Genome Wide Association Studies Using Multiple-lactation Breeding Value in Holsteins

Abstract

A genome wide association study was conducted using estimated breeding value (EBV) for milk production traits from 1st to 4th lactation. Significant single nucleotide polymorphism (SNP) markers were selected for each trait and the differences were compared by lactation. DNA samples were taken from 456 animals with EBV which are Holstein proven bulls whose semen is being sold or the daughters of old proven bulls whose semen is no longer being sold in Korea. High density genome wide SNP genotype was investigated and the significance of markers associated with traits was tested using the breeding value estimated by a multiple lactation model as a dependent variant. As the result of significance comparisons by lactations, several differences were found between the first lactation and subsequent lactations (from second to 4th lactation). A similar trend was noted in mean deviation and correlation of the estimated effects by lactation. Since there was a difference in the genes associated with EBV for each trait between first and subsequent lactations, a multi-lactation model in which lactation is considered as a different trait is genetically useful. Also, significant markers in all lactations and common markers for different traits were detected, which can be used as markers for quantitative trait loci exploration and marker assisted selection in milk production traits.

Single and longitudinal genome‐wide association studies for dairy traits available in goats with three recorded lactations

“…However, when we performed three GWAS (one per lactation), using the same 660 individuals in each analysis, we obtained identical results, and the very same lack of QTL positional concordance was detected. Cho et al (2015) carried out a GWAS in a population of 456 Holstein proven bulls with estimated breeding values of milk production traits recorded in different lactations (from first to fourth lactation) and genotyped with the Bovine SNP50 v2 chip (Illumina). They found that most of SNPs displaying significant associations with estimated breeding values showed different associations in first and subsequent lactations, and they also noted that genetic correlations between the first and subsequent lactations were weaker than those between the second, third, and fourth lactations (Cho et al, 2015).…”

“…Cho et al (2015) carried out a GWAS in a population of 456 Holstein proven bulls with estimated breeding values of milk production traits recorded in different lactations (from first to fourth lactation) and genotyped with the Bovine SNP50 v2 chip (Illumina). They found that most of SNPs displaying significant associations with estimated breeding values showed different associations in first and subsequent lactations, and they also noted that genetic correlations between the first and subsequent lactations were weaker than those between the second, third, and fourth lactations (Cho et al, 2015). Moreover, significant genotype by lactation stage interactions have been also reported (Lu et al, 2020).…”