Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design

The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F1 crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F1 hybrids, and all these F1 phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F1 hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study.

水稻、玉米与油菜的杂种优势（heterosis）利用彻底革新了作物生产格局。尽管优良杂交品种主要源自两组亲本杂交得到的F1代组合，该杂交设计被称为NCII交配设计（NCII mating design），但学界对于群体中互作效应如何影响数量性状表现的方法学机制仍知之甚少。为搭建遗传分析与杂交育种之间的桥梁，本研究针对部分NCII交配设计群体，将互作数量性状基因座（Quantitative Trait Locus，QTL）定位方法与设计育种理念相结合。本研究将所有潜在的主效效应与互作效应纳入同一全模型之中；若效应数量过多，则采用集群分离分析法（Bulked Segregant Analysis，BSA）筛选与目标性状相关的效应因子。对筛选得到的效应因子，进一步通过经验贝叶斯方法进行收缩估计，以甄别出具有统计学意义的效应。本研究通过一系列蒙特卡洛模拟（Monte Carlo simulation）对所提新方法进行验证。此外，利用所有甄别出的显著效应计算所有缺失F1杂交组合的基因型值，并基于这些F1代的表型或基因型值预测优良亲本及亲本组合。最后，将该新方法应用于解析441份油菜亲本与284份F1杂交组合的含油量遗传基础。研究结果显示，共鉴定出8个主效QTL与37个互作QTL，并利用这些位点预测得到10个优良恢复系、10个优良不育系以及10个优良亲本组合。本方法与多种现有方法及既往研究结果一致性良好，且预测表型与实测表型间的相关系数高达0.76，充分验证了本研究提出的方法的有效性。