Haplotypes Impacting Fertility
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Haplotypes Impacting Fertility With our growing knowledge about the bovine genome, experts have predicted for some time that we’d likely discover numerous cattle genetic defects. Human genetic researchers estimate that we each carry four or five genetic defects. It’s reasonable to expect that these exist at a similar level in cattle. USDA researchers along with international collaborators have now identified nine haplotypes that appear to cause embryo loss or stillbirths when these haplotypes exist in the homozygous state. These were discovered by taking the full SNP50 genotype database of cows and bulls used for genomic evaluations and studying the frequency of the various haplotypes. Those haplotypes that meet two conditions, 1) there are no live individuals that are homozygous for this haplotype and 2) there is an observed reduction in conception rate or increase in stillbirths when carrier sires were mated to cows sired by carrier bulls are added to the list of haplotypes that are labeled and tracked. These genetic conditions have not been directly observed and we do not know the exact genetic or biological cause of why the embryos or fetuses are not viable. Because of this, they’ve been given simple names of Holstein Haplotype 1 (HH1), Holstein Haplotype 2 (HH2), Holstein Haplotype 3 (HH3), Holstein Haplotype 4 (HH4), Holstein Haplotype 5 (HH5), Jersey Haplotype 1 (JH1) and Brown Swiss Haplotype 1 (BH1), Brown Swiss Haplotype 2 (BH2) and Ayrshire Haplotype 1 (AH1). These haplotypes appear to have a recessive mode of inheritance where animals with zero or one copy of the haplotype are completely normal. Those that inherit two copies of the haplotype are lost as embryos or are stillborn. The impacts of these haplotypes vary and are dependent on their frequency in the population and at what stage of gestation the pregnancies are lost. JHI has a frequency of 23.4%. BHI exists at a frequency of 14 percent and BH2 exists at a frequency of 20.5 percent. Only one haplotype has been discovered in the Ayrshire breed (AH1) and it exists at the highest frequency of 26.1 percent. HH1, HH2, HH3 and HH5 all have similar frequencies (4.5%, 4.6%, 4.7% and 4.8%, respectively). HH4 exists at a much lower frequency of 0.7 percent. Haplotypes with a higher population frequency and those that cause pregnancy loss later in gestation lead to larger losses of profitability. It’s important to realize that the negative impact of these haplotypes is already accounted for in the routinely published sire conception rate (SCR) evaluations and daughter pregnancy rate (DPR) genomic evaluations. So, if you are using these traits in selecting your A.I. sires, you’re already avoiding or compensating for these new genetic conditions. The haplotypes each represent a distinct and unique genetic condition. They are not related to each other. The haplotypes have no impact when a bull that is heterozygous for HH1 is mated to a cow that is heterozygous for HH2. The risk is only experienced when animals are heterozygous for the same haplotype. Select Mating Service (SMS) is an excellent tool for managing these genetic conditions. By using the SMS program, herds with at least one generation of pedigree information on their cows can use heterozygous bulls with less than 1 percent chance of lost pregnancies from known conditions. 7HO9222 Shot 7HO9281 Bigshot 7HO10375 Mr Mudd 7HO10406 Dashawn 7HO10429 Montney 7HO10585 Helix 7HO10702 Excel 7HO10723 Spur 7HO10884 Avery 7HO11279 Moonboy 7HO11283 Mayfield 7HO11402 Tavir 7HO11424 Offie 7HO11488 Branson 7JE1038 Valentino 7JE1151 Galvanize 7JE1163 Irwin 7AY109 Dixon 7BS871 Advisor 7BS873 Shaw 7BS878 Dimes-P 507HO12107 Loar 7HO12131 Mcgirt 7HO12175 Wonka 7HO12310 Bankroll HH5C HH3C HH3C HH2C HH3C HH5C HH4C HH3C HH3C HH3C HH3C HH3C HH2C HH5C JH1C JH1C JH1C AH1C BH1C BH2C BH1C HH5C HH3C HH3C HH3C 7HO12322 Delfino 7HO12357 Penley 7HO12387 Madron 7HO12409 Mirage-Red 7HO12431 Ridge-P 7HO12440 The Dude 7HO12441 Maven 7HO12443 Plus-PP 7HO12477 Radman 7HO12518 Snowboy 7HO12533 Hotshot 7HO12555 Mansfield-P 7HO12588 Oh Boy-PP 7HO13035 Modesto 7JE1348 Citation 7JE1385 Moore 7HO13035 Modesto 7JE1348 Citation 7JE1385 Moore 250HO1117 Caption 250HO12420 Miksa 250HO12589 Jacoby 250HO13165 Ripper HH2C HH3C HH3C HH3C HH5C HH3C HH5C HH2C HH3C HH3C HH5C HH3C HH3C HH5C JH1C JH1C HH5C JH1C JH1C HH3C HH3C HH5C HH3C 08/2015 Holstein Haplotype for Cholesterol Deficiency (HCD) At the 2015 Interbull Annual Meeting, German researchers reported that they had discovered a new genetic defect in Holstein dairy cattle. The defect, Haplotype for Cholesterol Deficiency (HCD), causes young calves to die if homozygous for HCD. Unlike previous haplotypes that cause early embryo loss, this haplotype creates a greater economic loss. Even though calf survival has a low heritability, Paul VanRaden of the USDA Animal Genomics and Improvement Laboratory (AIPL), recommends avoiding recessive defects by using sound selection and mating programs. The defective haplotype traces back to Maughlin Storm. Storm’s sire and maternal grandsire do not carry HCD. This suggests that HCD is a result of a recent mutation that first appeared in Storm or his dam. Influential descendants of Storm that also carry HCD are Stormatic, September Storm and Goldwyn. Unfortunately, the haplotype carrying the defect is difficult to track. Part of the difficulty is caused because descendants of Comestar Laurie Sheik and Comestar Outside appear to have the HCD haplotype but do not appear to produce affected calves. For animals that have the haplotype and have both Storm and Outside in their pedigrees, it’s difficult to know whether they transmit the defective condition or not. Animals that don’t have the haplotype will be labeled as non-carriers. Animals that have the haplotype and it’s determined the haplotype came from Storm will be labeled as carriers. Those animals that have the haplotype and it’s determined the haplotype came from Outside will be labeled as non-carriers. Those animals that have the haplotype and it can’t be determined whether it came from Storm or Outside will be labeled as suspect. 250HO1123 7HO9264 7HO10848 7HO10884 7HO11163 7HO11703 7HO12170 7HO12580 7HO12626 7HO13276 Motivator Dempsey Grafeeti Avery Ladd P-Red Armani Corey Bosa Manny-Red Bowen HCDC HCDC HCDC HCDC HCDC HCDC HCDC HCDC HCDC HCDS 08/2015