Genetic structure of Pinus henryi and Pinus tabuliformis: Natural landscapes as significant barriers to gene flow among populations

Mountains as natural barriers often have important effects on intraspecific genetic structure through restraining gene flow and enhancing differentiation among populations. While the Qinling and Daba mountains are considered significant geographic barriers, dividing China into temperate and subtropical regions, little is known about how this barrier influences the genetic patterns of sister species represented in distinct habitats. In this study, we analyzed genetic differentiation and the geographic boundary between Pinus henryi and Pinus tabuliformis using chloroplast microsatellite markers. Our data show high levels of among-population differentiation, consistent with the effects of historical demographic bottlenecks, local adaptation and climate effects. Three main geographic boundaries coinciding with mountain systems indicate natural landscapes, such as large rivers, and habitat loss caused by anthropogenic deforestation, are significant barriers to genetic exchange among populations. The divergence between populations in the eastern and western Qinling Mountains populations may possibly be ascribed to fragmentation driven by climate change. The genetic boundary of P. henryi and P. tabuliformis generally coincides with the previous morphological dividing line based on the unweighted pair group method using arithmetic averages and on spatial analysis of molecular variance.     

K、V、T型小麦细胞质雄性不育系叶绿体DNA的SSR分析及RuBP羧化酶活性比较

为了探讨小麦细胞质雄性不育(CMS)与叶绿体DNA(cpDNA)的关系,揭示CMS机理。以2套K、V、T型同核异质不育系(A)及其保持系(B)‘太911289’和‘冀5418’、育性恢复的F_1和各自的质供体粘果山羊草(Aegilops kotschyi)、偏凸山羊草(Aegilops ventricosa)、提莫菲维小麦(Triticum timopheevii)为试验材料,利用cpSSR引物对小麦cpDNA进行比较分析,筛选出代表不同胞质不育系的引物,探讨CMS与叶绿体的关系;同时测定由叶绿体DNA与核DNA共同编码的RuBP羧化酶的活性,为小麦K、V、T雄性不育类型的应用提供理论依据。结果表明:(1)K型、V型、T型不育系与保持系的cpDNA之间均呈现多态性,且不同的细胞质之间存在特异片段,这从DNA水平上提供了3类不育系胞质来源不同的证据,并分别找到5对和7对可以鉴定V型和T型不育系的特异引物。(2)除K型‘冀5418’与其胞质供体的cpDNA出现差异外,不育系与其胞质供体的cpDNA没有差异,而且不育系与其育性恢复的F_1代cpSSR扩增片段之间也没有差异,很好地遗传了其母本性状。(3)在起身期和开花期,不仅2套不育系的RuBP羧化酶活性显著高于保持系,且在不育系与恢复系杂交的F_1中,随着育性的恢复其RuBP羧化酶活性高于保持系而低于各自不育系;而在拔节期的不育系与保持系之间、不育系之间、以及F_1代与不育系和保持系之间的RuBP酶活性大小没有显著差异。这可能与拔节期主要是营养生长有关系。     

Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species

Chloroplast microsatellites, or simple sequence repeats (cpSSRs), are typically mononucleotide tandem repeats. When located in the noncoding regions of the chloroplast genome (cpDNA), they commonly show intraspecific variation in repeat number. Despite the growing number of studies applying cpSSRs, studies of economically important plants and their relatives remain over‐represented. Thus, the potential of cpSSRs to offer unique insights into ecological and evolutionary processes in wild plant species has yet to be fully realized. This review provides an overview of the technical resources available to aid cpSSR discovery including a list of cpSSR primer sets available and cpDNA sequencing resources. Our updated analysis of 99 whole chloroplast genomes downloaded from GenBank confirms that potentially variable cpSSRs are abundant in the noncoding cpDNA of plants. Overall variation in the frequency of cpSSRs was extreme, ranging from one to 700 per genome (median = 93), while in 81 vascular plants, between 35 and 160 cpSSRs were detected per genome (median = 86). We offer five recommendations to aid wider development and application of cpSSRs: (i) When genus‐specific cpSSR primers are available, cross‐species amplification can often be fruitful. (ii) While potentially useful, universal cpSSR primers at best provide access to only a small number of variable markers. (iii) De novo sequencing of noncoding cpDNA is the most effective and efficient way to develop cpSSR markers in wild species. (iv) DNA sequencing of cpSSR alleles is essential, given the complex nature of the genetic variation associated with hypervariable cpDNA regions. (v) The reliability of cpSSR length based genetic assays need to be validated in all studies.     

Mating system and fine-scale spatial genetic structure of Solanum lycocarpum St.Hil. (Solanaceae) in the Brazilian Cerrado

Restricted gene dispersion – resulting from both self-pollination and limited capability of pollen migration, as well as seed dispersion at short distances – has been considered the main reason for spatial genetic structuring in plant populations. This study evaluated the intrapopulation genetic structure and the mating system in four populations of Solanum lycocarpum, a woody bush occurring in Brazilian Cerrado vegetation. Two hundred and twenty-four individuals were genotyped through five nuclear SSR loci (30 alleles) and six cpSSR loci (82 haplotypes). The study evidenced that the species mates predominantly by outcrossings , that biparental inbreeding is not common, and that there are almost 10 trees participating as pollen donors per mother-tree. The populations were formed by many mother lineages, indicating efficient seed dispersion by the fauna and the occurrence of multiple foundation events. Spatial genetic structure was observed in three populations (average Sp=0.0184 ± 0.0030) and it resulted from both restricted seed dispersion and from vegetative reproduction. During the collection of seeds for ex situ conservation, seeds must be gathered from 150 to 200 mother trees, so that the effective size of 500 individuals is retained. The sampling must comprise the biggest possible number of populations in a wide area to enable the maintenance of the biggest possible haplotypic diversity.     

猕猴桃属植物的cpSSR遗传多样性及其同域分布物种的杂交渐渗与同塑

同域分布的近缘物种常常发生杂交而导致种间基因渐渗, 从而对相关物种的自然居群遗传结构产生重要影响, 近缘种间的杂交渐渗已成为进化生物学和保护生物学关注的热点。本研究采用8对cpSSR引物对我国西部高原台地向中东部丘陵平原过渡地带同域重叠分布的猕猴桃属(Actinidia)7个物种的自然居群遗传多样性、居群遗传结构和同域分布种间遗传分化进行了检测。结果表明: (1)在6个多态性位点检测到18个等位基因形成的42个单倍型, 尽管各单倍型间显示了复杂的网状进化关系, 但还是具有明显的物种特异性; (2)各物种有丰富的cpSSR遗传多样性, 但种间存在较大差异, 绵毛猕猴桃(Actinidia fulvicoma var. lanata)的遗传多样性水平最高(P = 62.50%, h_T = 0.173, H_T = 0.897), 美味猕猴桃(A. deliciosa)的最低(P = 37.5％, h_T = 0.041, H_T = 0.516); (3)尽管不同物种的居群分化程度存在较大差异, 但种内居群间存在明显分化(G_ST为0.319–0.780, F_ST为0.401–0.695), 居群间的基因流不足(N_m为0.219–0.747<1); 其中以美味猕猴桃的居群遗传分化度最高(G_ST = 0.780, F_ST = 0.695); (4)遗传分化系数G_ST(unordered alleles)与N_ST(ordered alleles)无显著差异, 揭示本研究的大多数猕猴桃属物种不存在系统地理结构, 与用Mantel检验得出的居群遗传距离和地理距离不存在显著性相关的结果一致; (5)除了中华/美味猕猴桃复合体(A. chinensis / A. deliciosa complex)的湖北五峰(HW)和广西资源(GZ)两个同域复合居群外, 同域分布的物种间遗传分化强烈(F_ST为0.476–0.990), 与UPGMA聚类时多数居群按各自物种聚类的结果一致。进一步分析表明, 中华/美味猕猴桃复合体近缘种间存在明显的共祖多态性和杂交渐渗现象, 近缘种植株分布的交错程度以及是否存在亚居群结构对杂交渐渗存在着重要影响。亲缘关系较远的物种间杂交渐渗事件稀少, 但存在个别同塑事件。本研究结果有助于进一步了解猕猴桃属植物自然居群cpDNA的遗传特性和渐渗杂交进化模式, 为我国猕猴桃野生种质资源保育及可持续开发利用提供基础数据和科学依据。     

A comparative plastomics approach reveals available molecular markers for the phylogeographic study of Dendrobium huoshanense,an endangered orchid with extremely small populations

Comparative plastomics approaches have been used to identify available molecular markers for different taxonomic level studies of orchid species. However, the adoption of such methods has been largely limited in phylogeographic studies. Therefore, in this study, Dendrobium huoshanense, an endangered species with extremely small populations, was used as a model system to test whether the comparative plastomic approaches could screen available molecular markers for the phylogeographic study. We sequenced two more plastomes of D. huoshanense and compared them with our previously published one. A total of 27 mutational hotspot regions and six polymorphic cpSSRs have been screened for the phylogeographic studies of D. huoshanense. The cpDNA haplotype data revealed that the existence of haplotype distribution center was located in Dabieshan Mts. (Huoshan). The genetic diversity and phylogenetic analyses showed that the populations of D. huoshanense have been isolated and evolved independently for long period. On the contrary, based on cpSSR data, the genetic structure analysis revealed a mixed structure among the populations in Anhui and Jiangxi province, which suggested that the hybridization or introgression events have occurred among the populations of D. huoshanense. These results indicated that human activities have played key roles in shaping the genetic diversity and distributional patterns of D. huoshanense. According to our results, both two markers showed a high resolution for the phylogeographic studies of D. huoshanense. Therefore, we put forth that comparative plastomic approaches could revealed available molecular markers for phylogeographic study, especially for the species with extremely small populations.     

Population genetics analysis in a relic population of silver fir (Abies alba Mill.) in southern Italy: A comparison with microsatellites and reference data

We investigated the genetic diversity of the last natural population of Abies alba Mill. in Campania region (southern Italy) using nuclear and chloroplast microsatellite markers. We found high genetic diversity despite small population size and geographic isolation, especially when comparing our microsatellite data with information from the literature.     

凉水国家自然保护区天然红松种群遗传多样性在时间尺度上变化的cpSSR分析

应用叶绿体微卫星（cpSSR）技术对凉水国家自然保护区天然红松种群的遗传多样性在时间尺度上的变化进行了遗传分析。共选择121个树龄在1 581~1 900年间的红松个体,连续分为6个龄级。从6对叶绿体SSR引物筛选出两对引物,共检测到7个位点,其中多态位点5个,多态位点比率为71.43%。利用POPGENE分析软件计算了红松各龄级内的遗传多样性指数,分析了遗传多样性在红松各龄级间的变化。研究结果表明,凉水保护区内的红松遗传多样性在这320年间没有发生太大的波动,龄级间遗传多样性分化不明显,红松遗传多样性主要存在于龄级内。