Data_Sheet_5_Integrated Analysis of mRNA and Non-coding RNA Transcriptome in Pepper (Capsicum chinense) Hybrid at Seedling and Flowering Stages.XLSX

Pepper is an important vegetable in the world. In this work, mRNA and ncRNA transcriptome profiles were applied to understand the heterosis effect on the alteration in the gene expression at the seedling and flowering stages between the hybrid and its parents in Capsicum chinense. Our phenotypic data indicated that the hybrid has dominance in leaf area, plant scope, plant height, and fruit-related traits. Kyoto Encyclopedia of Genes and Genomes analysis showed that nine members of the plant hormone signal transduction pathway were upregulated in the seedling and flowering stages of the hybrid, which was supported by weighted gene coexpression network analysis and that BC332_23046 (auxin response factor 8), BC332_18317 (auxin-responsive protein IAA20), BC332_13398 (ethylene-responsive transcription factor), and BC332_27606 (ethylene-responsive transcription factor WIN1) were candidate hub genes, suggesting the important potential role of the plant hormone signal transduction in pepper heterosis. Furthermore, some transcription factor families, including bHLH, MYB, and HSF were greatly over-dominant. We also identified 2,525 long ncRNAs (lncRNAs), 47 micro RNAs (miRNAs), and 71 circle RNAs (circRNAs) in the hybrid. In particular, downregulation of miR156, miR169, and miR369 in the hybrid suggested their relationship with pepper growth vigor. Moreover, we constructed some lncRNA–miRNA–mRNA regulatory networks that showed a multi-dimension to understand the ncRNA relationship with heterosis. These results will provide guidance for a better understanding of the molecular mechanism involved in pepper heterosis.

辣椒是全球重要的蔬菜作物。本研究以中华辣椒（Capsicum chinense）为材料，通过分析杂交种及其亲本在苗期与开花期的基因表达变化，解析杂种效应对基因表达的调控作用，采用了mRNA与非编码RNA（ncRNA）转录组谱技术。本研究的表型数据显示，该杂交种在叶面积、株幅、株高以及果实相关性状上均表现出显著优势。京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）分析结果表明，该杂交种在苗期与开花期的植物激素信号转导通路中有9个基因呈上调表达，该结论得到加权基因共表达网络分析的佐证；同时鉴定出BC332_23046（生长素响应因子8，auxin response factor 8）、BC332_18317（生长素响应蛋白IAA20，auxin-responsive protein IAA20）、BC332_13398（乙烯响应转录因子，ethylene-responsive transcription factor）以及BC332_27606（乙烯响应转录因子WIN1，ethylene-responsive transcription factor WIN1）为候选核心基因，这提示植物激素信号转导通路在辣椒杂种优势中具有重要潜在功能。此外，bHLH、MYB以及HSF等部分转录因子家族均呈现出显著的超显性效应。本研究还在该杂交种中鉴定出2525条长链非编码RNA（long ncRNAs，lncRNAs）、47条微小RNA（micro RNAs，miRNAs）以及71条环状RNA（circle RNAs，circRNAs）。尤为关键的是，该杂交种中miR156、miR169与miR369的下调表达，提示其与辣椒生长势密切相关。此外，本研究构建了多组lncRNA–miRNA–mRNA调控网络，从多维度阐释了非编码RNA与杂种优势之间的关联。上述研究结果可为深入解析辣椒杂种优势相关的分子机制提供重要理论参考与指导。