Application Of Multivariate Analysis For Body Conformation Traits In Shanghai Holstein

Information about genetic parameters is population specific and it is crucial for designing animal breeding programs and predicting response to selection.This study was carried out to estimate the genetic parameters for 23 body conformation traits of45,517 Shanghai Holstein reared in Eastern China from 1995 to 2017 with Bayesian inference method using a linear animal mixed model.The methods to integrate these traits included:1)using composite index from Dairy Association of China（DAC）;2)applying Principal Component Analysis（PCA）and Factor Analysis（FA）to explore the relationship between the conformation traits.Estimates of heritability using the composite index were low（0.04;feet and legs）to moderate（0.23;body capacity）.Strong genetic correlations were observed between the individual body conformation traits（IBCT）.Both principal components（PC1 to PC7;eigenvalues?1）and latent factor（F1 to F7;eigenvalues?1）explained 60.37%total variability.Both principal component analysis and factor analysis provided insight into new form of composite that could be used for selection program in Shanghai Holstein population.PC1 and F1accounted for the traits that are usually associated with milk production.Moderate to low heritability were estimated through multi-trait analysis for principal components（from 0.07 to 0.21）and latent factors（from 0.07 to 0.23）.Genetic correlations among the two multivariate techniques are typically lower compared to the one existing among the measured traits.Results from these analyses suggest the possibility of using both PCA and FA in morphological evaluation,simplifying the information given by the body conformation traits into new variables which could be useful for the genetic improvement of the Shanghai Holstein population.This information could also be used to avoid analyzing large number of correlated traits thereby improving precision and reducing computation burdens to analyze large and complex data.A genome-wide association analysis was carried out on a subsample of 621 cows genotyped with the genotyping by genome reducing and sequencing（GGRS）protocol.Three single nucleotide polymorphisms on chromosome 10,15 and 24 were significantly associated with PC1 and PC3 respectively.The gene discovery was carried out considering genes surrounding the significant markers and highlighted some interesting candidate genes such as ACOT4-like（acyl-CoA thioesterase 4-like）,STIM1（Stromal Interaction Molecule 1）and U6（U6 spliceosomal RNA）genes.None of these genes have been previously reported to be associated with body conformation traits.The ACOT4 genes have not yet been characterized in livestock species.The STIM1 has been found to be chiefly expressed in bovine aortic endothelial cells（BAECs）with positive effect on both the store-operated Ca²⁺entry（SOCE）and the inositol 1,4,5-trisphosphate receptor（IP3R）-dependent Ca²⁺release.The U6 gene has been found to be associated with reproductive traits in Nellore cattle.Further studies should be carried out to validate these genes in order to foster our understanding on their roles in body conformation traits in cattle.