title: Genomic prediction in maize breeding populations with genotyping-by-sequencing.
abstract: Genotyping-by-sequencing (GBS) technologies have proven capacity for delivering large numbers of marker genotypes with potentially less ascertainment bias than standard single nucleotide polymorphism (SNP) arrays. Therefore, GBS has become an attractive alternative technology for genomic selection. However, the use of GBS data poses important challenges, and the accuracy of genomic prediction using GBS is currently undergoing investigation in several crops, including maize, wheat, and cassava. The main objective of this study was to evaluate various methods for incorporating GBS information and compare them with pedigree models for predicting genetic values of lines from two maize populations evaluated for different traits measured in different environments (experiments 1 and 2). Given that GBS data come with a large percentage of uncalled genotypes, we evaluated methods using nonimputed, imputed, and GBS-inferred haplotypes of different lengths (short or long). GBS and pedigree data were incorporated into statistical models using either the genomic best linear unbiased predictors (GBLUP) or the reproducing kernel Hilbert spaces (RKHS) regressions, and prediction accuracy was quantified using cross-validation methods. The following results were found: relative to pedigree or marker-only models, there were consistent gains in prediction accuracy by combining pedigree and GBS data; there was increased predictive ability when using imputed or nonimputed GBS data over inferred haplotype in experiment 1, or nonimputed GBS and information-based imputed short and long haplotypes, as compared to the other methods in experiment 2; the level of prediction accuracy achieved using GBS data in experiment 2 is comparable to those reported by previous authors who analyzed this data set using SNP arrays; and GBLUP and RKHS models with pedigree with nonimputed and imputed GBS data provided the best prediction correlations for the three traits in experiment 1, whereas for experiment 2 RKHS provided slightly better prediction than GBLUP for drought-stressed environments, and both models provided similar predictions in well-watered environments.
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico DF, Mexico.
authors.forename: José
authors.initials: J
authors.lastname: Crossa
authors.forename: Yoseph
authors.initials: Y
authors.lastname: Beyene
authors.forename: Semagn
authors.initials: S
authors.lastname: Kassa
authors.forename: Paulino
authors.initials: P
authors.lastname: Pérez
authors.forename: John M
authors.initials: JM
authors.lastname: Hickey
authors.forename: Charles
authors.initials: C
authors.lastname: Chen
authors.forename: Gustavo
authors.initials: G
authors.lastname: de los Campos
authors.forename: Juan
authors.initials: J
authors.lastname: Burgueño
authors.forename: Vanessa S
authors.initials: VS
authors.lastname: Windhausen
authors.forename: Ed
authors.initials: E
authors.lastname: Buckler
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Jannink
authors.forename: Marco A
authors.initials: MA
authors.lastname: Lopez Cruz
authors.forename: Raman
authors.initials: R
authors.lastname: Babu
mesh_terms: D001947:Breeding; D002875:Chromosomes / Q000737:chemistry / Q000378:metabolism; D018745:Genome, Plant; D005838:Genotype; D006239:Haplotypes; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D003313:Zea mays / Q000235:genetics*
keywords: GBLUP; GenPred; RKHS; genomic selection; genotyping by sequencing; imputation; shared data resources
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: Genetics. 2012 Oct;192(2):693-704
references.pmid: 22813891
references.citation: PLoS Genet. 2009 Nov;5(11):e1000734
references.pmid: 19956538
references.citation: Nat Genet. 2010 Apr;42(4):322-7
references.pmid: 20305664
references.citation: Nat Genet. 2012 Jun 03;44(7):803-7
references.pmid: 22660545
references.citation: G3 (Bethesda). 2012 Nov;2(11):1427-36
references.pmid: 23173094
references.citation: BMC Genet. 2011 Sep 20;12:80
references.pmid: 21933416
references.citation: Genetics. 2013 Feb;193(2):327-45
references.pmid: 22745228
references.citation: G3 (Bethesda). 2012 Dec;2(12):1595-605
references.pmid: 23275882
references.citation: Genetics. 2010 Oct;186(2):713-24
references.pmid: 20813882
references.citation: BMC Genet. 2011 Oct 07;12:87
references.pmid: 21981731
references.citation: Theor Appl Genet. 2012 Aug;125(4):759-71
references.pmid: 22566067
references.citation: PLoS One. 2011 May 04;6(5):e19379
references.pmid: 21573248
references.citation: Bioinformatics. 2007 Oct 1;23(19):2633-5
references.pmid: 17586829
references.citation: Plant Genome. 2010;3(2):106-116
references.pmid: 21566722
references.citation: J Dairy Sci. 2010 Dec;93(12):5942-9
references.pmid: 21094768
references.citation: Genetics. 2006 Jul;173(3):1761-76
references.pmid: 16648593
references.citation: Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9573-8
references.pmid: 12060715
references.citation: Genetics. 2001 Apr;157(4):1819-29
references.pmid: 11290733
references.citation: Bioinformatics. 2008 Sep 15;24(18):2096-7
references.pmid: 18689808
references.citation: Genetics. 2009 May;182(1):375-85
references.pmid: 19293140
references.citation: Genet Res (Camb). 2010 Aug;92(4):295-308
references.pmid: 20943010
references.citation: Genome Biol. 2013 Jun 11;14(6):R55
references.pmid: 23759205
references.citation: Nucleic Acids Res. 2011 Oct;39(19):e132
references.pmid: 21813454
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Heredity (Edinb). 2014 Jan;112(1):48-60
references.pmid: 23572121
references.citation: Genetics. 2013 Apr;193(4):1073-81
references.pmid: 23410831
references.citation: J Dairy Sci. 2008 Nov;91(11):4414-23
references.pmid: 18946147
references.citation: PLoS One. 2011;6(9):e24861
references.pmid: 21949770
references.citation: Genetics. 2009 May;182(1):355-64
references.pmid: 19299342