多年生植物模式物种基因组研究的历史及进展

木本植物有许多不同于一年生草本植物的生物学特性,生物学家提出将木本植物 作为研究多年生植物的模式体系。杨属Populus树种由于研究基础较好且基因组较小,目前已 被广泛地接受作为多年生植物基因组研究的模式物种。随着杨属树种全基因组序列的测定, 杨属树种在多年生植物的功能基因组研究及一些基础科学问题的研究中将发挥重要作用。本 文综述了杨属树种基因组研究的历史、进展及将来的研究热点,旨在为我国多年生植物基因 组研究提供参考和借鉴。本文主要论述了以下几个方面的内容:（1）对杨属树种开展的细胞 遗传学研究;（2）在分子水平上对杨属树种进行的基因组研究,内容包括遗传作图、基因组 测序、物理图谱构建、基因芯片及连锁不平衡分析;（3）杨属树种基因组信息在探讨一些基 础科学问题中的潜在应用。     

基于cpDNA和rDNA ITS片段分析西南地区青杨派杨树的系统发育与进化关系

西南地区青杨派杨树种质资源丰富,可为杨树遗传改良提供珍贵的基因资源,但树种之间形态学差异细微,该研究以山杨作为外类群,测定了西南地区及其他地区杨属青杨派17个种(杂种)共36份样本的3个叶绿体片段(atpF-atpH、trnL-F和matK)和核糖体ITS片段,并对其进行系统发育分析,以探讨西南地区青杨派树种的系统进化关系。结果表明:(1)在所有样本中,3个叶绿体片段atpF-atpH、trnL-F、matK的长度分别为605~634bp、957~1 010bp、819bp,3个片段拼接后的联合序列包含29个变异位点和15个信息位点;ITS片段对齐后的长度为646bp,变异位点19个,信息位点17个。(2)基于叶绿体联合序列和ITS片段的杨属青杨派树种的平均遗传距离分别为0.001 3和0.003 6。叶绿体联合片段的MP和Bayes系统树树型基本一致,青杨派树种可以划分为2组,第1组由青杨、三脉青杨、大青杨和辽杨构成;第2组中的小叶杨、小青杨、川杨、德钦杨、昌都杨、乡城杨、康定杨、西南杨、滇杨和藏川杨不能有效区分,且均与缘毛杨的遗传关系较近。(3)基于ITS的系统树与叶绿体联合片段构建的系统树差异不大,仅在于第2组中的小青杨与小叶杨、川杨等差异明显,与第1组中的树种紧密聚拢。     

河狸,濒危在生态工程中

2005年,我怀着激动期盼的心情再次踏入布尔根河狸保护区,并沿乌伦古河进行了考察,亲身感受到了乌伦古河经过15年后的巨大变迁。布尔根已于1992年开放口岸(塔克什肯口岸),原来的小村子变成了目前的大镇子,随着河岸常居人口的迅猛增加并伴随着河谷水土开发,原来茂密的河谷林已变成"稀树荒漠草原",我以前曾多次留恋观察的几个河狸     

用ITS序列研究杨属各组之间的系统发育关系

杨树是重要的工业用材树种。我国杨树遗传资源丰富 ,分布范围广泛 ,不少种为我国特有。开展杨属系统发育和分子进化研究 ,对丰富的杨树遗传资源保存和利用有着重大意义。杨属 (Ｐｏｐｕｌｕｓ)全世界约 10 0余种 ,属下通常分 5个组[1] 。胡志昂等[2 ] 对杨属不同组间的过氧化物酶同工酶进行了研究 ;李宽钰等[3] 利用ＲＡＰＤ标记技术对白杨组、青杨组、黑杨组 2 0个种作了遗传分析。但是在杨属系统分类上还存在着许多混乱 ,同物异名、同名异物现象相当普遍。本文以杨属 5个派主要代表种为材料 ,用ＰＣＲ产物直接测序法测定杨树ＩＴＳ序列 ,…     

杨属的分支分析

根据被子植物大系统的资料和形态学观察确定了大凤子科山桐子属为杨属的外来群,即假设的祖先类群,借以确定杨属性状的极性,通过简约性分析构建了杨属有根的Wagner树,把杨属的五个组分为演化趋势上的三支:第一支为最原始的白杨组;第二支为变异较大的大叶杨组和青杨组;第三支是歧化的黑杨组和胡杨组。     

青藏高原杨属化石概述

杨属是北半球温带森林生态系统中一个重要的乔木属。文中概述了青藏高原古近纪和新近纪的杨属化石记录,并根据最新的地层学和年代学数据,对化石的时代进行厘定。化石记录显示杨属在青藏高原最早出现于始新世最晚期。在渐新世和中新世杨属在青藏高原的南部和北部都有较多的化石,但在高原中部尚未见记录。青藏高原具有杨属的化石植物群大多数都是温带落叶阔叶的河岸植被,进一步证实杨属在其演化历史早期就偏好温带近河岸的环境。青藏高原北部的早渐新世植物群中杨属多样性较高,并占据显著优势,表明这一地区在杨属早期分化中具有重要作用。     

怒江中游西藏境内干旱河谷荒漠植被特征

基于实地调查资料,对西藏境内怒江中游河谷的特殊荒漠型植被进行了研究。结果表明：（1）22个样方中有85种维管植物,其种子植物属的分布区类型以泛热带分布为主,占21．6％;种以中国特有分布中的西南特有成分为主,占53．2％;（2）生活型谱以矮高位芽植物为主,占41．2％,地面芽植物占40．0％;（3）采用Raunkiaer频度分析,出现在10个以上样方中的物种有白刺花、垫状卷柏、芸香草和阔盖中国蕨等,频度分别是68．2％、50．0％、50．0％、45．5％;（4）根据该河谷区域的气候特点、干旱程度、群落的生态外貌特征和生活型等,并结合《中国植被》对灌丛和荒漠的划分,认为该河谷区域的植被盖度极低,不属于灌丛类型,而是非地带性的干旱河谷型荒漠植被。     

青藏高原杨属化石概述（英文）

杨属是北半球温带森林生态系统中一个重要的乔木属。文中概述了青藏高原古近纪和新近纪的杨属化石记录,并根据最新的地层学和年代学数据,对化石的时代进行厘定。化石记录显示杨属在青藏高原最早出现于始新世最晚期。在渐新世和中新世杨属在青藏高原的南部和北部都有较多的化石,但在高原中部尚未见记录。青藏高原具有杨属的化石植物群大多数都是温带落叶阔叶的河岸植被,进一步证实杨属在其演化历史早期就偏好温带近河岸的环境。青藏高原北部的早渐新世植物群中杨属多样性较高,并占据显著优势,表明这一地区在杨属早期分化中具有重要作用。     

应用SRAP标记分析新疆地区主要杨属树种的遗传多样性

用30对SRAP引物对15个采集于新疆不同地区的杨属树种进行了遗传多样性分析,共扩增出881条具多态性的条带,平均多态性信息量为0．958,平均多态性比率为96．8％．通过聚类分析将15个杨树材料分为4个群．这一聚类结果与传统的分类基本上一致。这表明SRAP标记适用于研究杨属树种遗传多样性。     

荒漠英雄——胡杨

胡杨,维吾尔语称为托克拉克,意为“最美丽的树”。它主要分布于欧、亚、非沙漠和干旱荒漠的盆地与河谷两岸,在我国新疆、内蒙、甘肃、陕西和宁夏等地均有生长,其中在新疆塔里木流域呈走廊式分布的胡杨林有35.2万公顷,是目前世界上最大的一片天然原始树种。胡杨林在塔里木河、叶尔羌河、和田河和克里雅河的滋润下,犹如一条绿色长城环抱着塔克拉玛干大沙漠,不仅起到了防沙固沙、阻挡流沙移动的作     

Barrier to gene flow between two ecologically divergent Populus species, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history in gene introgression

The renewed interest in the use of hybrid zones for studying speciation calls for the identification and study of hybrid zones across a wide range of organisms, especially in long-lived taxa for which it is often difficult to generate interpopulation variation through controlled crosses. Here, we report on the extent and direction of introgression between two members of the "model tree" genus Populus: Populus alba (white poplar) and Populus tremula (European aspen), across a large zone of sympatry located in the Danube valley. We genotyped 93 hybrid morphotypes and samples from four parental reference populations from within and outside the zone of sympatry for a genome-wide set of 20 nuclear microsatellites and eight plastid DNA restriction site polymorphisms. Our results indicate that introgression occurs preferentially from P. tremula to P. alba via P. tremula pollen. This unidirectional pattern is facilitated by high levels of pollen vs. seed dispersal in P. tremula (pollen/seed flow = 23.9) and by great ecological opportunity in the lowland floodplain forest in proximity to P. alba seed parents, which maintains gene flow in the direction of P. alba despite smaller effective population sizes (N(e)) in this species (P. alba N(e)c. 500-550; P. tremula N(e)c. 550-700). Our results indicate that hybrid zones will be valuable tools for studying the genetic architecture of the barrier to gene flow between these two ecologically divergent Populus species.     

Detection of a variable number of ribosomal DNA loci by fluorescent in situ hybridization in Populus species

Fluorescent in situ hybridization (FISH) was applied to related Populus species (2n = 19) in order to detect rDNA loci. An interspecific variability in the number of hybridization sites was revealed using as probe an homologous 25S clone from Populus deltoides. The application of image analysis methods to measure fluorescence intensity of the hybridization signals has enabled us to characterize major and minor loci in the 18S-5.8S-25S rDNA. We identified one pair of such rDNA clusters in Populus alba; two pairs, one major and one minor, in both Populus nigra and P. deltoides; and three pairs in Populus balsamifera, (two major and one minor) and Populus euroamericana (one major and two minor). FISH results are in agreement with those based on RFLP analysis. The pBG13 probe containing 5S sequence from flax detected two separate clusters corresponding to the two size classes of units that coexist within 5S rDNA of most Populus species. Key words : Populus spp., fluorescent in situ hybridization, FISH, rDNA variability, image analysis.     

Evaluation of qPCR reference genes in two genotypes of Populus for use in photoperiod and low-temperature studies

ABSTRACT: BACKGROUND: Quantitative PCR (qPCR) is a widely used technique for gene expression analysis. A common normalization method for accurate qPCR data analysis involves stable reference genes to determine relative gene expression. Despite extensive research in the forest tree species Populus, there is not a resource for reference genes that meet the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) standards for qPCR techniques and analysis. Since Populus is a woody perennial species, studies of seasonal changes in gene expression are important towards advancing knowledge of this important developmental and physiological trait. The objective of this study was to evaluate reference gene expression stability in various tissues and growth conditions in two important Populus genotypes (P. trichocarpa "Nisqually 1" and P. tremula X P. alba 717 1-B4) following MIQE guidelines. RESULTS: We evaluated gene expression stability in shoot tips, young leaves, mature leaves and bark tissues from P. trichocarpa and P. tremula. x P. alba grown under long-day (LD), short-day (SD) or SD plus low-temperatures conditions. Gene expression data were analyzed for stable reference genes among 18S rRNA, ACT2, CDC2, CYC063, TIP4-like, UBQ7, PT1 and ANT using two software packages, geNormPLUS and BestKeeper. GeNormPLUS ranked TIP4-like and PT1 among the most stable genes in most genotype/tissue combinations while BestKeeper ranked CDC2 and ACT2 among the most stable genes. CONCLUSIONS: This is the first comprehensive evaluation of reference genes in two important Populus genotypes and the only study in Populus that meets MIQE standards. Both analysis programs identified stable reference genes in both genotypes and all tissues grown under different photoperiods. This set of reference genes was found to be suitable for either genotype considered here and may potentially be suitable for other Populus species and genotypes. These results provide a valuable resource for the Populus research community.     

Comparative genome mapping among Populus adenopoda, P. alba, P. deltoides, P. euramericana and P. trichocarpa

Among the genus Populus, the sections Populus (white poplar), Aigeiros Duby (black poplar) and Tacamahaca Spach contain many tree species of economical and ecological important properties. Two parental maps for the inter-specific hybrid population of Populus adenopoda × P. alba (two species of Populus section) were constructed based on SSR and SRAP markers by means of a two-way pseudo-test cross mapping strategy. The same set of SSR markers developed from the P. trichocarpa (belonging to Tacamahaca section) genome which were used to construct the maps of P. deltoides and P. euramericana (two species of Aigeiros section) was chosen to analyze the genotype of the experimental population of P. adenopoda × P. alba. Using the mapped SSR markers as allelic bridges, the alignment of the white and black poplar maps to each other and to the P. trichocarpa physical map was conducted. The alignment showed high degree of marker synteny and colinearity and the closer relationship between Aigeiros and Tacamahaca sections than that of Populus and Tacamahaca. Moreover, there was evidence for the chromosomal duplication and inter-chromosomal reorganization involving some poplar linkage groups, suggesting a complicated course of fission or fusion in one of the lineages. A poplar consensus map based on the comparisons could be constructed will be useful in practical applications including marker assisted selection.     

Admixture in European Populus hybrid zones makes feasible the mapping of loci that contribute to reproductive isolation and trait differences

The use of admixed human populations to scan the genome for chromosomal segments affecting complex phenotypic traits has proved a powerful analytical tool. However, its potential in other organisms has not yet been evaluated. Here, we use DNA microsatellites to assess the feasibility of this approach in hybrid zones between two members of the 'model tree' genus Populus: Populus alba (white poplar) and Populus tremula (European aspen). We analyzed samples of both species and a Central European hybrid zone (N=544 chromosomes) for a genome-wide set of 19 polymorphic DNA microsatellites. Our results indicate that allele frequency differentials between the two species are substantial (mean delta=0.619+/-0.067). Background linkage disequilibrium (LD) in samples of the parental gene pools is moderate and should respond to sampling schemes that minimize drift and account for rare alleles. LD in hybrids decays with increasing number of backcross generations as expected from theory and approaches background levels of the parental gene pools in advanced generation backcrosses. Introgression from P. tremula into P. alba varies strongly across marker loci. For several markers, alleles from P. tremula are slightly over-represented relative to neutral expectations, whereas a single locus exhibits evidence of selection against P. tremula genotypes. We interpret our results in terms of the potential for admixture mapping in these two ecologically divergent Populus species, and we validate a modified approach of studying genotypic clines in 'mosaic' hybrid zones.     

Camouflage and selective predation in caterpillars of the poplar and eyed hawkmoths (Laothoe populi and Smerinthus ocellata)

Final instar caterpillars of the poplar hawkmoth ( Laothoe populi ) are usually yellow-green when they have been feeding on Salix fragilis but white when on Populus alba. Similarly final instar caterpillars of the eyed hawkmoth (Smerinthus ocellata) vary in colour from yellow-green when fed on Salix cinerea or S. fragilis to grey-green when fed on Salix ripens or S. alba. Most caterpillars of these two moths are thus very cryptic to the human eye. It has already been shown that colour matching is brought about by young caterpillars changing colour depending on the colour of the substrate perceived by their eyes. Evidence is presented here for selective predation, probably by birds. Yellow-green poplar hawk caterpillars disappeared from P. alba more rapidly than did white caterpillars, but there was no significant difference in the survival of the two colour forms on S. fragilis. Yellow-green caterpillars survived better on S. fragilis than on P. alba , but there was no significant difference in the survival of white caterpillars on the two plants. Reasons why selective predation did not occur in all of the experiments are discussed.     

沈阳城市森林主要树种叶片形态生态特征与生长规律

利用统计和多元分析方法研究了沈阳城市森林10个主要树种叶片的形态生态特征和生长规律.结果表明,影响树木叶片生长发育节律的主要气象因子是≥5 ℃积温、累积日照时数和各物候期中旬平均温度.不同物候期树木所需要的气象因子有所变化,树木萌动期要求低温和寒冷指数,而在生长期需要一定的温暖指数和湿润指数.10个树种的叶片形态数量特征差异较大,按叶形指数依次为短序胡枝子＞华北丁香＞国槐＞银白杨＞红瑞木＞金银忍冬＞水腊＞水曲柳＞稠李＞黄菠萝;按叶面积依次为华北丁香＞银白杨＞黄菠萝＞稠李＞水曲柳＞红瑞木＞短序胡枝子＞金银忍冬＞国槐＞水腊.在10个树种叶长度与宽度、周长、叶面积之间相互关系中,基本属于异速生长类型,符合y=ax^k模型,但在叶长度与宽度之间关系中,除银白杨k＞1外,其它9个树种均k＜1;在叶长度与周长关系中,黄菠萝k＞1, 银白杨k≈1,呈线性关系,其它树种均k＜1;在叶长度与叶面积关系中,10个树种k＞1,而 银白杨k=2.1028,叶面积增长速率近似于叶长的2倍.建立了10个树种的叶面积最优回归估测模型,并对模型进行了估测检验.     

Proof of the indigenous nature of Populus alba L. in the western Mediterranean Basin

Around the western Mediterranean Basin, the ecological status of Populus alba, whether indigenous or introduced, is controversial. This note presents new palaeobotanical data based on analyses of leaf imprints from a travertine formation located in southern France. This travertine presents two levels with Populus alba imprints. The oldest level is dated back by 14C to the Early Holocene, i.e., 8890 +/- 70 BP. This demonstrates that Populus alba is an autochthonous species of the southern-France vegetation, removing speculations reporting that its distribution area was greatly influenced by Roman civilization. Finally, we discuss this new data in regard to other Pleistocene and Holocene deposits circum the Mediterranean Basin and in Europe, where this species was identified.     

干旱区人工防护林带不同林分凋落叶分解及养分释放

2007年10月下旬至2008年11月,采用原位模拟分解网袋法,对新疆克拉玛依市区北郊人工防护林新疆杨、紫穗槐及二者混合凋落叶进行为期365 d的分解及养分释放动态试验.结果表明：树种不同,凋落叶质量损失率的动态变化不同;凋落叶组成对质量损失率有显著影响,与单优林凋落叶相比,紫穗槐与新疆杨凋落叶混合后更易于分解.经修正Olson负指数衰减模型分析,新疆杨凋落叶分解系数最低(k=0.167),混合凋落叶分解系数最高(k=0.275),估测3种凋落叶半分解和95％分解所需时间为2.41～4.19 a和10.79～17.98 a.不同的分解时期3种凋落叶中N、P和K的残留率不同,分解1年后,K为净释放,N和P为固持或从周围环境中吸收而富集.分解过程中,除紫穗槐凋落叶在分解中期有机碳分解率下降外,其他处理凋落叶有机碳分解率均不断上升,1年后分解率在35.5%～44.2%之间.C/N值基本呈下降趋势,分解前期和中期下降幅度较小,后期下降较快.     

Preliminary interspecific genetic maps of the populus genome constructed from RAPD markers.

We have constructed RAPD-based linkage maps for an interspecific cross between two species of the genus Populus (P. adenopoda and P. alba), based on a double pseudo-test-cross strategy. Of a total of 360 polymorphic fragments scored, 290 showed a test-cross configuration, corresponding to DNA polymorphisms heterozygous in one parent and null in the other. In the female parent, P. adenopoda, 82 markers were grouped in 19 different linkage groups (553 cM), whereas in the male parent P. alba, 197 markers established a much more complete framework map with an observed genome length of 2300 cM covering 87% of the total P. alba genome. The larger number of test-cross markers detected for the P. alba parent than for the P. adenopoda parent might be due to a higher level of heterozygosity in the former than in the latter. In this study, we detected only a small percentage (2%) of the intercross dominant markers heterozygous in both parents and segregating 3:1 in the progeny. The further focus in this mapping study should be on the identification of more intercross markers, to align the two parent-specific maps into a consensus map for mapping important genes causing species differentiation during long evolutionary divergences.