Genomic prediction and validation strategies for reproductive traits in Holstein cattle across different Chinese regions and climatic conditions

ABSTRACT: Accurate genomic predictions of breeding values for traits included in the selection indexes are paramount for optimizing genetic progress in populations under selection. The size of the reference populations is a major factor influencing the accuracy of genomic predictions, which is even more important for lowly heritable traits, such as fertility and reproduction indicators. Combining data from different geographical regions or countries can be beneficial for genomic prediction of these lowly heritable traits. Therefore, the objectives of this study were to (1) evaluate the benefits of performing across-regional genomic evaluations for reproduction traits in Chinese Holstein cattle and (2) assess the feasibility of validating genomic predictions across environments based on reaction norm models (RNM) and the linear regression (LR) method after accounting for genotype-by-environment interactions. Phenotypic records from 194,574 cows collected across 47 farms located in 2 regions of China were used for this study. The reference and validation populations were defined based on birth year for applying the LR validation method. The traits evaluated included: interval from first to last insemination (IFL), conception rate at the first insemination (CR_f), and number of inseminations (NS) recorded in heifers and first-parity cows. The results indicated that combining data from different regions resulted in greater genomic prediction accuracies compared with using data from single regions, with increases ranging from 2.74% to 93.81%. This improvement was particularly notable for the region with the least amount of available data, where the increases ranged from 26.49% to 93.81%. Furthermore, the predictive abilities could be validated for all studied traits based on the LR method across different environments when fitting RNM. The prediction accuracies and bias of genomic breeding values based on RNM were better than regular single-trait animal models in extreme climatic conditions for IFL and NS, whereas limited increases in predictive abilities were observed for CR_f. Across-regional genomic prediction by RNM can account for genotype-by-environment interactions, potentially increase the accuracy of genomic prediction, and predict the performances of individuals in the environments with limited phenotypic data available.