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genomic evaluations with many more genotypes基因组评估更多的基因型
VanRaden et al. Genetics Selection Evolution 2011, 43:10 Ge n e t i c s
/content/43/1/10 Se l e c t i o n
Evolution
RESEARCH Open Access
Genomic evaluations with many more genotypes
1* 2 1 3
Paul M VanRaden , Jeffrey R O’Connell , George R Wiggans , Kent A Weigel
Abstract
Background: Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two
years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include
animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips
recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to
use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced
by genotyping most animals at less than the highest density and imputing their missing genotypes using
haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals
and markers may continue to grow quickly.
Methods: Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker
genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the
pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets
were created by keeping 50,000 (every tenth) of the markers for most animals.
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