Advances in genomic selection in domestic animals

Chinese Science Bulletin

Volumn 56, Issue 25, 2011, Pages 2655-2663

  Zhang, Zhe ^a   Zhang, Qin ^a   Ding, Xiang Dong ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

breeding; domestic animals; genomic estimated breeding value (GEBV); genomic selection (GS); marker assisted selection (MAS)

Indexed keywords

ANIMALIA; BOS;

EID: 80051603211     PISSN: 10016538     EISSN: 18619541     Source Type: Journal    
DOI: 10.1007/s11434-011-4632-7     Document Type: Review

References (69)

1. Goddard M E, Hayes B J. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat Rev Genet, 2009, 10: 381-391.
2. Meuwissen T H E, Hayes B J, Goddard M E. Prediction of total genetic value using genome-wide dense marker maps. Genetics, 2001, 157: 1819-1829.
3. Heffner E L, Sorrells M E, Jannink J L. Genomic selection for crop improvement. Crop Sci, 2009, 49: 1-12.
4. Sonesson A K, Meuwissen T H. Testing strategies for genomic selection in aquaculture breeding programs. Genet Sel Evol, 2009, 41: 37.
5. Habier D. More than a third of the WCGALP presentations on genomic selection. J Anim Breed Genet, 2010, 127: 336-337.
6. Goddard M E, Hayes B J. Genomic selection. J Anim Breed Genet, 2007, 124: 323-330.
7. Xu S. Estimating polygenic effects using markers of the entire genome. Genetics, 2003, 163: 789-801.
8. Calus M P L. Genomic breeding value prediction: Methods and procedures. Animal, 2010, 4: 157-164.
9. Verbyla K L, Hayes B J, Bowman P J, et al. Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle. Genet Res, 2009, 91: 307-311.
10. Meuwissen T H. Accuracy of breeding values of' nrelated' individuals predicted by dense SNP genotyping. Genet Sel Evol, 2009, 41: 35.
11. Meuwissen T H, Solberg T R, Shepherd R, et al. A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value. Genet Sel Evol, 2009, 41: 2.
12. Long N, Gianola D, Rosa G J, et al. Machine learning classification procedure for selecting SNPs in genomic selection: Application to early mortality in broilers. J Anim Breed Genet, 2007, 124: 377-389.
13. Solberg T R, Sonesson A K, Woolliams J A, et al. Reducing dimensionality for prediction of genome-wide breeding values. Genet Sel Evol, 2009, 41: 29.
14. Gianola D, Fernando R L, Stella A. Genomic-assisted prediction of genetic value with semiparametric procedures. Genetics, 2006, 173: 1761-1776.
15. Bennewitz J, Solberg T, Meuwissen T. Genomic breeding value estimation using nonparametric additive regression models. Genet Sel Evol, 2009, 41: 20.
16. de los Campos G, Naya H, Gianola D, et al. Predicting quantitative traits with regression models for dense molecular markers and pedigree. Genetics, 2009, 182: 375-385.
17. VanRaden P M. Efficient methods to compute genomic predictions. J Dairy Sci, 2008, 91: 4414-4423.
18. Visscher P M, Medland S E, Ferreira M A, et al. Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. PLoS Genet, 2006, 2: 316-325.
19. VanRaden P M, Tooker M E. Methods to explain genomic estimates of breeding value. J Dairy Sci, 2007, 90: 374.
20. Habier D, Fernando R L, Dekkers J C M. The impact of genetic relationship information on genome-assisted breeding values. Genetics, 2007, 177: 2389-2397.
21. Strandén I, Garrick D J. Technical note: Derivation of equivalent computing algorithms for genomic predictions and reliabilities of animal merit. J Dairy Sci, 2009, 92: 2971-2975.
22. Goddard M E. Genomic selection: Prediction of accuracy and maximisation of long term response. Genetica, 2009, 136: 245-257.
23. Hayes B J, Visscher P M, Goddard M E. Increased accuracy of artificial selection by using the realized relationship matrix. Genet Res, 2009, 91: 47-60.
24. Daetwyler H D, Villanueva B, Bijma P, et al. Inbreeding in genome-wide selection. J Anim Breed Genet, 2007, 124: 369-376.
25. Muir W M. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J Anim Breed Genet, 2007, 124: 342-355.
26. Calus M P, Meuwissen T H, de Roos A P, et al. Accuracy of genomic selection using different methods to define haplotypes. Genetics, 2008, 178: 553-561.
27. Zhang Z, Ding X D, Liu J F, et al. TA-BLUP: A New Genetic Evaluation Method for Genomic Selectionon. In: 9th World Congress on Genetics Applied to Livestock Production, 2010. Leipzig, Germany. 215.
28. Zhang Z, Liu J F, Ding X D, et al. Best linear unbiased prediction of genomic breeding values using trait-specific marker-derived relationship matrix. PLoS One, 2010, 5: e12648.
29. Solberg T R, Sonesson A K, Woolliams J A, et al. Genomic selection using different marker types and densities. J Anim Sci, 2008, 86: 2447-2454.
30. Calus M P L, Veerkamp R F. Accuracy of breeding values when using and ignoring the polygenic effect in genomic breeding value estimation with a marker density of one SNP per cM. J Anim Breed Genet, 2007, 124: 362-368.
31. Habier D, Fernando R L, Dekkers J C M. Genomic selection using low-density marker panels. Genetics, 2009, 182: 343-353.
32. Legarra A, Aguilar I, Misztal I. A relationship matrix including full pedigree and genomic information. J Dairy Sci, 2009, 92: 4656-4663.
33. Chen C Y, Misztal I, Aguilar I, et al. Genome-wide marker-assisted selection combining all pedigree phenotypic information with genotypic data in one step: An example using broiler chickens. J Anim Sci, 2011, 89: 23-28.
34. Daetwyler H D, Villanueva B, Woolliams J A. Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS One, 2008, 3: e3395.
35. Daetwyler H D, Pong-Wong R, Villanueva B, et al. The impact of genetic architecture on genome-wide evaluation methods. Genetics, 2010, 185: 1021-1031.
36. Zhang Z, Ding X D, Liu J F, et al. Accuracy of genomic prediction using low density marker panels. J Dairy Sci, 2011, Doi: 10. 3168/ jds. 2010-3917.
37. Sved J A. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol, 1971, 2: 125-141.
38. Moser G, Tier B, Crump R E, et al. A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers. Genet Sel Evol, 2009, 41: 56.
39. Schaeffer L R. Strategy for applying genome-wide selection in dairy cattle. J Anim Breed Genet, 2006, 123: 218-223.
40. Hayes B J, Bowman P J, Chamberlain A J, et al. Genomic selection in dairy cattle: Progress and challenges. J Dairy Sci, 2009, 92: 433-443.
41. VanRaden P M, van Tassell C P, Wiggans G R, et al. Reliability of genomic predictions for North American Holstein bulls. J Dairy Sci, 2009, 92: 16-24.
42. Hayes B, Bowman P, Chamberlain A, et al. Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genet Sel Evol, 2009, 41: 51.
43. Luan T, Woolliams J A, Lien S, et al. The accuracy of genomic selection in Norwegian red cattle assessed by cross-validation. Genetics, 2009, 183: 1119-1126.
44. Harris B L, Montgomerie W A. Current status of the use of genomic information in the national genetic evaluation in New Zealand. In: Proc of the Interbull International Workshop in Genomic Information in Genetic Evaluations, 2009. Interbull: Uppasla, Sweden. 35-38.
45. de Roos A P W, Schrooten C, Mullaart E, et al. Genomic selection at CRV. Interbull Bull, 2009, 39: 47-50.
46. Lund M S, Su G. Genomic selection in the Nordic countries. Interbull bulletin, 2009, 39: 39-42.
47. Habier D, Tetens J, Seefried F R, et al. The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet Sel Evol, 2010, 42: 5.
48. Berry D, Kearney F, Harris B. Genomic selection in Ireland. Interbull Bulletin, 2009, 39: 29-34.
49. Loberg A, Dürr J W. Interbull survey on the use of genomic information. Interbull Bull, 2009, 39: 3-14.
50. Tuggle C K, Dekkers J C M. Genotyping: How useful is it for producers? Pig Prog, 2009, 25: 9.
51. Simianer H. The potential of genomic selection to improve litter size in pig breeding programmes. In: European Association for Animal Production 2009 Annual Meetings, 2009. Barcelona, Spain.
52. van der Werf J H J. Potential benefit of genomic selection in sheep. In: The Association for the Advancement of Animal Breeding and Genetics 18th Conference, 2009. Barossa Valley, South Australia. 38-41.
53. McEwan J C. Current and future impact of DNA technologies on the New Zealand sheep industry. In: Proceedings of the New Zealand Society of Animal Production, 2009. Canterbury, New Zealand. 165-168.
54. Chen C Y, Misztal I, Aguilar I, et al., Genome wide marker assisted selection in chicken: Making the most of all data, pedigree, phenotypic, and genomic in a simple one step procedure. In: 9th World Congress on Genetics Applied to Livestock Production, 2010. Leipzig, Germany.
55. Legarra A, Calenge F, Mariani P, et al. Use of a reduced set of single nucleotide polymorphisms for genetic evaluation of resistance to Salmonella carrier state in laying hens. Poul Sci, 2011, 90: 731-736.
56. Wolc A, Stricker C, Arango J, et al. Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model. Genet Sel Evol, 2011, 43: 5.
57. Gonzalez-Recio O, Gianola D, Rosa G J, et al. Genome-assisted prediction of a quantitative trait measured in parents and progeny: Application to food conversion rate in chickens. Genet Sel Evol, 2009, 41: 3.
58. Daetwyler H D, Hickey J M, Henshall J M, et al. Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population. Anim Prod Sci, 2010, 50: 1004-1010.
59. Weigel K A, de los Campos G, Vazquez A I, et al. Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle. J Dairy Sci, 2010, 93: 5423-5435.
60. Ibánz-Escriche N, Fernando R L, Toosi A, et al. Genomic selection of purebreds for crossbred performance. Genet Sel Evol, 2009, 41: 12.
61. König S, Simianer H, Willam A. Economic evaluation of genomic breeding programs. J Dairy Sci, 2009, 92: 382-391.
62. de Roos A P, Hayes B J, Goddard M E. Reliability of genomic predictions across multiple populations. Genetics, 2009, 183: 1545-1553.
63. Toosi A, Fernando R L, Dekkers J C. Genomic selection in admixed and crossbred populations. J Anim Sci, 2010, 88: 32-46.
64. Kizilkaya K, Fernando R L, Garrick D J. Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. J Anim Sci, 2010, 88: 544-551.
65. Lund M S, Roos A P W D, Vries A G D, et al. Improving genomic prediction by EuroGenomics collaboration. In: 9th World Conference of Genetics Applied on Livestock Production, 2010. Leipzig, Germany. 880.
66. Harris B L, Johnson D L, Montgomerie W A. National genomic evaluations without genotypes. Interbull Bull, 2009, 40: 189-192.
67. Tian F, Bradbury P J, Brown P J, et al. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet, 2011, 43: 159-162.
68. Huang X H, Wei X H, Sang T, et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet, 2010, 42: 961-967.
69. Weigel K A, de los Campos G, Gonzalez-Recio O, et al. Predictive ability of direct genomic values for lifetime net merit of Holstein sires using selected subsets of single nucleotide polymorphism markers. J Dairy Sci, 2009, 92: 5248-5257.