title: Genomic predictability of interconnected biparental maize populations.
abstract: Intense structuring of plant breeding populations challenges the design of the training set (TS) in genomic selection (GS). An important open question is how the TS should be constructed from multiple related or unrelated small biparental families to predict progeny from individual crosses. Here, we used a set of five interconnected maize (Zea mays L.) populations of doubled-haploid (DH) lines derived from four parents to systematically investigate how the composition of the TS affects the prediction accuracy for lines from individual crosses. A total of 635 DH lines genotyped with 16,741 polymorphic SNPs were evaluated for five traits including Gibberella ear rot severity and three kernel yield component traits. The populations showed a genomic similarity pattern, which reflects the crossing scheme with a clear separation of full sibs, half sibs, and unrelated groups. Prediction accuracies within full-sib families of DH lines followed closely theoretical expectations, accounting for the influence of sample size and heritability of the trait. Prediction accuracies declined by 42% if full-sib DH lines were replaced by half-sib DH lines, but statistically significantly better results could be achieved if half-sib DH lines were available from both instead of only one parent of the validation population. Once both parents of the validation population were represented in the TS, including more crosses with a constant TS size did not increase accuracies. Unrelated crosses showing opposite linkage phases with the validation population resulted in negative or reduced prediction accuracies, if used alone or in combination with related families, respectively. We suggest identifying and excluding such crosses from the TS. Moreover, the observed variability among populations and traits suggests that these uncertainties must be taken into account in models optimizing the allocation of resources in GS.
authors.affiliation: Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Riedelsheimer
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Endelman
authors.forename: Michael
authors.initials: M
authors.lastname: Stange
authors.forename: Mark E
authors.initials: ME
authors.lastname: Sorrells
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Jannink
authors.forename: Albrecht E
authors.initials: AE
authors.lastname: Melchinger
mesh_terms: D001947:Breeding; D003433:Crosses, Genetic; D018745:Genome, Plant; D005874:Gibberella; D008957:Models, Genetic; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D018401:Sample Size; D012641:Selection, Genetic; D003313:Zea mays / Q000235:genetics* / Q000382:microbiology
keywords: Fusarium graminearum; G-BLUP; GenPred; shared data resources; whole-genome prediction
references.citation: BMC Genomics. 2012 Sep 04;13:452
references.pmid: 22947126
references.citation: PLoS One. 2008;3(10):e3395
references.pmid: 18852893
references.citation: Genetics. 2009 Sep;183(1):347-63
references.pmid: 19620397
references.citation: Theor Appl Genet. 2009 Dec;120(1):151-61
references.pmid: 19841887
references.citation: Nat Rev Genet. 2011 Dec 29;13(2):85-96
references.pmid: 22207165
references.citation: PLoS One. 2011;6(12):e28334
references.pmid: 22174790
references.citation: Methods Mol Biol. 2012;877:161-72
references.pmid: 22610627
references.citation: Genetics. 2007 Dec;177(4):2389-97
references.pmid: 18073436
references.citation: Nat Genet. 2012 Jan 15;44(2):217-20
references.pmid: 22246502
references.citation: Genet Res (Camb). 2009 Feb;91(1):47-60
references.pmid: 19220931
references.citation: Theor Appl Genet. 2012 Oct;125(6):1181-94
references.pmid: 22733443
references.citation: G3 (Bethesda). 2012 Nov;2(11):1427-36
references.pmid: 23173094
references.citation: Genetics. 2010 Jun;185(2):623-31
references.pmid: 20308278
references.citation: Genet Sel Evol. 2010 Feb 19;42:5
references.pmid: 20170500
references.citation: Genet Sel Evol. 2012 Feb 09;44:4
references.pmid: 22321529
references.citation: Genet Sel Evol. 2009 Jun 11;41:35
references.pmid: 19519896
references.citation: J Dairy Sci. 2008 Nov;91(11):4414-23
references.pmid: 18946147
references.citation: Genetics. 2010 Oct;186(2):713-24
references.pmid: 20813882
references.citation: Genet Res (Camb). 2011 Feb;93(1):47-64
references.pmid: 21226974
references.citation: Theor Appl Genet. 2011 Jul;123(2):339-50
references.pmid: 21505832
references.citation: Genetics. 2010 Jul;185(3):1021-31
references.pmid: 20407128
references.citation: Theor Appl Genet. 1987 Sep;73(5):759-63
references.pmid: 24241202
references.citation: J Dairy Sci. 2005 May;88(5):1865-72
references.pmid: 15829680
references.citation: Genetics. 2001 Apr;157(4):1819-29
references.pmid: 11290733
references.citation: Genetics. 2009 Dec;183(4):1545-53
references.pmid: 19822733
references.citation: Nat Rev Genet. 2009 Jun;10(6):381-91
references.pmid: 19448663