Genetic and genomic analysis of long insemination interval in Israeli dairy cattle as an indicator of early abortions.

One of the causes of observed low fertility is embryo loss after fertilization. Previous findings suggested that more than half of fertilizations result in embryo loss before pregnancy is detected. We proposed reinsemination between 49 and 100 d after the first insemination as an indicator trait for early abortion (EA) in dairy cattle based on the mean estrus interval of 21 d. This trait was compared with conception rate from first insemination and conception status, computed as the inverse of the number of inseminations to conception. Animal model variance components were estimated by REML, including parents and grandparents of cows with records. First-parity heritability for first insemination conception rate was 3%. In the multitrait analysis of parities 1 to 3 for putative EA, heritabilities ranged from 8.9% for first parity to 10.4% for second parity. All genetic correlations were >0.9, whereas all environmental correlations were <0.12. The variance component for the service sire effect for putative EA rate was less than half the variance component for conception rate. Thus, genetic control of the 2 traits is clearly different, and analysis of EA rate by a single-trait animal model is justified. Genetic evaluation for putative EA was computed using this model, including all first- through third-parity cows with freshening dates from January 1, 1985, through December 31, 2016, that either became pregnant on first insemination or were reinseminated between 49 and 100 d after the first insemination. All known parents and grandparents of cows with records were included in the analysis. The regression of the breeding value for non-abortion rate on the cows' birth year was 0.083%/yr. The genetic correlation between first-parity EA and conception status was 0.995. The genetic correlations between first-parity EA and milk, fat, and protein production were all negative, whereas the genetic correlation between EA and herd life was 0.33. Inclusion of putative EA in the selection index instead of conception status resulted in 10 to 20% greater genetic gain for both fertility traits. In a genome-wide association study based on 1,200 dairy bulls with reliabilities >50% for abortion rate genotyped for 41,000 markers, 6 markers were found with nominal probabilities of <10-12 to reject the null hypothesis of no effect on EA rate. The markers with the lowest probabilities for EA rate were also included among the markers with the lowest probabilities for female fertility, but not vice versa. The marker explaining the most variance for abortion rate is located within the ABCA9 gene, which is found within an ATP-binding cassette (ABC) genes cluster. The ABC family is the major class of primary active transporters in the placenta.