Grafting changed silicon metabolism and expression of bloom-forming related genes of cucumber pericarp. Cucumis sativus

Cucumber (Cucumis sativus L.) is an economically important vegetable cultivated all over the world. Grafting can produce bloomless or sparse-bloom cucumber, which is welcomed by increasing consumers. Bloom granule is tine glandular hair, which is hard and rare studied on its formation and related genes. Mutifunctional RNA-seq is a recently developed analytical approach for transcriptome profiling via high-throughput sequencing and has been recently applied to a wide variety of organisms, which provide us reliable technical means detect bloom formation and related genes. In this study, we chose a cucumber inbred line (Shannong No.5) and two pumpkin rootstock lines as materials, and constructed four tested cucumbers, grew plants in “Yamazaki cucumber nutrient solution formula” prepared by deionized water, treated plants with or without 1.7mM potassium silicate 2 hours before collecting pericarp. Each treatment were duplicated twice.16 cDNA libraries were constructed from pericarp of a cucumber inbred line (own-rooted cucumber), C/C (self-grafted cucumber), M/C (More bloom, cucumber grafted onto “3225” rootstock) and L/C(Less bloom, cucumber grafted onto “3212” rootstock). We obtained 17,215,769~17,529,047 high quality reads, and 18,804~19,358 genes from each sample. All reads can be mapped to the cucumber genome (Version 2). By RPKM comparing, we got 38 comparing combinations with differentially expressed genes (DEGs), obtained 38 significantly expressed combinations by FDR≤0.001 and the absolute value of log2Ratio≥1 as the thresholds. These results suggest that there are many differences and genes expression mode among effects of grafting or added silicon. This study addresses a preliminary analysis and offers a foundation for future genomic research in the bloom formation of cucumber. Overall design: Own-rooted cucumber,self-grafted cucumber and cucumber grafted onto two pumpkin rootstock lines, cultivated by deionized water nutrient solution with 1.7mM silicon added or not; RNA-Seq on cucumbers pericarp, analyse the data, and get differencially expressed genes

黄瓜（Cucumis sativus L.）是全球广泛栽培的重要经济蔬菜。嫁接可培育出无蜡粉或蜡粉稀疏的黄瓜品种，这类产品正受到越来越多消费者的青睐。蜡粉颗粒为细小的腺毛，质地坚硬，目前对其形成机制及相关基因的研究尚少。多功能RNA测序（RNA-seq）是近年依托高通量测序发展而来的转录组分析方法，现已被广泛应用于多种生物的研究，为我们解析黄瓜蜡粉形成机制及相关基因提供了可靠的技术手段。本研究以黄瓜自交系'山农5号'及两份南瓜砧木材料为试材，构建了4组试验黄瓜材料，采用去离子水配制的'山崎黄瓜营养液配方'进行植株栽培，并在采集果皮样本前2小时，对部分植株施加1.7mM硅酸钾处理，每组处理均设置2次生物学重复。本研究从黄瓜自交系（自根黄瓜）、自嫁接黄瓜（C/C）、强蜡粉型嫁接黄瓜（M/C，即黄瓜嫁接至'3225'砧木）、弱蜡粉型嫁接黄瓜（L/C，即黄瓜嫁接至'3212'砧木）的果皮组织中构建了16个cDNA文库。每个样本共获得17,215,769~17,529,047条高质量测序读段，检测到18,804~19,358个表达基因。所有读段均可比对至黄瓜参考基因组（版本2）。以每百万reads中基因长度每千碱基的reads数（Reads Per Kilobase per Million mapped reads, RPKM）进行标准化分析，以错误发现率（False Discovery Rate, FDR）≤0.001且log₂Ratio绝对值≥1作为筛选阈值，共得到38个包含差异表达基因（Differentially Expressed Genes, DEGs）的比较组合，最终筛选出38个显著差异表达的基因组合。研究结果表明，嫁接处理与硅元素施加对黄瓜基因表达模式均存在显著影响，相关差异基因数量较多。本研究为黄瓜蜡粉形成的相关基因组学研究提供了初步分析基础与研究思路。整体试验设计：设置自根黄瓜、自嫁接黄瓜及嫁接至两份南瓜砧木的黄瓜材料，采用去离子水配制的营养液进行栽培，分别施加1.7mM硅酸钾或不施加处理；对黄瓜果皮组织进行RNA测序，通过数据分析筛选差异表达基因。