Partitioning additive genetic variance into genomic and remaining polygenic components for complex traits in dairy cattle

BMC Genetics

Volumn 13, Issue , 2012, Pages

  Jensen, Just ^a   Su, Guosheng ^a   Madsen, Per ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

Chromosomes; Complex traits; Dairy cattle genetic markers; Genomic variance; Polygenic variance

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CHROMOSOME; CONTROLLED STUDY; DAIRY CATTLE; FEMALE FERTILITY; GENE LOCUS; GENETIC TRAIT; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; MASTITIS; MILK PRODUCTION; MILK YIELD; NONHUMAN; PEDIGREE ANALYSIS; PREDICTIVE VALUE; PROGENY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CATTLE; DAIRYING; GENETIC MARKERS; GENETIC VARIATION; PEDIGREE;

BOS;

EID: 84862183331     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-13-44     Document Type: Article

References (28)

1. Meuwissen TH, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics 2001, 157:1819-1829. 1461589, 11290733.
2. Schaeffer LR. Strategy for applying genome wide selection in dairy cattle. Journal of Animal Breeding and Genetics 2006, 123:218-223. 10.1111/j.1439-0388.2006.00595.x, 16882088.
3. Buch LH, Sørensen MK, Berg P, Pedersen LD, Sørensen AC. Genomic selection strategies in dairy cattle: Strong positive interaction between use of genotypic information and intensive use of young bulls on genetic gain. Journal of Animal Breeding and Genetics 2012, 129:138-151. 10.1111/j.1439-0388.2011.00947.x, 22394236.
4. Mc Hugh N, Meuwissen THE, Cromie AR, Sonesson AK. Use of female information in dairy cattle genomic breeding programs. Journal of dairy science 2011, 94:4109-4118. 10.3168/jds.2010-4016, 21787946.
5. VanRaden P, Cooper T. The genomic evaluation system in the United States: Past, present, future. Journal of dairy science 2011, 94:3202-3211. 10.3168/jds.2010-3866, 21605789.
6. Lund M, de Ross S, de Vries A, Druet T, Ducrocq V, Fritz S, et al. A common reference population from four European Holstein populations increases reliability of genomic predictions. Genetics Selection Evolution 2011, 43:43.
7. Jannink JL, Lorenz AJ, Iwata H. Genomic selection in plant breeding: from theory to practice. Briefings in Functional Genomics 2010, 9:166-177. 10.1093/bfgp/elq001, 20156985.
8. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, et al. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 2009, 4:e5350. 10.1371/journal.pone.0005350, 2669730, 19390634.
9. Harris BL, Johnson DL, Spelman RJ, Sattler JD. Genomic selection in New Zealand and the implications for national genetic evaluation. ICAR Technical Series 2009, 13:325-330.
10. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, et al. Common SNPs explain a large proportion of the heritability for human height. Nature genetics 2010, 42:565-569. 10.1038/ng.608, 3232052, 20562875.
11. Visscher PM, Hill WG, Wray NR. Heritability in the genomics era|[mdash]| concepts and misconceptions. Nature Reviews Genetics 2008, 9:255-266.
12. Gudbjartsson DF, Walters GB, Thorleifsson G, Stefansson H, Halldorsson BV, Zusmanovich P, et al. Many sequence variants affecting diversity of adult human height. Nature genetics 2008, 40:609-615. 10.1038/ng.122, 18391951.
13. Maher B. Personal genomes: The case of the missing heritability. Nature 2008, 456:18.
14. Johannes F, Colot V, Jansen RC. PersPeCTives. Epigenome dynamics: a quantitative genetics perspective. NATuRe ReVIeWS| genetics 2008, 9:883.
15. Habier D, Fernando RL, Dekkers JCM. The Impact of Genetic Relationship Information on Genome-Assisted Breeding Values. Genetics 2007, 177:2389-2397. 10.3168/jds.2007-0980, 2219482, 18073436.
16. VanRaden PM. Efficient methods to compute genomic predictions. Journal of dairy science 2008, 91:4414-4423. 10.1186/1297-9686-43-19, 18946147.
17. Liu Z, Seefried FR, Reinhardt F, Rensing S, Thaller G, Reents R. Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction. Genetics, selection, evolution: GSE 2011, 43:19. 10.1186/1297-9686-44-8, 3107172, 21586131.
18. Gao H, Christensen O, Madsen P, Nielsen U, Zhang Y, Lund M, et al. Comparison on genomic predictions using three GBLUP methods and two single-step blending methods in the Nordic Holstein population. Genetics Selection Evolution 2012, 44:8.
19. Christensen OF, Lund MS. Genomic prediction when some animals are not genotyped. Genet Sel Evol 2010, 42(2):1-8. 10.3168/jds.2009-2061, 2830933, 20100345.
20. Legarra A, Aguilar I, Misztal I. A relationship matrix including full pedigree and genomic information. Journal of dairy science 2009, 92:4656-4663.
21. Danish Cattle Federation Principles of Danish Cattle Breeding: Recording of Production Data, Recording of Breeding Data, Calculation Methods, Breeding Values. Eight Edition. Report The Danish Agricultural Advisory Center 2006, 126. Danish Cattle Federation.
22. Jensen J, Mantysaari EA, Madsen P, Thompson R. Residual maximum likelihood estimation of (co) variance components in multivariate mixed linear models using average information. Jour Ind Soc Ag Statistics 1997, 49:215-236.
23. Madsen P, Jensen J. A users guide to DMU. A package for analysing multivariate mixed models, Version 6, Release 5.0. 2010 http://dmu.agrsci.dk/dmuv6_guide.5.0.pdf.
24. Grisart B, Coppieters W, Farnir F, Karim L, Ford C, Berzi P, et al. Positional Candidate Cloning of a QTL in Dairy Cattle: Identification of a Missense Mutation in the Bovine DGAT1 Gene with Major Effect on Milk Yield and Composition. Genome Research 2002, 12:222-231. 10.3168/jds.S0022-0302(05)72861-7, 11827942.
25. Sørensen AC, Sørensen MK, Berg P. Inbreeding in Danish Dairy Cattle Breeds. Journal of dairy science 2005, 88:1865-1872. 10.3168/jds.2008-1762, 15829680.
26. Pimentel ECG, Erbe M, Koenig S, Simianer H. Frontiers: Genome Partitioning of Genetic Variation for Milk Production and Composition Traits in Holstein Cattle 2011, 2. Frontiers in Livestock, Genomics.
27. Cole JB, VanRaden PM, O'Connell JR, Van Tassell CP, Sonstegard TS, Schnabel RD, et al. Distribution and location of genetic effects for dairy traits. Journal of dairy science 2009, 92:2931-2946. 10.1007/s10709-008-9308-0, 19448026.
28. Goddard M. Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 2009, 136:245-257.