| Body conformation traits are highly important and play a crucial role in the economic development of dairy farming.By improving body conformation selection accuracy,the dairy.industry as a whole would benefit and individual farms profitability.This in turn will consequently contribute to the future profitability of the dairy industry in China.A registered body conformation trait is a reliable and cost-effective tool for use in national cattle breeding selection programs.Body conformation traits are significantly associated with cow production,longevity,locomotion,health,fertility,and environmental adaptation.Thus,these traits can be regarded as an indirect indicator of economically important traits for an animal.In this study,we systematically estimated the genetic parameters of 11 traits in the body conformation traits of dairy cows in Jiangsu province,including body size traits,rump traits（ReproductionRelated Body-Shape）traits,as well as feet and leg conformation traits,and then carried out non-genetic effect analysis and GWAS for these traits.Finally,we explored the feasibility of using genetically correlated information from other phenotype measurements to improve the estimation of genetic breeding value for single traits.Our results are expected to provide a foundation for understanding body conformation genetic architecture.Moreover,they will contribute to the development of breeding programs and genomic selection projects for Chinese Holstein cattle.The specific research results are as follows:（1）Evaluating the genetic parameters for body conformation traits have an economic interest to implement and develop efficient selection programs.It is the basis for research such as genome-wide association studies and genome-wide selection.Our study estimated genetic correlations between -0.35 and 0.84 among feet and leg traits.They also ranged from -0.08 to 0.36 for rump traits and 0.173 to 0.939 for body size traits.Accurate heritability estimates are necessary to predict selection response and breeding values.The heritability of body conformation traits ranges from low to medium.In the present study,estimates of heritability results ranged from 0.05（bone quality）to 0.17（rear leg-side view）for feet and leg conformation traits,Reproduction-Related Body Shape traits ranged from 0.20（Pin Width）to 0.38（loin strength）,while body size traits ranged from 0.1（body depth）to 0.48（body height）.Logistic regression models were used to analyze the effects of body conformation traits and age on lameness occurrence.Among the many body conformation traits,the rear leg-rear view has a significant effect on lameness（P<0.05）.In terms of the disease risk dimension,the ideal score for the rear leg-rear view might be 4 points.This is associated with a minimal lameness risk.（2）Utilizing a novel genetic method,such as a genome-wide association study（GWAS）,may provide greater insights into the genetic architecture of complex traits by identifying and applying genetic markers.Therefore,to better understand the genomic regions and biological pathways of body conformation traits in dairy cows,in the present study,we conducted GWAS using the fixed and random model circulating probability unification（FarmCPU）method on three groups（11 traits）of body conformation traits in Chinese Holstein cows.The feet and leg conformation traits include bone quality（BQ）,heel depth（HD）,rear leg-side view（RLSV）and rear leg-rear view（RLRV）.The rump（Reproduction-Related Body-Shape）traits,namely,rump angle（RA）,loin strength（LS）,and pin width（PW）.The body size traits（body depth（BD）,body height（BH）,chest width（CW）,and angularity（ANG））.In total,we identified 20,11 and 11 significant SNPs associated with feet and leg conformation,Reproduction-Related Body-Shape,and body size traits,respectively at the threshold of Bonferroni correction(5.90×10-7).Several genes within 200 kb distances（upstream or downstream）of the sigdificant SNPs were identified as candidate genes,including DNMT3A,ADIPOR2,INPP4A,ALDH1A2,PCDH7,CADPS and XKR4 for feet and leg conformation traits.For Reproduction-Related Body-Shape,five genes CDH12,TARP,ARAP2,DTHD1,and PCDH9 might affect LS,six genes FSTL4,LOC781835,ATG4C,DSPP,DMP1,and SH3BP4 that might affect RA,and five genes UPF2,ECHDC3,LOC101907665,USP6NL,and CNTN3 might affect PW.Moreover,six genes（KHDRBS3,MYH15,UBAPIL,DCC,AIP,and SQOR）were identified as the most promising candidate genes for body size traits.Further bioinformatics analyses（Gene Ontology（GO）terms and Kyoto Encyclopedia of Genes and Genomes（KEGG）pathway analysis）for genes within 200 kb of the identified SNPs showed 34 GO terms and two signaling pathways for Feet and Leg conformation traits,20 GO terms and six KEGG signaling pathways for Reproduction-Related Body-Shape traits,and 25 GO terms and five signaling pathways for body size traits were significantly enriched（p≤0.05）.（3）Our study found that the estimation accuracy of genomic breeding values using a Bayesian four-distribution mixed model was slightly better than the Genomic BLUP（GBLUP）-based method,especially for low heritable traits.At the same time,as the heritability of the predicted trait decreases,the accuracy of genome prediction by adding another trait’s phenotypic information gradually increases,and the accuracy of the predicted trait evaluation is positively correlated with the genetic correlation between the added another trait and the predicted trait,but in our study,only for traits with low heritability（ANG）,the accuracy of genome prediction was significantly improved by adding the phenotype information of traits with high genetic correlation（BH）.Therefore,the integration of genomic information is encouraged to improve the accuracy of genomic assessment,especially for low heritability traits. |
PDF Full Text Request