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

Abstract

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.

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

“…A total of 40,498 SNPs were retained. The GWAS files were prepared and formatted as described in Gershoni et al (2020Gershoni et al ( , 2021 and Weller et al (2021) using the Plink software (Purcell et al, 2007). The response variable was the sires' transmitting abilities (half of the EBV) for AFI.…”

Genes and pathways associated with pregnancy loss in dairy cattle

“…Numerous factors may cause fetal loss, including infectious diseases, toxic agents, heat stress, and genetic factors. Indeed, previous studies have reported that there is a substantial genetic variation underlying fetal loss in dairy catlle 8 – 10 . Known genetic factors include lethal recessive alleles, such as complex vertebral malformation (CVM) and deficiency of uridine monophosphate synthase (DUMPS), and an increasing list of recessive haplotypes 11 .…”

“…Known genetic factors include lethal recessive alleles, such as complex vertebral malformation (CVM) and deficiency of uridine monophosphate synthase (DUMPS), and an increasing list of recessive haplotypes 11 . Recently, Gershoni and colleagues identified ABCA9 gene as a candidate gene for early abortions in Israeli dairy cattle 10 . Interestingly, ABCA9 gene is located within an ATP-binding cassette (ABC) genes cluster on BTA19, and the ABC family is the major class of primary active transporters in the placenta.…”

Genetic and Genome-Wide Association Analysis of Yearling Weight Gain in Israel Holstein Dairy Calves

“…Genetic evaluations for first parity dystocia and calf mortality were compute by single-trait sire and maternal grandsire models, as described by [ 12 ]. The component traits in PD16 and their index coefficients are given in [ 13 ].…”

“…A total of 40,498 SNPs were retained. GWAS were computed as described in [ 13 , 14 ]. The response variable was the sires’ transmitting abilities for YG.…”