Improvement of genomic prediction in advanced wheat breeding lines by including additive-by-additive epistasis

Miguel Angel Raffo,Jeppe Reitan Andersen,Just Jensen,Huiming Liu,Pernille Sarup,Jihad Orabi,Ahmed Jahoor,Xiangyu Guo

doi:10.1007/s00122-021-04009-4

Miguel Angel Raffo, Jeppe Reitan Andersen + Show 6 more

Open Access

https://doi.org/10.1007/s00122-021-04009-4

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Abstract

Key messageIncluding additive and additive-by-additive epistasis in a NOIA parametrization did not yield orthogonal partitioning of genetic variances, nevertheless, it improved predictive ability in a leave-one-out cross-validation for wheat grain yield.Additive-by-additive epistasis is the principal non-additive genetic effect in inbred wheat lines and is potentially useful for developing cultivars based on total genetic merit; nevertheless, its practical benefits have been highly debated. In this article, we aimed to (i) evaluate the performance of models including additive and additive-by-additive epistatic effects for variance components (VC) estimation of grain yield in a wheat-breeding population, and (ii) to investigate whether including additive-by-additive epistasis in genomic prediction enhance wheat grain yield predictive ability (PA). In total, 2060 sixth-generation (F6) lines from Nordic Seed A/S breeding company were phenotyped in 21 year-location combinations in Denmark, and genotyped using a 15 K-Illumina-BeadChip. Three models were used to estimate VC and heritability at plot level: (i) “I-model” (baseline), (ii) “I + GA-model”, extending I-model with an additive genomic effect, and (iii) “I + GA + GAA-model”, extending I + GA-model with an additive-by-additive genomic effects. The I + GA-model and I + GA + GAA-model were based on the Natural and Orthogonal Interactions Approach (NOIA) parametrization. The I + GA + GAA-model failed to achieve orthogonal partition of genetic variances, as revealed by a change in estimated additive variance of I + GA-model when epistasis was included in the I + GA + GAA-model. The PA was studied using leave-one-line-out and leave-one-breeding-cycle-out cross-validations. The I + GA + GAA-model increased PA significantly (16.5%) compared to the I + GA-model in leave-one-line-out cross-validation. However, the improvement due to including epistasis was not observed in leave-one-breeding-cycle-out cross-validation. We conclude that epistatic models can be useful to enhance predictions of total genetic merit. However, even though we used the NOIA parameterization, the variance partition into orthogonal genetic effects was not possible.

Highlights

Genomic selection (GS, Meuwissen et al 2001) methods based on whole-genome prediction (WGP) have been successfully applied for a variety of quantitative traits of agronomic importance in animals and plants (Poland et al 2012; Gianola and Rosa 2015; Crossa et al 2017; Kristensen et al 2019).In quantitative genetics, a distinction is made between the genomic estimated breeding value (GEBVs, estimated additive genetic effects) and the total genetic value
There was a trend that lines coming from the first four breeding cycles were more separated by the first principal component from lines coming from last three breeding cycles
Further studies are required to: (i) investigate the influence of genetic relationships on the performance of epistatic predictions and develop CVs schemes that allow to capitalize the benefit of epistatic models in wheat breeding programs, (ii) develop breeding programs that consider more elaborate mating schemes in order to improve the genetic relationships between breeding cycles, and (iii) develop a genomic prediction (GP) model in which the inclusion of pairwise interaction effects has minimal impact on the estimates of additive effects and their variance

Summary

Introduction

Genomic selection (GS, Meuwissen et al 2001) methods based on whole-genome prediction (WGP) have been successfully applied for a variety of quantitative traits of agronomic importance in animals and plants (Poland et al 2012; Gianola and Rosa 2015; Crossa et al 2017; Kristensen et al 2019).In quantitative genetics, a distinction is made between the genomic estimated breeding value (GEBVs, estimated additive genetic effects) and the total genetic value (estimated additive plus non-additive genetic effects). The better performance of GS over phenotypic selection (Crossa et al 2011; Michel et al 2017; Tessema et al 2020) has led many wheat breeding programs to implement GS, and base the selection of lines on the prediction of GEBVs, which in general are used to select both breeding lines and commercial varieties. Separating additive and non-additive genetic effects can be favorable if it contributes to a more accurate estimate of both additive and total genetic merit. In this context, treating additive and non-additive effects separately can result in an improved strategy of selection, allowing to select crossing parents based exclusively on the additive effect, and develop commercial varieties, based on both additive plus non-additive effects

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