title: Accuracy of across-environment genome-wide prediction in maize nested association mapping populations.
abstract: Most of previous empirical studies with genome-wide prediction were focused on within-environment prediction based on a single-environment (SE) model. In this study, we evaluated accuracy improvements of across-environment prediction by using genetic and residual covariance across correlated environments. Predictions with a multienvironment (ME) model were evaluated for two corn polygenic leaf structure traits, leaf length and leaf width, based on within-population (WP) and across-population (AP) experiments using a large maize nested association mapping data set consisting of 25 populations of recombinant inbred-lines. To make our study more applicable to plant breeding, two cross-validation schemes were used by evaluating accuracies of (CV1) predicting unobserved phenotypes of untested lines and (CV2) predicting unobserved phenotypes of lines that have been evaluated in some environments but not others. We concluded that (1) genome-wide prediction provided greater prediction accuracies than traditional quantitative trait loci-based prediction in both WP and AP and provided more advantages over quantitative trait loci -based prediction for WP than for AP. (2) Prediction accuracy with ME was significantly greater than that attained by SE in CV1 and CV2, and gains with ME over SE were greater in CV2 than in CV1. These gains were also greater in WP than in AP in both CV1 and CV2. (3) Gains with ME over SE attributed to genetic correlation between environments, with little effect from residual correlation. Impacts of marker density on predictions also were investigated in this study.
authors: Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709, USA. zhigang.guo@syngenta.com
authors: Zhigang
authors: Z
authors: Guo
authors: Dominic M
authors: DM
authors: Tucker
authors: Daolong
authors: D
authors: Wang
authors: Christopher J
authors: CJ
authors: Basten
authors: Elhan
authors: E
authors: Ersoz
authors: William H
authors: WH
authors: Briggs
authors: Jianwei
authors: J
authors: Lu
authors: Min
authors: M
authors: Li
authors: Gilles
authors: G
authors: Gay
mesh_terms: D003433:Crosses, Genetic; D018745:Genome, Plant; D005838:Genotype; D008954:Models, Biological; D020412:Multifactorial Inheritance; D010641:Phenotype; D018515:Plant Leaves / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D040641:Quantitative Trait Loci; D003313:Zea mays / Q000235:genetics*
keywords: GenPred; best linear unbiased prediction; genetic correlation; maize; ridge regression; shared data resources
references: Theor Appl Genet. 2012 Aug;125(4):759-71
references: 22566067
references: Genet Sel Evol. 2009 Dec 31;41:56
references: 20043835
references: PLoS Genet. 2008 Oct;4(10):e1000231
references: 18949033
references: Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):10972-6
references: 8248199
references: Genetics. 2011 Jul;188(3):695-708
references: 21515573
references: Genetics. 2008 Sep;180(1):611-8
references: 18757934
references: Genetics. 2009 Nov;183(3):1119-26
references: 19704013
references: Brief Funct Genomics. 2010 Mar;9(2):166-77
references: 20156985
references: Genetics. 1994 Apr;136(4):1457-68
references: 8013918
references: BMC Genet. 2010 Jan 22;11:3
references: 20092655
references: Genetics. 2009 May;182(1):355-64
references: 19299342
references: PLoS Genet. 2012;8(3):e1002637
references: 22479213
references: BMC Genet. 2008 Dec 05;9:82
references: 19061502
references: PLoS Genet. 2011 Apr;7(4):e1002051
references: 21552331
references: Theor Appl Genet. 2009 Dec;120(1):151-61
references: 19841887
references: Genet Sel Evol. 2009 Jan 05;41:2
references: 19284681
references: Theor Appl Genet. 2012 Mar;124(4):769-76
references: 22075809
references: Genetics. 2007 Jan;175(1):361-74
references: 17110476
references: Genetics. 1989 Jan;121(1):185-99
references: 2563713
references: Theor Appl Genet. 2006 Jul;113(2):206-24
references: 16791688
references: Genetics. 1996 Jan;142(1):285-94
references: 8770605
references: Nat Genet. 2011 Feb;43(2):159-62
references: 21217756
references: Genetics. 1993 Sep;135(1):205-11
references: 8224820
references: Theor Appl Genet. 2012 Feb;124(2):261-75
references: 21938474
references: Ann Bot. 2012 Nov;110(6):1303-16
references: 22645117
references: J Dairy Sci. 2010 Dec;93(12):5942-9
references: 21094768
references: J Dairy Sci. 2009 Feb;92(2):433-43
references: 19164653
references: Genetica. 2002 Apr;114(3):217-30
references: 12206360
references: Nat Genet. 2012 Jan 15;44(2):217-20
references: 22246502
references: Genetics. 1990 Mar;124(3):743-56
references: 1968875
references: Genet Res (Camb). 2009 Feb;91(1):47-60
references: 19220931
references: Genetics. 2001 Apr;157(4):1819-29
references: 11290733
references: Genet Sel Evol. 2011 Jul 05;43:26
references: 21729282
references: J Anim Sci. 2011 Nov;89(11):3353-61
references: 21642493
references: Genet Res (Camb). 2010 Aug;92(4):295-308
references: 20943010
references: Heredity (Edinb). 1992 Oct;69(4):315-24
references: 16718932
references: Science. 2009 Aug 7;325(5941):714-8
references: 19661422
references: Genetics. 2009 May;182(1):375-85
references: 19293140
references: BMC Bioinformatics. 2011 May 23;12:186
references: 21605355
references: Theor Appl Genet. 2007 Sep;115(5):665-74
references: 17673971
references: Genetics. 1995 Jul;140(3):1111-27
references: 7672582
references: Genetics. 2003 Feb;163(2):789-801
references: 12618414
references: J Dairy Sci. 2008 Nov;91(11):4414-23
references: 18946147
references: Genet Sel Evol. 2011 Jan 21;43:5
references: 21255418
references: BMC Genet. 2010 Apr 19;11:24
references: 20403185
references: Genetics. 2000 Apr;154(3):1839-1849
references: 10866652
references: Genetics. 2010 Oct;186(2):713-24
references: 20813882