Genetic and genomic analysis of age at first insemination in Israeli dairy cattle

Abstract

We performed a genetic analysis of age at first insemination, including estimation of the heritability and genetic correlations with other economic traits, and the consequences of including this trait in the Israeli selection index. The genetic factors affecting age at first insemination were determined via GWAS. Five data sets were analyzed. Data sets 1, 2, and 3 were used to compute variance components among age at first insemination, first calving age, days from first insemination to calving, and the 9 traits included in the Israel breeding index. Heritabilities for age at first insemination, calving age, and days from first insemination to calving in Israeli Holsteins as computed by REML individual animal model analyses of 273,239 Israeli Holstein cows were 0.072, 0.042, and 0.014. The estimated genetic correlation between the first 2 traits was 0.88. In addition to the fact that heritability of age at first insemination is 1.7 times the heritability for calving, the former trait has the advantage that the number of records is greater, and the records are generated earlier. Absolute values of the genetic and residual correlations between age at first insemination and the 9 traits included in the Israeli index were all less than 0.2. Data set 4 included first insemination dates of 1,181,600 calves born from 1985 through 2018. Genetic evaluations were computed by a single trait animal model. Annual phenotypic and genetic trends for age at first calving for calves born since 1985 were "positive," that is, economically negative, at 0.320 ± 0.003 and 0.169 ± 0.005 d, respectively. Applying the GCTA-GREML software, 54% of variance in the transmitting ability of 1,585 sires could be explained by considering all 40,498 markers included in the GWAS analysis. The significant markers were mainly associated with milk production genes. The SNP UA-IFASA-8854 on chromosome 11 had the lowest probability value, 1.2 × 10 −24 . This marker is located between the genes RETSAT and ELMOD3, both of which are overexpressed in human mammary glands. The gene RETSAT is reported to be essential for lipid accumulation and adipogenesis promotion. Gene enrichment analysis found that genes in the genomic region flanking significant markers are associated with vasopressin receptor activity, which was shown to mediate puberty in humans. If age at first insemination is included in the index with a weighting to account for 9% of the index, reductions of 2.8 and 2.6 d for age at first insemination and first calving age after 10 yr of selection are predicted, as compared with reductions of 1.4 and 1.1 d with the current index. Gains for the other index traits are only marginally affected. We suggest selection on age at first insemination as an alternative to selection for early calving.

Genetic and Genomic Analysis of Cow Mortality in the Israeli Holstein Population

“…We thus analyzed the distribution of the genomic distances between markers as a function of the R 2 values for genetic linkage. About 85% of the marker pairs with R 2 > 0.9 are within 150 kb distance from each other, as we found recently in this population [ 32 ]. We therefore obtained QTL and genes within an interval of 150 kb spanning the significant markers for enrichment analysis.…”

Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation

“…The following supporting information can be downloaded at: . File S1: BTA14 association analysis of RFI [ 30 , 31 , 32 ]; Figure S1: ZHX2 polymorphism; Figure S2: imbalanced allele proportions in Sanger sequencing; Table S1: PCR primers; the basic dataset (Excel format).…”