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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #299003

Research Project: Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information

Location: Animal Genomics and Improvement Laboratory

Title: Haplotype tests for recessive disorders that affect fertility and other traits

Author
item Cole, John
item Vanraden, Paul
item Null, Daniel
item Hutchison, Jana - Edwards
item Cooper, Tabatha

Submitted to: AIPL Research Reports
Publication Type: Government Publication
Publication Acceptance Date: 9/23/2013
Publication Date: 9/23/2013
Citation: Cole, J.B., Van Raden, P.M., Null, D.J., Hutchison, J.L., Cooper, T.A. 2013. Haplotype tests for recessive disorders that affect fertility and other traits. AIPL Research Reports. Genomics (09-13).

Interpretive Summary:

Technical Abstract: Haplotype tests now are used routinely to identify new recessive disorders and to track the carrier status of genotyped animals. Changes in the reporting of recessive factors that affect fertility and stillbirth recently have been described in detail (VanRaden et al., 2013). Carrier status for Holstein haplotypes with mutations for bovine leucocyte adhesion deficiency, complex vertebral malformation, deficiency of uridine monophosphate synthase, mule foot, polledness, and red coat color now are reported in files distributed to the industry by the Council on Dairy Cattle Breeding. Brown Swiss haplotype tests for spinal dismyelination, spinal muscular atrophy, and Weaver Syndrome also are provided, but those tests do not directly include the causative mutation as an additional single nucleotide polymorphism because too few bulls were previously tested. An exact test of the loss-of-function mutation within haplotype JH1 now is used to determine carrier status for genotyped Jerseys. A new haplotype that affects conception rate in Ayrshires recently has been reported. This report provides detailed information about all of the recessive 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. Locations are exact (single bp) when the causative mutation is known and approximate (range of bp) when it is not. The frequency of carriers in the population is generally twice the haplotype frequency because carriers have 1 defective and 1 normal haplotype.