Validating genomic predictions for economic traits in purebred US dairy heifers

Abstract

ABSTRACT: Most genotypes in the National Cooperator Database now originate from cows, but most previous studies validating genomic predictions have primarily focused on bulls. This study paired official within-breed genomic PTA (GPTA) and parent average (PA) for genotyped heifer calves born between 2019 and 2021 using the August 2021 database with their corresponding performance deviations (PDEV) for 17 different traits. The PDEV data became available when the heifers completed their first lactation and were extracted from the August 2023 database in which at least one PDEV value for those 17 traits existed for each genotyped heifer record. The separate breed analyses included records for 219 Ayrshires (AY), 2,715 Brown Swiss (BS), 1,055 Guernseys (GU), 949,904 Holsteins (HO), and 125,275 Jerseys (JE). These validation cows were heifer calves born between 2019 and 2021. However, due to timing or recording patterns, each trait had missing or incomplete PDEV data, leading to unbalanced distributions of records across traits. The squared accuracy of genomic prediction, or genomic reliability (r2), was divided by the corresponding heritability for each trait, as only the heritable portion of cow records could be predicted, and this reliability varied across different traits and breeds. For HO and JE, the predictive ability of GPTA outperformed PA in predicting cow PDEV for yield, productive life, SCS, fertility, and health traits. The improvement ranged from 33% to 142% compared with the predictive ability of the PA. However, the results for AY, BS, and GU breeds were less consistent due to the smaller number of genotyped heifers. The r2 gains in those breeds were smaller and aligned with the published reliabilities of GPTA. Weighted and unweighted regressions of PDEV on GPTA and PA traits mostly exceeded the expected value of 2.00 when predicting the future trait PDEV using GPTA or PA. The larger number of observations and lower SE of the weighted regression coefficient prediction in HO and JE breeds contributed to more stable and consistent regression coefficients for all traits except milk fever and heifer livability. Our study suggests that herd owners may experience greater benefits from genomics than originally forecast.

Keywords

• cow validation
• genomic prediction
• performance deviation
• dairy breeds