Comparative transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus). Cucumis sativus

Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early fruit development directly determines the final fruit length and diameter, and consequently the fruit yield and quality. Different cucumber varieties display huge variations of fruit length, but how fruit length is determined at the molecular level remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-seq data were used to compare the transcriptomes of early fruit from two near isogenic lines with different fruit lengths. 3955 genes were found to be differentially expressed, among which 2368 genes were significantly up-regulated and 1587 down-regulated in the line with long fruit. Microtubule and cell cycle related genes were dramatically activated in the long fruit, and transcription factors were implicated in the fruit length regulation in cucumber. Thus, our results built a foundation to dissect the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance. Overall design: Comparative analysis of fruit from two near-isogenic lines, 408 (long fruit) and 409 (short fruit), was employed to discover genes and networks that regulate the fruit length. Two biological replicates were used from each line.

黄瓜（Cucumis sativus L.）果实为肉质果的一种，通常在未成熟阶段采收。果实早期发育直接决定最终的果实长度与直径，进而影响果实的产量与品质。不同黄瓜品种的果实长度存在显著差异，但目前对果实长度的分子调控机制仍缺乏深入认知。为解析调控黄瓜果实长度的基因及基因调控网络，本研究采用高通量RNA测序（RNA-seq）技术，对两个果实长度存在显著差异的近等基因系的早期果实转录组开展比较分析。共鉴定得到3955个差异表达基因，其中在长果近等基因系中，2368个基因显著上调，1587个基因显著下调。长果材料中，微管及细胞周期相关基因被显著激活，同时发现转录因子参与黄瓜果实长度的调控。综上，本研究结果为解析这一具有重要经济价值的关键农艺性状——黄瓜果实长度的分子调控机制奠定了重要基础。实验设计：本研究以两个果实长度不同的近等基因系408（长果）和409（短果）的果实为材料，通过比较转录组分析挖掘调控果实长度的基因及调控网络；每个品系设置两个生物学重复。