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Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement.

Spindel JE, Begum H, Akdemir D, Collard B, Redoña E, Jannink JL, McCouch S.

Heredity (Edinb). 2016 Apr;116(4):395-408. doi: 10.1038/hdy.2015.113. Epub 2016 Feb 10.


Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR.

PLoS Genet. 2015 Feb 17;11(2):e1004982. doi: 10.1371/journal.pgen.1004982. eCollection 2015 Feb. Erratum in: PLoS Genet. 2015 Jun;11(6):e1005350.


Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.).

Kwong QB, Teh CK, Ong AL, Chew FT, Mayes S, Kulaveerasingam H, Tammi M, Yeoh SH, Appleton DR, Harikrishna JA.

BMC Genet. 2017 Dec 11;18(1):107. doi: 10.1186/s12863-017-0576-5.


Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding.

Grenier C, Cao TV, Ospina Y, Quintero C, Châtel MH, Tohme J, Courtois B, Ahmadi N.

PLoS One. 2015 Aug 27;10(8):e0136594. doi: 10.1371/journal.pone.0136594. eCollection 2015. Erratum in: PLoS One. 2016;11(5):e0154976.


Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Xie W, Wang G, Yuan M, Yao W, Lyu K, Zhao H, Yang M, Li P, Zhang X, Yuan J, Wang Q, Liu F, Dong H, Zhang L, Li X, Meng X, Zhang W, Xiong L, He Y, Wang S, Yu S, Xu C, Luo J, Li X, Xiao J, Lian X, Zhang Q.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):E5411-9. doi: 10.1073/pnas.1515919112. Epub 2015 Sep 10.


Open access resources for genome-wide association mapping in rice.

McCouch SR, Wright MH, Tung CW, Maron LG, McNally KL, Fitzgerald M, Singh N, DeClerck G, Agosto-Perez F, Korniliev P, Greenberg AJ, Naredo ME, Mercado SM, Harrington SE, Shi Y, Branchini DA, Kuser-Falcão PR, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J.

Nat Commun. 2016 Feb 4;7:10532. doi: 10.1038/ncomms10532. Erratum in: Nat Commun. 2016;7:11346.


Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

Yabe S, Yamasaki M, Ebana K, Hayashi T, Iwata H.

PLoS One. 2016 Apr 26;11(4):e0153945. doi: 10.1371/journal.pone.0153945. eCollection 2016.


Improving the accuracy of whole genome prediction for complex traits using the results of genome wide association studies.

Zhang Z, Ober U, Erbe M, Zhang H, Gao N, He J, Li J, Simianer H.

PLoS One. 2014 Mar 24;9(3):e93017. doi: 10.1371/journal.pone.0093017. eCollection 2014.


Genomic Selection in Plant Breeding: Methods, Models, and Perspectives.

Crossa J, Pérez-Rodríguez P, Cuevas J, Montesinos-López O, Jarquín D, de Los Campos G, Burgueño J, González-Camacho JM, Pérez-Elizalde S, Beyene Y, Dreisigacker S, Singh R, Zhang X, Gowda M, Roorkiwal M, Rutkoski J, Varshney RK.

Trends Plant Sci. 2017 Nov;22(11):961-975. doi: 10.1016/j.tplants.2017.08.011. Epub 2017 Sep 28. Review.


Genome-wide association study, genomic prediction and marker-assisted selection for seed weight in soybean (Glycine max).

Zhang J, Song Q, Cregan PB, Jiang GL.

Theor Appl Genet. 2016 Jan;129(1):117-30. doi: 10.1007/s00122-015-2614-x. Epub 2015 Oct 30.


A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers.

Moser G, Tier B, Crump RE, Khatkar MS, Raadsma HW.

Genet Sel Evol. 2009 Dec 31;41:56. doi: 10.1186/1297-9686-41-56.


Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E, Oard J, Tohme J.

PLoS One. 2015 Apr 29;10(4):e0124617. doi: 10.1371/journal.pone.0124617. eCollection 2015.


Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding.

Zhou D, Chen W, Lin Z, Chen H, Wang C, Li H, Yu R, Zhang F, Zhen G, Yi J, Li K, Liu Y, Terzaghi W, Tang X, He H, Zhou S, Deng XW.

Plant Biotechnol J. 2016 Feb;14(2):638-48. doi: 10.1111/pbi.12409. Epub 2015 Jun 10.


Breeding schemes for the implementation of genomic selection in wheat (Triticum spp.).

Bassi FM, Bentley AR, Charmet G, Ortiz R, Crossa J.

Plant Sci. 2016 Jan;242:23-36. doi: 10.1016/j.plantsci.2015.08.021. Epub 2015 Sep 6. Review.


Resequencing rice genomes: an emerging new era of rice genomics.

Huang X, Lu T, Han B.

Trends Genet. 2013 Apr;29(4):225-32. doi: 10.1016/j.tig.2012.12.001. Epub 2013 Jan 4. Review.


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

Resende MD, Resende MF Jr, Sansaloni CP, Petroli CD, Missiaggia AA, Aguiar AM, Abad JM, Takahashi EK, Rosado AM, Faria DA, Pappas GJ Jr, Kilian A, Grattapaglia D.

New Phytol. 2012 Apr;194(1):116-28. doi: 10.1111/j.1469-8137.2011.04038.x. Epub 2012 Feb 6.


Toward integration of genomic selection with crop modelling: the development of an integrated approach to predicting rice heading dates.

Onogi A, Watanabe M, Mochizuki T, Hayashi T, Nakagawa H, Hasegawa T, Iwata H.

Theor Appl Genet. 2016 Apr;129(4):805-817. doi: 10.1007/s00122-016-2667-5. Epub 2016 Jan 20.


Accuracy of genomic selection for a sib-evaluated trait using identity-by-state and identity-by-descent relationships.

Vela-Avitúa S, Meuwissen TH, Luan T, Ødegård J.

Genet Sel Evol. 2015 Feb 25;47:9. doi: 10.1186/s12711-014-0084-2.


Assessment of Genetic Heterogeneity in Structured Plant Populations Using Multivariate Whole-Genome Regression Models.

Lehermeier C, Schön CC, de Los Campos G.

Genetics. 2015 Sep;201(1):323-37. doi: 10.1534/genetics.115.177394. Epub 2015 Jun 29.


Breeding technologies to increase crop production in a changing world.

Tester M, Langridge P.

Science. 2010 Feb 12;327(5967):818-22. doi: 10.1126/science.1183700. Review.


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