海草克隆性及其种群遗传效应

海草是适应在海洋环境中生存和繁殖的单子叶植物,由于所处环境常存在潮汐、风暴等的干扰,海草形成了一系列适应特征,克隆性是其中突出的一个.所有的海草都具有水平根状茎,许多海草也具有垂直根状茎,在一些海草中,也观察到无性生殖(无融合生殖).与克隆生长有关的参数(如节间长度、间隔子长度、分枝角度以及延伸速率和分枝率等)对于海草的克隆生长有着决定性影响,但繁育系统对克隆斑块大小也有较大影响.强烈的克隆性影响着海草的遗传变异.总体来看,海草种群内遗传多样性比陆生植物低,也低于另一类海洋高等植物-红树植物,利用DNA标记观察到的多样性高于等位酶标记.在一些海草植物种群中观察到较高的克隆多样性,但也有一些种群由单一基因型或少量基因型组成,其原因主要是由于奠基者效应和克隆生长.通常克隆植物中基因流有限,但是海草的克隆片段可能远距离扩散,从而提高种群间的基因流.就克隆生长对种群空间结构和交配系统的影响进行了综述.     

Microsatellite markers reveal two admixed genetic groups and an ongoing displacement within the French population of the invasive plant pathogen Phytophthora infestans

Potato late blight is an example of a re‐emerging disease of plants. Phytophthora infestans was first introduced into Europe during the 19th century, where it caused the Irish potato famine. During the 20th century several additional introduction events have been suspected, especially in the mid‐70s due to the import of large quantities of potato needed after the shortage caused by drought in 1976. Here, we investigate the genetic population structure of Phytophthora infestans, at the first stages of a recent invasion process in France. A total of 220 isolates was collected from 20 commercial fields of the potato susceptible cultivar Bintje, during two consecutive years (2004 and 2005). Clustering analyses based on eight recently developed microsatellite markers reveal that French P. infestans populations are made of two differentiated genetic clusters of isolates (F_ST = 0.19). This result suggests multiple introductions of P. infestans into France, either through the introduction of a composite population of isolates or through the successive introduction of isolates having differentiated genetic backgrounds. Both clusters identified have a strong clonal structure and are similar regarding genetic diversity and mating type composition. The maintenance of differentiation between the two genetic clusters should result from the low or non‐existent contribution of sexual reproduction in French P. infestans populations.     

Development and characterization of microsatellite markers in Populus euphratica (Populaceae)

In this study, we developed 12 microsatellite loci for Populus euphratica and checked their variability in 27 individuals. The number of alleles for 12 loci ranged from five to nine, the observed and expected heterozygosities ranged from 0.32 to 0.48 and from 0.53 to 0.67. Frequencies of null alleles of all loci are not significantly greater than zero. None of the loci showed significant deviation from Hardy-Weinberg equilibrium. No significant linkage disequilibrium was observed between pairs of studied loci. These markers are useful in studies of population genetic structure of P. euphratica.     

乌骨鸡蛋用系群体遗传结构的微卫星标记分析

用20对微卫星引物对丝羽乌骨鸡BM、BF两个蛋用新品系的基因组DNA进行扩增,应用多重PCR结合全自动电泳技术分析群体遗传结构。试验结果表明：18个微卫星标记表现出丰富的多态性,每个标记平均检测到7.444个等位基因（3～15个）,平均观测杂合度为0.3962,平均预期杂合度为0.7301,平均多态信息含量为0.669。本研究的标记检测结果比以前的研究报道值要高,说明全自动电泳分析技术比聚丙烯酰胺凝胶电泳结合银染法检测电泳结果的传统方法要精确,能更好地用于群体遗传结构的分析。      

Spatial genetic relationships in a population of the Japanese wood mouse Apodemus argenteus

Space-related relationships between individuals were investigated during the breeding season in a natural population of Apodemus argenteus (Temminck) by using the catch-mark-release method and microsatellite DNA markers. Several overlapping patterns of home ranges in breeding males and females were observed. Although this species is thought to be monogamous, DNA analysis revealed polygynous mating. In adults, relatedness between sexes was generally low and no apparent spatial genetic structure was observed. In juveniles, however, relatedness and geographical distance be-tween individuals were significantly negatively correlated. The relatedness between adult females decreased with distance, whereas there was not such a correlation in males. Long-distance movements were observed in current-year-born males. The differences in spatial genetic structure between adults and juveniles are thought to be produced by male-biased natal dispersal. An erratum to this article can be found at     

微卫星分子标记在濒危动物保护遗传学研究中的应用

微卫星DNA广泛分布于真核生物基因组中,具有多态性高、共显性遗传、选择中性、易于操作等特点,是一种极具应用价值的分子遗传标记,近年来在濒危动物保护遗传学研究中得到越来越多的应用。微卫星DNA高度多态性提供的高分辨率遗传信启,使其不仅适合个体水平的亲子鉴定与交配系统研究,而且也已成为种群遗传结构与多样性分析的有效分子标记。微卫星分析所需的DNA量极少,用非损伤性方法获取的极少量样品或陈旧样品就能用于有效分析,方便了濒危动物野外调查工作的开展,并且可以利用年代久远的馆藏历史标本揭示种群的重要历史进程。另外,某些微卫星DNA大小在近缘物种间可相互区分,这使得部分物种的DNA分子鉴别将更为简便。但微卫星分子标记的座位筛选和特异引物开发耗时费力,一定程度上限制了其广泛应用。针对不同的研究目的选择合适的分子标记方法将有助于更好的揭示问题本质。     

Polymorphic microsatellite DNA markers in the mangrove crab Ucides cordatus (Brachyura: Ocypodidae)

The isolation and characterization of the first polymorphic microsatellite markers for the mangrove crab Ucides cordatus are described. The number of alleles at each locus ranged from three to 25, mean of nine alleles, in 46 crabs captured in two Brazilian mangroves. The markers averaged high levels of observed (0.709 ± 0.183) and expected (0.716 ± 0.170) heterozygosities. Departures from Hardy-Weinberg equilibrium were observed at two loci. Linkage disequilibrium tests were not significant and no evidence of null alleles was detected. All these microsatellite loci are expected to be useful in estimating fine-scale population processes of this valuable mangrove species currently subjected to excessive fishing efforts.     

Impact of selective logging on inbreeding and gene dispersal in an Amazonian tree population of Carapa guianensis Aubl

Selective logging may impact patterns of genetic diversity within populations of harvested forest tree species by increasing distances separating conspecific trees, and modifying physical and biotic features of the forest habitat. We measured levels of gene diversity, inbreeding, pollen dispersal and spatial genetic structure (SGS) of an Amazonian insect-pollinated Carapa guianensis population before and after commercial selective logging. Similar levels of gene diversity and allelic richness were found before and after logging in both the adult and the seed generations. Pre- and post-harvest outcrossing rates were high, and not significantly different from one another. We found no significant levels of biparental inbreeding either before or after logging. Low levels of pollen pool differentiation were found, and the pre- vs. post-harvest difference was not significant. Pollen dispersal distance estimates averaged between 75 m and 265 m before logging, and between 76 m and 268 m after logging, depending on the value of tree density and the dispersal model used. There were weak and similar levels of differentiation of allele frequencies in the adults and in the pollen pool, before and after logging occurred, as well as weak and similar pre- and post-harvest levels of SGS among adult trees. The large neighbourhood sizes estimated suggest high historical levels of gene flow. Overall our results indicate that there is no clear short-term genetic impact of selective logging on this population of C. guianensis.     

Pollen flow in the wildservice tree, Sorbus torminalis (L.) Crantz. IV. Whole interindividual variance of male fecundity estimated jointly with the dispersal kernel

Interindividual variance of male reproductive success (MRS) contributes to genetic drift, which in turn interacts with selection and migration to determine the short-term response of populations to rapid changes in their environment. Individual relative MRS can be estimated through paternity analysis and can be further dissected into fecundity and spatial components. Existing methods to achieve this decomposition either rely on the strong assumption of a random distribution of pollen donors (TwoGener) or estimate only the part of the variance of male fecundity that is explained by few covariates. We developed here a method to estimate jointly the whole variance of male fecundity and the pollen dispersal curve from the genotypic information of sampled seeds and their putative fathers and geographical information of all individuals in the study area. We modelled the relative individual fecundities as a log-normally distributed random effect. We used a Bayesian approach, well suited to the hierarchical nature of the model, to estimate these fecundities. When applied to Sorbus torminalis , the estimated variance of male fecundity corresponded to an effective density of trees 13 times lower than the observed density ( d_obs / d_ep ~  13). This value is between the value ( ~ 2) estimated with a classical mating model including three covariates (neighbourhood density, diameter, flowering intensity) that affect fecundity and the value ( ~ 30) estimated with TwoGener. The estimated dispersal kernel was close to previous results. This approach allows fine monitoring of ongoing genetic drift in natural populations, and quantitative dissection of the processes contributing to drift, including human actions.     

Structure of Amylase Genes in Populations of Pacific Cupped Oyster (Crassostrea gigas): Tissue Expression and Allelic Polymorphism

Using the previously determined complementary DNA Sequence of Crassostrea gigas amylase (Y08370), we designed several oligonucleotide primers and used them with polymerase chain reaction (PCR) technology to characterize oyster amylase gene sequences. Two genes encoding 2 different amylases were characterized and sequenced. The 2 genes are similarly organized with 8 exons and 7 introns. Intron insertions are found at the same location in the 2 genes. Sizes and nucleotide sequences are different for the different introns inside each gene and different for the corresponding introns in the 2 genes. Comparing the 2 genes, around 10% of the nucleotides are different along the exons, and comparing the 2 deduced protein sequences, a mean value of 10.4% of amino acids are changed. Genes A and B encode mature proteins of, respectively, 500 and 499 amino acids, which present 94% similarity. A microsatellite (TC₃₇) that constitutes the largest part of intron 4 of gene A has been used as a polymorphic marker. A method consisting of a PCR step followed by EcoRI digestion of the obtained fragments was used to observe polymorphism in these 2 genes. Six and 4 alleles for genes A and B, respectively, have been sequenced, leading to a maximum of 2.9% base change. The 2 genes are ubiquitously expressed in the different digestive tissues with quantitative differences. Gene A is strongly expressed in the digestive gland and at a lower level in stomach, while gene B is preferentially expressed in the labial palps. The microsatellite repeat was used in the analysis of 4 populations of Crassostrea gigas from the French Atlantic coast. A high level of polymorphism observed with 30 different alleles of gene A inside the populations should allow their characterization using the mean value of the microsatellite allelic distribution. These populations showed a low level of differentiation (F _st between 0 and 0.011); however, the population of Bonne Anse appeared to be distinguished from the other populations.     

Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei (Primulaceae):implications for its conservation

Omphalogramma souliei Franch. Is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. Souliei in NW Yunnan, China. The genetic diversity at the species level is low with P= 42.5% (percentage of polymorphic bands) and Hsp=0.1762 (total genetic diversity). However, a high level of genetic differentiation among populations was detected based on different measures (Nei's genetic diversity analysis: Gst=0.6038; AMOVA analysis: Fst=0.6797). Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenog-amy predominated and autogamy played an assistant role in O. Souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed.     

Cross-species amplification of primers developed from Plantago major and P. intermedia in two Hawaiian Plantago species from the section Plantago

Thirty-nine primers, developed from the sister species Plantago major and P. intermedia, were tested in two Hawaiian Plantago species from the section Plantago. Eight primers were polymorphic, of which three were published earlier, and five are new ones presented here. Amplification and polymorphism levels appeared to be high in these Hawaiian species. These markers will be valuable for further mating system and evolutionary studies in species from the section Plantago that are closely related to P. major and P. intermedia.     

Genetic diversity in Chinese modern wheat varieties revealed by microsatellite markers

Genetic diversity of 1680 modern varieties in Chinese candidate core collections was analyzed at 78 SSR loci by fluorescence detection system. A total of 1336 alleles were detected, of which 1253 alleles could be annotated into 71 loci. For these 71 loci, the alleles ranged from 4 to 44 with an average of 17.6, and the PIC values changed from 0.19 to 0.89 with an average of 0.69. (1) In the three genomes of wheat, the average genetic richness was B>A>D, and the genetic diversity indexes were B>D>A. (2) Among the seven homoeologous groups, the average genetic richness was 2=7>3>4>6>5>1, and the genetic diversity indexes were 7>3>2>4>6>5>1. As a whole, group 7 possessed the highest genetic diversity, while groups 1 and 5 were the lowest. (3) In the 21 wheat chromosomes, 7A, 3B and 2D possessed much higher genetic diversity, while 2A, 1B, 4D, 5D and 1D were the lowest. (4) The highest average genetic diversity index existed in varieties bred in the 1950s, and then it declined continually. However, the change tendency of genetic diversity among decades was not greatly sharp. This was further illustrated by changes of the average genetic distance between varieties. In the 1950s it was the largest (0.731). Since the 1960s, it has decreased gradually (0.711, 0.706, 0.696, 0.695). The genetic base of modern varieties is becoming narrower and narrower. This should be given enough attention by breeders and policy makers.