Location: Animal Genomics and Improvement LaboratoryTitle: Haplotype tests for economically important traits of dairy cattle
Submitted to: AIPL Research Reports
Publication Type: Government Publication
Publication Acceptance Date: 12/3/2020
Publication Date: 12/3/2020
Citation: Cole, J.B., Van Raden, P.M., Null, D.J., Hutchison, J.L., Hubbard, S.M. 2020. Haplotype tests for economically important traits of dairy cattle. AIP Research Report. GENOMICS5 (12-20).
Technical Abstract: Haplotype tests are used routinely to identify animals with desirable traits of economic importance, discover new genetic disorders, and track carrier status of genotyped animals. Recessive haplotypes that affect fertility and stillbirth in dairy cattle (haplotypes BH1–BH2, HH1–HH5, and JH1–JH2 have been described in detail, and a recessive mutation that causes embryo death (haplotype HH6) has also been discovered. Carrier status for Holstein haplotypes with mutations for brachyspina (haplotype HH0), bovine leucocyte adhesion deficiency (BLAD; haplotype HHB), complex vertebral malformation (CVM; haplotype HHC), deficiency of uridine monophosphate synthase (DUMPS; haplotype HHD), mulefoot (syndactyly; haploptype HHM), polledness (haplotype HHP), red coat color (haplotypes HBR, HDR, and HHR), and cholesterol deficiency (HCD) are reported by the Council on Dairy Cattle Breeding (Bowie, MD). Brown Swiss haplotype tests for spinal dismyelination (SDM; haplotype BHD), spinal muscular atrophy (SMA; haplotype BHM), and Weaver Syndrome (haplotype BHW) also are provided. Polledness haplotypes are reported for Brown Swiss (BHP) and Jerseys (JHP). For Ayrshires, haplotypes that affects conception rate (AH1) and fertility (AH2) have been discovered. A haplotype associated with Jersey neuropathy with splayed forelimbs (JNS) has recently been identified. Haplotypes BH1 and JH2 were discontinued in December 2018. This report provides detailed information about all of the haplotypes currently tracked in the U.S. genomic evaluation system, the frequency of the minor (less common) haplotype, and the location in base pairs (bp) of the haplotype based on the 2018 ARS-UCD1.2 genome assembly. Locations are exact (single bp) when the causative mutation is known and approximate (range of bp) when it is unknown, a duplication, a deletion, or multiple mutations. The frequency of carriers in the population is generally twice the haplotype frequency because carriers have 1 defective and 1 normal haplotype. Recessives with very low frequencies (e.g., HH4) can be identified because many Holsteins have been genotyped. Generally, recessives in breeds with fewer genotyped animals and smaller populations will not be detected until they have a high frequency in the population. Haplotype tests are less accurate than loss-of-function (LOF) mutation tests, and retesting valuable animals that have been identified as carriers using a haplotype test is recommended if an exact test is available.