G and THRSP) has also been found high expression in Y2. Nine fat metabolism related genes(APOM, APOL3, APOA1, APOE and FOXC2gene) lowly expressed in Y2. In fructose and mannose metabolic pathways, FBP1, HK2and TSTA3genes highly expressed in low marbling group (Y1), while PFKFB2and PFKFB3highly expressed in Y2. Twelve DEGs related with fibrogenesis, the expression of TGF-β111, TGF-β3, IGFBP6and FGFR-4genes increased in Y1. At the same time, DKK1genes which reduce fiber deposition and COL11A2and COL22A1genes highly expressed in Y2. MPP19, COL14A1, COL16A1, COL1A1, COL1A2and ITGA8, ITGB4, ITGBL1(except ITGB6) genes also highly expressed in Y1. Six DEGs related with rnyogenesis including MyoD, MyoG, Myf6, MYL3, MYL6B and MYL9genes were highly expressed in Y1.Using first-generation sequencing technology, analysis SNPs in introns of UCP3and THRSP genes, and their correlation analysis with marbling traits in FLW cattle, five SNPs in UCP3intron5were detected, in which CG genetype cattie’s fat coior grade and fat content were significantly higher than CC genetype cattle at C786G and C782G loci (P＜0.05), AG genetype cattle’s fat color grade and fat content is significantly higher than AA genetype cattle at A559G loci (P＜0.05), GT genetype cattle related traits (muscle length, triangle beef brisket grade, thickness, back fat fat fat color level, color grade, marbling level) is significantly higher than GG genetype cattle at G457T loci (P<0.05). At the same time, homozygous genetype cattle fresh water content is significantly higher than that of hybrid type cattle at the above loci (P＜0.05). Six SNPs in THRSP introns were detected, in which TC genetype cattle marbling level is significantly higher than TT type at T448C loci (P＜0.05), the remaining five SNPs were not significant differences with beef marbling related traits in FLW cattle.In this paper, studied bovine muscle transcriptome, selected a series of genes, SNPs and new transcripts associated with IMF deposition using high-throughput sequencing, and provides the direction for further research on IMF deposition, also provides valuable data for breeding high quality beef cattle using modern biotechnology. In addition, SNPs were significantly correlation with marbling related traits at UCP3and THRSP introns gene provided test data for applicating the two genes in beef cattle breeding work.