Analysis Of Goat BHLH And PLAG Gene Families And Mining Of Genetic Markers Associated With Growth

Goat is one of the oldest domesticated animals.It provides various animal products such as meat,skin,hair,and dairy products for human life.It is an important source of food and industrial raw materials.Growth traits such as body weight and body size are important factors affecting the performance and economic value of livestock,and targeted improvement of important economic traits such as meat production and body size is an important part of modern goat breeding programs.Due to the low meat yield and lagging growth performance of the excellent goat breeds in many parts of my country,the development of the local goat industry is limited.Germplasm resources or genetic resources are the material basis for animal breeding,and the mining and utilization of high-quality genetic resources is the key to breeding excellent breeds.It is of great significance to mine important candidate genes and molecular markers,and use molecular marker-assisted selection breeding(MAS)for genetic improvement and breeding of important growth traits in goats.The basic helix-loop-helix(bHLH)transcription factor family plays an important role in the regulation of eukaryotic growth and development.The members of the animal bHLH gene family are widely involved in important biological processes related to myogenesis and organogenesis,cell proliferation and differentiation,intestinal tissue development and circadian rhythm.It is important in differentiation and apoptosis,as well as in the regulation of the cell cycle.Current studies have shown that it has an important regulatory function in the regulation of animal growth rate and body size.According to a large number of studies,genes such as Myo D1 in the bHLH family and PLAG1 gene in the PLAG family are one of the major genes that determine important economic traits such as muscle growth and body height regulation in mammals.In this study,through a comprehensive analysis of two candidate gene families,the key gene and molecular markers that may affect the main growth traits of goats were mined,and the experimental verification of genetic effects was carried out in a total of 1920 ewes,with a view to providing insights into goats.Molecular breeding provides a theoretical basis.The main results of this study are as follows:1.Goat bHLH and PLAG gene family annotation and systematic bioinformatics analysisBased on the whole genome data of goat,a total of 101 bHLH family members in goat were identified for the first time,and they were divided into five subfamilies A,B,C,D,and E according to phylogenetic relationship,including family members 17,17,16,30,21,the results show that goat bHLH family genes have a slight shrinkage phenomenon in evolution compared with other species;PLAG gene family is 3 genes consistent with previous studies.Through systematic and comprehensive analysis of conserved motifs and gene structure analysis,chromosome positioning,collinearity analysis,phylogenetic analysis,enrichment analysis,etc.,the basic characteristics of the two families of genes were characterized and annotated,and the genes in the goat genome were also described.Evolutionary relationships among multiple species.2.Analysis of gene expression patterns of goat bHLH and PLAG families and identification of spatiotemporal expression profiles of key growth-related genesThrough the quantification of transcriptome data in different tissues,the tissue expression profiles of each gene in the bHLH family were analyzed and analyzed,and the spatiotemporal expression patterns of potential candidate genes related to important growth traits in different periods and between different tissues were verified by RT-q PCR.The relative expression levels of Myo D1 and Myo G genes are higher in the adipose tissue of adult sheep,and the relative expression levels of Myf5 and Myf6 genes are higher in the skin tissue of fetal sheep.These four genes have the highest expression in skeletal muscle tissue in adult goat tissues.The relative expression of PLAG1 gene was highest in goat lung and kidney tissue,and the expression level in fetal period was higher than that in adult period.Combined with the construction of protein interaction network,key candidate genes Myo D1,Myo G,Myf5,Myf6 and PLAG1 genes that may be related to important growth traits such as meat production and body size in goat were identified.3.Molecular marker mining of key genes of goat bHLH and PLAG families and verification of their genetic effects in goat breedingPotential molecular breeding markers were mined for important genes related to meat production and body size in the bHLH and PLAG gene families,and the polymorphic loci of local elite goat breeds such as Shaanbei white cashmere goat with a large sample size(n=1914)were identified.Identification and detection of genetic effects.Finally,a CNV(NC＿030822.1:g: 47532801-47536000)spanning the entire CDS region of the Myo D1 gene was determined,which can significantly affect all the growth and developmental traits tested,and has the dominant genotype Gain type with significantly excellent growth phenotypes;In the PLAG1 gene,CNV1(NC＿030821.1:g:58704401-58707600)spanning both the first exon and the bidirectional promoter of the PLAG1 and CHCHD7 genes was identified.,chest circumference,and tube circumference traits had extremely significant effects(P<0.01),of which Loss type was the dominant genotype for all tested traits;CNV2 located on the first intron of PLAG1 gene(NC＿030821.1:g:58711201-58715600)significantly affected body weight,recommended height,chest circumference,hip width and chest depth(P < 0.01 or P< 0.05),and the dominant genotype was Medium;CNV3 located on the first intron of the PLAG1 gene(NC＿030821.1: g:58716801-58718800)significantly affected body weight,recommended height,body length,chest circumference,tube circumference,and hip width(P<0.01 or P<0.05),and the dominant genotype was Medium.To sum up,this study made a comprehensive annotation and analysis of the two gene families in the goat genome,and carried out molecular marker mining and identification of candidate genes that may affect key growth traits in goats,in order to provide evidence for the development of bHLH and PLAG families in the goat genome.The follow-up research in goat provides theoretical basis and technical support for more accurate and efficient molecular marker-assisted selection breeding in goat.