Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/5/2020
Publication Date: 1/5/2020
Citation: Cole, J.B. 2020. Identification, validation, and management of Mendelian traits in livestock breeding programs [abstract]. Plant and Animal Genome Conference. San Diego, California, January 11-15, 2020, W216.
Technical Abstract: The number of known Mendelian traits has increased rapidly as the cost of genotyping has decreased rapidly in all livestock species. In 2011, VanRaden and colleagues reported five previously unknown recessive defects in the Brown Swiss, Holstein, and Jersey breeds based on a deficiency of expected homozygotes and undesirable effects of those loci on fertility and stillbirth traits. As the number of genotyped animals has increased globally, exceeding 3.5 million in the US dairy population alone, new defects have been reported in many breeds. A number of loci associated with polled status and coat color also have been identified, and the same methodology could be used to track desirable milk protein or fatty acid profiles. In the US, 25 haplotypes currently are tracked, and carrier status is reported for all genotyped animals. Several haplotypes affecting fertility have been identified in commercial pig populations, including a mutation in BMPER associated with mummified piglets. Causal variants are known for most of these haplotypes, but identification efforts are hampered by the quality of annotation for livestock genomes and validation of causal variants often is based on statistical, rather than biological, association. The rapid growth in the number of Mendelian traits being reported has raised many questions. Three of the most common will be addressed in this presentation: 1) how best to manage haplotypes in a population, and 2) how to validate putative causal variants with lower-quality genome annotations than model species, and 3) if the rate of de novo mutations is increasing.