Use of Haplotypes to Estimate Mendelian Sampling Effects and Selection Limits

Authors: Cole, John; Vanraden, Paul

Submitted to: Journal of Animal Breeding and Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/13/2011
Publication Date: 4/13/2011
Citation: Cole, J.B., Van Raden, P.M. 2011. Use of Haplotypes to Estimate Mendelian Sampling Effects and Selection Limits. Journal of Animal Breeding and Genetics. 128(6):446-455.

Interpretive Summary: Every individual receives two copies of each chromosome during fertilization, one from its sire and one from its dam. In the past, only the average of the gene effects on the two chromosomes could be calculated. Using new computing procedures and large numbers of DNA markers for thousands of cows and bulls the gene effects now can be identified for individual chromosomes. An analysis of 1,455 Brown Swiss, 40,351 Holstein, and 4,064 Jersey animals found that there is more variation among individual chromosomes than previously calculated, and that the populations can be changed more than reported in earlier studies. It is not currently possible to predict which chromosomes will be inherited by individual animals, but improvements in technology may permit the screening of large numbers of embryos to identify those inheriting desirable combinations of chromosomes, which could then be bred to other animals with favorable sets of chromosomes. The best chromosomal genotypes generally consisted of two copies of the same haplotype. 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.

Technical Abstract: Limits to selection and Mendelian sampling 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 Mendelian sampling (MS) variance were calculated for daughter pregnancy rate (a measure of fertility), milk yield, lifetime net merit (NM$; 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.