摘要
萝卜(Raphanus sativus L.)是十字花科萝卜属一、二年生根菜类蔬菜作物,在我国的种植面积位居前列,是出口创汇的主要蔬菜品种。萝卜的主要产品器官是肉质根,其发育的好坏直接关系到萝卜的品质和产量。肉质根的形成膨大是个复杂的形态建成过程,但目前对其形成的研究多是集中于解剖结构、形态学描述和生理生化机制方面,而对萝卜肉质根形成的分子生物学基础研究还较少。本研究利用双向电泳技术、mRNA差异显示技术和构建cDNA文库技术分析肉质根不同发育时期蛋白质组变化、差异表达基因的表达情况以及分析肉质根不同发育时期的表达谱,研究结果将有助于从不同水平上分析萝卜肉质根形成的分子生物学特征,为萝卜品质与产量的遗传改良提供一定的理论依据。主要研究结果如下：
1.以'NAU-ZQH'为材料,采用改良的三氯乙酸-丙酮-酚提取法分别提取破肚期、叶片生长盛期、膨大期萝卜肉质根总蛋白,进行双向电泳并用软件PDQuest8.0对电泳图谱进行分析。结果表明,在肉质根发育不同时期有25个蛋白点表现出明显差异,其中6个蛋白质点从破肚期开始表现为下调、13个蛋白质点表现为上调、3个蛋白质点仅在肉质根膨大盛期才出现、3个蛋白质点先下调后上调。对其中18个有代表性的、可靠的差异蛋白点进行MALDI-TOF/TOF质谱分析,成功鉴定出17个差异蛋白。生物信息学分析表明,它们参与到糖和能量代谢、蛋白质合成和代谢以及稳定、信号转导、抗性与调控相关等生命过程。利用RT-PCR技术对相应差异蛋白基因的表达情况进行了分析,结果显示有11个差异蛋白的变化趋势与其对应的基因转录水平变化相一致,有4个表现为不一致。
2.利用]nRNA差异显示技术分析肉质根不同发育时期的差异基因表达情况,用3条锚定引物与78条随机引物共234个组合进行扩增。经过二次扩增验证,成功分离到50条cDNA差异片段。将差异片段回收测序,结果显示,这些差异片段分别参与了转录调控、信号转导、普通新陈代谢、转运通道、防卫与胁迫反应、蛋白质代谢等功能,如NADH脱氢酶亚基、TIFY、翻译调控蛋白、钙依赖蛋白激酶29、18S核糖体RNA、水通道蛋白等,表明萝卜肉质根的发育是一个复杂的过程,涉及到多种代谢途径与抗逆反应的协同调控。
3.以不同发育阶段的肉质根为材料,成功构建了萝卜肉质根全长cDNA文库。对该cDNA文库测序获得8,807条高质量的EST序列,拼接后产生5088个unigenes(包括1,510个contig和3,578个sigleton),长度在100－1,592bp之间,平均长度为545bp。基于相似性比对,分别有4,684(92.1%)、4,512(88.7%)和3,168(62.3%)个unigene与Nt、Nr、SWISSPORT数据库的序列有相似性。进一步按照COG(Cluster of Orthologous Groups of proteins)功能分类,有1,475个unigene被分为24类,其中所占比例最大的是预测仅有全局功能(268,20.3%),其次是翻译后修饰、蛋白质折叠及伴侣蛋白分子(162,12.27%),其他的参与能量、氨基酸、核苷酸等的运输和代谢,以及防御机制、细胞结构与运动等功能。KEGG (Kyoto Encyclopedia of Genes and Genomes)注释结果表明,有4,490个unigene被归为145条KEGG pathway,其中与代谢途径相关的unigenes序列最多,包括碳水化合物代谢、氨基酸代谢以及次级代谢物的生物合成等。
4.通过Solexa高通量测序的方法分析肉质根不同发育时期的表达谱,构建了两个Solexa文库。测序结果产生了大量标签,在两个文库中分别产生了254,922个和145,414个清晰标签。通过与已知数据库进行比对,分别有53,941个和35,435个清晰标签能够匹配到参考基因上,所占的比例分别为21.16%和24.37%。按照筛选差异基因的标准,找到了166个上调基因和292个下调的基因。COG功能分类分析表明,这些差异基因共分为17个类别,主要是参与代谢(35.6%)、细胞过程和信号(28.0%)。KEGG pathway分析显示,其参与了63个pathway。随机筛选20个差异基因采用RT-PCR方法验证,证明试验结果与测序结果基本一致,证实了本试验测序数据的可靠性。
5.基于构建的cDNA文库,在5,088条unigene上检测到了179个SSR,分布于176条unigene上。萝卜EST-SSR的重复类型比较丰富,从二核苷酸到六核苷酸都存在,其中二核苷酸所占全部SSR比例最大(50.8%),其次是三核苷酸(29.6%)其他类型所占比例较小。在萝卜的EST-SSR中,共观察到55种重复基元类型,其中在二核苷酸重复基元中,GA/TC (50.55%)和AG/CT (45.55%)是最主要的类型；在三核苷酸重复基元中,GAA/TTC位居首位,占24.53%,其次是TCA/TGA (9.43%), AAG/CTT (9.43%)和ACA/TGT (9.43%)。基于检测到的EST-SSR,共设计了125对引物,并有110对得到扩增产物。筛选其中28对引物对32个萝卜品种进行遗传多样性分析,结果显示等位基因数从2到7不等,平均为3.5；PIC(polymorphism information content)值平均为0.5。32个萝卜品种在遗传相似系数0.62处分为三大组,主要与萝卜品种皮色及根形等性状相关联。利用这28对引物在十字花科3个属的12个作物上进行SSR通用性的验证,结果显示有18对引物可以在这12个作物上得到扩增产物,通用性达到64.2%。测序结果表明,等位基因的多样性主要表现在重复基元数目上的差异。结果表明新开发的EST-SSR标记可以作为萝卜种质鉴定和遗传改良的一种有力的工具。
6.根据文库中鉴定到的蔗糖磷酸合成酶基因(SPS)片段,利用同源克隆技术分离到该基因的全长,命名为RsSPS1.其编码区基因组序列长度为4,945bp,包括13个外显子和12个内含子；cDNA长度为3,261bp,‘开放阅读框(ORF)为3,135bp,推导编码1,044个氨基酸,含有GT1-Sucrose-synthase功能域。ORF序列与拟南芥ATSPS1(GenBank accession No.AY039911)同源性达到91%。系统发育树分析显示,RsSPSl与拟南芥ATSPS1聚为一组,亲缘关系很近。半定量RT-PCR与实时定量RT-PCR分析表明,该基因在肉质根发育的不同时期不同部位中都有表达,但表达量有明显差异,在膨大后期木质部中表达量明显高于其他时期和部位。
Radish (Raphanus sativus L.) belongs to the Brassicaceae family and is an important worldwide vegetable crop with high nutrition and medical value. Fleshy tap root is the main edible part and its development is much related to the yield and quality in radish. The development of taproot is a complex morphogenetic process. The research of fleshy taproot development experiences a long period of morphological, physiological and biochemical description. However, the scarcity of knowledge on root development molecular mechanism contributes to difficulties in breeding, production, and storage. In the present study, the changes on proteome and the difference of gene expression during the taproot development of radish were analyzed by two-dimensional electrophoresis, differential display reverse transcription and cDNA library construction. The results would provide theoretical basis for studying the molecular characterization of taproot development and improving important horticultural traits in radish breeding program. Main research results were as follows.
1. A proteomic approach was employed to study the mechanism of radish taproot development with the high advanced inbred line'NAU-ZQH'as material. Proteins were extracted from roots by using modified TCA-acetone-phenol extraction method and profiled by two-dimensional gel electrophoresis. The differentially expressed proteins were determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). A total of25protein spots displayed significant difference and17were successfully identified as either up-regulation (11spots) or down-regulation (6spots) in intensity relative to the development stages, of which,15had known functions. The identified proteins had functions related to sucrose and energy metabolism, protein metabolism and stability, resistance related proteins, signal transduction and regulation proteins. RT-PCR approach based on peptide sequences was used to compare transcript and protein accumulation patterns for17differential proteins. Of these proteins,11patterns of induced transcript accumulation were consistent with those of induced protein accumulation.
2. Differential-display reverse transcription-PCR (DDRT-PCR) was used to investigate the difference of gene expression during the taproot development of radish. A total of50differential fragments had been obtained in total of234selective amplifications.43fragments showed high sequence similarity to the genes of known or putative function, which were involved in transcriptional regulation, signal transduction, metabolism, transport channel and stress responding as well as protein metabolism such as NADH dehydrogenase, TIFY, translationally-controlled tumor protein, calcium-dependent protein kinase29,18S ribosomal RNA, aquaporin TIP2. The results indicated that the development of taproot was a complex process involving several pathways and stress responding.
3. In this study, a full-length cDNA library from the taproot tissue was constructed and characterized. A total of10,052ESTs were generated from cDNA libraries of radish, of which were8,807high quality ESTs with an average length of515bp. Cluster analysis revealed the presence of1,510contigs and3,578singletons, representing5,088unigenes. Based on the sequence similarity search,4,684(92.1%),4,512(88.7%) and3,168(62.3%) of the unigenes showed homology with sequences in the Nr, Nt and SwissProt databases, respectively. According to molecular function of COG (Cluster of Orthologous Groups of proteins) classification,1,475unigenes were assigned and sorted into24groups. Based on the known or predicted annotation, the unigenes involved in general function prediction only ranked the first, followed by those in posttranslational modification, protein turnover, chaperones. A total of4,490unigenes were assigned to specific Kyoto Encyclopedia of Genes and Genomes pathways. The enzymes in the metabolism group were most represented and dominated by'carbohydrate'followed by'energy'metabolism.
4. To investigate the profile of gene expression in radish taproot of different development stages, solexa sequencing was used to produce genome-wide gene expression profiling. The sequencing results showed that a large number of tags were generated from the taproot of two different stages, including254,922and145,414clean tags with more than one copy in the two libraries, respectively. Of these,53,941(21.16%) and35,435(24.37%) tags were matched to the reference genes. The tags with log2ratio>2or<-2(P<0.001) and FDR<0.01were characterized as the most differentially expressed genes and further analyzed, representing166up-regulated and292down-regulated genes, which were classified into17functional categories based on COG functional category. Moreover, the differentially expressed genes were queried against the KEGG pathway database and mapped to63KEGG pathways. Furthermore, the expression patterns of20genes selected were assessed by semi-quantitative RT-PCR, and the results showed general agreement with the Solexa data, which basically confirmed the reliability of our transcriptome analysis.
5. To develop novel expressed sequence tags-simple sequence repeats (EST-SSR) markers in radish, a set of179SSRs, distributing in176unigene sequences, were detected by the software SSR Locator Ⅰ v.1, of which,50.84%were di-nucleotide, followed by tri-(29.61%), hexa-(9.49%), penta-(6.15%) and tetra-nucleotide (3.91%), respectively. GA/TC (25.69%) was the most frequent repeat type of all repeat types. Out of125primer pairs designed,110(88%) could generate unambiguous amplification products. Totally28EST-SSR primer pairs were selected for genetic diversity analysis in32radish genotypes. It was found that two to seven alleles could be detected with a mean of3.5and the polymorphism information content (PIC) values of these primers ranged from0.000to0.825with the average of0.500. The32accessions were generally divided into three main clusters at a similarity index value of0.60, which was mainly in accordance with the different biological characterizations of the accessions. In addition, the28EST-SSR primer pairs were further used to test the transferability on12accessions from three genera of Raphanus, Brassica and Arabidopsis in Brassicaceae. The results showed that18primer pairs (64.2%) could produce target PCR bands in the12accessions. The EST-SSR markers developed herein represented a valuable resource for the genetic diversity analysis, genetic mapping and marker-assisted selection in radish.
6. An EST homolog to sucrose phosphate synthase (SPS) was found from the cDNA library, and the full length sequence of RsSPS1was obtained by homology cloning. The genome sequence was4,945bp including13extrons and12introns. The cDNA consisted of an open reading frame (ORF) of3,141bp and the predicted protein of1,044amino acids. The sequence of coding region showed the high homology of91%with SPS gene reported on Arabidopsis (GenBank accession No.AY039911). Phylogenetic tree analysis indicated that RsSPS1had a very close relationship with AtSPSl of Arabidopsis. Semi-quantitative reverse transcriptional-polymerase chain reaction and Real-time quantitative RT-PCR were performed to analyze the temporal and spatial expression pattern of RsSPS1. It was found that RsSPS1expressed in leaves, phloem and xylem of taproot with significantly different transcript level over the whole development stages.
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