Genetic Parameter Estimation,GWAS-based Identification Of Single Nucleotide Polymorphisms(SNPs) And Candidate Genes,and Population Genetic Structure Research For Mammary System Conformation Traits Of Chinese Holstein Cattle

The mammary system conformation traits are economically important for dairy animals in the dairy industry.These conformation traits of dairy cows are closely related to their milk yield,milk fat%,and milk protein%,which are among the most important traits in dairy breeding.Milk production loss can be reduced via a better udder structure in dairy cattle.At the same time,milk production of dairy cows has always been the focus of attention at the dairy cattle farm.The studied of trial population consisted of 1000 Holstein cows and 301 Jersey cattle raised from 5(First 4 animal farm included Holstein cattle and only last farm consisted Jersey cow)dairy farms in Jiangsu Province,China(Sihong Aideweigang Dairy Farm 1:199;Xuyi Weigang Dairy Farm 2:214;Xuzhou Yonghao Dairy Farm 3:224;Huaxia,Animal Husbandry Farm 4:363 cattle,and Yinbao Guangming Farm 5:301).This project carried out an estimate of phenotype and genotype research data,and genome-wide analysis on the Chinese Holstein cattle such as genetic parameter estimation(phenotype and genotype correlation,heritability),and finally,a comparison of population genetics structure of two breeds was done(Chinese Holstein and Jersey cattle)through whole genome sequencing on the base of genotype data in Jiangsu province.First,the eight mammary system conformation(teat consisted 3,and udder has 5)traits were measured individually by scores ranging from 1 to 9 points;including eight mammary system traits(anterior teat position(ATP),posterior teat position(PTP),front teat length(FTL),anterior udder attachment(AUA),central suspensory ligament(CSL),posterior udder attachment height(PUAH),posterior udder attachment width(PUAW),udder depth(UD)),and while three milk production traits(305d milk yield,milk fat percentage,and milk protein percentage)of 1000 Chinese Holstein cattle from four animals farm.However,hair samples(50)were collected from each animal of two breeds(999 Holstein and 301 Jersey cattle)for genotyping analysis in this research.Then,estimated genetic parameter analysis was performed for descriptive heritability,Phenotypic and genotypic correlation in Holstein cows using SPSS(v.19.)and AI-REML module in DMU software(v.5.6).So,all genotype data of mammary system traits were assessed by EM algorithm,and multi-trait animal model.A genome-wide association study(GWAS)was carried out to identify SNPs,and candidate genes between phenotypes that cause genetic variation in Chinese Holstein cattle.Afterward,we performed a genome-wide association study on mammary system conformation traits of total 8 traits(3 teats,and 5 udder traits)that included ATP(anterior teat position),PTP(posterior teat position),FTL(front teat length),AUA(anterior udder attachment),CSL(central suspensory ligament),PUAH(posterior udder attachment height),PUWA(posterior udder attachment width),and UD(udder depth),in which the FarmCPU(fixed and random model circulating probability unification model)model was used for association analyses.Identification of SNPs and candidate genes would be providing useful information about genetic architecture of mammary system traits for genetic selection,breeding planning in dairy cattle.Based on the GGP(GeneSeek Genomic Profiler)Bovine 100K single-nucleotide polymorphisms(SNP)chip was used for cattle genotyping data analysis.The GGP Bovine 100k of genotyping data was used to comparison of two breeds through Whole genome sequencing data,and it analyzed by principal components analysis,genetic population analysis,Fst test,and gene ontology for finding information about population genetics structure variations between two cattle breeds(Holstein,and Jersey cattle)that is essential for genetic improvement,understanding the genetic architecture,environmental adaptation as well as utilization and conservation of dairy cattle breeds.The following experimental data,models,and analysis were performed in this study,and pertinent results were achieved.1.To investigate that the 1000 animal selected from four animal farm including(Sihong Aideweigang Dairy Farm 1:199;Xuyi Weigang Dairy Farm 2:214;Xuzhou Yonghao Dairy Farm 3:224;Huaxia,Animal Husbandry Farm 4:363 cattle)in Jiangsu Province,China.The eight mammary system(Teats and Udder)traits were selected for estimated parameter genetic analysis.The DMU software(v.5.6)AI-REML module was used for the genetic analysis.The genetic parameters of mammary system conformation traits were estimated by the EM algorithm and multi-trait animal model.Pearson correlation coefficient was used to analyze the phenotypic correlation between mammary structure within traits and only udder conformation traits between milk production traits(305-day Milk yield,milk fat%,milk protein%).The estimated heritability of conformation traits was low(0.04)to medium(0.49)between PUAH and UD,and the genetic correlation between conformation traits ranged from-0.09(PTP)and(ATP)to 0.60(PUAH and PTP).Milk yield at 305d was significantly negatively correlated with UD(-0.14)and AUA(-0.11),and significantly positively correlated with CSL(0.09)and PUAH(0.10).Milk fat%was positively correlated with PUAH(0.34),and negatively correlated with UD(-0.07),and CSL(-0.117).Milk protein%was positively correlated with UD(0.08),CSL(0.15),and AUA(0.07),and negatively correlated with PUAH(-0.20).The logistic regression model was used to screen out the mammary system(udder)traits which greatly influenced on the milk yield in 305d.The UD and CSL had early predictive value on milk yield at 305d(P<0.01),and milk yield at 305d was significantly negatively correlated with UD(-0.15),and positively correlated with CSL(0.10).These results identified that the UD and CSL traits of Chinese Holstein cattle in Jiangsu had medium heritability that was related to milk production traits.Improving the selection of these two udder traits is significant for dairy cow breeding plans and milk yield enhancement in dairy cattle.2.Moreover,a genome-wide association study was performed on mammary systemrelated teat conformation traits;which included anterior teat position(ATP),posterior teat position(PTP),and front teat length(FTL)in which the FarmCPU method was used for association analyses.Phenotype and genotype data were collected from the first 4 dairy animal farm(Holstein cattle).Based on the GeneSeek Genomic Profiler Bovine(GGPB)100K single-nucleotide polymorphisms(SNP)chip was used for cattle genotyping data.After the quality control process,984 individual cows and 84,406 SNPs remained for GWAS analysis.While nine SNPs identified significantly that was associated with mammary-system-related teat traits after a Bonferroni correction(p<5.92 × 10-7),and genes within a region of 200 kb upstream or downstream of these SNPs were done bioinformatics analysis.A total of 36 GO(gene ontology)terms and 3 KEGG(Kyoto Encyclopedia of Genes and Genomes)pathways were significantly enriched(p<0.05),and these GO terms and KEGG pathways are mainly related to immune response,cellular,and amino acid catabolic processes.Eleven genes including MMS22L,E2F8,CSRP3,CDH11,PEX26,HAL,TAMM41,HIVEP3,SBF2,MYO16,and STXBP6 were identified as candidate genes that might play roles in the teat conformation traits of cows.So,these results identify SNPs and candidate genes that give valuable biological information for the genetic architecture of these mammary-related teat traits,thus participating in the health,and genetic selection of Holstein dairy cattle production.3.While a same GWAS study was conducted for five udder conformation traits;including AUA,CSL,PUAH,PUAW,and UD,in which the fixed and random model circulating probability unification(FarmCPU)model was applied for the association analysis.So,the GGPB 100 K SNP chip was used to analyze genotypic data in Holstein cattle.For GWAS analysis,984 individual cattle,and 84,407 SNPs(single-nucleotide polymorphisms)remained after quality control;a total of 18 SNPs were identified at the GW significant threshold(p<5.90 × 10-7).Several candidate genes were found within 200kb upstream or downstream of the significant SNPs,which include MGST1,MGST2,MTUS1,PRKN,STXBP6,GRID2,E2F8,CDH11,FOXP1,SLF1,TMEM117,SBF2,GC,ADGRB3,and GCLC.Pathway analysis revealed that 58 GO(Gene Ontology)terms and 18 KDGG(Kyoto Encyclopedia of Genes and Genomes)pathways were enriched with adjusted p values,and these GO terms and the KEGG pathway analysis was associated with growth,development processes,biological information,metabolism and hormonal.These results could give significant biological information for the genetic architecture of udder conformation traits in Chinese Holstein cattle.4.Since the study stated that information about population genetic structure differentiation between two cattle breeds is essential for genetic improvement,genetic architecture,understanding of environmental adaptation as well as utilization and conservation of cattle breeds.In this study,we investigated the population structure between two cattle breeds(999 Holstein,and 301 Jersey),and all animals were selected from five experimental farms in Jiangsu province China.So,VCF Tools and Plink software were used for the whole genome data analysis of the two breeds.The population structure of cattle breeds was differentiated based on genotyping data through whole genome sequencing data analysis.PCA1,PCA2,PCA3,and PCA4 contributed 7.47%,1.46%,1.22%,and 0.98%,at the same time,for total population structure variation.An LD decay was similar in the Jersey population and Holstein population,indicating that the selection caused the enhancement of LD degree in Jersey and Holstein cattle.Two populations of cows were observed for determining the relationship number of a genomic region in the Identity by descent(IBD)plot,and also Parallel Coordinates Plot(PCP)was identified a genomic region in breeds through VCF Tools.Hierarchical clustering analysis was showed the population structure of the cattle breeds by individual dissimilarity.For relatedness analysis,the method of moments(MOM)identified the genetic variance of two breeds which can be used to assess the degree of differentiation between populations.The variance among populations is the same as the variance within populations,there is no population substructure.Pi results were determined by Nucleotide diversity which is the average pairwise difference between all possible pairs of individuals in a population structure breed.Pi of the Holstein population was higher on Chr 6,7,11,and 19 than other chromosomes,while the nucleotide diversity(Pi)value of the Jersey population was less on several chromosomes than except Chr 23,28 and 29.Tajima’s D was a higher polymorphism frequency in Holstein cattle than in Jersey cattle populations.So,the Fixation index test was applied for two breeds of whole genome data analysis on the basis of SNPs.To collect genotype data,the study of population genetic structure was carried out in Holstein,and Jersey cattle by using GGP Bovine 100 k SNP chip.A total of(Holstein 999.and 301 Jersey)cows and 84,407 single-nucleotide polymorphisms(SNPs)remained after quality control.The common Population structure variations detected by the Fst test.Genetic variations depend on Fst value,Fst value 0 show no genetic between two breeds.The Fst>0.35 value was show high genetic structure variations in Chine Holstein and Jersey breeds.Fst score value of two breeds was 0.111,and mean of Fst value showed 0.099.Fst SNPs were distributed on base of chromosomes,and were dissimilar three chromosomes(Chr3,7,and 26).These genes were clustered in 16 gene ontology(GO)functional terms.The GO terms were revealed on base of genetic population structure in two breeds,including transmembrane receptor protein tyrosine kinase signaling pathway,cyclic-nucleotide-mediated signaling,memory,positive chemotaxis,Chemotaxis,Taxis,Locomotion,regulation of B cell proliferation,cyclic-nucleotide-mediated signaling,and cAMP-mediated signaling e.g.,Based on the findings,some potential candidate genes(DEFB1,PPP2CA,CRIP1,SKP1,and MZB1)were revealed from both population structure breeds.Our results will helpful to improve the understanding of the genetic architecture of population structure in cattle breeds and provide essential sources for future bovine cattle breeding.