Bioinformatics Analysis On The Relationship Of Beef Cattle Intramuscular Fat And Related Functional Gene Set

Intramuscular fat(IMF)content and skeletal muscle growth rate are the key factors to influence the meat quality and meat yield of beef cattle.To further understand the mechanism of intramuscular adipogenesis and skeletal muscle development would help to solve the industrial problems in China including relatively low meat quality and beef yield.To date,the mechanism of IMF development has been well established.However,there are some inherent defects of the current technologies to estimate IMF,such as low accuracy and high cost.In addition,although it is reported that the intramuscular adipocyte number in ruminants is set around weaning period,IMF development is affected by various factors,thus to accurately predict the future marbling status is always the focus in order to produce high quality beef more efficiently.Furthermore,besides muscle fiber,there are many kinds of cells and tissues in skeletal muscle.All kinds of components would affect the skeletal muscle growth thus to make it a complex biological process.Therefore,for the sake of manipulating beef cattle growth rate,it is a critical point to learn the stem cell resources of the main components of skeletal muscle.Based on the transcriptome and phenotypical dataset of skeletal muscle from various beef cattle breeds,this current dissertation has established a biology-based,low-cost and accurate methodology to estimate IMF content,and a model to predict future marbling status.Moreover,on the basis of transcriptome data of skeletal muscle development,this dissertation also has identified the potential markers of skeletal muscle growth rate and major cell types.Our research could provide the theoretical basis for Chinese beef cattle industry to solve the basic problems,such as the relatively low beef yield and meat quality.The detailed contents and results are shown as follows.1 Identification of the genes most correlated with beef cattle IMF%by using transcriptomic dataIn this study,the genes correlated with intramuscular fat percentage(IMF%)from boththe statistical and biological perspectives were selected by using transcriptome data andIMF of cattle and sheep longissimus muscle(LM).These genes can be used to estimate thedeposition rate of IMF%,which is not able to be simply measured by currentmethodologies.Two groups of cattle with divergent IMF were used to validate amethodology based on these genes to estimate IMF with lower cost and higher accuracy.The advantage of gene expression based methodology compared with other conventionalapproaches was discussed.The results showed that,after filter and validation,CIDEA,THRSP,ACSM1,DGAT2 and FABP4 were identified to be most correlated with IMF inboth cattle and sheep,which were assigned as "IMF 5 gene set".Compared with theconventional approaches,such as ultrasound and NIRS,the gene expression based methodscould estimate IMF of cattle and sheep using fewer animals and more accurate.Geneexpression levels are much more sensitive to the environmental and nutritional challenge ortreatment than phenotypical IMF,which is considered to be the main reason of betterperformance of the gene expression estimator of IMF.2 Establishment of a qPCR based prediction model of future marbling status in beefcattleBased on the rule of thumb,of which IMF was proportional to hot slaughter carcassweight(HSCW,easy to convert from bodyweight),this study was aimed to establish aqPCR assay to predict IMF%by using IMF 5 gene set in cattle.A set of 31 beef cattle withvariation in breeds,age and IMF were used as the animal sources.The results showed thatexpression level of the single gene in IMF 5 gene set was not correlated with IMF acrossthe 31 cattle,so was the combination of all the 5 genes.However,two groups of outlierswere identified based on the plot of IMF 5 gene set expression against IMF.The correlationbetween gene expression level of IMF 5 gene set and IMF was greatly improved(from 0.2to 0.8)when the outliers were excluded.An integrated analysis of HSCW,current IMF%and gene expression level of the IMF 5 gene set was conducted.The result indicated thatunder normal nutrition status and a certain HSCW scale(200kg to 400kg),the future IMF%in the animals with normal current IMF but disordered gene expression level was predicted to stay stable or had a substantial increase in short time;whereas the rest animal wouldfollow the IMF developmental trajectory to reach the limit of their IMF%potential.3 Transcriptome analysis of cattle muscle identifies potential markers for skeletal muscle growth rate and major cell typesIn this study,transcriptome data of three cattle breeds,Brahman steers,Piedmontese xHereford(PxH)and Wagyu x Hereford(W×H)and the corresponding average daily gain(ADG)were used to identify the gene markers and cell population correlated with skeletalmuscle growth rate.Based on the correlation analysis and gene ontology enrichmentanalysis,the genes most correlated with ADG in Brahman steers were identified to berelated to the mitotic cell cycle and extracellular matrix(ECM)remodeling processes.Twosets of genes were generated by the analysis above,which were designated.as "cell cycle 5gene set" and "ECM 5 gene set".From the transcriptome data in PxH and WxH cattleacross development,a large set of 5,596 genes co-expressed with the "ECM 5 gene set"were filtered for the clustering analysis.By combining the clustering analysis and publishedcell markers of the main components in skeletal muscle,we found that the cell cycle geneswere mainly derived from the cell populations generating ECM throughout development.Moreover,the variation of expression level of ECM related genes was highly correlatedwith IMF development.The analysis also indicated that the muscular adipocytes andfibroblasts shared a common progenitor stem cells pool,which was consistent with theconsensus in human and rodents.