Inclusion of imputed genotypes from non-genotyped dairy cattle in a Thai multibreed genomic-polygenic evaluation

This study assessed the impact of incorporating imputed single nucleotide polymorphism (SNP) information from non-genotyped animals on genomic-polygenic evaluations in a Thai multibreed dairy population under various levels of imputation accuracy.

Data encompassed pedigree and phenotypic records for 305-day milk yield (MY), 305-day fat (Fat), and age at first calving (AFC) from 12,859 first-lactation cows, and genotypic records of various densities from 4,364 animals. A set of 64 animals genotyped with GeneSeek Genomic Profiler 80K and with four or more genotyped progenies was defined as target animals to simulate imputation scenarios for non-genotyped individuals. Actual and imputed genotypes were utilized to construct three SNP sets. All SNP Sets contained actual and imputed SNP markers from genotyped animals. SNP Set 1 contained no SNPs from target animals, whereas SNP Set 2 incorporated imputed SNPs from target animals, and SNP Set 3 added actual SNPs from target animals. Genomic-polygenic evaluations were conducted using a 3-trait single-step model that included contemporary group, calving age, and heterozygosity as fixed effects and animal additive genetic and residual as random effects.

The imputation accuracy was similar across non-genotyped animals irrespective of the number of genotyped progenies (average: 40.55%; range: 34.68% to 53.82%). Estimates of additive genetic and environmental variances and covariances for MY and AFC varied across SNP sets. SNP Sets 1 and 2 had slightly higher additive genetic and lower environmental variances and covariances than SNP Set 3. Heritabilities and additive genetic, environmental, and phenotypic correlations between MY, Fat, and AFC were similar across all SNP Sets. Spearman rank correlations between genomic-polygenic estimated breeding values from SNP Sets 2 and 3 were high for all traits (0.9990±0.0003).

Utilization of phenotypic and pedigree data from imputed non-genotyped animals enhanced the efficiency and cost-effectiveness of the genetic improvement program in the Thai multibreed dairy cattle population.