High Coverage Methylation Re-sequencing For Tissue Specifie And Sequential Specific Loci Of Bamaxiang Pig And A Whole Genome Sequence Association Study Of Muscle Fiber Trarits In A F2 Resource Population

Bamaxiang pig is small,tolerant inbreeding,and is an important animal model for pharmacological test,disease model construction and xenotransplantation.DNA methylation is more and more popular in science research,and plays a very important role in regulating gene expression.The genome-wide methylation research of different age has not been reported in pig.This experiment using WGBS technology study testis and muscle tissue of Bamaxiang boars in 1,4 and 9 years.This study is the first time with high coverage methylation re-sequencing system analyzing tissue specificity and scheduling loci of Bamaxiang boars,for the first time mapped the single-base high resolution genome-wide methylation pattern of testicles and muscle tissue,and discusses the function of DNA methylation in the breeding recession and muscle aging mechanism of Bamaxiang pigs,provide important theoretical basis bide for animals breeding and human medical research.The genome-wide total methylation level of each sample is about 4.4%,methylation mainly occurs in the CG sequence context,methylation rate is about 70%(mCG/CG),and accounts for 89.57% of the total methylation level.Methylation level of mCHG and mCHH context are simile with the level of total methylation(mC)distribution trend on different chromosomes.The methylation level of chromosome is inversely proportional to the chromosome length.Different organizations,the methylation pattern of gene function area is similar in different organs of different ages.The DMRs length distribution on each chromosome is similar in different organs of Different ages.DMRs mainly concentrated in the intergenic,intron and exon in Different groups of different ages under different sequences environment,few scattered DMRs in other functional areas.The DMRs number of muscle and testis decreases as aging,and the methylation level as growth lowered after at first.The DMRs number of different organs decrease as the growth of the age,confirmed the tempornal specificity of DNA methylation.The DMRs methylation level of testis in different ages is higher than muscle tissue,the DMRs number and methylation level are not change with age.Methylation levels were highest in the intron region and 3 'UTR region,and lowest in 5' UTR region.GO and KEGG analysis,we obtained the GO items which we are interested in,such as: skeletal muscle development,muscle cells,muscle cells homoestasis and steroid hormone interfece signal pathways.Three candidate genes DMD,SGO1 and CITED1 were identified in muscle and testis.For different organizational DMGs intersection,we got 148 genes.Using the String database analysis those DMGs,we obtained four candidate genes DMGs:WT1?NCOA1?NR3C1 and NEOD4 L can be used in the study of the candidate.Pork is the main source of meat,muscle related traits has vital significance for pig production.Muscle fiber types,numbers and area are crucial aspects associated with meat production and meat quality,such as meat colour,p H,water dropping loss,holing capacity and tenderness.Previously,we examined swine muscle fiber traits by performing a genome scan using 183 microsatellites and detected 8 significant QTLs with confidence intervals ranging from 11 to 127 c M.This approach was used to identify hundreds of genes that hampered the identification of quantitative trait gene(QTG).Herein,GWAS was performed in a White Duroc × Erhualian pig resource population based on the phenotypic data,genotype data and re-sequencing data.Genotyping was performed for 1,020 individuals and SNPs were identified.The pinpoint of this study is identify QTL area,key marker and causal genes influence muscle fiber types.The deep sequencing data of 19 F0 and 98 unrelated individuals were used to build haploid reference library.The 60 k data of 1020 individuals were imputed on complete genome sequence by IMPUTE2 software,and 21,624,800 SNPs were identified,quality control filter,14,749,450 SNPs were then examined for associations to 11 longissimus muscle fiber traits.A total of 14 significant SNPs comprising 4 novel QTLs were identified and associated with the relative area of fiber type I(I_RA),the fiber number per square centimeter(FN)and the total fiber number(TFN).Moreover,one QTL on SSC14 was found to affect both FN and TFN.Furthermore,three plausible candidate genes associated with FN(ADAM8 and BIN1),TFN(ADAM8)and I_RA(FAM105A)were identified.In summary,whole genome sequence association in this study identified four QTLs for muscle fiber traits.The findings paved the load to fine mapping the interest loci,and to develop molecular breeding technologies for primal cut in pigs.