“Use of Haplotypes to Estimate Mendelian Sampling Effects and Selection Limits”, 2011-04-13 (; backlinks; similar):
Limits to selection and Mendelian sampling (MS) terms can be calculated using haplotypes by summing the individual additive effects on each chromosome. Haplotypes were imputed for 43 382 single-nucleotide polymorphisms (SNP) in 1,455 Brown Swiss, 40,351 Holstein and 4,064 Jersey bulls and cows using the Fortran program
findhap.f90, which combines population and pedigree haplotyping methods. Lower and upper bounds of MS variance were calculated for daughter pregnancy rate (a measure of fertility), milk yield, lifetime net merit (a measure of profitability) and protein yield assuming either no or complete linkage among SNP on the same chromosome. Calculated selection limits were greater than the largest direct genomic values observed in all breeds studied. The best chromosomal genotypes generally consisted of two copies of the same haplotype even after adjustment for inbreeding. Selection of animals rather than chromosomes may result in slower progress, but limits may be the same because most chromosomes will become homozygous with either strategy. Selection on functions of MS could be used to change variances in later generations.…Lifetime net merit: Lower selection limits for NM$ with no adjustment for inbreeding were $5,408.81$3,8572011 (BS), $10,538.56$7,5152011 (HO) and $6,560.13$4,6782011 (JE). Adjusted values were slightly smaller and were $5,352.72$3,8172011 (BS), $10,509.11$7,4942011 (HO) and $6,459.16$4,6062011 (JE). Upper bounds had values of $12,817.35$9,1402011 (BS), $33,078.31$23,5882011 (HO) and $16,150.71$11,5172011 (JE) and were not adjusted for inbreeding because they were calculated from individual loci rather than complete haplotypes. The largest DGV among all genotyped animals in each breed were $1,545.37$1,1022011 (BS), $3,545.11$2,5282011 (HO) and $2,182.04$1,5562011 (JE). The top active bulls (AI and foreign bulls with semen distributed in the US that are in or above the 80th percentile, based on NM) in each breed following the August 2010 genetic evaluation had GEBV (Genomic estimated breeding value) for NM$ of +$1,534.16$1,0942011 (BS: 054BS00374), +$2,226.91$1,5882011 (HO: 001HO08784) and +$1,811.82$1,2922011 (JE: 236JE00146).
…If two copies of each of the 30 best haplotypes in the US Holstein population were combined in a single animal (Lower bounds of selection limit/SLC for NM\$), it would have a GEBV for NM\$ of +$10,538.56$7,5152011 (Figure 5), ~5× larger than that of the current best Holstein bull in the US, whose GEBV for NM$ are +$2,226.91$1,5882011.