Fine-Tuning Quantitative Trait Loci Identified in Immortalized F<sub>2</sub> Population Are Essential for Genomic Prediction of Hybrid Performance in Maize
Pingxi Wang,
Xingye Ma,
Xining Jin,
Xiangyuan Wu,
Xiaoxiang Zhang,
Huaisheng Zhang,
Hui Wang,
Hongwei Zhang,
Junjie Fu,
Yuxin Xie,
Shilin Chen
Affiliations
Pingxi Wang
Henan Collaborative Innovation Center of Modern Biological Breeding, School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China
Xingye Ma
Henan Collaborative Innovation Center of Modern Biological Breeding, School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China
Xining Jin
Henan Collaborative Innovation Center of Modern Biological Breeding, School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China
Xiangyuan Wu
Henan Collaborative Innovation Center of Modern Biological Breeding, School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China
Xiaoxiang Zhang
Henan Collaborative Innovation Center of Modern Biological Breeding, School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China
Huaisheng Zhang
Henan Collaborative Innovation Center of Modern Biological Breeding, School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China
Hui Wang
Henan Collaborative Innovation Center of Modern Biological Breeding, School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China
Hongwei Zhang
State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Junjie Fu
State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Yuxin Xie
State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Shilin Chen
Henan Collaborative Innovation Center of Modern Biological Breeding, School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China
Maize breeding is greatly affected by hybrid vigor, a phenomenon that hybrids exhibit superior performance than parental lines. The immortalized F2 population (IMF2) is ideal for the genetic dissection and prediction of hybrid performance. Here, in this study, we conducted the QTL mapping and genomic prediction of six traits related to plant architecture using an IMF2 population. Broad-sense heritability of these traits ranged from 0.85 to 0.94. Analysis of genetic effects showed that additive variance was the main contributor to phenotypic variations. The mapping of quantitative trait loci (QTLs) revealed 10 to 16 QTLs (including pleiotropic loci and epistatic QTLs) for the six traits. Additionally, we identified 15 fine-tuning QTLs for plant height (PH). For genomic prediction (GP), the model of additive and dominance (AD) exhibited higher prediction accuracy than those fitting general combining ability (GCA) and its combination with special combining ability (SCA) effects for all tested traits. And adding the epistasis (E) effect into the AD model did not significantly increase its prediction accuracy. Moreover, the identified 15 fine-tuning QTLs of PH, which exerted large genomic prediction effects, were verified by the marker effect of GP. Our results not only provide an approach for the fine-mapping of fine-tuning QTLs but also serve as references for GP breeding in crops.
