Table_1_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）是一类胆固醇衍生的分子，在番茄中参与病原菌防御过程，但对人类具有毒性，被视作抗营养化合物。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，涵盖植物生长发育、果实成熟、生物与非生物胁迫响应以及SGAs的生物合成。本研究在栽培番茄（Solanum lycopersicum）的番茄变异组中，鉴定得到176个分别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（每百万转录本（Transcripts Per Million，TPM）>1）的ERF基因可划分为6个基因簇。加权基因共表达网络分析（Weighted gene co-expression network analysis，WGCNA）与基于代谢物的全基因组关联分析（metabolite-based genome-wide association study，mGWAS）结果显示，第6基因簇中的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SGAs合成通路中多个基因的表达，进而影响果实中的SGAs含量。病毒诱导基因沉默（Virus-induced gene silencing，VIGS）实验表明，沉默SlERF.D6会延缓果实成熟并改变果实中的SGAs含量。本研究数据为番茄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，同时为番茄育种与改良提供了新的研究资源。