Accuracy of genomic selection in European maize elite breeding populations

Zhao, Yusheng; Gowda, Manje; Liu, Wenxin; Würschum, Tobias; Maurer, Hans Peter; Longin, Friedrich; Ranc, Nicolas; Reif, Jochen C.

doi:10.1007/s00122-011-1745-y

Cited by 242 publications

(248 citation statements)

References 30 publications

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“…It would then be required to have an important coverage of the genome to capture ancestral LD, otherwise the reliability would be overestimated as discussed before. Breeders are also interested in applying genomic selection in multifamilial populations (Albrecht et al 2011;Zhao et al 2012). Albrecht et al (2011) showed that in such situations the prediction reliabilities are highly dependent on the composition of the calibration set.…”

Section: Discussionmentioning

confidence: 99%

Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea maysL.)

et al. 2012

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Genomic selection refers to the use of genotypic information for predicting breeding values of selection candidates. A prediction formula is calibrated with the genotypes and phenotypes of reference individuals constituting the calibration set. The size and the composition of this set are essential parameters affecting the prediction reliabilities. The objective of this study was to maximize reliabilities by optimizing the calibration set. Different criteria based on the diversity or on the prediction error variance (PEV) derived from the realized additive relationship matrix-best linear unbiased predictions model (RA-BLUP) were used to select the reference individuals. For the latter, we considered the mean of the PEV of the contrasts between each selection candidate and the mean of the population (PEVmean) and the mean of the expected reliabilities of the same contrasts (CDmean). These criteria were tested with phenotypic data collected on two diversity panels of maize (Zea mays L.) genotyped with a 50k SNPs array. In the two panels, samples chosen based on CDmean gave higher reliabilities than random samples for various calibration set sizes. CDmean also appeared superior to PEVmean, which can be explained by the fact that it takes into account the reduction of variance due to the relatedness between individuals. Selected samples were close to optimality for a wide range of trait heritabilities, which suggests that the strategy presented here can efficiently sample subsets in panels of inbred lines. A script to optimize reference samples based on CDmean is available on request.A MONG the different methods that use molecular markers for selection, genomic selection (GS) has received considerable attention in the last decade. The objective of this approach is to predict the breeding values of candidates based on their molecular marker genotypes. A prediction formula is developed using the genotypes and phenotypes of reference individuals forming a calibration set (Meuwissen

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Section: Discussionmentioning

confidence: 99%

Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea maysL.)

et al. 2012

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“…Previous studies have shown that prediction accuracy is impaired when performing genomic selection across connected biparental populations (Zhao et al 2012;Riedelsheimer et al 2013). This may be explained at least partially by epistatic effects as the genetic relatedness across connected populations may be better exploited by modeling epistasis in addition to additive effects.…”

Section: Enhancing Prediction Accuracy Across a Biparental Populationmentioning

confidence: 99%

Modeling Epistasis in Genomic Selection

Jiang¹,

2015

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Modeling epistasis in genomic selection is impeded by a high computational load. The extended genomic best linear unbiased prediction (EG-BLUP) with an epistatic relationship matrix and the reproducing kernel Hilbert space regression (RKHS) are two attractive approaches that reduce the computational load. In this study, we proved the equivalence of EG-BLUP and genomic selection approaches, explicitly modeling epistatic effects. Moreover, we have shown why the RKHS model based on a Gaussian kernel captures epistatic effects among markers. Using experimental data sets in wheat and maize, we compared different genomic selection approaches and concluded that prediction accuracy can be improved by modeling epistasis for selfing species but may not for outcrossing species.KEYWORDS epistasis; genomic selection; genomic best linear unbiased prediction (G-BLUP); extended G-BLUP (EG-BLUP); reproducing kernel Hilbert space regression (RKHS); GenPred; shared data resource E PISTASIS has long been recognized as an important component in dissecting genetic pathways and understanding the evolution of complex genetic systems (Phillips 2008). It is hence a biologically influential component contributing to the genetic architecture of quantitative traits (Mackay 2014). The influence of epistasis on genome-wide QTL mapping ranges from limited (e.g., Buckler et al. 2009;Tian et al. 2011) to high (e.g., Carlborg et al. 2006;Würschum et al. 2011;Huang et al. 2014). These discrepancies can be explained by the complexities of the examined traits, which are controlled by many loci exhibiting small effects entailing a low QTL detection power. In addition, the estimation of QTL main and interaction effects is very likely biased (Beavis 1994), which makes it challenging to reliably elucidate the role of epistasis through genome-wide QTL mapping studies.Genomic selection has been suggested as an alternative to tackle complex traits that are regulated by many genes, each exhibiting a small effect (Meuwissen et al. 2001). Genomic selection approaches based on additive and dominance effects have been successfully applied to predict complex traits in human (Yang et al. 2010), animal (Hayes et al. 2009, and plant populations (Jannink et al. 2010;Zhao et al. 2015). Moreover, several genomic selection approaches have been developed to model both main and epistatic effects (Xu 2007;Cai et al. 2011;Wittenburg et al. 2011;Wang et al. 2012). While in some studies prediction accuracies increased (Hu et al. 2011), in others modeling epistasis adversely affected prediction accuracies (Lorenzana and Bernardo 2009).Despite these first attempts, epistasis is often ignored in genomic selection approaches using parametric models mainly because of the high associated computational load, especially if a large number of markers are available. An attractive solution to reduce the computational load is to extend genomic best linear unbiased prediction (G-BLUP) models (VanRaden 2008) by adding marker-based epistatic relationship matrices [extended genomic...

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“…The obvious advantages of GS over traditional MAS have been successfully proven in animal breeding [116]. Rapid evolution of sequencing technologies and HTP SNP genotyping systems are enabling generation and validation of millions of markers, giving a "cautious optimism" for successful application of GS in breeding for complex traits [117][118][119][120].…”

Section: Implementation Of Snp Markers In Plant Breedingmentioning

confidence: 99%

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

2014

The Role of Bioinformatics in Agriculture

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The use of molecular markers has revolutionized the pace and precision of plant genetic analysis which in turn facilitated the implementation of molecular breeding of crops. The last three decades have seen tremendous advances in the evolution of marker systems and the respective detection platforms. Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms. Computational approaches dominate SNP discovery methods due to the everincreasing sequence information in public databases; however, complex genomes pose special challenges in the identification of informative SNPs warranting alternative strategies in those crops. Many genotyping platforms and chemistries have become available making the use of SNPs even more attractive and efficient. This paper provides a review of historical and current efforts in the development, validation, and application of SNP markers in QTL/gene discovery and plant breeding by discussing key experimental strategies and cases exemplifying their impact.

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Accuracy of genomic selection in European maize elite breeding populations

Cited by 242 publications

References 30 publications

Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea maysL.)

Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea maysL.)

Modeling Epistasis in Genomic Selection

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

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