Identity-by-descent genomic selection using selective and sparse genotyping

Genetics Selection Evolution

Volumn 46, Issue 1, 2014, Pages

  Ødegård, Jørgen ^a   Meuwissen, Theo H E ^b  

^a Aqua Gen AS   (Norway)

^b NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; AQUACULTURE; ARTICLE; BIOLOGICAL MODEL; BREEDING; COMPUTER SIMULATION; FEMALE; GENETIC SELECTION; GENOME; GENOMICS; GENOTYPE; GENOTYPING TECHNIQUE; MALE; METHODOLOGY; PHENOTYPE;

ALGORITHMS; ANIMALS; AQUACULTURE; BREEDING; COMPUTER SIMULATION; FEMALE; GENOME; GENOMICS; GENOTYPE; GENOTYPING TECHNIQUES; MALE; MODELS, GENETIC; PHENOTYPE; SELECTION, GENETIC;

EID: 84892450336     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/1297-9686-46-3     Document Type: Article

References (22)

1. Prediction of total genetic value using genome-wide dense marker maps. Meuwissen THE, Hayes BJ, Goddard ME, Genetics 2001 157 1819 1829 11290733 (Pubitemid 32298846)
2. The importance of identity-by-state information for the accuracy of genomic selection. Luan T, Wooliams JA, Ødegård J, Dolezal M, Roman-Ponze SI, Bagnato A, Meuwissen THE, Genet Sel Evol 2012 44 28 10.1186/1297-9686-44-28 22937985
3. Genomic selection using low-density marker panels. Habier D, Fernando RL, Dekkers JCM, Genetics 2009 182 343 353 10.1534/genetics.108.100289 19299339
4. The effect of linkage disequilibrium and family relationships on the reliability of genomic prediction. Wientjes YCJ, Veerkamp RF, Calus MPL, Genetics 2013 193 621 631 10.1534/genetics.112.146290 23267052
5. The impact of genetic relationship information on genome-assisted breeding values. Habier D, Fernando RL, Dekkers JCM, Genetics 2007 177 2389 2397 18073436 (Pubitemid 350277013)
6. QMSim: a large-scale genome simulator for livestock. Sargolzaei M, Schenkel FS, Bioinformatics 2009 25 680 681 10.1093/bioinformatics/btp045 19176551
7. The use of family relationships and linkage disequilibrium to impute phase and missing genotypes in up to whole-genome sequence density genotypic data. Meuwissen THE, Goddard ME, Genetics 2010 185 1441 1449 10.1534/genetics.110.113936 20479147
8. Marker assisted selection using best linear unbiased prediction. Fernando R, Grossman M, Genet Sel Evol 1989 21 467 477 10.1186/1297-9686-21-4-467
9. Madsen P, Jensen J, DMU: a user's guide. A package for analysing multivariate mixed models. Version 6, release 5.0 Tjele, Denmark: University of Aarhus, Faculty of Agricultural Sciences (DJF), Dept of Genetics and Biotecnology 2010
10. Inbreeding in artificial selection programmes. Robertson A, Genet Res 1961 2 189 194 10.1017/S0016672300000690
11. An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Hauser L, Baird M, Hilborn R, Seeb LW, Seeb JE, Mol Ecol Resour 2011 11 Suppl 1 150 161 21429171
12. Evaluation of three strategies using DNA markers for traceability in aquaculture species. Hayes B, Sonesson AK, Gjerde B, Aquaculture 2005 250 70 81 10.1016/j.aquaculture.2005.03.008 (Pubitemid 41525586)
13. Estimation of heritability from limited family data using genome-wide identity-by-descent sharing. Ødegård J, Meuwissen T, Genet Sel Evol 2012 44 16 10.1186/1297-9686-44-16 22568689
14. Bias in genomic predictions for populations under selection. Vitezica ZG, Aguilar I, Misztal I, Legarra A, Genet Res 2011 93 357 366 10.1017/ S001667231100022X
15. The Accuracy of Genomic Selection in Norwegian Red Cattle Assessed by Cross-Validation. Luan T, Woolliams JA, Lien S, Kent M, Svendsen M, Meuwissen THE, Genetics 2009 183 1119 1126 10.1534/genetics.109.107391 19704013
16. Accuracy of genomic selection using different methods to define haplotypes. Calus MPL, Meuwissen THE, de Roos APW, Veerkamp RF, Genetics 2008 178 553 561 10.1534/genetics.107.080838 18202394 (Pubitemid 351398768)
17. The effect of selection on genetic variability. Bulmer MG, Am Nat 1971 105 201 211 10.1086/282718
18. More than the sum of its parts: a complex epistatic network underlies natural variation in thermal preference behavior in Caenorhabditis elegans. Gaertner BE, Parmenter MD, Rockman MV, Kruglyak L, Phillips PC, Genetics 2012 192 1533 1542 10.1534/genetics.112.142877 23086219
19. Epistatic analysis of carcass characteristics in pigs reveals genomic interactions between quantitative trait loci attributable to additive and dominance genetic effects. Duthie C, Simm G, Doeschl-Wilson A, Kalm E, Knap PW, Roehe R, J Anim Sci 2010 88 2219 2234 10.2527/jas.2009-2266 20228239
20. Does heritability hide in epistasis between linked SNPs? Haig D, Eur J Hum Genet 2011 19 123 123
21. Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. Jablonka E, Raz G, Q Rev Biol 2009 84 131 176 10.1086/598822 19606595
22. Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. Visscher PM, Medland SE, Ferreira MAR, Morley KI, Zhu G, Cornes BK, Montgomery GW, Martin NG, PLoS Genet 2006 2 41 10.1371/journal.pgen.0020041 16565746