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Increased accuracy of artificial selection by using the realized relationship matrix

  • B. J. HAYES (a1), P. M. VISSCHER (a2) and M. E. GODDARD (a1) (a3)
Abstract
Summary

Dense marker genotypes allow the construction of the realized relationship matrix between individuals, with elements the realized proportion of the genome that is identical by descent (IBD) between pairs of individuals. In this paper, we demonstrate that by replacing the average relationship matrix derived from pedigree with the realized relationship matrix in best linear unbiased prediction (BLUP) of breeding values, the accuracy of the breeding values can be substantially increased, especially for individuals with no phenotype of their own. We further demonstrate that this method of predicting breeding values is exactly equivalent to the genomic selection methodology where the effects of quantitative trait loci (QTLs) contributing to variation in the trait are assumed to be normally distributed. The accuracy of breeding values predicted using the realized relationship matrix in the BLUP equations can be deterministically predicted for known family relationships, for example half sibs. The deterministic method uses the effective number of independently segregating loci controlling the phenotype that depends on the type of family relationship and the length of the genome. The accuracy of predicted breeding values depends on this number of effective loci, the family relationship and the number of phenotypic records. The deterministic prediction demonstrates that the accuracy of breeding values can approach unity if enough relatives are genotyped and phenotyped. For example, when 1000 full sibs per family were genotyped and phenotyped, and the heritability of the trait was 0·5, the reliability of predicted genomic breeding values (GEBVs) for individuals in the same full sib family without phenotypes was 0·82. These results were verified by simulation. A deterministic prediction was also derived for random mating populations, where the effective population size is the key parameter determining the effective number of independently segregating loci. If the effective population size is large, a very large number of individuals must be genotyped and phenotyped in order to accurately predict breeding values for unphenotyped individuals from the same population. If the heritability of the trait is 0·3, and Ne=1000, approximately 5750 individuals with genotypes and phenotypes are required in order to predict GEBVs of un-phenotyped individuals in the same population with an accuracy of 0·7.

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*Corresponding author. Tel: +61 (0)3 9479 5439. Fax: +61 (0)3 9479 3113. e-mail: ben.hayes@dpi.vic.gov.au
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G. R. Abecasis , S. S. Cherny , W. O. Cookson & L. R. Cardon (2002). Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nature Genetics 30, 97101.

A. M. Dunning , F. Durocher , C. S. Healey , M. D. Teare , S. E. McBride , F. Carlomagno , C. F. Xu , E. Dawson , S. Rhodes , S. Ueda , E. Lai , R. N. Luben , E. J. Van Rensburg , A. Mannermaa , V. Kataja , G. Rennart , I. Dunham , I. Purvis , D. Easton & B. A. J. Ponder (2000). The extent of linkage disequilibrium in four populations with distinct demographic histories. American Journal of Human Genetics 67, 15441554.

I. R. Franklin (1977). The distribution of the proportion of the genome which is homozygous by descent in inbred individuals. Theoretical Population Biology 11, 6080.

S. W. Guo (1996). Variation in genetic identity among relatives. Human Heredity 46, 6170.

B. J. Hayes & M. E. Goddard (2001). The distribution of the effects of genes affecting quantitative traits in livestock. Genetics Selection Evolution 33, 209229.

B. J. Hayes , P. M. Visscher , H. McPartlan & M. E. Goddard (2003). A novel multi-locus measure of linkage disequilibrium and it use to estimate past effective population size. Genome Research 13, 635.

B. J. Hayes , A. C. Chamberlain , H. McPartlan , I. McLeod , L. Sethuraman & M. E. Goddard (2007). Accuracy of marker assisted selection with single markers and marker haplotypes in cattle. Genetics Research 89, 215220.

W. G. Hill (1993). Variation in genetic identity within kinships. Heredity 71, 652653.

W. G. Hill , M. E. Goddard & P. M. Visscher (2008). Data and theory point to mainly additive genetic variance for complex traits. PLoS Genetics 4(2), e1000008. doi:10.1371/journal.pgen.1000008.

T. H. Meuwissen & M. E. Goddard (2004). Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data. Genetics Selection Evolution 36(3), 261279.

M. Rasmusson (1993). Variation in genetic identity within kinships. Heredity 70, 266268.

D. E. Reich , M. Cargill , S. Bolk , J. Ireland , P. C. Sabeti , D. J. Richter , T. Lavery , R. Kouyoumjlan , S. F. Farhadian , R. Ward & E. S. Lander (2001). Linkage disequilibrium in the human genome. Nature 411, 199204.

S. Sanna , A. U. Jackson , R. Nagaraja , C. J. Willer , W. M. Chen , L. L. Bonnycastle , H. Shen , N. Timpson , G. Lettre , G. Usala , P. S. Chines , H. M. Stringham , L. J. Scott , M. Dei , S. Lai , G. Albai , L. Crisponi , S. Naitza , K. F. Doheny , E. W. Pugh , Y. Ben-Shlomo , S. Ebrahim , D. A. Lawlor , R. N. Bergman , R. M. Watanabe , M. Uda , J. Tuomilehto , J. Coresh , J. N. Hirschhorn , A. R. Shuldiner , D. Schlessinger , F. S. Collins , G. Davey Smith , E. Boerwinkle , A. Cao , M. Boehnke , G. R. Abecasis & K. L. Mohlke (2008). Common variants in the GDF5-UQCC region are associated with variation in human height. Nature Genetics 40, 198203.

P. Stam (1980). The distribution of the fraction of the genome identical by descent in finite random mating populations. Genetical Research 35, 131155.

A. Tenesa , P. Navarro , B. J. Hayes , D. L. Duffy , G. M. Clarke , M. E. Goddard & P. M. Visscher (2007). Recent human effective population size estimated from linkage disequilibrium. Genome Research 17, 520526.

The International HapMap Consortium (2007). A second generation human haplotype map of over 3·.1 million SNPs. Nature 449(7164), 851861.

P. M. Visscher (2008). Sizing up human height variation. Nature Genetics 40, 489490.

P. M. Visscher , S. E. Medland , M. A. Ferreira , K. I. Morley , G. Zhu , B. K. Cornes , G. W. Montgomery & N. G. Martin (2006). Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. PLoS Genetics 2, e41.

N. R. Wray , M. E. Goddard & P. M. Visscher (2007). Prediction of individual genetic risk to disease from genome-wide association studies. Genome Research 17, 15201528.

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Genetics Research
  • ISSN: 0016-6723
  • EISSN: 1469-5073
  • URL: /core/journals/genetics-research
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