<p> 番茄(Solanum lycopersicum)是世界种植最为广泛的蔬菜作物之一。番茄生产过程中容易遭受各种生物和非生物胁迫，对其产量和产品质量都造成了严重影响。栽培番茄是一种喜温作物，低于13℃的温度下生长发育缓慢、叶片萎蔫，还可能造成落花落果，果实畸形等。因此，低温是影响番茄分布、生长发育和生产力的主要非生物因素之一。此外，番茄生产还经常受到灰霉病菌(Botrytis cinerea)等生物因子的侵染。因此，挖掘与番茄耐低温性和抗灰霉病相关基因，解析基因的作用机制具有重要的研究意义。本研究以野生潘那利番茄渐渗系IL6-2为材料，采用图位克隆的方法对其在低温下表现出植株矮化、叶片坏死性状的调控基因进行定位，并进行候选基因的功能验证。现将主要研究结果总结如下：<br /> 1. 对50份番茄渐渗系（背景材料为M82）的表型进行观察，发现IL6-2在低温下表现为植株矮化，萎缩，叶片甚至出现坏死斑，而其他渐渗系中并没有出现该表型。生理指标测定结果显示，12℃低温下IL6-2叶片相对电导率、丙二醛含量、过氧化氢积累均极显著高于M82，而脯氨酸含量极显著低于M82，说明IL6-2对低温更敏感。<br /> 2. 对IL6-2和M82的幼苗低温处理0 h、24 h、48 h后，进行RNA-seq 转录组分析，共鉴定到3,459个基因在M82和IL6-2之间显著差异表达，低温处理0 h、24 h、48 h分别有1,439、2,170和888个差异表达基因（DEGs），对DEGs进行功能聚类分析，发现IL6-2与M82之间的差异表达基因显著富集在跨膜受体蛋白激酶活性、跨膜受体活性、转移酶活性、蛋白激酶活性等分子功能类，主要涉及次生代谢产物生物合成、植物激素信号转导和植物病原菌互作途径。<br /> 3. 为了对IL6-2低温下矮化坏死性状的调控基因进行定位，将IL6-2与M82杂交，构建F2代遗传分离群体，通过性状遗传规律分析，得出IL6-2低温下矮化坏死属于单基因隐性性状。利用遗传分离群体，开发InDel分子标记进行基因分型，连锁分析结果将候选区段粗定位至6号染色体37.95 Mb~39.14 Mb之间约640 kb范围。进一步扩大遗传分离群体，开发新的InDel分子标记进行精细定位，最终将候选区段缩小至38.68 Mb~38.76 Mb之间约77.4 kb的范围内。<br /> 4. 根据番茄参考基因组数据库，预测候选区段内有7个ORFs，根据基因注释信息，分别为蛋白质精氨酸甲基转移酶（ORF1）、3个类受体蛋白激酶（ORF2、ORF3、ORF4）、糖基转移酶（ORF5）、过氧化物酶起源因子（ORF6）和锌指蛋白（ORF7）。7个ORFs在IL6-2和M82之间的gDNA序列在启动子、外显子、内含子区域都存在核苷酸的差异。RNA-seq分析IL6-2和M82之间差异基因的差异表达倍数，结合qRT-PCR对7个ORFs表达量分析结果，表明ORF2（Solyc06g060680.1.1）和ORF3(Solyc06g060690.2.1)在IL6-2中表达量极低，而ORF5（Solyc06g060710.2.1）在IL6-2中表达量显著上调，这3个基因在M82和IL6-2之间的相对表达量呈现极显著差异，因此将这3个基因作为调控潘那利渐渗系IL6-2低温下矮化坏死表型的重要候选基因。<br /> 5. 对3个候选基因分别构建超量表达载体和RNA干涉表达载体，并进行番茄的遗传转化，获得转基因植株。对转基因材料进行阳性检测和候选基因表达量分析，选择阳性且基因表达量显著上调的超量转基因株系、基因表达量显著下调的干涉转基因株系进行表型鉴定，结果表明超量表达ORF3(Solyc06g060690.2.1)基因，使IL6-2低温下矮化坏死的表型得到了恢复，表型接近于M82，12℃低温下3个超量转基因株系的株高极显著高于IL6-2，相对电导率、丙二醛含量极显著低于IL6-2，而脯氨酸含量极显著高于IL6-2。ORF2（Solyc06g060680.1.1）、ORF5（Solyc06g060710.2.1）转基因株系12℃低温下的表型与非转基因材料之间没有显著差异。因此，候选基因功能鉴定结果表明，ORF3 (Solyc06g060690.2.1) 即为正确的目的基因NDW，在番茄生长和耐低温性方面发挥重要作用。<br /> 6. 对NDW转基因株系接种灰霉菌的抗性进行鉴定，通过对离体叶片接种灰霉菌3d后病斑面积的测量及灰霉菌生长量的测定，结果表明与IL6-2相比，超表达NDW基因降低了植株对灰霉菌的敏感性，而在M82中抑制NDW基因的表达则提高了对灰霉菌的敏感性，说明NDW基因在调控番茄对灰霉菌的敏感性方面发挥一定作用。<br /> 7. 基因序列分析显示，NDW基因组全长序列为1122 bp，包含有两个外显子和一个内含子，编码一个342个氨基酸的蛋白质，在SGN数据库中的注释信息是一个类受体蛋白激酶（Receptor-like protein kinase），其氨基酸序列包含一个PKC-like保守结构域。番茄NDW氨基酸序列与茄属其它作物具有高度的同源性，与马铃薯、辣椒、烟草中同源蛋白存在多处的保守结构域。系统进化树分析结果表明，NDW与茄属的马铃薯(Solanum tuberosum)亲缘关系最近，同源性约为79.12%，与茄属以外作物同源性较低。<br /> 8. 对NDW基因的表达模式进行分析，明确了NDW基因呈组成型表达，在番茄的根、茎、叶片、花蕾、花和果实中均有表达，其中在根和茎中的表达量较高。亚细胞定位结果显示NDW蛋白定位于细胞的质膜，同时在细胞质中也有少量表达，说明其发挥着类受体蛋白激酶的功能，负责对胞外信号进行感知并向胞内进行传导。<br /> 9. 分析NDW转基因株系和M82、IL6-2中涉及ABA合成代谢、分解及信号转导通路相关基因的表达水平，结果表明NDW基因上调了部分ABA受体基因、信号转导正向调控基因、合成相关基因的表达水平，下调了部分ABA信号转导负向调控基因，分解相关基因的表达水平，说明NDW基因与ABA的积累有关，可能通过依赖ABA途径调控植物的生长发育及逆境胁迫应答。</p>

<p> Tomato (Solanum lycopersicum) is one of the extensively grown vegetable crops around the world. However, tomato is subject to various biotic and abiotic stresses, thereby limiting its productivity and quality. As a thermophilic plant, cultivated tomato suffers damage resulting in slow growth, leaf wilting, even flowers and fruits falling, and fruit deformity, when exposed to temperatures below 13 &deg;C. Thus, low temperature is one of the main limiting abiotic factors affecting tomato distribution, growth, development, and production. In addition, tomato production is strongly challenged by biotic factors such as tomato grey mold (Botrytis cinerea). Therefore, exploration of the key genes responding to cold tolerance, and Botrytis cinerea disease resistance, analyzing the mechanism of gene function have important value in tomato.In this study, we used S.pennellii introgression line IL6-2 as material, map-based cloning was used to locate the regulatory genes of the semi-dwarf and necrotic phenotype in IL6-2 under low temperature, and the function of the candidate genes was verified. The main research results are summarized as follows:<br /> 1. The phenotypes of 50 introgression lines (M82 as the background material) were observed. It was found that IL6-2 showed dwarfism, stunting, leaf curl, and even progressive necrosis compared with M82 plants when plants grew at 12 &deg;C, while this phenotype did not appear in other introgression lines. Physiological index measurement showed that the relative electrolyte leakage, MDA content and H2O2 were remarkably higher in IL6-2 than those in M82 at 12℃. By contrast, the proline content was significantly lower in IL6-2 than that in M82. The results suggest that IL6-2 is more sensitive to low temperatures compared to M82.<br /> 2. The leaves of IL6-2 and M82 seedlings were treated with low temperature for 0h, 24h and 48h, respectively, and RNA-seq analysis was performed. A total of 3,459 genes were identified as significantly differentially expressed between M82 and IL6-2, and there were 1,439, 2,170 and 888 differentially expressed genes (DEGs) at 0h, 24h and 48h, respectively. Functional cluster analysis of DEGs showed that the differentially expressed genes between IL6-2 and M82 were mainly in transmembrane receptor protein kinase activity, transmembrane receptor activity, transferase activity, protein kinase activity, which were mainly involved in biosynthesis of secondary metabolites pathway, plant hormone signal transduction pathway and plant-pathogen interaction pathway.<br /> 3. For mapping the gene that regulate the dwarfing necrosis of IL6-2 at low temperature, an F2 mapping population was created by self-pollination of a cross of IL6-2&times;M82. Through the genetic analysis of characters indicating that ndw mutant IL6-2 is controlled by a single recessive gene. Based on the mapping population, insertion/deletion (InDel) markers were developed, NDW was delimited to an interval between 37.95 Mb-39.14 Mb on chromosome 6, a fragment of approximately 640 kb. Further expanding the genetic isolation population, developing new InDel markers for fine mapping, and finally NDW gene was mapped to an approximately 77.4 kb fragment between 38.68 Mb-38.76 Mb.<br /> 4. Seven putative ORFs were predicted by sequencing and analyzing the target ~77.4 kb sequence in M82 using gene prediction software GENESCAN and FGENESH. According to genomic annotation information, the best hits of these ORFs included the protein arginine N-methyl transferase (ORF1), receptor-like protein kinases (ORF2&ndash;ORF4), glycosyltransferase (ORF5), peroxisomal biogenesis factor (ORF6), and zinc finger protein (ORF7). Sequence alignments showed that each candidate gene had nucleotide differences in the promoter, exon, or intron regions. RNA-seq analysis of differentially expressed genes, combined with qRT-PCR analysis of the relative expression of seven candidate ORFs, indicated that ORF2 (Solyc06g060680.1.1) and ORF3 (Solyc06g060690.2.1) were extremely lower in IL6-2 than in M82, while ORF5 (Solyc06g060710.2.1) was significantly up-regulated in IL6-2. ORF2, ORF3 and ORF5 showed significant difference between IL6-2 and M82. Therefore, we speculated that these three ORFs are the candidate genes which regulate the semi-dwarf and necrotic phenotype in IL6-2.<br /> 5. Over-expression vectors and RNA interference expression vectors were constructed for the three candidate genes, respectively, and the transgenic plants were obtained by genetic transformation of tomato. The transgenic plants were tested positive and the candidate gene relative expression level was measured. The expression level of candidate gene was evidently up-regulated in overexpression transgenic lines and down-regulated in RNAi transgenic lines were selected for phenotype identification. The results showed that overexpression of ORF3(Solyc06g060690) restored necrotic phenotype in IL6-2 under low temperature, the plant heights of transgenic plants OE-2, OE-7, and OE-9 were significantly higher than that of IL6-2, and were almost the same as that of M82. The relative electrolyte leakage and MDA content were remarkably lower in OE plants and M82 compared with IL6-2. In contrast, the proline content was significantly higher in OE plants and M82 compared with IL6-2. There was no significant difference between the phenotype of ORF2 (Solyc06g060680.1.1) and ORF5 (Solyc06g060710.2.1) transgenic lines and the non-transgenic control materials at 12℃. Taken together, these results indicated that Solyc06g060690 was NDW, and played an important role in plant growth and cold tolerance in tomato.<br /> 6. In the disease assays, we measured the average disease lesion area per leaflet and analyzed the planta fungal growth in transgenic plants. These results indicated that overexpression of NDW reduced susceptibility to Botrytis cinerea compared to IL6-2, and knockdown NDW in M82 plants resulted in increased sensitivity to Botrytis cinerea compared to M82.These results indicated that NDW played a role in regulating the sensitivity to Botrytis cinerea in tomato.<br /> 7. Sequence alignment analysis showed that NDW contains an ORF of 1122 bps in length, and contains two exons and an intron, encoding a 342 amino acid protein. The annotation information is a receptor-like protein kinase in the SGN database, and its amino acid sequence contains a conserved domain of the PKC-like super family. The kinase domain shared high sequence homology with that of other RLK genes in the Solanaceae species, and there are many conserved domains with potato, pepper and tobacco. Phylogenetic tree analysis shows that NDW shares the highest homology with Solanum tuberosum, and exhibited approximately 79.12% identity with XP_015161010.1 (S. tuberosum), and it has low homology with other crops.<br /> 8. It was confirmed that NDW gene was constitutively expressed in all tissues, including roots, stems, leaves, flower buds, flowers, and fruits, most highly in the root and stem of M82 plants. The results of subcellular distribution showed that NDW protein was localized to the plasma membrane and cytosol. It shows that it plays the function of receptor-like protein kinase, perceiving extracellular signals and conducting them into the cell.<br /> 9. Analysis the expression levels of some genes related to ABA synthesis, decomposition and signal transduction pathway in NDW transgenic lines. The results showed that NDW up-regulated the expression level of some ABA receptor genes, ABA synthesis related genes, and ABA signal transduction positive regulatory genes. On the contrary, the expression levels of some ABA signal transduction negative regulatory genes and ABA decomposition pathway genes were significantly decreased. These results indicated that NDW gene is related to ABA accumulation, and may regulate plant growth and stress response through ABA-dependent pathway in tomato.</p>

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