860 resultados para population genetic structure


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本文以采自云南、贵州和台湾三个地区的九个台湾杉群体为材料,应用同工酶分析技术对其群体遗传结构进行了测定和分析,结果发现台湾杉的遗传多样性的几个指标P,A He(P=44.4%,A=1.5,He=0.141)均比一般针叶树种的平均值(P=67.7%,A=2.29,He=0.207)为低,推此较低的遗传多样性主要与台湾杉的进化历史有关,台湾杉的基因分化系数Gst(Gst=0.109)为0.109,符合其风媒异花授粉的特点。利用所获得的有关遗传多样性和群体遗传结构方面的数据不仅能对台湾杉属的分类提供新的佐证,更为实现对其更好的保护和利用提供了不可缺少的本底资料。

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青杨(Populus cathayana Rehd.)是青杨派杨树的主要树种之一,为我国特有乡土树种,其主要分布区之一是我国的青藏高原,集中分布地带在甘肃省中部及青海省东部,四川省西北部岷江上游和松潘等地区。本研究以青藏高原东缘青杨天然分布区的6个群体143个个体为材料,用AFLP、SSR和叶绿体SSR分子标记分析青杨天然群体的遗传多样性,分析其遗传结构和分化,比较6个群体间遗传多样性的高低和群体间的遗传关系。旨在为青杨基因资源评价、保护与保存、遗传改良策略制定等提供科学理论依据。通过以上研究,得出如下主要研究结果: 1 AFLP分子标记研究结果 采用4对选择性引物对6个青杨天然群体143个个体进行分析,扩增谱带分析共检测到175个位点,其中173个位点表现为多态,多态位点百分率高达98.9%。从整体上表现出较高的遗传多样性,Nei’s基因多样度(h)水平为0.306。从青杨天然群体位点分布来看,有高达20%的位点(32位点)为群体所特有,仅有9.14%的位点(16位点)在所有群体中存在。群体间的遗传分化极大,所有遗传变异中,有48.9%的遗传变异存在于群体间。在个体群丛(Individuals cluster)和主坐标(PCO analysis)分析中,青杨各群体未呈现任何地理模式,Mantel检测也显示各群体间遗传距离与地理距离无明显相关。研究认为,由于地理和空间上大尺度的隔离和地形地貌复杂使得群体间无法进行基因交流,导致群体间遗传分化极大,另外各群体在不同的选择压力下,经历各自独立的进化历程,这些都可能导致群体间遗传距离与地理距离的不相关。 2 SSR分子标记研究结果 在SSR分析中,7个位点在6个青杨天然群体143个个体中共检测到79个等位基因,每位点检测到的等位基因数在5-16之间,平均11.3个,总体上多态位点百分率达100%。平均观察杂合度和期望杂合度分别为0.792和0.802。Hardy-Weinberg平衡检验表明青杨大部分群体都处于非平衡状态,群体大部分位点都是偏离哈迪-温伯格平衡(76.3%),只有23.7%的测验满足哈迪-温伯格平衡。分析青杨天然群体内和群体间的遗传变异,基因分化系数(GST)为0.373,即有62.7%的遗传变异存在群体内,37.3%的遗传变异存在群体间。群体内的遗传变异高于群体间水平。根据各群体遗传距离UPGMA聚类分析,有来自相临分布区、近似气候类型的群体聚在一起的趋势,但Mantel检测反映遗传距离与地理距离间并无明显相关性。 3 cpSSR分子标记研究结果 分析来自青藏高原东缘6个青杨天然群体,所用cpSSR引物中有5对cpSSR引物(CCMP2、CCMP5、SCUO01、SCU03、SCU07)都表现较高的多态性,单个引物检测的片段数都在4以上。5对cpSSR引物共检测片段数26个,组成了12种叶绿体DNA单倍型。各群体的单倍型分布和频率有较大差异,群体单倍型多样性范围为0-0.4926,TS、JZ、PW和SHY群体单倍型多样性高于QHY和LED群体水平。本研究发现,分布在青藏高原东缘的青杨天然群体,群体间不存在共享的单倍型,各群体间存在极大的遗传分化(GST=0.9223)。从青藏高原东缘地区经历的地质历史事件来看,第四纪的冰期气候变迁可能是造成青杨现今遗传结构模式的主要因素之一。根据单倍型在各群体的分布情况,进行青杨群体聚类分析结果,各群体无明显的分组现象,青杨各群体也未呈现任何清晰地理模式。 由于不同分子标记在对群体遗传多样性检测能力与效率上存在差异,所以三种标记检测的青藏高原东缘青杨天然群体遗传多性水平也不尽一致,但在与用同种方法检测其它物种或同一物种不同种源群体比较,三种分子标记方法都揭示了青藏高原东缘青杨天然群体具有中等偏上的遗传多样性水平。结果分析表明,群体间遗传分化极大,这是由于青杨天然群体分布于青藏高原东缘,既有高原又有高山峡谷,由于地理和空间上大尺度的隔离和地形地貌复杂导致了基因流物理上的阻隔。三种分子标记研究结果经Mantel分析检测,遗传距离与地理距离之间都无明显相关性。较为一致的解释是,青杨分布区域地理和空间上大尺度的隔离和和地形地貌复杂导致群体之间不存在均匀扩散现象,另外各群体在不同的选择压力下,经历各自独立的进化历程,这些都可能导致群体间遗传距离与地理距离的不相关。 The wide geographical and climatic distribution of P. cathayana Rehd. indicates that there is a large amount of genetic diversity available, which can be exploited for conservation, breeding programs and afforestation schemes. The results are as follows: 1 Research results of AFLP genetic diversity In present study, genetic diversity was evaluated in the natural populations of P. cathayana originating from southern and eastern edge of the Qinghai-Tibetan Plateau of China by means of AFLP markers. For four primer combinations, a total of 175 bands were obtained, of which 173 (98.9%) were polymorphic. Six natural populations of P. cathayana possessed different levels of genetic diversity, high level of genetic differentiation existed among populations (GST=0.489) of P. cathayana. Individuals cluster and PCO analysis based on Jaccard’s similarity coefficient also showed evident population genetic structure with high level population genetic differentiation. The long evolutionary process coupled with genetic drift within populations, rather than contemporary gene flow, are the major forces shaping genetic structure of P. cathayana populations. Moreover, there is no correspondence between geographical and genetic distances in the populations of P. cathayana, seldom gene exchange among populations and different selection pressures may be the causes. Our finding of different levels of genetic diversity within population and high level of genetic differentiation among populations provided promising condition for further breeding or conservation programs. 2 Research results of SSR genetic diversity In this study, the genetic diversity of P. cathayana was investigated using microsatellite markers. In a total of 150 individuals collected from six natural populations in the southeastern part of the Qinghai-Tibetan Plateau in China, a high level of microsatellite polymorphism was detected. At the seven investigated microsatellite loci, the number of alleles per locus ranged from 5 to 16, with a mean of 11.3, the observed heterozygosities across populations ranged from 0.408 to 0.986, with a mean of 0.792, and the expected heterozygosities across populations ranged from 0.511 to 0.891, with a mean of 0.802. The proportion of genetic differentiation among populations accounted for 37.3% of the whole genetic diversity. The presence of such a high level of genetic diversity could be attributed to the features of the species and the habitats where the sampled populations occur: The southeastern part of the Qinghai-Tibetan Plateau is regarded as the natural distribution and variation center of the genus Populus in China. Variation in environmental conditions and selection pressures in different populations, and topographic dispersal barriers could be factors associated with the high level of genetic differentiation found among populations. The populations possessed significant heterozygosity excesses, which may be due to extensive population mixing at the local scale. The cluster analysis showed that the populations are not strictly grouped according to their geographic distances but the habitat characteristics also influence the divergence pattern. In addition, we suggest that population SHY should be regarded as an ecologically divergent species of P. cathayana. 3 Research results of cpSSR genetic diversity Genetic diversity of six natural populations of P. cathayana originating from the southeastern part of the Qinghai-Tibetan Plateau in China was studied by use of cpSSR markers. Based on 5 pairs of polymorphic primers screened from 12 pairs of primers, twenty-six different length fragments and twelve different kinds of haplotypes were reduced in 143 samples. There were significant variant haplotypes among the populations.There were no shared haplotypes found among populations, analysis of molecular variance indicated that a high proportion of the total genetic variance was attributable to variations among populations (92.23%). The pattern of genetic structure which is associated with spatial separation, variation in environmental conditions and selection pressures in different populations, is also the result of geological historical factor. A molecular phylogenetic tree based on the 12 haplotypes showed that the populations are not strictly grouped according to their geographic distances.

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青藏高原东南缘由于特殊的生态地理条件,有着丰富的森林资源,这些资源是长江上游涵养水源、保持水土的生态屏障,是生物多样性的资源宝库。但随着过量的森林采伐,使该区曾经丰富的生物多样性资源遭受了前所未有的破坏,天然林的质量严重下降,生态系统退化,功能减弱。与此同时,许多物种的种群规模正在锐减,物种的遗传多样性也严重丧失。川西云杉是西部地区分布最广的云杉树种之一,在较高海拔的地区有着重要的生态学功能,是一种适应性很强的乡土树种。本项目采用简单序列重复标记(SSR)和特定序列位点(STS)研究不同生境条件下川西云杉群体的遗传变异及其时空分布格局,考察遗传变异与复杂的山地生态环境间的潜在联系,系统地揭示川西云杉天然群体与环境系统相互作用的生态适应与分子进化机制。研究成果能有效地为该树种遗传资源的科学保护与合理利用提供理论依据和科学指导,可为中国西南部亚高山天然林的可持续经营及退化生态系统的恢复与重建提供依据。主要研究结果如下: 1 STS和SSR两种分子标记的研究结果表明:川西云杉群体拥有中等水平的遗传多样性(基于SSR标记,平均He = 0.640;基于STS标记,平均He = 0.553)。造成这种中等水平的遗传多样性,可能是由于历史原因,川西云杉天然林被大量采伐,导致了遗传多样性的丧失。两种方法都检测出群体BT有着最高水平的遗传多样性。 2 两种标记的结果都一致说明:检测的10个川西云杉群体间遗传分化比较高,其存在群体间的遗传变异比例要明显地高于广泛分布的挪威云杉、横贯大陆的黑云杉以及兼有连续分布和不连续分布的西加云杉等,但要低于分布范围狭窄且呈不连续分布的粗枝云杉。青藏高原东南部的片段化生境可能是导致高水平遗传分化的主要原因。 3 基于两种标记的UPGMA 聚类和PCA分析结果,以及基于SSR标记的FCA分析结果都显示:群体BY遗传上明显区别于其它群体,其可能原因是青藏高原东南缘山脉阻隔而导致的生殖隔离的结果。 4 根据软件Bottleneck 1.2.02的检测以及不依赖哈迪一温伯格平衡的M比率检测结果:川西云杉种群很有可能经历了近期的遗传瓶颈效应。在本研究中遗传瓶颈效应并没有显著影响到物种的遗传多样性。然而,在这些片断化群体未来的子代群体中很可能出现遗传瓶颈导致的遗传多样性下降的效应。 Due to the extremely complex topography and climatic conditions, the southeast of the Qinghai-Tibet Plateau is region abundant in forest resource, which is benefit to the upper reaches of the Yangtze River water conservation, and protecting natural environment and biodiversity resources. However, by the reason of a plenty of trees were cut in these yeas, the biodiversity resource was destroy with degraded ecosystem and imperfect funcation. Picea balfouriana is one of the regionally distributed conifer species in the southeast of the Qinghai-Tibet Plateau and considered as a constructive species within its distribution area. It is an optimal species for the production of biomass. Moreover, it is well adapted to stressful environments at high altitude, especially to cold and drought conditions which are generally harsh for other trees. In our study, two types of molecular markers (SSR and STS) were used to estimate the genetic diversity and genetic structure of P. balfouriana populations originating from the southeast of the Qinghai-Tibet Plateau with varying climatic and geographical conditions. The results will not only provide a deep insight into its genetic diversity and population genetic structure but also valuable information for further management and breeding programs in P. balfouriana. In summary, the results obtained in this study revealed that: 1 A moderate degree of genetic variation is present in P. balfouriana in the southeast of the Qinghai-Tibet Plateau and it may caused by many trees were cut in the past. Population BT owns the highest level of genetic diversity by both two types of markers. 2 Considerable population differentiation exists among the ten P. balfouriana populations based on both SSR and STS markers, possibly caused by habitat fragmentation and heterogeneous environments. 3 The UPGMA clustering and PCA analyses based on SSR and STS marker, and FCA analyses based on SSR marker congruously separated population BY from other populations, which is likely due to the presence of mountain barriers. 4 The results of bottleneck analysis indicated that P. balfouriana populations that have undergone recent declines. In our research, the bottleneck effect don’t have a significant impact on the genetic diversity of species, however, the level of genetic diversity of P. balfouriana offspring populations growing in the fragmented habitats will decline in the future.

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同源四倍体水稻(2N=4X=48,AAAA)是由二倍体水稻(2N=2X=24,AA)通过秋水仙素诱导染色体加倍后得到的新品系,具有优良的抗病性以及较高的蛋白质含量。因此,在四倍体水平上挖掘水稻的增产潜力成为水稻育种的新手段。同源四倍体水稻具有很强的遗传可塑性和很弱的遗传保守性,利用其作为水稻远缘杂交的桥梁,从野生物种中不断地引进有益的基因,这将有助于杂交水稻的多代利用和固定水稻的杂种优势。但是迄今为止,还没有关于同源四倍体水稻遗传多样性,遗传背景的报道。目前世界关于同源四倍体水稻的研究主要集中在中国,主要研究方向为培育、筛选结实正常的亲本材料,配置和筛选结实率正常或接近正常的组合。经过几十年研究,虽然在材料构建,细胞学研究等方面取得了较大进展,但同样由于结实率低的瓶颈问题未解决,而使多倍体水稻育种未能取得实质性进展。而近年来一些关于同源四倍体水稻低结实率机理的细胞学研究也由于缺乏统计学数据而缺乏说明性。本文用SSR标记,对选取的36个结实率正常同源四倍体水稻三系亲本和14个来源二倍体亲本,分析他们的遗传差异和群体遗传结构。本文还利用我们培育的高、低结实率的同源四倍体水稻恢复系、优良保持系和杂种F1及二倍体对照为材料,进行系统深入的细胞遗传学研究,进一步探讨同源四倍体水稻有性传递后代的发育过程,探索分裂期染色体行为特征与遗传性状稳定性的关系,为进一步选育多倍体水稻品种并将其应用于生产提供理论依据。同源四倍体水稻突变株D4063-1直链淀粉含量比来源二倍体明恢63下降一半,即其直链淀粉含量为5.23%,为研究其直链淀粉含量下降的原因,本文还根据普通水稻Wx基因设计引物,扩增测序获得了D4063-1Wx基因的全序列,与已报道Wx基因进行比对分析,并根据D4063-1和籼稻、粳稻的序列差异并根据D4063-1在该片段上的特征序列位点设计了用于识别D4063-1的寡核苷酸片段,为快速、准确的鉴别低直链淀粉的D4063-1创造了条件。 SSR标记具有基因组分布广泛、数量丰富、多态性高、容易检测、共显性、结果稳定可靠、实验重现性好、操作简单、经济、易于高通量分析等许多优点,被认为是用于遗传多样性、品种鉴定、物种的系统发育、亲缘关系及起源等研究的非常有效的分子标记。本研究选取了中国科学院成都生物所培育的同源四倍体和二倍体水稻亲本,并用36个微卫星标记进行了遗传差异和种群遗传结构分析。在50个品系中,我们观察到较高水平的多态性,每基因等位基因数(Ae)分布于2至6之间(平均值3.028),多态性信息含量(PIC)分布于0.04至0.76之间(平均值0.366);期望杂合度(He)分布于0.04至0.76之间(平均值0.370),Shannon指数(I)分布于0.098至1.613之间(平均值0.649)。同源四倍体品系的等位基因数,期望杂合性和Shannon指数都比二倍体品系高。在供试50个品系中,较多材料均发现Rare基因,根据SSR多态性指数我们构建了同源四倍体和二倍体水稻的核心指纹库。F-统计值表明遗传差异主要存在于同源四倍体品系中(Fst=0.066)。聚类分析结果表明50个品系可以分为4个组。I组包括所有的同源四倍体和二倍体籼稻保持系,以及一个同源四倍体籼稻雄性不育系及其来源二倍体。II组仅包括IR来源的品系。III组比II组和IV组更复杂,包括同源四倍体和二倍体籼稻恢复系品系。IV组包括同源四倍体和二倍体粳稻品系。此外,由于等位基因及配子的遗传差异,同源四倍体与二倍体品系中存在单位点和双位点的遗传差异。分析结果表明,二倍体和四倍体水稻基因库的不同,其中遗传变异可以区分四倍体与二倍体水稻。同源四倍体水稻具有长期而独立的遗传性,我们能够选育并得到与二倍体亲本相比有特殊优良农艺性状的品系。 本研究以高结实率的同源四倍体水稻恢复系DTP-4、D明恢63及优良保持系D46B为材料进行农艺性状及细胞遗传学比较研究。DTP-4、D明恢63及保持系D46B的的染色体组成均为2N=4X=48,花粉母细胞具有较为理想的减数分裂行为,配对染色体的比率在99%以上,这与理论染色体组构成相符。DTP-4和D明恢63PMC减数分裂各个时期单价体和三价体的比例都非常低,而在MI, PMC观察到较多的二价体和四价体且四价体多以环状形式出现,其最大频率的染色体构型分别为12II 6IV和10II 7IV。恢复系DTP-4和D明恢63在MI四价体频率分别为2.00/PMC和2.26/PMC,而保持系D46B在MI四价体频率为6.00/PMC,极显著地高于恢复系品系,表明保持系D46B具有更好的染色体配对性质;AI保持系D46B的染色体滞后频率为10.62%,远低于恢复系材料DTP-4和D明恢63的19.44%和23.14%,接近二倍体对照明恢63的7.30%水平;TI保持系D46B具有比恢复系更低频率的微核数。而在TII,D46B的正常四分小孢子比率不但高于恢复系品系甚至高于二倍体对照。对高低结实率的同源四倍体水稻恢复系和杂种F1代的花粉育性,结实率和细胞遗传学行为进行了比较研究。DTP-4, D明恢63, D46A´DTP-4和D46A´D明恢63的花粉育性和结实率比D什香和D46A´D什香显著提高。减数分裂分析的结果表明,DTP-4,D明恢63,D什香,D46A´DTP-4,D46A´D明恢63和D46A´D什香其减数分裂染色体构型分别为:0.05I +19.96 II (9.89棒状+10.07环状) +0.01III + 2.20 IV, 0.11I +19.17 II (8.90 棒状+10.37 环状) +0.09III + 2.26 IV + 0.01 VI, 1.33I +9.46 II (4.50 棒状+4.96 环状) +0.44III + 6.02 IV + 0.09VI + 0.09 VIII, 0.02I +14.36 II (6.44 棒状+7.91 环状) +0.01III + 4.80IV + 0.01VIII, 0.06 I +17.67 II (11.01 棒状+6.67 环状) +0.06 III + 3.10 IV + 0.01 VI and 1.11 I +11.31 II (5.80 棒状+5.51 环状) +0.41 III + 5.63 IV+0.03VI+0.03VIII。在同源四倍体水稻恢复系和杂种F1代材料中,最常见的染色体构型为16II +4IV和12II +6IV。在减数分裂过程中,结实率较高的材料染色体异常现象较少而结实率较低的材料染色体异常现象较严重。在杂种F1代中,二价体的比例要低于其相应的恢复系亲本,同样的,单价体,三价体和多价体的比例相比其恢复系亲本也偏低。然而,在减数分裂MI,杂种F1代中四价体的比例要显著高于其恢复系亲本。在中期I,每细胞单价体的比例和花粉育性呈现出极高的负相关(-0.996),当单价体数目升高时,花粉育性下降。其次是每细胞三价体的比例(-0.987),之后则是每细胞多价体的比例与花粉育性的负相关(-0.948)。但是统计分析表明,二价体和四价体的比例对花粉育性和结实率没有显著影响。这一结果表明出了花粉育性和细胞减数分裂行为的相关性,同源四倍体的减数分裂行为为筛选高结实率的同源四倍体种系提供了理论依据。 突变体是遗传学研究的基本材料。利用突变体克隆水稻基因,并进而研究基因的生物学功能是水稻功能基因组学的重要研究内容。本课题组在多年的四倍体水稻育种研究中已获得多个低直链淀粉含量突变体,其中一些突变体在直链淀粉含量下降的同时,胚乳外观也发生了显著改变,呈半透明或不透明。同源四倍体水稻突变株D4063-1直链淀粉含量比来源二倍体明恢63下降一半,即其直链淀粉含量为5.23%。为研究其直链淀粉含量下降的原因,我们根据普通水稻Wx基因设计引物,扩增测序获得了D4063-1Wx基因的全序列,与已报道Wx基因进行比对分析;同源四倍体水稻D4063-1Wx基因最显著变化为在外显子序列中发生了碱基缺失,导致移码突变,在第9外显子终止密码子提前出现。D4063-1Wx基因碱基位点的变化还导致了其序列上的酶切位点的变化,对常用限制性内切酶位点分析分析结果表明同源四倍体水稻相对于籼稻和粳稻多了2个sph1酶切位点,相对于粳稻减少了6个Acc1,增加了4个Xba1,1个Xho1,1个Pst1和1个Sal1酶切位点。聚类分析表明D4063-1Wx基因序列与籼稻亲源关系较近,由此推测D4063-1Wx基因来源于籼稻的Wxa基因型。另外,根据D4063-1Wx基因的碱基差异,我们推测D4063-1Wx基因外显子碱基变化导致的RNA加工障碍是其直链淀粉降低的主要原因,并可能与其米饭较软等品质相关。本文还根据D4063-1和籼稻、粳稻的序列差异并根据D4063-1在该片段上的特征序列位点设计了用于识别D4063-1的寡核苷酸片段,并作为PCR反应的引物命名为AUT4063-1,将该引物与我们设计的扩增普通籼稻、粳稻的Wx基因引物F5配合使用建立了识别D4063-1的显性和共显性两种检测方式的分子标记,为快速、准确的鉴别低直链淀粉的D4063-1创造了条件。 研究同源四倍体水稻基因组的遗传差异,探索同源四倍体水稻的遗传规律,研究分裂期染色体行为特征与遗传性状稳定性的关系,旨在揭示四倍体水稻中同源染色体配对能力的遗传差异,为进一步选育多倍体水稻品种并将其应用于生产提供理论依据。 Autotetraploid rice (2N=4X=48, AAAA) is a new germplasm developed from diploid rice (2N=2X=24, AA) through chromosomes doubling with colchicines and is an excellent resource for desirable resistance genes to the pathogens and high protein content. Therefore, heterosis utilization on polyploidy is becoming a new strategy in rice breeding. At present, the main research on autotetraploid rice centralizes in China. Breeding effort has been made to improve autotetraploid rice genetically, however, the progresses are limited due to higher degree of divergence between hybrid sterility and polygenic nature. But to date, almost nothing is reported about the genetic diversity, original and genetic background of autotetraploid rice. Despite several reports on cytological analysis of the mechanisms of low seed set in autotetraploid rice still the results are inconclusive due to lack the statistical evaluation. Therefore, the study on the mechanisms of low seed set in autotetraploid is a priority for rice breeding. Microsatellites or simple sequence repeats (SSRs) are the widely used marker for estimating genetic diversity in many species, including wild, weedy, and cultivated rice. In our research, genetic diversity and population genetic structure of autotetraploid and diploid populations collected from Chengdu Institute of Biology, Chinese Academy of Sciences were studied based on 36 microsatellite loci. For the total of 50 varieties, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus (Ae) ranging from 2 to 6 (mean 3.028) and PIC ranging from 0.04 to 0.76 (mean 0.366). The expected heterozygosity (He) varied from 0.04 to 0.76 with the mean of 0.370 and Shannon’s index (I) ranging from 0.098 to 1.613 (mean 0.649). The autotetraploid populations showed a slightly higher level of effective alleles, the expected heterozygosity and Shannon’s index than that of diploid populations. Rare alleles were observed at most of the SSR loci in one or more of the 50 accessions and core fingerprint database of the autotetraploid and diploid rice was constructed. The F-statistics showed that genetic variability mainly existed among autotetraploid populations rather than among diploid populations (Fst=0.066). Cluster analysis of the 50 accessions showed four major groups. Group I contained all of the autotetraploid and diploid indica maintainer lines and a autotetraploid and its original diploid indica male sterile lines. Groups II contained only original of IR accessions. Group III was more diverse than either group II or IV and comprised of both autotetraploid and diploid indica restoring lines. Group IV included japonica cluster of the autotetraploid and diploid rices. Furthermore, genetic differences at the single-locus and two-locus levels, as well as components due to allelic and gametic differentiation, were revealed between autotetraploid and diploid varieties. This analysis indicated that the gene pools of diploid and autotetraploid rice are somewhat dissimilar, which made a variation that distinguishes autotetraploid from diploid rices. Using this variation, we can breed new autotetraploid varieties with some new important agricultural characters but the diploid rice has not. Cytogenetic characteristics in restorer lines DTP-4, DMinghui63 and maintainer line D46B of autotetraploid rices were studied. DTP-4, DMinghui63 and D46B showed the advantage of high seed set and biological yield. The meiotic chromosome behavior was slightly irregular in DTP-4, DMinghui63 and D46B. We observed less univalent, trivalent and multivalent at MI, but more bivalent and quadrivalent were observed. The most frequent chromosome configurations were 12II 6IVand 10II 7IV in restorer and maintainer lines, respectively. The quadrivalent frequency of DTP-4 and Dminghui63 at metaphase(MI) was respectively 2.00/PMC and 2.26/PMC. However that frequency of D46B was 6.00/PMC, which was greatly significantly higher than DTP-4 and Dminghui63. That indicates the maintainer D46B has better chromosome pairing capability in metaphase (MI). The frequency of lagging chromosomes of the maintainer D46B at anaphaseI (AI) was 10.62%, which was significantly lower than that of DTP-4(19.44%) and Dminghui63(23.14%) and nearly reaching the level of diploid CK(7.30%). In telophaseI (TI) maintainer D46B showed lower frequency of microkernel at TI and lower frequency of abnormal spores at telophaseII(TII). We also studied pollen fertility, seed set and cytogenetic characteristics of restorer lines and F1 hybrids of autotetraploid rice. DTP-4, DMinghui63, D46A´DTP-4 and D46A´DMinghui63 showed significantly higher pollen fertility and seed set than DShixiang and D46A´DShixiang. Pairing configurations in PMC of DTP-4, DMinghui63, DShixiang, D46A´DTP-4, D46A´DMinghui63 and D46A´DShixiang were 0.05 I+19.96 II (9.89 rod+10.07 ring)+0.01 III+2.20 IV, 0.11 I+19.17 II (8.90 rod+10.37 ring)+0.09 III+2.26 IV+0.01 VI, 1.33 I+9.46 II (4.50 rod+4.96 ring)+0.44 III+6.02 IV+0.09 VI+0.09 VIII, 0.02 I+14.36 II (6.44 rod+7.91 ring)+0.01 III+4.80 IV+0.01V III, 0.06 I+17.67 II (11.01 rod+6.67 ring)+0.06 III+3.10 IV+0.01 VI and 1.11 I+11.31 II (5.80 rod+5.51 ring)+0.41 III+5.63 IV+0.03 VI+0.03 VIII, respectively. Configuration 16 II+4 IV and 12 II+6 IV occurred in the highest frequency among the autotetraploid restorers and hybrids. Meiotic chromosome behaviors were less abnormal in the tetraploids with high seed set than those with low seed set. The hybrids had fewer frequencies of bivalents, univalents, trivalents and multivalents than the restorers, but higher frequency of quatrivalents than the restorers at MI. The frequency of univalents at M1 had the most impact on pollen fertility and seed set, i.e., pollen fertility decreased with the increase of univalents. The secondary impact factors were trivalents and multivalents, and bivalents and quatrivalents had no effect on pollen fertility and seed set. The correlative relationship between pollen fertility and cytogenetic behaviors could be utilized to improve seed set in autotetraploidy breeding. The amylose content of autotetraploid indica mutant Rice D4063-1 dropped by half than diploid Minghui 63, that is, its amylose content of 5.23%.The whole sequence of Waxy gene of D4063-1 is amplified and sequenced. And the discrepancy of bases is found comparing to the reported Waxy gene. The Waxy gene of autotetraploid Rice D4063-1 had a base deletion in exon sequence, which resulted frameshift mutation in exon 9 and termination codon occur early. The mutation of Wx also led to the change of some common restriction endonuclease sites. Results showed compared to indica and japonica, D4063-1 had two adding sph1 sites. Compared to japonica, D4063-1 had six decreasing Acc1, a adding Xho1, Pst1 and Sal1 restriction sites. Phylogeny analysis shows that the DNA sequence of Waxy gene of D4063-1 is closer to Indica, and we suppose that the Waxy gene of D4063-1 is origin from genotype Wxa. In addition, according to the base differences of Wx in D4063-1, we deduce that RNA processing obstacle led by base change of intron is the main cause to low the amylose content, and related to phenotype of its soft rice. Based on analysis of fragments of D4063-1, indica and japonica and according to the special point of the three species, primers as markers-AUT4063-I were designed for distinguishing the D4063-1 from other rice. Combining with primer pair F5, dominant and codominant ways were established for discriminating them., rapid and correct identification of D4063-1 from other rice could be done. The genetic analysis is important to ensure the original of autotetraploid rice, for maintaining the “distinctiveness” of autotetraploid varieties, and to differentiate between the various genetic background of autotetraploid rice. The autotetraploid breeding will benefit from detailed analysis of genetic diversity in the germplasm collections. Further investigation on mechanisms of meiotic stability should benefit polyploid breeding. These findings demonstrated opportunity to improve meiotic abnormalities as well as grain fertilities in autotetraploid rice.

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课题组在不断地创制新的同源四倍体材料的同时,连续多年以提高结实率为目的培育、筛选自交系材料,已获得自交繁殖十二年的高代自交系材料。相对于诱导创制初期,材料表现出的结实率低,同种系单株间的差异较大;高代材料已表现出较显著的结实率提升和较一致的农艺性状表型。 本实验选取课题组多年培育的同源四倍体水稻高代自交系材料,通过形态学、农艺性状和细胞遗传学比较,研究水稻同源四倍体与二倍体之间的异同。结果显示,所有同源四倍体材料的染色体组成均为2N=4X=48,花粉母细胞(PMC)减数分裂行为较正常,99%以上的染色体都能在减数分裂中期I(MI)发生联会、配对,形成四价体和二价体,这与理论染色体组构成相符。在减数分裂过程中,结实率较高的材料染色体异常现象较少而结实率较低的材料染色体异常现象较严重。统计分析表明,二价体和四价体的比例对结实率没有显著影响,但是三价体的数目对结实率有一定影响。这一结果表明了结实率和细胞减数分裂行为可能存在相关性,同源四倍体的减数分裂行为为筛选高结实率的同源四倍体种系提供了依据。 然后,对同源四倍体水稻高代自交系材料进行农艺性状和品质性状的统计与分析。主要针对结实率、每穗实粒数、有效分蘖和穗长等主要农艺性状,以及直链淀粉含量这一重要的品质性状进行统计。将统计结果与1996年诱导加倍的初代材料的数据相对比分析,结果显示所有材料经过多代选育培养,其农艺性状已经有了较显著的提高,同时同源四倍体材料的农艺性状稳定性也有了较显著的提升。如结实率的提高幅度较大,所有材料的平均结实率均显著高于加倍初代,而同种材料不同单株间的结实率差异也显著地减少,变异系数(CV)的平均值由1996年的41.15%减少到了2008年的28.81%。其他重要农艺性状也有不同程度的改良,种内变异系数也相应地降低。此外,实验测量了同源四倍体材料和来源二倍体材料的直链淀粉含量。分析结果显示,部分材料的直链淀粉含量与二倍体亲本产生了较显著的差异,这可能是诱导加倍过程中的遗传变异造成的;同源四倍体材料的种内变异系数(CV)平均值由1996年的6%下降到了2008年的3.88%,显示出在品质性状方面,同源四倍体材料的遗传稳定性也有较显著的增加。同源四倍体材料农艺性状经过多年的选育,表现出一定的提升,同时,经过多年自交纯化,所有材料种系内的性状差异逐渐缩小,说明同源四倍体水稻的遗传稳定性随着自交纯化而增强,这为同源四倍体水稻的进一步选育打下了良好的基础。 最后,通过测量连续两年的自交系材料的遗传多态性,分析材料间遗传差异和种群遗传结构,深入研究连续两代材料间的遗传差异,研究同源四倍体水稻与二倍体材料遗传稳定性之间的差异。实验采用18对SSR微卫星标记对连续两代15个材料,共94份样本进行差异分析。通过扩增条带长度多态性分析,计算不同材料以及同种材料不同世代间的遗传距离,构建同源四倍体和二倍体水稻的分子指纹库,并绘制聚类图。结果显示,同源四倍体和二倍体不同材料间的遗传差异比较大,遗传距离处于0.4757至0.2816之间;而相同品种不同世代材料间的遗传差异较小,但也表现出一定的遗传差异。同种同源四倍体材料不同世代间的遗传差异比二倍体材料更大,两代四倍体材料间遗传距离处于0.1359至0.0485之间;而两代二倍体材料间的遗传距离处于均小于0.0388。结果表明,同源四倍体水稻高代材料具有一定的遗传稳定性,但与来源二倍体材料相比,其世代间的遗传变异性仍然较强。这种结果说明,经过多代的自交纯化培育,同源四倍体水稻材料能够建立起相对稳定的遗传结构,同时,其强于二倍体亲本的变异性有能够为新品种的选育,农艺性状、品质性状的改良提供一定的遗传基础。此外,分析结果表明通过分子标记辅助检验,水稻材料间的遗传多态性能够有效地区分不同的品种,这为水稻品种的分子鉴定提供了一定的依据。 本研究从细胞学鉴定,农艺性状统计分析以及分子标记辅助聚类分析多方面地对同源四倍体水稻高代系进行了研究,对探究同源四倍体水稻的遗传规律,进一步揭示其遗传特性、农艺性状的遗传构成,为进一步选育优质的多倍体水稻提供了一定的理论依据。 This group insists on creating new Autotetraploid Rice (Oryza sativa L.) materials, while improving the seed-setting of them for many years, cultivated and selected the inbred line materials, has obtained the high generation inbred lines after twelve years cultivation. Compared to the early induced materials, which shown the low seed setting, and the large difference between the different plants in the same germ-line; the high generation materials have shown significant improvement in seed setting and more uniform phenotype agronomic traits. The autotetraploid rice high generation inbred lines material, which has been cultivated for more than 12 years, was chose in this experiment. The similarities and differences between autotetraploid and diploid rice was studied through morphological, agronomic and cytogenetic ways. The results showed that all the chromosome of autotetraploid materials are composed of 2N=4X=48, the pollen mother cells (PMC) meiosis behavior is normal, more than 99% chromosomes in metaphase I(MI) were federated and paired to form tetravalents or bivalents, which constitutes a consistent theory of genome. In the meiosis process, the material with a higher seed setting showed less chromosome abnormal than the material whose seed setting is lower. However, statistical analysis showed that the bivalent and tetravalent rate had no significant impact on seed setting, but the number of trivalent had a certain impact on seed setting. The result shows that the seed setting may be related to the meiosis behavior, which provides a basis to cultivate new autotetraploid germ line with high seed setting through the meiotic behavior. Furthermore, the agronomic and quality traits of autotetraploid rice high generation inbred material were statistically analyzed. The statistically analysis was focused on major agronomic traits such as: seed setting, grains per panicle, effective tillers and panicle length, as well as the important quality trait amylose content. The statistic data was compared with the data in 1996, when the first induced generation of autotetraploid material, and the result shows that after a multi-generation breeding, the agronomic traits has been significantly improved in all the materials, while the stability of agronomic traits also significant upgraded. For instant, the seed setting increased significantly, the average seed setting of all materials was significantly higher than the first induced generation, and the differences between different plants in the same species also significantly reduced, the average of the coefficient of variation (CV) was reduced from 41.15% in 1996 to 28.81% in 2008. Other important agronomic traits had improved in different degrees; the coefficient of variation within species is also reduced accordingly. In addition, the amylose content of autotetraploid and diploid materials was measured in this experiment. The results shows that the amylose content of some of the material differed from diploid parents significantly, it may caused by the genetic change during the inducing, autotetraploid materials intra-specific coefficient of variation (CV) average reduced from 6% in 1996 to 3.88% in 2008, shows that this is a significant increase of quality traits stability in autotetraploid rice. Agronomic traits of autotetraploid material shows some improvement after years of breeding, at the same time, after years of purification, all material within the germ-line gradually narrow the differences in traits indicates that autotetraploid rice genetic stability was enhanced, which laid a good foundation for the further autotetraploid rice breeding. Finally, this experiment studied the genetic differences between materials of two generations and researched the difference of genetic stability between diploid and autotetraploid rice materials through investigating the genetic polymorphism, genetic differences between materials and population genetic structure of inbred line materials of two consecutive years.18 pairs of SSR microsatellite markers for 15 materials of two generations were used in this experiment, and the total of 94 samples were analyzed. Through the amplification length polymorphism analysis of different materials and materials in different generations, the genetic distance between materials and generations was analyzed, a diploid and autotetraploid rice molecular fingerprint database and map rendering cluster were constructed. The result shows that the genetic distance is between 0.4757 to 0.2816 among different autotetraploid and diploid materials; the genetic distance between different generations of same species was less, but also shows a certain degree of genetic differences. The inter-generational genetic differences of autotetraploid materials were greater than of the diploid materials, which are 0.1359 to 0.0485 as the genetic distance; comparing with the 0.0388 of diploid materials. The result shows that high generation inbred autotetraploid rice material has a certain genetic stability, but the genetic variation between generations is still strong comparing with the source diploid materials. It indicates that, after many generations of purification cultivation, autotetraploid rice materials established a relatively stable genetic structure, at the same time, stronger variability than its diploid parents are useful in the breeding of new varieties, provides a genetic foundation to the agronomic and quality traits improvement. In addition, the analysis result shows that the through the molecular marker-assisted testing, rice genetic polymorphism between materials can effectively distinguish different species, provides a certain basis for molecular identification of varieties of rice. A series of investigation such as cytological identification, statistical analysis of agronomic traits, molecular marker-assisted cluster analysis was applied in this experiment to research genetic pattern of autotetraploid rice high generation inbred lines, revealed the genetic characteristics and the genetic composition of agronomic traits, provides a theoretical basis for the further selection of high quality autotetraploid rice.

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为了进一步研究青蟹属系统进化的科学问题,并揭示我国东南沿海青蟹群体遗传结构和群体进化细节信息,本论文主要开展了以下两个方面的研究:(1)基于线粒体12S rRNA、16S rRNA和COI三种基因序列探讨中国东南沿海青蟹的种类归属与青蟹属的系统进化;(2)利用线粒体COI基因标记分析中国东南沿海拟穴青蟹的群体遗传结构。序列特征、遗传距离和系统进化分析结果都表明本文研究的青蟹均为S. paramamosain。NJ、BAYES和ML系统进化树显示S. paramamosain与S. tranquebarica互为姐妹种,S. olivecea应该是4种青蟹中最早分化出来的种类。10个地理群体130只拟穴青蟹的线粒体DNA(mitochondrial DNA,mtDNA)细胞色素氧化酶亚基I(COI)基因序列Mantel检验结果显示群体间的遗传分化程度与地理距离没有显著的相关性。分子进化中性检验结果表明自然选择在分子进化过程中起了重要作用,并暗示该物种在最近经历了一个快速的群体爆发及扩张事件。

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The pinnotherid crab Dissodactylus primitivus lives parasitically on 2 burrowingechinoid species, Meoma ventricosa and Plagiobrissus grandis. The fecundity of female crabsvaries between hosts, and is higher when parasitizing P. grandis than M. ventricosa. Moreover, thehosts present great variations in morphology (size and density of spines). These characteristicssuggest the potential to differentiate crabs according to host species. We investigated the genetic(microsatellites) and morphometric (outline analysis) differentiation of this parasitic crab between2 host species at 1 Jamaican site (Western Lagoon, Discovery Bay), and compared it with geographicdifferentiation among 4 sites along the north coast of Jamaica. Greater genetic differencesbetween parasites of the 2 sympatric hosts than between parasites of a single host at different geographiclocations would indicate host differentiation. Genetic analyses (microsatellites) did notdetect spatial differentiation (probably due to local hydrography) or differentiation according tohost species. This lack of host differentiation could be explained by mobility of adult crabsbetween hosts. However, there was weak but significant morphological differentiation betweenfemale crabs from the 2 hosts. This morphological difference may reflect constraints due to hostmorphology.

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It is increasingly evident that evolutionary processes play a role in how ecological communities are assembled. However the extend to which evolution influences how plants respond to spatial and environmental gradients and interact with each other is less clear. In this dissertation I leverage evolutionary tools and thinking to understand how space and environment affect community composition and patterns of gene flow in a unique system of Atlantic rainforest and restinga (sandy coastal plains) habitats in Southeastern Brazil.

In chapter one I investigate how space and environment affect the population genetic structure and gene flow of Aechmea nudicaulis, a bromeliad species that co-occurs in forest and restinga habitats. I genotyped seven microsatellite loci and sequenced one chloroplast DNA region for individuals collected in 7 pairs of forest / restinga sites. Bayesian genetic clustering analyses show that populations of A. nudicaulis are geographically structured in northern and southern populations, a pattern consistent with broader scale phylogeographic dynamics of the Atlantic rainforest. On the other hand, explicit migration models based on the coalescent estimate that inter-habitat gene flow is less common than gene flow between populations in the same habitat type, despite their geographic discontinuity. I conclude that there is evidence for repeated colonization of the restingas from forest populations even though the steep environmental gradient between habitats is a stronger barrier to gene flow than geographic distance.

In chapter two I use data on 2800 individual plants finely mapped in a restinga plot and on first-year survival of 500 seedlings to understand the roles of phylogeny, functional traits and abiotic conditions in the spatial structuring of that community. I demonstrate that phylogeny is a poor predictor of functional traits in and that convergence in these traits is pervasive. In general, the community is not phylogenetically structured, with at best 14% of the plots deviating significantly from the null model. The functional traits SLA, leaf dry matter content (LDMC), and maximum height also showed no clear pattern of spatial structuring. On the other hand, leaf area is strongly overdispersed across all spatial scales. Although leaf area overdispersion would be generally taken as evidence of competition, I argue that interpretation is probably misleading. Finally, I show that seedling survival is dramatically increased when they grow shaded by an adult individual, suggesting that seedlings are being facilitated. Phylogenetic distance to their adult neighbor has no influence on rates of survival though. Taken together, these results indicate that phylogeny has very limited influence on the fine scale assembly of restinga communities.

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Allozyme analyses have suggested that Neotropical orchid bee (Euglossini) pollinators are vulnerable because of putative high frequencies of diploid males, a result of loss of sex allele diversity in small hymenopteran populations with single locus complementary sex determination. Our analysis of 1010 males from 27 species of euglossine bees sampled across the Neotropics at 2-11 polymorphic microsatellite loci revealed only 5 diploid males at an overall frequency of 0.005 (95% CIs 0.002-0.010); errors through genetic non-detection of diploid males were likely small. In contrast to allozyme-based studies, we detected very weak or insignificant population genetic structure, even for a pair of populations >500 km apart, possibly accounting for low diploid male frequencies. Technical flaws in previous allozyme-based analyses have probably led to considerable overestimation of diploid male production in orchid bees. Other factors may have a more immediate impact on population persistence than the genetic load imposed by diploid males on these important Neotropical pollinators.

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Orchid or euglossine bees are conspicuous Hymenoptera of the Neotropics, where they pollinate numerous plants, including orchids. Allozyme-based analyses have suggested that their populations suffer from inbreeding, as evidenced by so-called diploid male production. We have developed nine polymorphic microsatellite loci for the widespread Euglossa annectans, with observed heterozygosities ranging from 0.143 to 0.952 and between 2 and 9 alleles per species. These loci will be useful for analysis of relatedness, population genetic structure and diploid male production in this and related species.

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Sweat bees display considerable variation in social organization and a few species, such as Halictus rubicundus, are even facultatively eusocial. Fourteen polymorphic, unlinked microsatellite loci were isolated from H. rubicundus and characterized in 45 females. The number of alleles per locus ranged from two to 18 (mean 10.1), observed heterozygosity ranged from 0.24 to 0.98 (mean 0.71) and expected heterozygosity ranged from 0.24 to 0.98 (mean 0.70). Six or more loci cross-amplified in four other sweat bees. These loci will be useful for the study of social evolution and population genetic structure in H. rubicundus and many other sweat bees.

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Background: Many deep-sea benthic animals occur in patchy distributions separated by thousands of kilometres, yet because deep-sea habitats are remote, little is known about their larval dispersal. Our novel method simulates dispersal by combining data from the Argo array of autonomous oceanographic probes, deep-sea ecological surveys, and comparative invertebrate physiology. The predicted particle tracks allow quantitative, testable predictions about the dispersal of benthic invertebrate larvae in the south-west Pacific. Principal Findings: In a test case presented here, using non-feeding, non-swimming (lecithotrophic trochophore) larvae of polyplacophoran molluscs (chitons), we show that the likely dispersal pathways in a single generation are significantly shorter than the distances between the three known population centres in our study region. The large-scale density of chiton populations throughout our study region is potentially much greater than present survey data suggest, with intermediate ‘stepping stone’ populations yet to be discovered. Conclusions/Significance: We present a new method that is broadly applicable to studies of the dispersal of deep-sea organisms. This test case demonstrates the power and potential applications of our new method, in generating quantitative, testable hypotheses at multiple levels to solve the mismatch between observed and expected distributions: probabilistic predictions of locations of intermediate populations, potential alternative dispersal mechanisms, and expected population genetic structure. The global Argo data have never previously been used to address benthic biology, and our method can be applied to any non-swimming larvae of the deep-sea, giving information upon dispersal corridors and population densities in habitats that remain intrinsically difficult to assess.

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Eight new microsatellite loci were isolated and characterized for the Natterer's bat Myotis nattereri from a microsatellite-enriched genomic library. The usefulness of these markers was assessed by screening a sample comprising 100 specimens collected from throughout the species range in Europe. Both moderately and highly polymorphic loci were identified with 3-17 alleles segregating per locus (mean 8.1 SE +/- A 0.048). No evidence for departure from HWE or linkage disequilibrium among loci was observed. These markers will provide a valuable addition to the molecular toolbox currently available for studies of population genetic structure, parentage and social organisation of M. nattereri and related species.

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Atlantic mackerel (Scomber scombrus L.) is a widely distributed commercially important pelagic species. Little is known about the stock structure of this species, but it is thought to be undergoing a range extension due to environmental changes. Knowledge of the stock structure under these changing conditions is fundamental for effective management. In this paper, 30 highly polymorphic microsatellite loci developed with next generation sequencing are described. The number of alleles per locus ranged from 4 to 39 in two geographically distant populations, observed and expected heterozygosities ranged between 0. 370-0. 978 and 0. 426-0. 962, respectively. These loci are an important resource that will allow assessment of the current population genetic structure of this species, and enable monitoring of climate related changes in the species range and distribution. 

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Lumpfish (Cyclopterus lumpus L. 1758) are widely distributed on both sides of the North Atlantic. They are a commercially important species, but stock size estimates have declined since the mid-1980s in Canada, Norway and Iceland. Little is known about the biology of this species, in particular the breeding migrations and population structure which are fundamental for effective management. This paper describes the development and characterization of twenty-two polymorphic microsatellite loci using next generation sequencing. The number of alleles per locus ranged from 3 to 27 in two geographically distant North Atlantic populations, with observed and expected heterozygosities ranging between 0. 0625-0. 979 and 0. 0618-0. 946, respectively. These loci are an important resource that will allow assessment of the population genetic structure of this species, and contribute to its appropriate management.