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Thursday, July 16, 2015

Frontiers in cattle genomics

A correspondent updates us on advances in genomic cattle breeding. See also Genomic Prediction: No Bull and It's all in the gene: cows.
More than a million cattle in the USDA dairy GWAS system (updated with new breeding value predictions weekly), as cost per marker drops exponentially: https://www.cdcb.us/Genotype/cur_freq.html
The NM$ (Net Merit in units of dollars) utility function for selection is more and more sophisticated (able to avoid bad trade-offs from genetic correlations): http://www.ars.usda.gov/research/publications/publications.htm?SEQ_NO_115=310013
Cheap genotyping has allowed mass testing of cows, and made it practical to use dominance in models and to match up semen and cow for dominance synergies and heterosis (the dominance component is small compared to the additive one, as usual: for milk yield 5-7% dominance variance, 21-35% additive): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103934
[Note: additive heritability for the traits cattle breeders work on is significantly lower than for cognitive ability.]
Matching mates to reduce inbreeding (without specific markers for dominance effects) by looking at predicted ROH: http://www.ars.usda.gov/research/publications/publications.htm?SEQ_NO_115=294115
Identifying recessive lethals and severe diseases: http://aipl.arsusda.gov/reference/recessive_haplotypes_ARR-G3.html http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054872
For humans, see Genetic architecture and predictive modeling of quantitative traits.

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