Hybrid Performance of an Immortalized F2 Rapeseed Population Is Driven by Additive, Dominance, and Epistatic Effects.

Peifa Liu,Jun Hu,Dandan Hu,Yusheng Zhao,Jochen C Reif,Jun Zou,Guozheng Liu,Meng Wang,Jinling Meng

doi:10.3389/fpls.2017.00815

Abstract

Genomics-based prediction of hybrid performance promises to boost selection gain. The main goal of our study was to investigate the relevance of additive, dominance, and epistatic effects for determining hybrid seed yield in a biparental rapeseed population. We re-analyzed 60,000 SNP array and seed yield data points from an immortalized F2 population comprised of 318 hybrids and 180 parental lines by performing genome-wide QTL mapping and predictions in combination with five-fold cross-validation. Moreover, an additional set of 37 hybrids were genotyped and phenotyped in an independent environment. The decomposition of the phenotypic variance components and the cross-validated results of the QTL mapping and genome-wide predictions revealed that the hybrid performance in rapeseed was driven by a mix of additive, dominance, and epistatic effects. Interestingly, the genome-wide prediction accuracy in the additional 37 hybrids remained high when modeling exclusively additive effects but was severely reduced when dominance or epistatic effects were also included. This loss in accuracy was most likely caused by more pronounced interactions of environments with dominance and epistatic effects than with additive effects. Consequently, the development of robust hybrid prediction models, including dominance and epistatic effects, required much deeper phenotyping in multi-environmental trials.

Highlights

Hybrid breeding is a promising approach to boost selection gain in crop improvement (Duvick, 2001; Kempe and Gils, 2011; Zhang et al, 2016)
We further decomposed the genetic variance for seed yield of the TabtinemNtdwResseCpel-enaFcr2eigfinehcrvyibctrhoroimandnmbpiσoennG2pintCusAglaa,taniabodninldSitiCnytAhteoeffevevffacaretricsaitans(nσcσceS2E2eCsnAdvoi)ufr.oeinTntmohteeegnretaσ×ncS2SteCCiroAAanlww(eσaaffG2sseC21cA..t34s) times larger than σE2nvironment×general combining ability (GCA)
The immortalized TNRC-F2 population used in our study was initially designed to determine the genetic basis of midparent heterosis of hybrids between the European winter-type cultivar Tapidor and the Chinese semi-winter type cultivar Ningyou7 (Shi et al, 2011)

Summary

Introduction

Hybrid breeding is a promising approach to boost selection gain in crop improvement (Duvick, 2001; Kempe and Gils, 2011; Zhang et al, 2016). The establishment of hybrid breeding programs for rapeseed (Brassica napus, 2n = 38, AACC) resulted in an up to 30% increase in seed yield compared with open-pollinated cultivars (Brandt et al, 2007). Hybrid breeding in rapeseed profited strongly from the exploration of different hybrid seed production systems, such as the Polima cytoplasmic male sterility (CMS) (Fu et al, 1995), Ogura CMS (Brown et al, 2003), genic male sterility (Yan et al, 2016), and ecotype male sterility (Yu et al, 2015). Hybrids replaced open-pollinated cultivars in most rapeseed growing regions (Fu, 2000). In genome-wide prediction, many markers are used, and their effects are estimated in populations that have been genotyped and phenotyped. The estimated marker effects are applied to predict the performance of non-phenotyped hybrids based on their molecular marker profiles

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