Impact of pedigree completeness on genomic–polygenic evaluations for milk yield, fat percentage, and age at first calving in Thai multibreed dairy cattle

Abstract. Pedigree completeness is fundamental for accurate estimation of genetic parameters and reliable prediction of breeding values, yet incomplete pedigree records remain a persistent limitation in smallholder dairy systems, especially in multibreed populations. Although genomic data capture genetic relationships and compensate for missing pedigree information, the extent of this compensation under varying pedigree losses is not fully understood. This study evaluated the impact of pedigree completeness on genomic–polygenic evaluations of 305 d milk yield (MY), fat percentage (FP), and age at first calving (AFC) in the Thai multibreed dairy cattle population. Phenotypic records from 14 239 first-lactation cows and genotypes from 5175 animals imputed to 117 796 single-nucleotide polymorphisms (SNPs) were analyzed using a three-trait single-step genomic–polygenic model across nine scenarios (SO1–SO9). These ranged from full pedigree (SO1) to progressive exclusion of records for up to 50 % of phenotyped animals (SO9). Declining pedigree completeness altered variance structures, increasing additive genetic variance and heritability estimates for MY but reducing them for FP and AFC. Genomic–polygenic estimated breeding value (GPEBV) accuracies and ranking stability also declined with pedigree losses, particularly for FP and AFC, once more than 20 % of phenotyped animals lacked pedigree information. While genomic data partially compensated for moderate pedigree omissions, this capacity was trait-specific and dependent on the accuracy of imputation. The findings underscore that pedigree completeness remains indispensable for robust genomic–polygenic evaluations, particularly for low-heritability traits, where genomic information alone cannot ensure reliable selection. This study highlights the importance of systematic pedigree recording in smallholder-based tropical dairy systems to safeguard the accuracy of genetic evaluations and sustain long-term genetic improvement in multibreed populations.