Qi Xiaoxiao, Wu Jun, Wang Lifen, Li Leiting, Cao Yufen, Tian Luming, Dong Xingguang, Zhang Shaoling
College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
BMC Genomics. 2013 Oct 23;14(1):727. doi: 10.1186/1471-2164-14-727.
'Kuerlexiangli' (Pyrus sinkiangensis Yu), a native pear of Xinjiang, China, is an important agricultural fruit and primary export to the international market. However, fruit with persistent calyxes affect fruit shape and quality. Although several studies have looked into the physiological aspects of the calyx abscission process, the underlying molecular mechanisms remain unknown. In order to better understand the molecular basis of the process of calyx abscission, materials at three critical stages of regulation, with 6000 × Flusilazole plus 300 × PBO treatment (calyx abscising treatment) and 50 mg.L-1GA3 treatment (calyx persisting treatment), were collected and cDNA fragments were sequenced using digital transcript abundance measurements to identify candidate genes.
Digital transcript abundance measurements was performed using high-throughput Illumina GAII sequencing on seven samples that were collected at three important stages of the calyx abscission process with chemical agent treatments promoting calyx abscission and persistence. Altogether more than 251,123,845 high quality reads were obtained with approximately 8.0 M raw data for each library. The values of 69.85%-71.90% of clean data in the digital transcript abundance measurements could be mapped to the pear genome database. There were 12,054 differentially expressed genes having Gene Ontology (GO) terms and associating with 251 Kyoto Encyclopedia of Genes and Genomes (KEGG) defined pathways. The differentially expressed genes correlated with calyx abscission were mainly involved in photosynthesis, plant hormone signal transduction, cell wall modification, transcriptional regulation, and carbohydrate metabolism. Furthermore, candidate calyx abscission-specific genes, e.g. Inflorescence deficient in abscission gene, were identified. Quantitative real-time PCR was used to confirm the digital transcript abundance measurements results.
We identified candidate genes that showed highly dynamic changes in expression during the calyx abscission process. These genes are potential targets for future functional characterization and should be valuable for exploration of the mechanisms of calyx abscission, and eventually for developing methods based on small molecule application to induce calyx abscission in fruit production.
“库尔勒香梨”（新疆梨，学名Pyrus sinkiangensis Yu）是中国新疆本土的一种梨，是重要的农产品且主要出口到国际市场。然而，宿萼果会影响果实形状和品质。尽管已有多项研究探究了萼片脱落过程的生理方面，但潜在的分子机制仍不清楚。为了更好地理解萼片脱落过程的分子基础，我们收集了处于调控关键的三个阶段的材料，分别进行了6000倍氟硅唑加300倍PBO处理（促萼片脱落处理）和50 mg.L-1赤霉素处理（宿萼处理），并通过数字转录本丰度测量对cDNA片段进行测序以鉴定候选基因。
使用高通量Illumina GAII测序对在萼片脱落过程的三个重要阶段收集的七个样本进行数字转录本丰度测量，这些样本经过化学试剂处理以促进萼片脱落和宿存。每个文库共获得超过251,123,845条高质量读数，每个文库约有8.0 M原始数据。数字转录本丰度测量中69.85% - 71.90%的清洁数据值可映射到梨基因组数据库。有12,054个差异表达基因具有基因本体（GO）术语并与251条京都基因与基因组百科全书（KEGG）定义的途径相关。与萼片脱落相关的差异表达基因主要参与光合作用、植物激素信号转导、细胞壁修饰、转录调控和碳水化合物代谢。此外，还鉴定出了候选的萼片脱落特异性基因，如脱落缺陷花序基因。使用定量实时PCR对数字转录本丰度测量结果进行了验证。
我们鉴定出了在萼片脱落过程中表达呈现高度动态变化的候选基因。这些基因是未来功能表征的潜在靶点，对于探索萼片脱落机制具有重要价值，最终对于开发基于小分子应用的水果生产中诱导萼片脱落的方法也具有重要意义。
