Evaluation of approaches for estimating the accuracy of genomic prediction in plant breeding

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Ould Estaghvirou, Sidi B ^a   Ogutu, Joseph O ^a   Schulz Streeck, Torben ^a,b   Knaak, Carsten ^b   Ouzunova, Milena ^b   Gordillo, Andres ^c   Piepho, Hans Peter ^a  

^a UNIVERSITY OF HOHENHEIM   (Germany)

^b KWS SAAT SE Co KGaA   (Germany)

^c KWS Lochow GMBH ^*  (Germany)

Author keywords

Cross validation; Genomic selection; Heritability; Plant breeding; Predictive ability; Predictive accuracy; Ridge regression BLUP; SNP markers; Zea mays

Indexed keywords

ACCURACY; ARTICLE; COMPUTER PREDICTION; GENETIC CORRELATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMICS; GENOTYPE; HERITABILITY; MAIZE; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; NONHUMAN; PERFORMANCE MEASUREMENT SYSTEM; PLANT BREEDING; PLANT GENOME; PREDICTIVE VALUE; QUALITY CONTROL; VALIDATION PROCESS;

ANIMALIA; ZEA MAYS;

ALGORITHMS; BREEDING; COMPUTER SIMULATION; GENOMICS; MODELS, GENETIC; PLANTS; REPRODUCIBILITY OF RESULTS; ZEA MAYS;

EID: 84889057158     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-860     Document Type: Article

References (27)

1. Meuwissen THE, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker map. Genetics 2001, 157:1819-1829. 1461589, 11290733.
2. Piepho HP. Ridge regression and extensions for genomewide selection in maize. Crop Sci 2009, 49:1165-1176.
3. Whittaker JC, Thomson R, Denham MC. Marker-assisted selection using ridge regression. Genetic Research 2000, 75:249-252.
4. Bernardo R, Yu J. Prospects for genomewide selection for quantitative traits in maize. Crop Sci 2007, 47:1082-1090.
5. Goddard ME, Hayes BJ. Genomic selection. J Anim Breed Genet 2007, 124:323-330. 10.1111/j.1439-0388.2007.00702.x, 18076469.
6. Schulz-Streeck T, Ogutu JO, Karaman Z, Knaak C, Piepho HP. Genomic selection using multiple populations. Crop Sci 2012, 52:2453-2461.
7. Visscher PM, Hill WG, Wray NR. Heritability in the genomics era-concepts and misconceptions. Nat Rev Genet 2008, 9:255-266.
8. Dekkers JCM. Prediction of response to marker-assisted and genomic selection using selection index theory. J Anim Breed Genet 2007, 124:331-341. 10.1111/j.1439-0388.2007.00701.x, 18076470.
9. Habier D, Tetens J, Seefried FR, Lichtner P, Thaller G. The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet Sel Evol 2010, 41:5.
10. Schulz-Streeck T, Ogutu JO, Piepho H-P. Comparisons of single-stage and two-stage approaches to genomic selection. Theor Appl Genet 2013, 126:69-82. 10.1007/s00122-012-1960-1, 22903736.
11. Petersen RG. Agricultural Field Experiments/Design and analysis 1994, New York: Marcel Dekker.
12. Albrecht T, Wimmer V, Auinger HJ, Erbe M, Knaak C, Ouzunova M, Simianer H, Schön CC. Genomic-based prediction of testcross values in maize. Theor Appl Genet 2011, 123:339-350. 10.1007/s00122-011-1587-7, 21505832.
13. SAS Institute Inc SAS Institute Inc 2013, NC: Cary, SAS Institute Inc.
14. Legarra A, Robert-Granie C, Manfredi E, Elsen J. Performance of genomic selection in mice. Genetics 2008, 180:611-618. 10.1534/genetics.108.088575, 2535710, 18757934.
15. Hastie T, Tibshirani R, Friedman J. The Elements of Statistical Learning: Data Mining, Inference and Prediction 2009, New York: Springer, 2.
16. Piepho HP, Möhring J. Computing heritability and selection response from unbalanced plant breeding trials. Genetics 2007, 177:1881-1888. 10.1534/genetics.107.074229, 2147938, 18039886.
17. Gonçalves E, Carrasquinho I, St Aubyn A, Martins A. Broad-sense heritability in mixed models for grapevine initial selection trials. Euphytica 2013, 189:379-391.
18. Cullis BR, Smith A, Coombes N. On the design of early generation variety trials with correlated data. J Agr Biol Envir St 2006, 11:381-393.
19. Johnson NL, Kotz S, Kemp AW. Univariate Discrete Distribution 1993, New York: Wiley, 2.
20. Mrode RA, Thompson R. Linear Models for the Prediction of Animal Breeding Values 2005, Wallingford: UK, 2.
21. Henderson CR. Comparison of alternative sire evaluation methods. J Anim Sci 1975, 41:760-770.
22. VanRaden PM. Efficient methods to compute genomic predictions. J Dairy Sci 2008, 91:4414-4423. 10.3168/jds.2007-0980, 18946147.
23. McLean RA, Sanders WL, Stroup WW. A unified approach to mixed linear models. Am Stat 1991, 45:54-63.
24. Henderson CR. Best linear unbiased prediction of breeding values not in the model for records. J Dairy Sci 1977, 60:783-787.
25. Searle SR, Casella G, McCulloch CE. Variance Components 1992, New York: Wiley.
26. Gauch HG, Gene Hwang JT, Fick GW. Model evaluation by comparison of model-based predictions and measured values. Agron J 2003, 95:1442-1446.
27. Holland JB, Nyquist WE, Cervantes-Martinez CT. Estimating and interpreting heritability for plant breeding: an update. J Plant Breed 2003, 22:9-112.