葡萄cDNA文库构建及鲜食与酿酒葡萄果实发育相关基因的表达分析
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摘要
葡萄是世界性的重要果树,也是我国的重要果树树种之一,它在我国果树产业中占据重要地位,其栽培面积和产量位于世界水果的前列,特别是鲜食葡萄已连续多年稳居世界首位,但葡萄新基因的发掘和果实发育相关基因研究方面进展较慢。本研究在构建葡萄花和果实EST文库的基础上,进一步进行了EST-SSR标记的开发,同时还利用基因芯片技术对鲜食和酿酒葡萄果实发育相关基因的表达情况进行了初步分析。主要结果如下：
1.构建葡萄花、果cDNA文库是开展葡萄花及果实发育的分子机理研究的重要工作基础,有助于重要相关基因的克隆、功能分析、调控及其利用。本研究以生产上广泛栽培、性状优良且极具代表性的‘夏黑’葡萄为试材,应用优化的Creator SMART cDNA Construction Kit技术,构建了‘夏黑’葡萄花和果实的cDNA文库。文库的滴度为1.2x106pfu/mL,库容为6.0×106pfu。从文库中随机挑取30个克隆进行菌落PCR鉴定的结果显示：插入片段大小为1.0-3.0kb,重组率为99%。研究结果表明,该葡萄cDNA文库具备较高的质量。
2.本研究通过‘夏黑’花和果实cDNA文库的构建,获得了7,561个阳性克隆,有6,320个携带cDNA片段,进一步经序列拼接共获得3,582个unigenesi(登录号：GW836604-GW840185)。BLASTx比对结果表明,在所获得的3,582unigenes中,有913个为已知功能基因,主要涉及原料的运输与代谢、翻译与修饰、功能预测、能量代谢等；12个为功能未知基因；381个为新基因。基因定位结果表明,在所获得的381个新的EST序列中,有289个能够匹配到葡萄基因组的19条染色体上。
3.本研究利用MISA软件对来自所构建文库的3,582个unigenes进行SSR位点的搜索,结果在459条序列中共发掘出SSR位点540个,候选SSR位点出现的频率为15.08%。二核苷酸、三核苷酸、四核苷酸、五核苷酸以及六核苷酸重复单元的SSR数目分别为135(3.77%)、270(7.54%)、59(1.65%)、29(0.81%)和47(1.31%)。利用Primer3.0Plus软件随机设计了47对引物用于PCR扩增,用6%的非变性聚丙烯酰胺凝胶分析这些SSR引物的PCR扩增产物多态性。47对引物中有20对引物能在20个葡萄品种中扩增出理想的PCR产物,占总引物的42.55%。其中,18对引物扩增条带具有多态性。
4.为获取鲜食和酿酒葡萄果实发育过程中与品质形成有关基因的差异表达情况,本研究制备了一个含有15,403条EST序列的基因芯片对其进行分析。结果表明在果实的整个生长发育阶段,鲜食和酿酒葡萄之间共有2,493个差异表达基因,其中在鲜食葡萄中上调表达基因1,244个,下调表达基因1,249个。利用荧光定量PCR技术对随机选择的19个基因的表选情况进行验证分析,其中有18个基因的表达水平与芯片检测结果相一致。BLAST2G0分析结果显示：共有172个差异表达基因(52个上调,120个下调)具有功能注释,分属于生物过程、分子功能和细胞成分三类不同水平。差异表达基因主要参与代谢、细胞生理、应激反应等生物过程,与结合、催化活性等分子功能有关,作用空间分布在细胞或细胞器中。KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway分析结果显示鲜食与酿酒葡萄差异表达基因主要参与碳水化合物代谢、次生代谢、脂代谢、能量代谢等多个代谢途径。
Grape is an important fruit tree in the word and is also one of the most important fruit crop in China. The planting area and output of the grape in China list top position in the world, especially for the table grape, the cultivate area and yield have been in the first place in the world for many years. But the discovery of novel genes and the study of genes related to the fruit quality of grapevine just start the first step. In this research, EST-SSR markers were developed and microarray was also used to analysis the different expression of genes related to the development of table and wine grape on the basis of a constructed cDNA library from flower and fruit of grapevine. The main results are as follows:
1. Construction of the cDNA library of grape flower and berry is the importantly fundamental work for the study on the molecular mechanism of the development of grape flower and berry, in which it can facilitate the cloning, characterization and utilization of the important genes involved. In this research, a cDNA library of flower and berry of grapevine'Summer Black', a well known grape cultivar in its high popularity in cultivation and great berry quality, was constructed with Creator SMART cDNA Construction Kit. This library has a titer of1.2×106pfu/mL, and a capacity of6.0x106pfu. The recombination efficiency was about99%, and the insert sizes were about1.0-3.0kb based on PCR analysis of30randomly chosen clones, suggesting that the cDNA library of grape flower and fruit has been successfully constructed for the use in further study.
2. A total of6,230EST sequences were produced from7,561clones in a cDNA library generated from grapevine'Summer Black'(Vitis vinifera x V. labrusca.) flower and fruit tissues in this study. After cluster and assembly analysis of the datasets,3,582unigenes (GenBank accession numbers GW836604to GW840185) were established. The BLASTx result showed that all of the3,582unigenes including913unigenes with known function, mainly involved to material transport and metabolism, translation and modification category, general function prediction, energy production and conversion and so on,12unigenes with unknown function, and381new genes. The mapping result showed that289 new grapevine EST sequences could be mapped on the19grapevine chromosomes.
3. A total of3,582grapevine EST sequences that were from the cDNA library were screened by the use of MISA software to search for SSR motifs and540SSR loci were identified from the459grape EST sequences. The frequency of EST-SSRs identified was15.08%. All the540SSR loci included135(3.77%) dinucleotides,270(7.54%) trinucleotides,59(1.65%) tetranucleotides,29(0.81%) pentanucleotides, and47(1.31%) hexanucleotides. Fourty-seven pairs of primers were designed against the some EST sequences by the software Primer3.0Plus, and the PCR products of these primers were detected by PAGE. Among the47pairs of EST-SSR primers,20pairs could amplify distinct PCR bands that were the anticipated products. Eighteen pairs of the EST-SSR primers could amplify polymorphic bands.
4. A microarray system comprising15,403ESTs was used to obtain an overall view on the different expression profiles of quality formation-related genes involved in fruit development of table and wine grapes. The result showed that2,493genes exhibited at least2.0-fold differences in expression levels, with1,244genes being up-regulated and1,249being down-regulated during the entire fruit development stage. The expression patterns from the microarray analysis were validated with quantitative real-time polymerase chain reaction analysis of19selected genes of interest, and only18genes show patterns similar to the changes measured by microarray analysis. Following BLAST2GO analysis, only172differentially expressed genes (including52up-regulated and120down-regulated) got GO annotation, which belong to the different leves of molecular function, cellular component and biology process. According to annotation, the differently expressed genes were mainly involved in the metabolism process of metabolic, cellular and so on, related to binding, catalytic activity and so on, distributed in the whole cell or organelle. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the differently expressed genes between table and wine grape were involved in several pathways primarily focused on Carbohydrates metabolism, Biosynthesis of secondary metabolism, Lipid metabolism and Energy metabolism.
1.构建葡萄花、果cDNA文库是开展葡萄花及果实发育的分子机理研究的重要工作基础,有助于重要相关基因的克隆、功能分析、调控及其利用。本研究以生产上广泛栽培、性状优良且极具代表性的‘夏黑’葡萄为试材,应用优化的Creator SMART cDNA Construction Kit技术,构建了‘夏黑’葡萄花和果实的cDNA文库。文库的滴度为1.2x106pfu/mL,库容为6.0×106pfu。从文库中随机挑取30个克隆进行菌落PCR鉴定的结果显示：插入片段大小为1.0-3.0kb,重组率为99%。研究结果表明,该葡萄cDNA文库具备较高的质量。
2.本研究通过‘夏黑’花和果实cDNA文库的构建,获得了7,561个阳性克隆,有6,320个携带cDNA片段,进一步经序列拼接共获得3,582个unigenesi(登录号：GW836604-GW840185)。BLASTx比对结果表明,在所获得的3,582unigenes中,有913个为已知功能基因,主要涉及原料的运输与代谢、翻译与修饰、功能预测、能量代谢等；12个为功能未知基因；381个为新基因。基因定位结果表明,在所获得的381个新的EST序列中,有289个能够匹配到葡萄基因组的19条染色体上。
3.本研究利用MISA软件对来自所构建文库的3,582个unigenes进行SSR位点的搜索,结果在459条序列中共发掘出SSR位点540个,候选SSR位点出现的频率为15.08%。二核苷酸、三核苷酸、四核苷酸、五核苷酸以及六核苷酸重复单元的SSR数目分别为135(3.77%)、270(7.54%)、59(1.65%)、29(0.81%)和47(1.31%)。利用Primer3.0Plus软件随机设计了47对引物用于PCR扩增,用6%的非变性聚丙烯酰胺凝胶分析这些SSR引物的PCR扩增产物多态性。47对引物中有20对引物能在20个葡萄品种中扩增出理想的PCR产物,占总引物的42.55%。其中,18对引物扩增条带具有多态性。
4.为获取鲜食和酿酒葡萄果实发育过程中与品质形成有关基因的差异表达情况,本研究制备了一个含有15,403条EST序列的基因芯片对其进行分析。结果表明在果实的整个生长发育阶段,鲜食和酿酒葡萄之间共有2,493个差异表达基因,其中在鲜食葡萄中上调表达基因1,244个,下调表达基因1,249个。利用荧光定量PCR技术对随机选择的19个基因的表选情况进行验证分析,其中有18个基因的表达水平与芯片检测结果相一致。BLAST2G0分析结果显示：共有172个差异表达基因(52个上调,120个下调)具有功能注释,分属于生物过程、分子功能和细胞成分三类不同水平。差异表达基因主要参与代谢、细胞生理、应激反应等生物过程,与结合、催化活性等分子功能有关,作用空间分布在细胞或细胞器中。KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway分析结果显示鲜食与酿酒葡萄差异表达基因主要参与碳水化合物代谢、次生代谢、脂代谢、能量代谢等多个代谢途径。
Grape is an important fruit tree in the word and is also one of the most important fruit crop in China. The planting area and output of the grape in China list top position in the world, especially for the table grape, the cultivate area and yield have been in the first place in the world for many years. But the discovery of novel genes and the study of genes related to the fruit quality of grapevine just start the first step. In this research, EST-SSR markers were developed and microarray was also used to analysis the different expression of genes related to the development of table and wine grape on the basis of a constructed cDNA library from flower and fruit of grapevine. The main results are as follows:
1. Construction of the cDNA library of grape flower and berry is the importantly fundamental work for the study on the molecular mechanism of the development of grape flower and berry, in which it can facilitate the cloning, characterization and utilization of the important genes involved. In this research, a cDNA library of flower and berry of grapevine'Summer Black', a well known grape cultivar in its high popularity in cultivation and great berry quality, was constructed with Creator SMART cDNA Construction Kit. This library has a titer of1.2×106pfu/mL, and a capacity of6.0x106pfu. The recombination efficiency was about99%, and the insert sizes were about1.0-3.0kb based on PCR analysis of30randomly chosen clones, suggesting that the cDNA library of grape flower and fruit has been successfully constructed for the use in further study.
2. A total of6,230EST sequences were produced from7,561clones in a cDNA library generated from grapevine'Summer Black'(Vitis vinifera x V. labrusca.) flower and fruit tissues in this study. After cluster and assembly analysis of the datasets,3,582unigenes (GenBank accession numbers GW836604to GW840185) were established. The BLASTx result showed that all of the3,582unigenes including913unigenes with known function, mainly involved to material transport and metabolism, translation and modification category, general function prediction, energy production and conversion and so on,12unigenes with unknown function, and381new genes. The mapping result showed that289 new grapevine EST sequences could be mapped on the19grapevine chromosomes.
3. A total of3,582grapevine EST sequences that were from the cDNA library were screened by the use of MISA software to search for SSR motifs and540SSR loci were identified from the459grape EST sequences. The frequency of EST-SSRs identified was15.08%. All the540SSR loci included135(3.77%) dinucleotides,270(7.54%) trinucleotides,59(1.65%) tetranucleotides,29(0.81%) pentanucleotides, and47(1.31%) hexanucleotides. Fourty-seven pairs of primers were designed against the some EST sequences by the software Primer3.0Plus, and the PCR products of these primers were detected by PAGE. Among the47pairs of EST-SSR primers,20pairs could amplify distinct PCR bands that were the anticipated products. Eighteen pairs of the EST-SSR primers could amplify polymorphic bands.
4. A microarray system comprising15,403ESTs was used to obtain an overall view on the different expression profiles of quality formation-related genes involved in fruit development of table and wine grapes. The result showed that2,493genes exhibited at least2.0-fold differences in expression levels, with1,244genes being up-regulated and1,249being down-regulated during the entire fruit development stage. The expression patterns from the microarray analysis were validated with quantitative real-time polymerase chain reaction analysis of19selected genes of interest, and only18genes show patterns similar to the changes measured by microarray analysis. Following BLAST2GO analysis, only172differentially expressed genes (including52up-regulated and120down-regulated) got GO annotation, which belong to the different leves of molecular function, cellular component and biology process. According to annotation, the differently expressed genes were mainly involved in the metabolism process of metabolic, cellular and so on, related to binding, catalytic activity and so on, distributed in the whole cell or organelle. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the differently expressed genes between table and wine grape were involved in several pathways primarily focused on Carbohydrates metabolism, Biosynthesis of secondary metabolism, Lipid metabolism and Energy metabolism.
引文
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