Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (<i>Oryza sativa</i> L.)
Yingheng Wang,
Jing Xia,
Likun Huang,
Qiang Lin,
Qiuhua Cai,
Hongguang Xie,
Wei He,
Yidong Wei,
Huaan Xie,
Weiqi Tang,
Weiren Wu,
Jianfu Zhang
Affiliations
Yingheng Wang
Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
Jing Xia
College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Likun Huang
College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Qiang Lin
Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
Qiuhua Cai
Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
Hongguang Xie
Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
Wei He
Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
Yidong Wei
Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
Huaan Xie
Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
Weiqi Tang
Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
Weiren Wu
College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Jianfu Zhang
Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
The heterosis in hybrid rice is highly affected by the environment and hybrid weakness occurs frequently depending on the genotypes of the hybrid and its parents. Hybrid weakness was also observed in our field experiments on nine rice hybrids produced by 3 × 3 incomplete diallel crosses. Among the nine hybrids, five displayed mid-parent heterosis (MPH) for grain yield per plant, while four showed mid-parent hybrid weakness (MPHW). A sequencing analysis of transcriptomes in panicles at the seed-filling stage revealed a significant association between enhanced non-additive gene expression (NAE) and allele-specific gene expression (ASE) with hybrid weakness. High proportions of ASE genes, with most being of mono-allele expression, were detected in the four MPHW hybrids, ranging from 22.65% to 45.97%; whereas only 4.80% to 5.69% of ASE genes were found in the five MPH hybrids. Moreover, an independence test indicated that the enhancements of NAE and ASE in the MPHW hybrids were significantly correlated. Based on the results of our study, we speculated that an unfavorable environment might cause hybrid weakness by enhancing ASE and NAE at the transcriptome level.
