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The effects of training population design on genomic prediction accuracy in wheat.

ABSTRACT: Genomic selection offers several routes for increasing the genetic gain or efficiency of plant breeding programmes. In various species of livestock, there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeder's equation. Accurate predictions of genomic breeding value are central to this, and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable predictions with higher accuracy. To quantify the effect of some of the properties of training sets on the accuracy of genomic selection in crops, we performed an extensive field-based winter wheat trial. In summary, this trial involved the construction of 44 F_2:4 bi- and tri-parental populations, from which 2992 lines were grown on four field locations and yield was measured. For each line, genotype data were generated for 25 K segregating SNP markers. The overall heritability of yield was estimated to 0.65, and estimates within individual families ranged between 0.10 and 0.85. Genomic prediction accuracies of yield BLUEs were 0.125-0.127 using two different cross-validation approaches and generally increased with training set size. Using related crosses in training and validation sets generally resulted in higher prediction accuracies than using unrelated crosses. The results of this study emphasise the importance of the training panel design in relation to the genetic material to which the resulting prediction model is to be applied.

SUBMITTER: Edwards SM

PROVIDER: S-EPMC6588656 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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The effects of training population design on genomic prediction accuracy in wheat.

Edwards Stefan McKinnon SM Buntjer Jaap B JB Jackson Robert R Bentley Alison R AR Lage Jacob J Byrne Ed E Burt Chris C Jack Peter P Berry Simon S Flatman Edward E Poupard Bruno B Smith Stephen S Hayes Charlotte C Gaynor R Chris RC Gorjanc Gregor G Howell Phil P Ober Eric E Mackay Ian J IJ Hickey John M JM

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 20190319 7

Genomic selection offers several routes for increasing the genetic gain or efficiency of plant breeding programmes. In various species of livestock, there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeder's equation. Accurate predictions of genomic breeding value are central to this, and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close r ...[more]

PMID: 30888431

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Project description:Agronomically important traits generally have complex genetic architecture, where many genes have a small and largely additive effect. Genomic prediction has been demonstrated to increase genetic gain and efficiency in plant breeding programs beyond marker-assisted selection and phenotypic selection. The objective of this study was to evaluate the impact of allelic origin, marker density, training population size, and cross-validation schemes on the accuracy of genomic prediction models in an interspecific soybean nested association mapping (NAM) panel. Three cross-validation schemes were used: (a) Within-Family (WF): training population and predictions are made exclusively within each family; (b) Across All families (AF): all the individuals from the three families were randomly assigned to either the training or validation set; (c) Leave one Family out (LFO): each family is predicted using a training set that contains the other two families. Predictive abilities increased with training population size up to 350 individuals, but no significant gains were noted beyond 250 individuals in the training population. The number of markers had a limited impact on the observed predictive ability across traits; increasing markers used in the model above 1000 revealed no significant increases in prediction accuracy. Predictive abilities for AF were not significantly different from the WF method, and predictive abilities across populations for the WF method had a range of 0.58 to 0.70 for maturity, protein, meal, and oil. Our results also showed encouraging prediction accuracies for grain yield (0.58–0.69) using the WF method. Partitioning genomic prediction between G. max and G. soja alleles revealed useful information to select material with a larger allele contribution from both parents and could accelerate allele introgression from exotic germplasm into the elite soybean gene pool. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01203-6.

Project description:Genomic selection (GS) models use genome-wide genetic information to predict genetic values of candidates of selection. Originally, these models were developed without considering genotype × environment interaction(G×E). Several authors have proposed extensions of the single-environment GS model that accommodate G×E using either covariance functions or environmental covariates. In this study, we model G×E using a marker × environment interaction (M×E) GS model; the approach is conceptually simple and can be implemented with existing GS software. We discuss how the model can be implemented by using an explicit regression of phenotypes on markers or using co-variance structures (a genomic best linear unbiased prediction-type model). We used the M×E model to analyze three CIMMYT wheat data sets (W1, W2, and W3), where more than 1000 lines were genotyped using genotyping-by-sequencing and evaluated at CIMMYT's research station in Ciudad Obregon, Mexico, under simulated environmental conditions that covered different irrigation levels, sowing dates and planting systems. We compared the M×E model with a stratified (i.e., within-environment) analysis and with a standard (across-environment) GS model that assumes that effects are constant across environments (i.e., ignoring G×E). The prediction accuracy of the M×E model was substantially greater of that of an across-environment analysis that ignores G×E. Depending on the prediction problem, the M×E model had either similar or greater levels of prediction accuracy than the stratified analyses. The M×E model decomposes marker effects and genomic values into components that are stable across environments (main effects) and others that are environment-specific (interactions). Therefore, in principle, the interaction model could shed light over which variants have effects that are stable across environments and which ones are responsible for G×E. The data set and the scripts required to reproduce the analysis are publicly available as Supporting Information.

Project description:BackgroundA multi-population genomic prediction (GP) model in which important pre-selected single nucleotide polymorphisms (SNPs) are differentially weighted (MPMG) has been shown to result in better prediction accuracy than a multi-population, single genomic relationship matrix ([Formula: see text]) GP model (MPSG) in which all SNPs are weighted equally. Our objective was to underpin theoretically the advantages and limits of the MPMG model over the MPSG model, by deriving and validating a deterministic prediction equation for its accuracy.MethodsUsing selection index theory, we derived an equation to predict the accuracy of estimated total genomic values of selection candidates from population [Formula: see text] ([Formula: see text]), when individuals from two populations, [Formula: see text] and [Formula: see text], are combined in the training population and two [Formula: see text], made respectively from pre-selected and remaining SNPs, are fitted simultaneously in MPMG. We used simulations to validate the prediction equation in scenarios that differed in the level of genetic correlation between populations, heritability, and proportion of genetic variance explained by the pre-selected SNPs. Empirical accuracy of the MPMG model in each scenario was calculated and compared to the predicted accuracy from the equation.ResultsIn general, the derived prediction equation resulted in accurate predictions of [Formula: see text] for the scenarios evaluated. Using the prediction equation, we showed that an important advantage of the MPMG model over the MPSG model is its ability to benefit from the small number of independent chromosome segments ([Formula: see text]) due to the pre-selected SNPs, both within and across populations, whereas for the MPSG model, there is only a single value for [Formula: see text], calculated based on all SNPs, which is very large. However, this advantage is dependent on the pre-selected SNPs that explain some proportion of the total genetic variance for the trait.ConclusionsWe developed an equation that gives insight into why, and under which conditions the MPMG outperforms the MPSG model for GP. The equation can be used as a deterministic tool to assess the potential benefit of combining information from different populations, e.g., different breeds or lines for GP in livestock or plants, or different groups of people based on their ethnic background for prediction of disease risk scores.

Dataset Information

The effects of training population design on genomic prediction accuracy in wheat.

Publications

The effects of training population design on genomic prediction accuracy in wheat.

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