Genomic selection for growth and wood quality in Eucalyptus: Capturing the missing heritability and accelerating breeding for complex traits in forest trees

New Phytologist

Volumn 194, Issue 1, 2012, Pages 116-128

  Resende, Marcos D V ^a,b   Resende Jr , Márcio F R ^b   Sansaloni, Carolina P ^c,d   Petroli, Cesar D ^c,d   Missiaggia, Alexandre A ^e   Aguiar, Aurelio M ^e   Abad, Jupiter M ^e   Takahashi, Elizabete K ^f   Rosado, Antonio M ^f   Faria, Danielle A ^c   Pappas Jr , Georgios J ^c,g   Kilian, Andrzej ^h   Grattapaglia, Dario ^c,g  

^a EMBRAPA CERRADOS   (Brazil)

^b FEDERAL UNIVERSITY OF VIÇOSA   (Brazil)

^c EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^d UNIVERSITY OF BRASILIA   (Brazil)

^e Centro de Tecnologia   (Brazil)

^f CENIBRA Celulose Nipo Brasileira SA   (Brazil)

^g UNIVERSIDADE CATÓLICA DE BRASÍLIA   (Brazil)

^h DArT Diversity Arrays Technology   (Australia)

Author keywords

Applied genomics; DArT; Effective population size; Eucalyptus; Genome wide selection (GWS); Genomic selection (GS); Tree breeding

Indexed keywords

ALLELE; EFFECTIVE POPULATION SIZE; EVERGREEN TREE; FORESTRY PRACTICE; GENETIC ANALYSIS; GENETIC MARKER; GENOMICS; GENOTYPE-ENVIRONMENT INTERACTION; GROWTH RATE; HERITABILITY; PARADIGM SHIFT; PHENOTYPE; PLANT BREEDING; REGRESSION ANALYSIS; SELECTIVE BREEDING; WOOD QUALITY;

ARTICLE; BIOLOGICAL MODEL; BREEDING; EUCALYPTUS; GENETIC MARKER; GENETIC SELECTION; GENETICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; INHERITANCE; PLANT GENOME; QUANTITATIVE TRAIT; TREE; WOOD;

BREEDING; EUCALYPTUS; GENETIC MARKERS; GENOME, PLANT; GENOTYPE; INHERITANCE PATTERNS; MODELS, GENETIC; QUANTITATIVE TRAIT, HERITABLE; SELECTION, GENETIC; TREES; WOOD;

EUCALYPTUS;

EID: 84857384716     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2011.04038.x     Document Type: Article

References (65)

1. Albrecht T, Wimmer V, Auinger HJ, Erbe M, Knaak C, Ouzunova M, Simianer H, Schon CC. 2011. Genome-based prediction of testcross values in maize. Theoretical and Applied Genetics 123: 339-350.
2. Apiolaza LA, Raymond CA, Yeo BJ. 2005. Genetic variation of physical and chemical wood properties of Eucalyptus globulus. Silvae Genetica 54: 160-166.
3. Bernardo R, Yu JM. 2007. Prospects for genomewide selection for quantitative traits in maize. Crop Science 47: 1082-1090.
4. Brondani RP, Williams ER, Brondani C, Grattapaglia D. 2006. A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus. BMC Plant Biology 6: 20.
5. Crossa J, de los Campos G, Perez P, Gianola D, Burgueno J, Araus JL, Makumbi D, Singh RP, Dreisigacker S, Yan JB et al. 2010. Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers. Genetics 186: 713-724.
6. Daetwyler HD, Hickey JM, Henshall JM, Dominik S, Gredler B, van der Werf JHJ, Hayes BJ. 2010. Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population. Animal Production Science 50: 1004-1010.
7. Dekkers JCM. 2007. Prediction of response to marker-assisted and genomic selection using selection index theory. Journal of Animal Breeding and Genetics 124: 331-341.
8. Dillen S, Storme V, Marron N, Bastien C, Neyrinck S, Steenackers M, Ceulemans R, Boerjan W. 2009. Genomic regions involved in productivity of two interspecific poplar families in Europe. 1. Stem height, circumference and volume. Tree Genetics & Genomes 5: 147-164.
9. Eathington SR, Crosbie TM, Edwards MD, Reiter R, Bull JK. 2007. Molecular markers in a commercial breeding program. Crop Science 47: S154-S163.
10. Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J, Gonzalez-Martinez SC, Neale DB. 2010. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185: 969-982.
11. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. 2011. A robust, simple genotyping-by-sequencing (GbS) approach for high diversity species. PLoS ONE 6: e19379.
12. Garrick DJ, Taylor JF, Fernando RL. 2009. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genetics Selection Evolution 41: 55.
13. Gianola D, de los Campos G, Hill WG, Manfredi E, Fernando R. 2009. Additive genetic variability and the Bayesian alphabet. Genetics 183: 347-363.
14. Goddard M. 2009. Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 136: 245-257.
15. Goddard ME, Hayes BJ. 2009. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nature Reviews Genetics 10: 381-391.
16. Gonzalez-Martinez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB. 2007. Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175: 399-409.
17. Grattapaglia D, Bertolucci FL, Sederoff RR. 1995. Genetic mapping of QTLs controlling vegetative propagation in Eucalyptus grandis and E. urophylla using a pseudo-testcross strategy and RAPD markers. Theoretical and Applied Genetics 90: 933-947.
18. Grattapaglia D, Kirst M. 2008. Eucalyptus applied genomics: from gene sequences to breeding tools. New Phytologist 179: 911-929.
19. Grattapaglia D, Plomion C, Kirst M, Sederoff RR. 2009. Genomics of growth traits in forest trees. Current Opinion in Plant Biology 12: 148-156.
20. Grattapaglia D, Resende MDV. 2011. Genomic selection in forest tree breeding. Tree Genetics & Genomes 7: 241-255.
21. Habier D, Fernando RL, Dekkers JCM. 2009. Genomic selection using low-density marker panels. Genetics 182: 343-353.
22. Hamblin MT, Buckler ES, Jannink JL. 2011. Population genetics of genomics-based crop improvement methods. Trends in Genetics 27: 98-106.
23. Hayes B, Goddard ME. 2001. The distribution of the effects of genes affecting quantitative traits in livestock. Genetics Selection Evolution 33: 209-229.
24. Hayes B, Goddard M. 2010. Genome-wide association and genomic selection in animal breeding. Genome 53: 876-883.
25. Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME. 2009b. Invited review: genomic selection in dairy cattle: progress and challenges. Journal of Dairy Science 92: 433-443.
26. Hayes BJ, Bowman PJ, Chamberlain AC, Verbyla K, Goddard ME. 2009a. Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genetics Selection Evolution 41: 51.
27. Heffner EL, Lorenz AJ, Jannink JL, Sorrells ME. 2010. Plant breeding with genomic selection: gain per unit time and cost. Crop Science 50: 1681-1690.
28. Heffner EL, Sorrells ME, Jannink JL. 2009. Genomic selection for crop improvement. Crop Science 49: 1-12.
29. Iwata H, Hayashi T, Tsumura Y. 2011. Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica. Tree Genetics & Genomes 7: 747-758.
30. Jannink JL, Lorenz AJ, Iwata H. 2010. Genomic selection in plant breeding: from theory to practice. Briefings in Functional Genomics 9: 166-177.
31. Jannink JL, Zhong SQ, Dekkers JCM, Fernando RL. 2009. Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study. Genetics 182: 355-364.
32. Lee SH, van der Werf JHJ, Hayes BJ, Goddard ME, Visscher PM. 2008. Predicting unobserved phenotypes for complex traits from whole-genome SNP data. Plos Genetics 4: e1000231.
33. Legarra A, Robert-Granie C, Manfredi E, Elsen JM. 2008. Performance of genomic selection in mice. Genetics 180: 611-618.
34. Lorenzana RE, Bernardo R. 2009. Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theoretical and Applied Genetics 120: 151-161.
35. Luan T, Woolliams JA, Lien S, Kent M, Svendsen M, Meuwissen THE. 2009. The accuracy of genomic selection in Norwegian red cattle assessed by cross-validation. Genetics 183: 1119-1126.
36. Lynch M, Walsh B. 1998. Genetics and analysis of quantitative traits. Sunderland, MA, USA: Sinauer Associates, Inc.
37. Makowsky R, Pajewski NM, Klimentidis YC, Vazquez AI, Duarte CW, Allison DB, de los Campos G. 2011. Beyond missing heritability: prediction of complex traits. Plos Genetics 7: e1002051.
38. Mamani EMC, Bueno NW, Faria DA, Guimaraes LMS, Lau D, Alfenas AC, Grattapaglia D. 2010. Positioning of the major locus for Puccinia psidii rust resistance (Ppr1) on the Eucalyptus reference map and its validation across unrelated pedigrees. Tree Genetics & Genomes 6: 953-962.
39. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A et al. 2009. Finding the missing heritability of complex diseases. Nature 461: 747-753.
40. McKeand SE, Bridgwater FE. 1998. A strategy for the third breeding cycle of loblolly pine in the Southeastern US. Silvae Genetica 47: 223-234.
41. Meuwissen T, Goddard M. 2010. Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics 185: 623-631.
42. Meuwissen TH, Hayes BJ, Goddard ME. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
43. Moser G, Khatkar MS, Hayes BJ, Raadsma HW. 2010. Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers. Genetics Selection Evolution 42: 37.
44. Muir WM. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. Journal of Animal Breeding and Genetics 124: 342-355.
45. Namkoong G, Kang HC, Brouard JS. 1988. Tree breeding: principles and strategies. New York, NY, USA: Springer Verlag.
46. Neale DB, Kremer A. 2011. Forest tree genomics: growing resources and applications. Nature Reviews Genetics 12: 111-122.
47. Neale DB, Savolainen O. 2004. Association genetics of complex traits in conifers. Trends in Plant Science 9: 325-330.
48. Rae A, Pinel M, Bastien C, Sabatti M, Street N, Tucker J, Dixon C, Marron N, Dillen S, Taylor G. 2008. QTL for yield in bioenergy Populus: identifying G×E interactions from growth at three contrasting sites. Tree Genetics & Genomes 4: 97-112.
49. Raymond CA, Schimleck LR. 2002. Development of near infrared reflectance analysis calibrations for estimating genetic parameters for cellulose content in Eucalyptus globulus. Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere 32: 170-176.
50. Resende MDV, de Assis TF. 2008. Seleção recorrente recíproca entre populações sintéticas multi-espécies (SRR-PSME) de eucalipto. Pesquisa Florestal Brasileira 57: 57-60.
51. Resende MDV, Lopes PS, Silva RL, Pires IL. 2008. Seleção genômica ampla (GWS) e maximização da eficiência do melhoramento genético. Pesquisa Florestal Brasileira 56: 63-77.
52. Resende MFRJ, Muñoz P, Acosta JJ, Peter GF, Davis JM, Grattapaglia D, Resende MDV, Kirst M. 2012. Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytologist 193: 617-624.
53. Resende MDV, Oliveira EB. 1997. Sistema Selegen - Seleção genética computadorizada para o melhoramento de espécies perenes. Pesquisa Agropecuaria Brasileira 32: 931-939.
54. Resende MDV, Resende MFRJ, Aguiar AM, Abad JIM, Missiaggia AA, Sansaloni CP, Petroli CD, Grattapaglia D. 2010. Computação da Seleção Genômica Ampla (GWS). Documentos EMBRAPA 210. Brasilia, Brazil: EMBRAPA.
55. Rosado AM, Rosado TB, Resende MFR, Bhering LL, Cruz CD. 2009. Predicted genetic gains by various selection methods in Eucalyptus urophylla progenies. Pesquisa Agropecuaria Brasileira 44: 1653-1659.
56. Sansaloni CP, Petroli CD, Carling J, Hudson CJ, Steane DA, Myburg AA, Grattapaglia D, Vaillancourt RE, Kilian A. 2010. A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus. Plant Methods 6: 16.
57. Steane DA, Nicolle D, Sansaloni CP, Petroli CD, Carling J, Kilian A, Myburg AA, Grattapaglia D, Vaillancourt RE. 2011. Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping. Molecular Phylogenetics and Evolution 59: 206-224.
58. Strauss SH, Lande R, Namkoong G. 1992. Limitations of molecular-marker-aided selection in forest tree breeding. Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere 22: 1050-1061.
59. Sved JA. 1971. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theoretical Population Biology 2: 125-141.
60. Thumma BR, Matheson BA, Zhang DQ, Meeske C, Meder R, Downes GM, Southerton SG. 2009. Identification of a cis-acting regulatory polymorphism in a eucalypt COBRA-like gene affecting cellulose content. Genetics 183: 1153-1164.
61. Ukrainetz N, Ritland K, Mansfield S. 2008. Identification of quantitative trait loci for wood quality and growth across eight full-sib coastal Douglas-fir families. Tree Genetics & Genomes 4: 159-170.
62. VanRaden PM, Van Tassell CP, Wiggans GR, Sonstegard TS, Schnabel RD, Taylor JF, Schenkel FS. 2009. Invited review: reliability of genomic predictions for North American Holstein bulls. Journal of Dairy Science 92: 16-24.
63. Wegrzyn JL, Eckert AJ, Choi M, Lee JM, Stanton BJ, Sykes R, Davis MF, Tsai CJ, Neale DB. 2010. Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. New Phytologist 188: 515-532.
64. Wong CK, Bernardo R. 2008. Genomewide selection in oil palm: increasing selection gain per unit time and cost with small populations. Theoretical and Applied Genetics 116: 815-824.
65. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW et al. 2010. Common SNPs explain a large proportion of the heritability for human height. Nature Genetics 42: 565-569.