DNA序列在悬钩子属植物分子系统学研究中的应用进展

悬钩子属植物种类繁多,类群复杂,而且多为多倍体和杂种。该文就近年来国内外有关DNA序列在悬钩子属植物分子系统学研究中的应用现状和进展进行了综述,并对中国悬钩子属植物系统发育研究进行了展望。研究认为:叶绿体DNA序列多应用非编码区,且多与ITS序列联合分析;核基因组中ITS序列应用最为广泛,主要用于研究悬钩子属空心莓组与木莓组的进化关系、栽培品种间亲缘关系及部分杂种和多倍体的起源等;在该属植物中发现了ITS个体内多态性,但未进行ITS假基因检测,其系统学应用价值需重新评价;低拷贝核基因只有GBSSI和LEAFY有相关应用。同时认为,悬钩子属植物系统学研究中应用的DNA序列及研究类群均较少,缺乏对整个悬钩子属全面而系统的研究。指出应进一步选择具有代表性的样本、筛选合适的DNA片段,并结合形态学、孢粉学和细胞学等手段对中国悬钩子属植物系统关系进行深入研究。     

稻属分类的现状及存在问题

稻属(Oryza L．是禾本科中重要的植物类群,该属含20余种,广泛分布于全球热带和亚热带地区。未来水稻育种的重大突破还将有赖于对稻属基因库中丰富种质资源,特别是野生稻资源的利用和开发。由于稻属植物在农业生产中的重要作用,引起了众多的植物分类学家、遗传学家、育种学家和分子生物学家的广泛研究。稻属自Linnaeus于1753年建立以来的200多年中,无论在物种的数量和分类系统上都产生了很大的变化。多位学者对稻属的属以下等级和种间的分类都做了详细的工作,对稻属现代分类系统的建立起到了重要的作用。Roschevicz(1931)对稻属全面深入的研究为后来的稻属系统分类奠定了基础。Sharma &; Shastry (1965) 建立的稻属分类系统在很大程度上受了 Roschevicz(1931)工作的影响,对属以下种以上的分类等级也处理得较合理,但是他们对稻属的分类定义较为广泛,包括了好几个如今已不放在稻属的物种。Vaughan(1989)对全球的稻属标本进行了较为全面的查证和研究,他建立的稻属系统不仅在属的界定上更为合理,而且对稻属中各物种的形态变异、地理分布和种间的关系,都有更清楚的描述。遗憾的是,Vaughan (1989)采用的属下等级——“复合体”(complex),不符合国际植物命名法规(ICBN)的规定。Lu(1999)在对前人大量工作的基础上,结合现代对稻属的研究成果并包括了近年来发表的一些新种,建立了稻属3组7系24种的分类系统。本文结合最新的研究成果对稻属作了进一步的修订,列出了以形态特征为基础的分种检索表,并对稻属分类中仍存在的一些问题进行了讨论。     

绞股蓝属植物系统进化研究进展述评

绞股蓝属植物为典型的热带亚洲分布类型,中国是绞股蓝属的现代分布中心和多样化中心。绞股蓝属植物多倍体的系统进化研究表明,该属内广布物种绞股蓝多倍体种群经历了同源多倍化起源的过程。同时,形态学结合分子生物学证据的研究解决了绞股蓝属部分物种间的系统发育关系。分子标记研究结果表明,绞股蓝属植物具有低水平的群体遗传多样性和高水平的种群分化。另外,分子亲缘地理学研究表明,绞股蓝属植物发生了冰期后的种群范围扩张事件,气候波动和环境变迁可能驱使了该属植物的物种分化。本文从以上几方面进行研究述评,以期为绞股蓝属植物资源利用、保护和评价提供科学依据和理论基础。     

利用多基因序列探讨稻属药稻复合体二倍体物种的系统发育关系

稻属药稻复合体Oryza officinalis complex中有5个二倍体物种,涉及B、C和E3个染色体组,分布在亚洲、非洲和大洋洲。其中,O.australiensis是稻属中惟一含E染色体组的物种;O.punctata则是惟一含B染色体组的物种。虽然O.officinalis、O.rhizomatis和O.eichingeri都含C染色体组,但由于它们间断分布在亚洲和非洲,可能在稻属异源多倍体成种中发挥了不同作用。染色体组B、C和E之间,以及上述二倍体物种之间的系统发育关系及其在稻属多倍体物种形成     

基于低拷贝核基因GBBSI的禺毛茛复合体系统进化研究

禺毛茛多倍体复合体及其近缘种系统进化关系复杂,杂交与多倍化现象同时存在。该复合体内高倍性植物的形成及扩散过程仍需进一步研究。首次克隆了毛茛属植物低拷贝核基因颗粒结合型淀粉合成酶 I (GBBSI )基因,并利用其构建禺毛茛多倍体复合体及其近缘种的系统进化树和网状进化关系,进而证明其适合于研究毛茛属植物种下系统发育研究。结果表明：匍枝毛茛与多倍体复合体关系密切,参与了该多倍体复合体的起源和进化;禺毛茛起源于茴茴蒜和卷喙毛茛,扬子毛茛起源于茴茴蒜和匍枝毛茛;在该类群中茴茴蒜是个关键种,它在多倍体复合体中可能起着枢纽基因组的重要作用。     

稻属植物的基因组进化

水稻所在的稻属(Oryza)共有24个左右的物种。由于野生稻含有大量的优良农艺性状基因, 在水稻遗传学研究中日益受到重视。随着国际稻属基因组计划的开展, 越来越多的稻属基因组序列被测定, 稻属成为进行比较、功能和进化基因组学研究的模式系统。近期开展的一系列研究对稻属不同基因组区段以及全基因组序列的比较分析, 揭示了稻属在基因组大小、基因移动、多倍体进化、常染色质到异染色质的转化以及着丝粒区域的进化等方面的分子机制。转座子的活性以及转座子因非均等重组或非法重组而造成的删除, 对稻属基因组的扩增和收缩具有重要作用。DNA双链断裂修复介导的基因移动, 特别是非同源末端连接, 是稻属基因组非共线性基因形成的主要来源。稻属基因组从常染色质到异染色质的转换过程, 伴随着转座子的大量扩增、基因片段的区段性和串联重复以及从基因组其他位置不断捕获异染色质基因。对稻属不同物种间基因拷贝数、特异基因和重要农艺性状基因的进化等研究, 可揭示稻属不同物种间表型和适应性差异的分子基础, 将加速水稻的育种和改良。     

芸薹属植物比较基因组学研究进展

芸薹属(Brassica)植物是双子叶植物比较基因组学研究的重点对象。经过十几年的研究, 芸薹属植物比较基因组学研究已取得很大进展。宏观共线性和微观共线性两个层次的研究均发现, 芸薹属植物之间以及芸薹属和拟南芥之间都存在广泛的共线性, 表明拟南芥信息在芸薹属中具有重要应用价值。芸薹属作物基因组内存在着多个拷贝的共线性区域, 支持二倍体芸薹属作物起源于多倍体祖先的假设。     

芸薹属植物比较基因组学研究进展

芸薹（Brassica）植物是双子叶植物比较基因组学研究的重点对象。经过十几年的研究,芸薹属植物比较基因组学研究已取得很大进膜。宏观共线性和微观共线性两个层次的研究均发现,芸薹属植物之间以及芸薹属和拟南芥之间都存在广泛的共线性,表明拟南芥信息在芸薹属中具有重要应用价值。芸薹属作物基因组内存在着多个拷贝的共线性区域,支持二倍体芸薹属作物起源于多倍体祖先的假设。     

山茶属植物的染色体数目和核型

本文对已报道的(包括作者的研究)山茶属植物的染色体数目和核型作一简单的讨论,结合地理分布情况,提出由二倍体向多倍体进化可能是山茶属植物进化的一个重要途径。山茶属植物的核型多为Stebbins核型分类的“2A”型,表明山茶属植物是一个较原始的种系。本文中12种的染色体数目和2种的核型为首次报道。     

青藏高原六种棘豆属植物的染色体数目及核型报道

对6种棘豆属植物（Oxytropis）的13个居群样进行细胞学研究,其中黄花棘豆（O．ochrocephala）、绢毛棘豆（O．tatarica）、甘肃棘豆（O．kansuensis）和铺地棘豆（0．humifusa）为首次报道染色体数目（2n=16）和核型;在胀果棘豆（O．stracheyana）中（2n=48）首次发现B染色体。现有的细胞学资料表明：棘豆属植物中多倍体占总报道数的58％,这说明多倍化在本属植物的进化过程中起着非常重要的作用,但青藏高原仅有一种植物发现多倍体,多倍化并不占主导地位,而主要表现为二倍体水平上的结构变异,即核型不对称性的变化。     

Origins and introgression of polyploid species in Mentzelia section Trachyphytum (Loasaceae)

? Premise of the study: Polyploid speciation has been important in plant evolution. However, the conditions that favor the origination and persistence of polyploids are still not well understood. Here, we examine origins of 16 polyploid species in Mentzelia section Trachyphytum. ? Methods: We used phylogeny reconstructions based on DNA sequences from plastid regions and the nuclear gene isocitrate dehydrogenase (idh) to construct hypotheses of introgression and polyploidization. ? Key results: Molecular data suggest that homoploid hybridization has been surprisingly common in Trachyphytum. Diploid species had unequal involvement in polyploid origins, but most polyploid taxa had allopolyploid origins from extant progenitors. A few polyploids with extreme phenotypes did not appear to have extant progenitors. We infer that the progenitors of these species were derived from extinct diploid lineages or ancestral lineages of multiple extant diploids. In agreement with other recent studies, we recovered molecular evidence of multiple phylogenetically distinct origins for several polyploid taxa, including the widespread octoploid M. albicaulis. ? Conclusions: Evidence of high levels of introgression and allopolyploidy suggests that hybridization has played an important role in the evolution of Trachyphytum. Although idh sequences exhibited complicated evolution, including gene duplication, deletion, and recombination, they provided a higher percentage of informative characters for phylogeny reconstruction than the most variable plastid regions, allowing tests of hypotheses regarding polyploid origins. Given the necessity for rapidly evolving low-copy nuclear genes, researchers studying hybridization and polyploidy may increasingly turn to complex sequence data.     

High-resolution phylogeny for Helianthus (Asteraceae) using the 18S-26S ribosomal DNA external transcribed spacer

The sunflower genus, Helianthus, is recognized widely for the cultivated sunflower H. annuus and scientifically as a model organism for studying diploid and polyploid hybrid speciation, introgression, and genetic architecture. A resolved phylogeny for the genus is essential for the advancement of these scientific areas. In the past, phylogenetic relationships of the perennial species and polyploid hybrids have been particularly difficult to resolve. Using the external transcribed spacer region of the nuclear 18S-26S rDNA region, we reveal for the first time a highly resolved gene tree for Helianthus. Phylogenetic analysis allowed the determination of a monophyletic annual H. sect. Helianthus, a two-lineage polyphyletic H. sect. Ciliares, and the monotypic H. sect. Agrestis, all of which were nested within a large perennial and polyphyletic H. sect. Divaricati. The distribution of perennial polyploids and known annual diploid hybrids on this phylogeny suggested multiple independent hybrid speciation events that gave rise to at least four polyploids and three diploid hybrids. Also provided by this phylogeny was evidence for homoploid hybrid speciation outside H. sect. Helianthus. Finally, previous hypotheses about the secondary chemistry in the genus were tested in a phylogenetic framework to obtain a better understanding of the evolution of these compounds in Helianthus.     

Polyploid plants have faster rates of multivariate niche differentiation than their diploid relatives

Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids. We found that polyploids are often more climatically differentiated from their diploid parents than the diploids are from each other. Consistent with this pattern, we estimated that polyploid species generally have higher rates of multivariate niche differentiation than their diploid relatives. In contrast to recent analyses, our results confirm that ecological niche differentiation is an important component of polyploid speciation and that niche differentiation is often significantly faster in polyploids.     

Assessing the monophyly of polyploid Gossypium species

The origin and monophyly of the polyploid cotton (Gossypium) species has been largely accepted, despite the lack of explicit phylogenetic evidence. Recent studies in other polyploid systems have demonstrated that multiple origins for polyploid species are much more common than once thought, raising the possibility that Gossypium polyploids also had multiple origins, as postulated by some authors. To test the monophyly of polyploid cotton, we sequenced a 2.8-kb intergenic region from all diploid species belonging to the genome groups from which the polyploid originates. The resulting phylogenetic analyses strongly support a single origin of polyploid cotton involving a D-genome ancestor related to Gossypium raimondii and an A-genome ancestor that was sister to both extant A-genome species.     

Chromosomes associate premeiotically and in xylem vessel cells via their telomeres and centromeres in diploid rice (<Emphasis Type="Italic">Oryza sativa</Emphasis>)

Studies of the meiosis of diploid plants such as Arabidopsis, maize and diploid progenitors of wheat have revealed no premeiotic association of chromosomes. Premeiotic and somatic association of chromosomes has only been previously observed in the anther tissues and xylem vessel cells of developing roots in polyploid plants such as hexaploid and tetraploid wheat, polyploid relatives of wheat and artificial polyploids made from the progenitor diploids of wheat. This suggested that this association was confined specifically to polyploids or was induced by polyploidy. However, we developed procedures for in situ hybridization on structurally well-preserved tissue sections of rice, and analysed two diploid rice species (Oryza sativa and O. punctata). Contrary to expectation, this has revealed that centromeres and telomeres also associate both in the xylem vessel cells of developing root and in undifferentiated anther cells in these diploids. However, in contrast to wheat and related polyploids, where the initial association in undifferentiated anthers is between either non-homologous or related chromosomes, and not homologous chromosomes, the initial association of rice chromosomes seems to be between homologues. Thus, in contrast to the diploid dicot model Arabidopsis, meiotic studies on the diploid model cereal, rice, will now need to take into account the effects of premeiotic chromosome association.Pilar Prieto and Ana Paula Santos are joint first authors.     

The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae)

BACKGROUND: In studies looking at individual polyploid species, the most common patterns of genomic change are that either genome size in the polyploid is additive (i.e. the sum of parental genome donors) or there is evidence of genome downsizing. Reports showing an increase in genome size are rare. In a large-scale analysis of 3008 species, genome downsizing was shown to be a widespread biological response to polyploidy. Polyploidy in the genus Nicotiana (Solanaceae) is common with approx. 40 % of the approx. 75 species being allotetraploid. Recent advances in understanding phylogenetic relationships of Nicotiana species and dating polyploid formation enable a temporal dimension to be added to the analysis of genome size evolution in these polyploids. METHODS: Genome sizes were measured in 18 species of Nicotiana (nine diploids and nine polyploids) ranging in age from <200,000 years to approx. 4.5 Myr old, to determine the direction and extent of genome size change following polyploidy. These data were combined with data from genomic in situ hybridization and increasing amounts of information on sequence composition in Nicotiana to provide insights into the molecular basis of genome size changes. KEY RESULTS AND CONCLUSIONS: By comparing the expected genome size of the polyploid (based on summing the genome size of species identified as either a parent or most closely related to the diploid progenitors) with the observed genome size, four polyploids showed genome downsizing and five showed increases. There was no discernable pattern in the direction of genome size change with age of polyploids, although with increasing age the amount of genome size change increased. In older polyploids (approx. 4.5 million years old) the increase in genome size was associated with loss of detectable genomic in situ hybridization signal, whereas some hybridization signal was still detected in species exhibiting genome downsizing. The possible significance of these results is discussed.     

Propagule pressure and the establishment of emergent polyploid populations

BackgroundWhereas the incidence or rate of polyploid speciation in flowering plants is modest, the production of polyploid individuals within local populations is widespread. Explanations for this disparity primarily have focused on properties or interactions of polyploids that limit their persistence.HypothesisThe emergence of local polyploid populations within diploid populations is similar to the arrival of invasive species at new, suitable sites, with the exception that polyploids suffer interference from their progenitor(s). The most consistent predictor of successful colonization by invasive plants is propagule pressure, i.e. the number of seeds introduced. Therefore, insufficient propagule pressure, i.e. the formation of polyploid seeds within diploid populations, ostensibly is a prime factor limiting the establishment of newly emergent polyploids within local populations. Increasing propagule number reduces the effects of genetic, environmental and demographic stochasticity, which thwart population survival. As with invasive species, insufficient seed production within polyploid populations limits seed export, and thus reduces the chance of polyploid expansion.ConclusionThe extent to which propagule pressure limits the establishment of local polyploid populations remains to be determined, because we know so little. The numbers of auto- or allopolyploid seed in diploid populations rarely have been ascertained, as have the numbers of newly emergent polyploid plants within diploid populations. Moreover, seed production by these polyploids has yet to be assessed.     

Phylogeny and molecular evolution of the DMC1 gene within the StH genome species in Triticeae (Poaceae)

To estimate the phylogeny and molecular evolution of a single-copy nuclear disrupted meiotic cDNA (DMC1) gene within the StH genome species, two DMC1 homoeologous sequences were isolated from nearly all the sampled StH genome species and were analyzed with those from seven diploid taxa representing the St and H genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) there is a close relationship among North American StH genome species; (2) the DMC1 gene sequences of the StH genome species from North America and Eurasia are evolutionarily distinct; (3) the StH genome polyploids have higher levels of sequence diversity in the St genome homoeolog than the H genome homoeolog; (4) the DMC1 sequence may evolve faster in the polyploid species than in the diploids; (5) high dN and dN/dS values in the St genome within polyploid species could be caused by low selective constraints or AT-biased mutation pressure. Our result provides some insight on evolutionary dynamics of duplicate DMC1 gene, the polyploidization events and phylogeny of the StH genome species.     

普通小麦7B染色体两类低拷贝专化DNA序列的特性

研究表明 ,多倍体小麦基因组中存在一类低拷贝、染色体专化的DNA序列 ,其在多倍体形成时常表现出不稳定性。这类序列被认为在异源多倍体的建立和稳定中起着关键作用。为进一步研究这一问题 ,对通过染色体显微切割从普通小麦 (TriticumaestivumL .)中分离的 5个 7B染色体专化DNA序列的特性进行了研究。以这些序列为探针对大量的多倍体小麦和它们的二倍体祖先物种进行了Southern杂交分析。结果表明 ,这些序列可被分为两种类型 :其中的 4个序列与所有的多倍体物种均杂交 ,但是在二倍体水平上 ,它们却只与和多倍体小麦B基因组紧密相关的物种杂交 ,这说明这些序列是在二倍体物种分化以后产生的 ,然后垂直传递给多倍体 ;其中的 1个序列与所有的二倍体及多倍体物种均杂交 ,暗示在多倍体形成后这些序列从A和D基因组中消除了。用这一序列分别与一个人工合成的六倍体和四倍体小麦进行Southern杂交的结果表明 ,序列消除是一个迅速的事件而且很可能与这些序列的甲基化状态有关。认为这些低拷贝的染色体专化序列对于多倍体形成后部分同源染色体之间的进一步分化起着重要作用。     

A bivalent polyploid model for mapping quantitative trait loci in outcrossing tetraploids

Two major aspects have made the genetic and genomic study of polyploids extremely difficult. First, increased allelic or nonallelic combinations due to multiple alleles result in complex gene actions and interactions for quantitative trait loci (QTL) in polyploids. Second, meiotic configurations in polyploids undergo a complex biological process including either bivalent or multivalent formation, or both. For bivalent polyploids, different degrees of preferential chromosome pairings may occur during meiosis. In this article, we develop a maximum-likelihood-based model for mapping QTL in tetraploids by considering the quantitative inheritance and meiotic mechanism of bivalent polyploids. This bivalent polyploid model is implemented with the EM algorithm to simultaneously estimate QTL position, QTL effects, and QTL-marker linkage phases by incorporating the impact of a cytological parameter determining bivalent chromosome pairings (the preferential pairing factor). Simulation studies are performed to investigate the performance and robustness of our statistical method for parameter estimation. The implication and extension of the bivalent polyploid model are discussed.