魔芋软腐病病原菌果胶杆菌ZX67菌株全基因组测序及分析

菌株ZX67是魔芋软腐病病原菌胡萝卜果胶杆菌胡萝卜亚种(Pectobacterium carotovorum subsp. carotovorum),为进一步了解该病原菌的特性,便于更好地研究防治软腐病的方法,对该菌株进行了全基因组测序和分析。该菌株基因组总长度为4,909,724 bp,GC含量为51.27%,包含4,977个编码基因,其序列长度占总基因组的85.25%,预测的非编码RNA主要包括74个tRNA、22个rRNA及100个sRNA,有10个基因岛,6个转座子,预测存在2个前噬菌体,每个前噬菌体的平均长度为26,258 bp,有5个CRISPR序列,每个序列的平均长度为621 bp,并分析了与降解寄主细胞壁相关的裂解酶、与侵染植物相关的5种蛋白分泌系统。以上结果,为进一步了解软腐病病原菌的特性提供了机会,也为研究新的防治方法提供了新的出发点和思路。     

雷蒙德氏棉PIF-like转座元件鉴定与特征分析

PIF-like转座元件在植物基因组中含量丰富,是植物DNA转座子的重要组成部分。利用基因组学和生物信息学的研究手段,系统研究了雷蒙德氏棉全基因组水平PIF-like转座元件的数量、染色体分布、结构特征、表达模式及相邻基因的种类和功能等,共鉴定了440条包含转座酶且插入位置明确的PIF-like转座元件。这些元件几乎均匀地分布在13条染色体上,上下游2 kb内共有171个相邻编码蛋白的基因,其中132个基因注释到了GO数据库中,且这些基因的功能分布广泛;部分PIF-like转座元件表达,且具有组织特异性。这些遗传信息为深入研究棉花PIF-like转座元件介导的基因和基因组的进化规律以及棉花基因的功能奠定基础。     

Tomato: a crop species amenable to improvement by cellular and molecular methods

Summary Tomato is a crop plant with a relatively small DNA content per haploid genome and a well developed genetics. Plant regeneration from explants and protoplasts is feasable which led to the development of efficient transformation procedures.In view of the current data, the isolation of useful mutants at the cellular level probably will be of limited value in the genetic improvement of tomato. Protoplast fusion may lead to novel combinations of organelle and nuclear DNA (cybrids), whereas this technique also provides a means of introducing genetic information from alien species into tomato. Important developments have come from molecular approaches. Following the construction of an RFLP map, these RFLP markers can be used in tomato to tag quantitative traits bred in from related species. Both RFLP's and transposons are in the process of being used to clone desired genes for which no gene products are known. Cloned genes can be introduced and potentially improve specific properties of tomato especially those controlled by single genes. Recent results suggest that, in principle, phenotypic mutants can be created for cloned and characterized genes and will prove their value in further improving the cultivated tomato.     

尖孢镰刀菌专化型及生理小种分子检测研究进展

摘 要：尖孢镰刀菌分子检测工作在枯萎病病原菌分子诊断与防治中具有重要意义。本文综述了DNA分子标记、毒性基因和转座子等技术在尖孢镰刀菌专化型及其生理小种鉴别方面的应用,指出了各检测方法优缺点,并对今后的研究方向进行展望。     

中棉所12配制的2个杂交棉DNA甲基化遗传与传递

DNA甲基化在真核生物的生长发育过程中起着重要的调控作用。本研究用MSAP方法分析了中棉所12配制的2个杂交棉和亲本不同发育时期的基因组DNA 5′-CCGG位点胞嘧啶的甲基化水平及其遗传传递模式。研究表明: (1)杂交棉及其亲本不同发育时期的胞嘧啶甲基化水平不同,随着生育期的逐步推进,出现两头低而中间高现象;(2)两个杂交棉组合的DNA 甲基化总体水平为12.41%~20.05%,其中以内侧胞嘧啶全甲基化为主(约占6.90%~11.47%);(3)棉花中绝大多数CCGG胞嘧啶甲基化位点是由亲本稳定遗传给杂交种的,但杂交棉仍有1.14%~3.39%的位点显示了变异,其变异频率在不同亲本组合之间和不同发育时期都存在差异;(4)对甲基化差异条带测序分析发现,其功能涉及到富含亮氨酸重复、类PDR的ABC转运蛋白、GTP结合蛋白、病程相关蛋白、磷酸激酶、功能未知的蛋白质和反转录酶等,部分差异序列没有产生有意义的匹配。     

全基因组分析玉米MuDR转座因子插入突变体库

在功能基因组研究中,插入诱变被广泛用于基因敲除。玉米Mutator转座子因其具有较高的转座活性常被用于构建大型玉米插入突变体库。本研究利用具有活性MuDR因子的玉米材料与优良玉米自交系Z31杂交,获得1 000个M1单株,自交构建M2群体,并研究MuDR因子在基因组中插入位点特性。利用优化的MuTAIL-PCR方法分离出695条MuDR插入位点侧翼序列,经初步生物信息学分析得到374条非冗余的插入位点,其中的298条序列能够被定位在玉米基因组物理图谱单个位点上。实验结果揭示了MuDR因子插入的一些特性：在10条染色体上随机分布,偏向于插入到基因序列中,并在某些功能基因中有明显插入偏好。     

水稻突变群体的构建及功能基因组学

随着水稻基因组全序列的测定完成，功能基因组学已成为重点研究内容。功能基因组学主要研究生物有机体内各基因的生物学功能进而了解所有基因如何协调发挥作用完成一系列的生长发育过程。目前已经发展了多种分析鉴定基因功能的方法，其中最直接最有效的方法是构建饱和的基因突变群体，通过突变体分析鉴定基因功能。本文主要阐述了各种构建方法及其优缺点以及在功能基因分离鉴定上的应用。自发突变的频率极低，且自发突变基因的分离难度比较大，只能作为突变群体构建的辅助方法。利用EMS等化学诱变剂可以在短时间内构建大量点突变群体，并可用TILLING进行突变检测，但多位点的点突变使突变表型难以鉴定。由快中子等物理诱变也可以在短时间内构建大量缺失突变体，且可用Ddeteagene系统进行检测；但多基因缺失、多位点缺失和内含子缺失等使突变表型的分析可能无法进行。利用T—DNA、转座子和反转录转座子等构建插入突变体已经成为突变库构建的主要方法。T—DNA插入已成功应用于水稻大规模突变体的构建，但只限于转基因效率较高的品种；T—DNA在基因组中整合的复杂性以及转基因过程中由组织培养等引发的突变等，增加了突变体表型和分子分析的难度。Tos17是目前应用最为成功的反转录转座子，但多拷贝的插入使突变体的表型鉴定和分子鉴定较为困难，因为只有10％左右的突变性状是由Tos17插入引起的。理论上，Ac／Ds双因子系统是目前最理想的水稻插入突变库构建体系，Ds的单拷贝插入，大大方便了突变体的表型分析和分子鉴定；Ds的回复突变，可以验证突变表型是否由Ds插入引起；但在血转座酶驱动下Ds可能发生的多次跳动所形成的痕迹(footprint)也可能影响突变表型的分析。RNAi可以有效地使目标基因沉默，但并不是所有基因均可被RNAi沉默；对多因一效基因或同源性较高的基因家族，RNAi会同时作用这些基因，沉默表型很难鉴定。可见，每一种方法都有各自的优缺点，但不同的方法是可以互补的，通过各种方法是能够构建成理想的水稻突变库的。     

重离子辐照诱变育种应用及其生物学效应研究进展

重离子辐射育种以其程序简单、突变效率高、突变谱广等特点,受到育种工作者的广泛关注。其作用的机制是通过注入的高能带电粒子与生物体内的分子或原子发生弹性、非弹性的碰撞,导致生物体内的电离损伤,进而使染色体发生序列或结构改变。其生物学效应在个体水平主要表现为叶形、花色、花形、株型等变化,在生理水平主要表现为过氧化物酶类含量的改变,在分子水平主要表现为生物体内基因表达变化、转座子、甲基化的激活等。本文简要介绍了重离子辐射作用的基本原理,重离子辐射对生物体的生物学效应以及在育种应用中的最新研究进展。     

野生二粒小麦（Triticum dicoccoides）与普通小麦（T. aestivum）A、B染色体组的同源性分析

以普通小麦农家种、野生二粒小麦和野生二粒小麦与节节麦合成的双二倍体为材料,运用SSR分子标记方法对野生二粒小麦与普通小麦A、B染色体组的同源性进行了研究。结果表明：（1）野生二粒小麦与普通小麦A、B染色体组的遗传相似系数仅为0.189,存在较大的差异,推测野生二粒小麦与普通小麦的A、B染色体组在长期的进化过程中,     

基于全长cDNA序列的小麦cSNP发掘

以测序得到的来自小麦不同基因组的基因序列为源序列,用AutoSNP软件,在GenBank中的小麦EST库中检测到一批cSNP,开辟了一条发掘小麦基因组特异候选cSNP的新途径。在2089个源序列中,检测到1 296个cSNP,其中有397个来自A基因组,322个来自S基因组,420个来自D基因组;另外,A和D基因组共有的SNP有154个,A和S,S和D,A、S和D基因组共有的SNP各仅有1个,这一结果也同时表明,小麦的3个基因组供体种中,A、D基因组关系比较近,而它们与S基因组的关系比较远。统计分析表明,小麦中SNP出现的频率约为0.914‰。     

Effect of genome and ploidy on photosynthesis of wheat

We assessed (1) the effects of addition and doses of the D genome from different sources and (2) the addition of either the A genome or the D genome on the photosynthesis of synthesized hexaploid wheats. On average, the increased doses of the D genome reduced photosynthesis, but the depression was dependent on the source of the D genome. Two accessions of Aegilops squarrosa had depressed photosynthetic rates, but not another accession of Ae. squarrosa. The D genome of cv. Thatcher did not contribute to depress photosynthetic rate. Triticum monococcum had considerably higher photosynthetic rates than Ae. squarrosa. However, addition of the A genome from T. monococcum did not increase the photosynthetic rates of hexaploids. Chlorophyll a : b ratio, functional photosystem II and the core complex of photosystem II did not account for the variation in photosynthetic rate among the genotypes studied. In our experiment, photosynthesis of polyploids was not dependent on photosynthesis rates of the donor genomes. This revised version was published online in July 2006 with corrections to the Cover Date.     

利用SNP分型技术鉴别油菜FLC1与FLC3基因的A、C组基因型

甘蓝犁油菜是由白菜型油菜(A组基因型)与甘蓝(C组基因型)杂交后自然加倍的异源四倍体芸薹属植物.其中含有A组与C组两种基因型的染色体,而FLC1与FLC3是A、C组中共同拥有的FLC基因.通过序列比对,分别寻找出A、C组基因中FLC1与FLC3基因的特异性SNP位点,并设计了3对SNP特异性引物对.采用特异性引物延伸法,分别对来自白菜型油菜、甘蓝以及甘蓝型油菜的不同材料进行检测.利用这3对特异性SNP引物对,成功地对油菜中A、C组的FLC1与FLC3基因进行了有效的分型,为研究甘蓝型油菜中A、C组来源的FLC1与FLC3表达奠定了基础.     

Hexaploid triticales from hybrids of 'Langdon' durum D-genome substitutions with 'Gazelle' rye

The formation of unreduced gametes in some hybrids between disomic D‐genome substitutions (DS) of durum wheat cv.‘Langdon’ and rye provides a convenient approach for the rapid introduction of D‐genome chromosomes into hexaploid triticale. Meiotic pairing at metaphase I and seed fertility in spontaneous and colchicine‐induced amphidiploids derived from F₁ hybrids between a set of ‘Langdon’ DS and ‘Gazelle’ rye were analysed. The purpose was to determine the effects of the substitution of D‐genome chromosomes for their A‐ and B‐genome homoeologues on hexaploid triticale and to select stable disomic D‐genome substitutions of hexaploid triticale. The results showed that the disomic substitutions with D‐genome slightly increased the frequency of univalents (1.0‐3.13) compared with the ‘Langdon’ control primary hexaploid triticale (0.76). Substitutions 2D(2A) and 3D(3B) were partly desynaptic. The substitutions 1D(1A), 1D(1B) and 7D(7B) exhibited high seed fertility but the others had decreased fertility. Except for 2D(2A), 5D(5A), 3D(3B) and 5D(5B), 10 of the 14 possible hexaploid triticale D‐genome disomic substitutions have been obtained. The results suggest that the poor compensation ability of some D‐genome chromosomes for their homoeologous A‐ and B‐genome chromosomes is a major factor affecting meiotic stability and fertility in the hexaploid triticale D‐genome substitutions.     

小麦(T.aestivum L.)D基因组的研究进展

普通小麦是一个异源六倍体物种,具有ABD三个染色体组,D染色体组在来源和进化过程中都与A、B染色体组不同,D染色体组来自于粗山羊草,含有丰富的抗病、抗虫、抗寒、优质等有益基因,因此D染色体组的研究对小麦的产量、品质改良具有重要意义。但是由于长期的定向遗传改良,我国普通小麦的遗传差异较小,遗传基础狭窄,特别是在D染色体组上尤为突出。一些对作物产量和品质有益的基因未被挖掘利用。本文对小麦D基因组的起源、遗传多样性和拓宽遗传基础的方法及基因定位等进行了综述,并结合本实验室的研究工作对其研究前景进行展望。     

Retrotransposons - a major driving force in plant genome evolution and a useful tool for genome analysis

As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to unforeseen transposition activities. Regulation of transposition is relatively complex and three factors such as maintaining structure for none- or cis- or trans-acting transposition, being controlled by the host genome and induction by biotic and abiotic stress may contribute altering its transposition activity. The important roles of retrotransposons to modify genome size, remodel genome structure, and displace gene functions in the plant genome have been proven by a growing number of research studies till date, which indicates that retrotransposons are important driving force in genome evolution. For this review, we summarized the latest theoretic and practical research progresses on plant retrotransposons for their distribution, regulation of activity, the impact on the architecture of plant genomes, and put forward the future prospects.     

DaizuBase,an integrated soybean genome database including BAC-based physical maps

Soybean [Glycine max (L) Merrill] is one of the most important leguminous crops and ranks fourth after to rice, wheat and maize in terms of world crop production. Soybean contains abundant protein and oil, which makes it a major source of nutritious food, livestock feed and industrial products. In Japan, soybean is also an important source of traditional staples such as tofu, natto, miso and soy sauce. The soybean genome was determined in 2010. With its enormous size, physical mapping and genome sequencing are the most effective approaches towards understanding the structure and function of the soybean genome. We constructed bacterial artificial chromosome (BAC) libraries from the Japanese soybean cultivar, Enrei. The end-sequences of approximately 100,000 BAC clones were analyzed and used for construction of a BAC-based physical map of the genome. BLAST analysis between Enrei BAC-end sequences and the Williams82 genome was carried out to increase the saturation of the map. This physical map will be used to characterize the genome structure of Japanese soybean cultivars, to develop methods for the isolation of agronomically important genes and to facilitate comparative soybean genome research. The current status of physical mapping of the soybean genome and construction of database are presented.     

红莲型水稻不育系和保持系线粒体基因组BAC文库的构建

以红莲型(HL)细胞质雄性不育系和保持系为材料, 构建了水稻线粒体基因组的BAC文库. 每个文库保存约2300个菌落, 外源插入片段介于9～25 kb之间. 以线粒体基因为探针对文库进行菌落原位杂交验证, 均筛选到了阳性克隆. 构建的两个文库为进一步研究水稻线粒体基因组的结构特点, 为克隆与红莲型水稻细胞质雄性不育相关的线粒体基     

The Effect of the "D" Genome from Synthetic Wheat Lines in Anther Culture Responses

Synthetic lines of wheat were compared in order to determine the effect of the “D” genome on embryo induction and plant regeneration from anther culture. The experiments were performed using 6 genotypes of wheat in a randomized block design with 4 replications. In all cases except one, addition of the “D” genome from T. tauschii increased the efficiency of embryo formation and green plantlet production. This positive effect of the “D” genome does not exclude the existence of possible interactions between the three genomes (A, B and D) and/or the effect of each genome separately.     

偏凸山羊草的核型和C-带研究

通过对偏凸山羊草的核型和C-带分析研究表明,偏凸山羊草的D染色体组与节节麦的D染色体组很相似,其可能来自于节节麦;M^V染色体组臂比较大,有2对普通小麦所没有的近端着丝粒染色体,且所显C-带带型与普通小麦的染色体组有明显区别。     

马协型细胞质雄性不育水稻的线粒体DNA研究

采用ＲＦＬＰ分析与分子杂交实验,研究马协型及野败型不育系线粒体基因组的组成,初步证实它们属于不同来源的细胞质;马协型不育系及其保持系线粒体基因组之间也存在明显的限制酶酶切片段长度多态性。