Meat Quality-related Genes Screening And Breeding Improvements Analysis Of Xinjiang Brown Cattle Based On The Transcriptome-whole Genome Sequencing

Xinjiang brown cattle is a type of milk-meat cattle that is bred for long-term selection and breeding with Kazakh cattle native to Xinjiang as the female parent,which has been crossed with Swiss brown cattle,Alatawu cattle and Kostrom cattle.After years of improvement,its meat and milk production has been effectively increased.Currently,Xinjiang brown cattle and Kazakh cattle are the main breeds of Xinjiang beef cattle.This study took Xinjiang brown cattle and Kazak cattle breeding populations as the research objects.First,the slaughter traits,carcass traits,muscle nutritional content,and eating quality of the two breeds were compared;then,the two breeds of cattle were compared through transcriptome sequencing.The transcriptome of the longissimus dorsi muscle is different,and the differentially expressed genes and the biological pathways that may affect the meat quality are discovered;finally,the genome resequencing technology is used to clarify the genes selected by humans in the improvement process of Xinjiang brown cattle and use the transcriptome to date.The method of combined analysis with genome sequencing results has clarified the progress of molecular improvement of meat quality traits in Xinjiang brown cattle breeding process.The main results are as follows:1.The comparative analysis of slaughter and carcass traits and meat quality traits between Xinjiang brown cattle and Kazak cattle shows that Xinjiang brown cattle have better meat production performance,body surface fat deposition and carcass indicators than Kazakh cattle;The shear force value and cooking loss of xinjiang brown cattle are better than Kazak cattle2.RNA high-throughput sequencing results showed that there were 673 differentially expressed genes in the longissimus dorsi of Kazakh cattle and Xinjiang brown cattle while 286 of which are highly expressed in Kazakh cattle and 387 are highly expressed in Xinjiang brown cattle.Among them,(1)ABLIM2,ACTB,ARPC1 A,DNAAF1,COL12A1,STC1,ITGA7 and other genes can potentially affect the formation and distribution of muscle fibers,thereby affecting meat production and meat quality;(2)ADCY6,ATP5 E,POR,LDHA,ACACB,ACOT2,CPT1 A,FADS3 and other genes can affect energy production,utilization,lipid transport and metabolism,thereby potentially affecting the content of intermuscular fat,which in turn affects meat quality;(3)CH1,NMNAT3,PTS,CFB,FBXO32,NAMPT,PANK1,ANXA9,BIN3,CRYAB,SIRT5,DCLRE1 C,MCM6,ARNTL,HLX,ADCY10,AOX1,ADAMTS10,ATAD3 and other genes can affect carbohydrates,coenzymes,inorganic ion transport and metabolism,and glycosylate transport/metabolism,transcription,post-translational modification,protein renewal,and signal transduction,and then regulate the basic biological functions of cells;In addition,a large number of genes such as UBIAD1,C1H21ORF7,CMYA1,CCDC138,etc.are also differentially expressed,but the specific biological functions are not yet clear;(4)CFB,GLUL,FBXO32,FUT11,GCNT1,GLCE,ACTB,ARPC1 A,STC1,ADCY6,POR,LDHA,ACACB,ACOT2,CPT1 A genes in the quadriceps femoris,psoas major,trapezius,semitendinosus,and intercostal muscles of Xinjiang brown cattle and Kazakh cattle The muscles and intercostal muscles are differentially expressed in meat,and they may be candidate genes that affect meat quality.3.The whole genome resequencing results showed that there were more than 5 million SNP loci and more than 700,000 small Indel loci between Kazak cattle and Xinjiang brown cattle.All SNP/small Indel loci were related to 10,000 functional genes and 258 biological pathways.The conjoint analysis showed that compared with Kazakh cattle,more than 4,000 genome segments were selected during the breeding process as well as many genes and 85 biological pathways involving Rap1 signaling,Ras signaling,Chemokine signaling,Fox O signaling,Neuroactive ligand-receptor interaction,Protein processing in endoplasmic reticulum,PI3K-Akt signaling,Regulation of actin cytoskeleton,Hippo signaling,Focal adhesion,MAPK signaling.This study preliminarily clarified the changes in the genome and transcriptome during the selection and breeding of Xinjiang brown cattle.The breeding improvements of Xinjiang brown cattle at the genome and transcript levels were also explored.These provided a theoretical basis for the next step in the breeding of Xinjiang brown cattle.