Table_3_Multi-Omics Analysis Reveals That SlERF.D6 Synergistically Regulates SGAs and Fruit Development.XLSX

Steroidal glycoalkaloids (SGAs) are cholesterol-derived molecules that contribute to the pathogen defense in tomato but are toxic and considered to be antinutritional compounds to humans. APETALA2/Ethylene Responsive Factor (AP2/ERF) family transcription factors (TFs) play an indispensable role in various biological processes, such as plant growth and development, fruit ripening, biotic and abiotic stresses responses, and SGA biosynthesis. In this study, we identified 176 AP2/ERF genes that were domesticated or improved SlAP2/ERF in the tomato variome (Solanum lycopersicum) within either domestication or improvement sweeps, respectively. According to the RNA-sequencing data, 93 of the ERF genes with high transcriptional level (Transcripts Per Million, TPM > 1) belong to six clusters. Weighted gene co-expression network analysis (WGCNA) and metabolite-based genome-wide association study (mGWAS) analyses revealed that the expression level of the Solyc04g071770 (SlERF.D6) gene in the cluster six gradually increased as the fruit matured. Transient transformation verified that the overexpression of SlERF.D6 significantly promoted fruit ripening and regulated the expression of multiple genes in the SGA synthesis pathway, thereby affecting the SGA content of the fruit. Virus-induced gene silencing (VIGS) showed that the silencing of SlERF.D6 delayed fruit ripening and influenced the content of SGAs. Our data provide new insights into AP2/ERF TFs in tomato, offer a candidate TF for fruit development and steroidal glycoalkaloids, and provide new resources for tomato breeding and improvement.

甾体糖苷生物碱（Steroidal glycoalkaloids, SGAs）是一类源自胆固醇的分子，可参与番茄的病原菌防御过程，但同时具有毒性，被认为是对人体具有抗营养作用的化合物。APETALA2/乙烯响应因子（APETALA2/Ethylene Responsive Factor, AP2/ERF）家族转录因子（transcription factors, TFs）在诸多生物学过程中发挥不可或缺的作用，包括植物生长发育、果实成熟、生物与非生物胁迫响应以及甾体糖苷生物碱的生物合成。本研究在栽培番茄（Solanum lycopersicum）的变异组中，分别鉴定出176个位于驯化选择扫荡或改良选择扫荡区间内的驯化型或改良型SlAP2/ERF基因。基于RNA测序数据，93个转录水平较高的ERF基因（每百万转录本（Transcripts Per Million, TPM）>1）可划分为6个聚类模块。加权基因共表达网络分析（WGCNA）与基于代谢物的全基因组关联分析（mGWAS）结果显示，聚类6中的Solyc04g071770（SlERF.D6）基因的表达水平随果实成熟逐渐升高。瞬时转化实验证实，SlERF.D6过表达可显著促进果实成熟，并调控甾体糖苷生物碱合成通路中多个基因的表达，进而影响果实中的甾体糖苷生物碱含量。病毒诱导基因沉默（VIGS）实验表明，沉默SlERF.D6会延迟果实成熟，并改变甾体糖苷生物碱的含量。本研究结果为番茄AP2/ERF家族转录因子的研究提供了新视角，为果实发育与甾体糖苷生物碱相关研究提供了候选转录因子，同时为番茄育种与遗传改良提供了新的研究资源。