基因组分析揭示番茄育种的历史

番茄(Solanum lycopersicum)适应性广,产量高,营养丰富,风味独特,栽培方式多样,是世界范围内广泛种植的第一大蔬菜作物。2012年全球产量达到1.62亿吨(联合国粮农组织(FAO)统计),产值超过550亿美元。番茄也是植物遗传、发育和生理研究的重要模式系统。番茄起源于南美洲的安第斯山脉,随着人类迁移和驯化逐渐传到中美洲和墨西哥一代,16世纪传到欧洲,在随后的几百年中番茄被传播到世界各地,在这一过程中受到不同的人工选择,产生了丰富的变异类型。番茄果实大小的变化是驯化的一个重要特征,今天人们食用的大果栽培番茄是由野生醋栗番茄(Solanum pimpinellifolium)驯化而来,野生番茄果实非常小,只有1~2g 重,经过人工的长期驯化,现代栽培番茄的果重是其祖先的100多倍。然而,番茄果实变大的人工驯化过程一直未有全面的研究,人类选择如何改变番茄基因组仍是知之甚少。     

一个园艺植物基因组序列和注释的在线批量实时提取平台

目前, 大量园艺植物基因组测序已经完成或接近尾声, 它们的基因组序列和注释数据极大地促进了功能基因组学研究。为给科研人员提供批量下载特定的基因组区段序列和注释平台, 笔者开发了一个称为OBRRP的生物信息学工具。OBRRP具有提取葡萄(Vitis vinifera)、桃(Prunus persica)、草莓(Fragaria vesca)、黄瓜(Cucumis sativus)、西瓜(Citrullus lanatus)、番茄(Solanum lycopersicum)、甜橙(Citrus sinensis)、苹果(Malus x domestica)、猕猴桃(Actinidia chinensis)、马铃薯(Solanum tuberosum)、香蕉(Musa acuminata)和拟南芥(Arabidopsis thaliana) 12种植物基因组序列及注释数据的功能; 同时, 也具有扩展到其它Gbrowser浏览器架构的数据库功能。测试结果表明, OBRRP是一个快捷简便的在线、批量和实时提取工具, 其登录地址为http://bioinfo.jit.edu.cn/OBRRP/。     

银川番茄斑萎病毒的分子鉴定

为明确银川番茄(Lycopersicon esculentum)是否遭受了番茄斑萎病毒(TSWV)的危害, 采用国家标准TSWV RT- PCR检测技术对银川番茄上采集的14份疑似感染TSWV病叶样本进行分子鉴定, 对克隆得到的核衣壳蛋白基因N (Nucleocapsid)序列进行多序列比对和系统进化树分析, 随后对PCR阳性样本进行蛋白检测。结果表明, 14份病叶样本中有8份扩增出长度为394 bp的TSWV N基因序列, 且8条序列完全一致; 获得的银川番茄TSWV分离物与云南番茄、中国莴苣(Lactuca sativa)、中国鸢尾(Iris tectorum)和重庆辣椒(Capsicum annuum) TSWV分离物相对近缘, 与山东、黑龙江和北京等地及国外TSWV分离物相对远缘; 利用TSWV的抗体通过Western blot对8个PCR阳性样本进一步检测, 结果也证实8个阳性样本中存在TSWV感染。该研究首次通过分子鉴定及蛋白检测证明银川番茄上存在TSWV感染, 需要加快抗TSWV番茄品种的选育工作。     

外源褪黑素与钙离子互作对高温胁迫下黄瓜幼苗过氧化伤害的缓解效应

为了探明褪黑素(MT)和钙离子(Ca²⁺)在调控植物耐热性中是否存在互作关系,以黄瓜幼苗为试材,分析了内源MT和Ca²⁺对高温胁迫的响应;并通过叶面喷施100 μmol·L^-1 MT、10 mmol·L^-1 CaCl₂、3 mmol·L^-1乙二醇二乙醚二胺四乙酸(EGTA,Ca²⁺螯合剂)+100 μmol·L^-1 MT、0.05 mmol·L^-1氯丙嗪(钙调素拮抗剂,CPZ)+100 μmol·L^-1 MT、100 μmol·L^-1氯苯丙氨酸(p-CPA,MT合成抑制剂)+10 mmol·L^-1 CaCl₂和去离子水(H₂O),研究高温下(42/32 ℃)外源MT和Ca²⁺对黄瓜幼苗活性氧积累、抗氧化系统及热激转录因子(HSF)和热激蛋白(HSPs)等的影响。结果表明: 黄瓜幼苗内源MT和Ca²⁺均受高温胁迫诱导;外源MT可上调常温下钙调素蛋白(CaM)、钙依赖蛋白激酶(CDPK5)、钙调磷酸酶B类蛋白(CBL3)、CBL结合蛋白激酶(CIPK2)mRNA表达;CaCl₂处理的MT合成关键基因色氨酸脱羧酶(TDC)、5-羟色胺-N-乙酰转移酶(SNAT)和N-乙酰-5-羟色胺甲基转移酶(ASMT)水平也显著升高,MT含量快速增加。MT和CaCl₂可显著增强高温下黄瓜的抗氧化能力,减少活性氧(ROS)积累,同时上调HSF7、HSP70.1和HSP70.11 mRNA表达,从而减轻高温胁迫引起的过氧化伤害,植株热害症状明显减轻,热害指数和电解质渗漏率显著降低。加入EGTA和CPZ后,MT对黄瓜幼苗抗氧化能力和热激蛋白表达的促进效应明显减弱,Ca²⁺对高温下黄瓜幼苗过氧化伤害的缓解效应也被p-CPA逆转。可见,MT和Ca²⁺均可诱导黄瓜幼苗的耐热性,二者在热胁迫信号转导过程中存在互作关系。     

多功能菌群混合施用的生态效应

从蔬菜地黄瓜根围土壤中经分离筛选,得到两个对黄瓜枯萎病菌(Fusarium oxysporum f.sp.cucumerinum)有抑制作用,并能明显促进黄瓜生长的菌株ZJY-1(Brevibacillus brevis)和ZJY-116(Bacillus subtilis).将这两菌株与一株毒死蜱降解菌DSP3(Alcaligenes faecali)按照不同组合处理黄瓜种子,以研究多功能菌群在环境中发挥生态效应的可行性.结果表明,这两株具有生防和促生功能的菌株与DSP3按不同组合混合后,对黄瓜的防病促生作用均不受影响.同时对黄瓜根围土中毒死蜱含量检测分析发现,DSP3与这两株细菌混和施用后其降解率与单独施用相比没有明显差异.实验初步证明,不同功能的菌株混合施用后可以发挥其生态效应.     

sly-miR399在番茄抗晚疫病中的初步探究*

背景: 番茄(Solanum lycopersicum)是广泛种植的最具价值的果蔬之一,番茄晚疫病会导致其产量和品质降低。microRNAs(miRNAs)是一类内源性非编码RNA,广泛参与基因转录后调控。已有研究表明miR399家族可参与调控植物抗病过程。目的:探究番茄miR399(sly-miR399)对番茄抗晚疫病的影响。方法:构建sly-miR399的过表达和沉默载体,利用农杆菌介导在番茄叶片中瞬时表达;实时荧光定量PCR(qRT-PCR)技术检测相关基因表达水平;台盼蓝染色并统计分析瞬时过表达和瞬时沉默sly-miR399的番茄叶片的病斑情况。结果:瞬时过表达sly-miR399导致其靶基因UBC24的表达量下降了75%,病程相关蛋白(pathogenesis related proteins,PRs)SlPR1、SlPR2、SlPR3和SlPR5的表达量分别上升了3.6倍、2.2倍、2.3倍和6.4倍,茉莉酸(JA)信号通路相关基因SlJA1、SlLOX1和SlLOX2的表达量分别上升了1.3倍、2.5倍和1.5倍,JA转录抑制因子SlJAZ1的表达量下降了50%,接种晚疫病菌后,叶片上相对病斑面积明显减小;瞬时沉默导致其靶基因的表达量上升了1.8倍,PRs基因的表达量分别下降了65%、82%、52%和80%,SlJA1、SlLOX1和SlLOX2的表达量分别下降了84%、50%和65%,SlJAZ1的表达量上升了1.8倍,病菌接种后叶片上相对病斑面积明显变大。结论:初步揭示了sly-miR399在番茄抗晚疫病过程中的正调控因子作用。     

利用多组学手段解析番茄育种过程中代谢物变化的机制

番茄(Solanum lycopersicum)在育种过程中经历了驯化、改良、分化和渐渗等不同阶段, 在这一选择过程中番茄的果重和风味等均发生了显著改变, 但是目前对于番茄育种过程中代谢物的变化及其遗传基础却不是十分清楚。近期, 中国农业科学院深圳农业基因组研究所黄三文研究组与华中农业大学罗杰研究组利用多组学(变异组、转录组及代谢组)手段系统解析了番茄育种过程中代谢物的变化。结果表明, 在番茄驯化过程中有46个甾醇糖基生物碱类物质(SGAs)含量逐渐降低, 并获得了7个与其中44个物质显著相关的遗传位点。因此, 在番茄育种过程中通过优异等位位点的组合可以显著降低SGAs的含量; 同时发现在番茄以果重为目标的选择过程中, 控制果重基因周围其它基因的“搭车效应”是引起许多代谢物变化的重要遗传因素, 及在育种过程中对某一性状的选择会对其它性状产生重要影响。该研究首次利用多组学手段系统解析了选择对作物代谢物的影响, 为番茄品质改良奠定了良好的理论基础。     

番茄属(Lycopersicon)四个种的过氧化物酶同工酶分析

本文报告了应用连续浓度梯度聚丙烯酰胺凝胶电泳对番茄属Lyco-persicon的四个种:秘鲁番茄L.peruviaunm Mill.,多毛番茄L.hirsutum Humb.et Bonp,醋栗番茄L.pimpinellifolium(Jusl)Mill和普通番茄L.esculentum Mill.的86份材料,15个不同生育时期,不同器官以及同一器官的不同部位的过氧化物酶同工酶的分析结果。结果表明:L.Peruvianum的各个生育期和不同器官的过氧化物酶同工酶谱带叠加共有28条带,L.hirsutum有29条带,L.pimpinellifolium有28条带,L.esculentum有27条带。种间过氧化物酶同工酶谱型差异明显,种内不同生育期叠加总酶谱基本一致。在根、茎和叶中,这四个种的过氧化物酶同工酶酶谱和活性具有相似的生育期变化规律和器官分布规律.在果实发育过程中,种间过氧化物酶同工酶酶谱、活性及变化律规都不相同。本文还就同工酶谱型相似值的意义,野生资源及同工酶分析技术在番茄育种中的应用等问题进行了讨论。     

是金子无论在何处都发光: 玉米和水稻驯化中的趋同选择

野生植物的驯化为人类定居与文明起源奠定了重要基础。在世界范围内不同地区生活的古人类分别对当地不同的野生植物进行了驯化, 而经过驯化的作物常常表现出相似的驯化综合性状。在基因组层面上对趋同选择规律的解析, 可为作物育种提供重要信息与遗传资源。近日, 中国农业大学杨小红/李建生和华中农业大学严建兵领衔的团队从单基因和全基因组2个层次系统解析了玉米(Zea mays)和水稻(Oryza sativa)趋同选择的遗传基础, 发现玉米KRN2与水稻OsKRN2受到了趋同选择, 并通过相似的途径调控玉米与水稻的粒数与产量。他们还发现玉米与水稻在全基因组范围内存在大量趋同选择同源基因对(gene pair), 这些基因在淀粉代谢、糖及辅酶合成等途径特异富集。该研究不仅克隆了在玉米与水稻中均具有重要育种价值的趋同选择同源基因对KRN2/OsKRN2, 而且在全基因组水平上揭示了玉米与水稻趋同选择的规律, 为进一步解析驯化综合性状形成的分子机理及其在育种中的应用奠定了重要理论基础。     

不同光强下高锰对黄瓜光合作用特性的影响

采用营养液培养的方法,研究了不同光强下高锰对黄瓜植株生长、叶绿素含量、叶绿素荧光参数和光合作用的影响.结果表明,高锰处理抑制了黄瓜植株的生长,与弱光处理相比强光下抑制幅度更加显著.强光下,高锰处理显著降低叶绿素含量,但降低光强却增加其含量.强光下,高锰处理显著降低原初光能转换效率(F_v/F_m)、光合电子传递量子效率(ΦPSII)和光化学猝灭系数(qP);弱光下,高锰处理对F_v/F_m和qP无显著影响.高锰处理使净光合速率(P_n)和气孔导度(G_s)下降.尤其是在强光下下降幅度更大.高锰处理使细胞间CO₂浓度(C_i)在强光下升高,而在弱光下则下降.与C_i相反,高锰处理使气孔限制值(L_s)在强光下下降,而在弱光下上升.因此,强光下高锰胁迫使净光合速率下降可能是由非气孔限制引起的,而弱光下高锰处理使净光合速率下降可能是由气孔因子限制引起的.     

黄瓜的冷害及耐冷性

随着蔬菜反季节栽培面积的不断扩大,如何提高黄瓜(Cucumis sativus L.)耐冷性已成为选育新品种的研究重点。系统地综述近几年黄瓜耐冷性的鉴定、获得途径、冷害机理以及遗传和分子遗传学等方面的研究,以促进对黄瓜冷害机制的研究, 加速耐冷品种的培育。耐冷性鉴定时要从耐冷指数、低温发芽能力、MDA (丙二醛)含量和电解质渗漏率等几个方面综合鉴定。耐冷性的获得途径主要有冷驯化、激素处理、热激处理和培育耐低温品种,最重要的途径是耐冷品种选育。黄瓜冷害机理包括细胞膜的流动性降低及透性增加,光合作用被抑制,根系吸收减弱,可溶性糖含量减少,淀粉粒积累增加,微管的稳定性受到破坏等。黄瓜低温发芽能力由非加性基因决定,而幼苗时期主要由加性基因控制。黄瓜 耐冷的分子遗传学研究进展缓慢,目前已克隆出在低温锻炼中特异表达的功能未知的基因CCR18。今后还应研究黄瓜低温胁迫时的信号转导系统,以进一步揭示黄瓜的冷害机理;利用野生资源的抗逆性状,拓宽栽培黄瓜的遗传基础,选育适于保护地栽培的耐低温品种。     

黄瓜的冷害及耐冷性

随着蔬菜反季节栽培面积的不断扩大,如何提高黄瓜(Cucumis sativus L.)耐冷性已成为选育新品种的研究重点.系统地综述近几年黄瓜耐冷性的鉴定、获得途径、冷害机理以及遗传和分子遗传学等方面的研究,以促进对黄瓜冷害机制的研究,加速耐冷品种的培育.耐冷性鉴定时要从耐冷指数、低温发芽能力、MDA(丙二醛)含量和电解质渗漏率等几个方面综合鉴定.耐冷性的获得途径主要有冷驯化、激素处理、热激处理和培育耐低温品种,最重要的途径是耐冷品种选育.黄瓜冷害机理包括细胞膜的流动性降低及透性增加,光合作用被抑制,根系吸收减弱,可溶性糖含量减少,淀粉粒积累增加,微管的稳定性受到破坏等.黄瓜低温发芽能力由非加性基因决定,而幼苗时期主要由加性基因控制.黄瓜耐冷的分子遗传学研究进展缓慢,目前已克隆出在低温锻炼中特异表达的功能未知的基因CCRl8.今后还应研究黄瓜低温胁迫时的信号转导系统,以进一步揭示黄瓜的冷害机理;利用野生资源的抗逆性状,拓宽栽培黄瓜的遗传基础,选育适于保护地栽培的耐低温品种.     

Ethylene perception is involved in female cucumber flower development

It is well established that ethylene promotes female flower development in cucumber. However, little is known about how the gaseous hormone selectively affects female flowers, and what mechanism it uses. Previously, we found organ‐specific DNA damage in the primordial anther of female cucumber flowers. This finding led to a hypothesis that ethylene might promote female flower development via the organ‐specific induction of DNA damage in primordial anthers. In this study, we tested this hypothesis first by demonstrating ethylene induction of DNA damage via the ethylene signaling pathway using cucumber protoplasts. Then, using representative component genes of the ethylene signaling pathway as probes, we found that one of the ethylene receptors, CsETR1, was temporally and spatially downregulated in the stamens of stage‐6 female cucumber flowers, especially along with the increase of the nodes. Furthermore, by constructing transgenic Arabidopsis plants with organ‐specific expression of antisense CsETR1 under the control of an AP3 promoter to downregulate ETR1 expression in the stamens, we generated Arabidopsis ‘female flowers’, in which the abnormal stamens mimic those of female cucumber flowers. Our data suggest that ethylene perception is involved in the arrest of stamen development in female cucumber flowers through the induction of DNA damage. This opens up a novel perspective and approach to solve the half‐century‐long puzzle of how gaseous ethylene selectively promotes female flowers in the monoecious cucumber plant.     

Response of rhizosphere microbial diversity and soil physico-chemical properties in a rotation of cucumber with Volvariella volvacea

Crop rotation can significantly increase yield by improving soil conditions through reducing soil pathogens and increasing the microbial diversity near the root system of the plant. Cucumber is widely consumed across the world, and monoculture of cucumber under greenhouse conditions is often threatened by Fusarium wilt, which is caused by fungi belonging to the genus Fusarium. In Jiangsu province of China, rotating cucumber crops with Volvariella volvacea is used as a way to control Fusarium wilt. Here, we tested how rotating cucumber with V. volvacea influences soil physico-chemical and biological properties. We found that rotating with V. volvacea improved bacterial diversity near the cucumber root system. We also found an increase in nitrogen-fixing bacteria that have been used for biological control of plant pathogens, and a decrease in Fusarium species. In the treated soil, we found increased activity of the soil enzymes catalase, dehydrogenase, polyphenol oxidase and alkaline phosphatase by 2–22%, 14–29%, 16–58% and 9–64%, respectively. Lastly, the total and available nitrogen, phosphorus and potassium content significantly increased one to three weeks after V. volvacea residual substrate was mixed into the soil, up to 39%, 24%, 17%, 28%, 18% and 70, but declined slowly afterwards. These results suggested that rotating cucumber with V. volvacea could aid in resetting the structure of the microbial community of the cucumber root system. Increase in beneficial microbes and improved soil conditions are likely to contribute to improved yield of this commercially important crop.     

Characterization of an ethylene-inducible, calcium-dependent nuclease that is differentially expressed in cucumber flower development

? Production of unisexual flowers is an important mechanism that promotes cross-pollination in angiosperms. We previously identified primordial anther-specific DNA damage and organ-specific ethylene perception responsible for the arrest of stamen development in female flowers, but little is known about how the two processes are linked. ? To identify potential links between the two processes, we performed suppression subtractive hybridization (SSH) on cucumber (Cucumis sativus L.) stamens of male and female flowers at stage 6, with stamens at stage 5 of bisexual flowers as a control. ? Among the differentially expressed genes, we identified an expressed sequence tag (EST) encoding a cucumber homolog to an Arabidopsis calcium-dependent nuclease (CAN), designated CsCaN. Full-length CsCaN cDNA and the respective genomic DNA sequence were cloned and characterized. The CsCaN protein exhibited calcium-dependent nuclease activity. CsCaN showed ubiquitous expression; however, increased gene expression was detected in the stamens of stage 6 female flowers compared with male flowers. As expected, CsCaN expression was ethylene inducible. It was of great interest that CsCaN was post-translationally modified. ? This study demonstrated that CsCaN is a novel cucumber nuclease gene, whose DNase activity is regulated at multiple levels, and which could be involved in the primordial anther-specific DNA damage of developing female cucumber flowers.     

Development and characterization of microsatellite markers in Cucumis

This study provides a set of useful SSR markers and describes their development, characterization and application for diversity studies.Sixty one Cucumis SSR markers were developed, most of them (46) from melon (Cucumis melo L.) genomic libraries. Forty of the markers (30 melon and 10 cucumber SSRs) were evaluated for length polymorphism in a sample of 13 melon genotypes and 11 cucumber (Cucumis sativus L.) genotypes. PCR-amplification revealed up to six size alleles among the melon genotypes and up to five alleles among the cucumber genotypes, with mean gene-diversity values of 0.52 and 0.28 for melon and cucumber, respectively. These differences are in accordance with the known narrower genetic background of the cucumber. SSR data were applied to phylogenetic analysis among the melon and cucumber genotypes. A clear distinction between the ’exotic’ groups and the sweet cultivated groups was demonstrated in melon. In cucumber, separation between the two sub-species, C.sativus var. sativus and C.sativus var. hardwickii,was obtained. Conservation of SSR loci between melon and cucumber was proven by sequence comparisons. Received: 17 April 2000 / Accepted: 16 May 2000     

Consumptive and non‐consumptive effects of wolf spiders on cucumber beetles and cucumber plant damage

Biological control research often focuses on the ability of predators to reduce pest densities and protect crops through consumption. Less studied is their ability to protect crops by altering pest behaviour (non‐consumptive effects). Lab experiments were conducted to test predation rates of striped cucumber beetles (Acalymma vittatum; Coleoptera: Chrysomelidae) and spotted cucumber beetles (Diabrotica undecimpunctata howardi; Coleoptera: Chrysomelidae) by large (>10 mm) wolf spiders (Araneae: Lycosidae). Field experiments were conducted to examine how the physical presence and/or cues of spiders impact the behaviour and mortality of A. vittatum (specialist) and D. undecimpunctata (generalist) cucumber beetles as well as growth and damage of cucumber plants (Cucumis sativus; Cucurbitaceae). A. vittatum and D. undecimpunctata adults were added to caged cucumber plants without a spider, with spider cues only (spider removed before beetle inclusion), with spider only (spider introduced to plants immediately before beetle inclusion), and with spiders and their cues present (spiders introduced 24 hr in advance of beetle inclusion). A. vittatum responded to spider cues primarily by emigrating from plants. Contrarily, D. undecimpunctata did not display obvious responses, such as reduced feeding or increased emigration, to spider foraging and/or cues. Actively foraging lycosids increased A. vittatum mortality and reduced densities of D. undecimpunctata in the field when cucumber plants were flowering. This study highlights how non‐consumptive and consumptive effects can play a role in modifying pest populations, and how these effects can vary across species and plant growth stages.     

Oviposition preference of western flower thrips for cucumber leaves from different positions along the plant stem

While the distribution of herbivorous insects over leaves along the stem often shows a peak at some distance from the apex this does not necessarily reflect an innate preference as alternative explanations can be provided such as impact of predators and inter- or intraspecific competitors. It is of interest to determine which factors shape the distribution of insects over the leaves of a plant. Do leaves from different positions differ in suitability for insects and is that reflected in the insect's preference, or are other factors involved? In this paper we assess how the herbivorous insect western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), chooses among leaves from different positions relative to the apex of cucumber, Cucumis sativus (L.) plants. On leaf discs of a susceptible and three partially resistant cucumber accessions, thrips reproduction was highest on apical leaves and lowest on basal leaves. In dual-choice essays thrips females preferred younger leaves over older leaves for oviposition in all cucumber accessions tested, as was predicted from the no-choice assay. This indicates that differences in leaf suitability are an important factor in determining thrips distribution on cucumber plants.