Effects of native forest regeneration practices on genetic diversity in Eucalyptus consideniana

Impacts of forest harvesting and regeneration practices on genetic diversity in the Australian native forest species Eucalyptus consideniana Maiden (yertchuk) were examined using 29 Mendelian DNA markers (18 RFLPs and 11 microsatellites). Two replicate logging coupes were studied from each of the two most commonly employed silvicultural treatments: clear felling with aerial re-sowing and the seed tree system. For each coupe, genetic diversity measures were compared between a sample of the sapling regeneration and a corresponding control sample from bordering unharvested trees. When calculations were performed over all 29 loci, significant reductions of allelic richness (AR), effective number of alleles (AE) and/or expected heterozygosity (HE) were detected on one or both of seed tree coupes, but on neither of the clear falls. When calculations were performed over the 11 microsatellites alone, all three measures, AR, AE and HE, were significantly reduced on both of the seed replicates but on neither of the two clear falls. In contrast, when the RFLPs were examined separately, there were no significant reductions of diversity on either of the two seed tree coupes or on the two clear falls. These results suggest that genetic erosion is more likely under the seed tree system than under clear-felling with aerial re-sowing and that there is greater statistical power to detect it with microsatellites than with RFLPs. A Monte Carlo simulation to test the statistical significance of the number of apparently lost or gained alleles showed that significant losses of alleles above specified threshold frequencies occurred only in the two seed tree replicates. Three of the four control and regeneration population pairs were significantly differentiated, as indicated by exact tests or by pairwise FST estimates. Comparisons of CONTML dendrograms, constructed for the regeneration populations only versus the control populations only, indicated that genetic drift was significantly promoted under forest management. No significant decreases in observed heterozygosity, or increases in the panmictic index (f), were observed in any of the comparisons suggesting that inbreeding was not promoted by a single rotation of forest management.     

Development of microsatellite markers in black locust (Robinia pseudoacacia) using a dual‐supression‐PCR technique

Black locust (Robinia pseudoacacia) is an economically and ecologically important tree species in the world. We isolated seven polymorphic microsatellite loci from R. pseudoacacia using a dual‐suppression‐PCR technique. These loci provided microsatellite markers with high polymorphism ranging from three to 12 alleles per locus and expected heterozygosity between 0.538 and 0.944. The markers are now available for more detailed investigation of population genetic structure and pollen and seed dispersal.     

Development of microsatellite markers for Dryobalanops aromatica (Dipterocarpaceae), a tropical emergent tree in Southeast Asia

Eight polymorphic microsatellite markers were developed in Dryobalanops aromatica, an emergent tree in tropical rain forests in Southeast Asia, using an enriched library method. For the assessment of microsatellite variation, 36 individuals from a natural population were analysed. The number of alleles per locus ranged from three to 16, with observed heterozygosity of 0.056–0.833 and expected heterozygosity of 0.054–0.882. These microsatellite markers will be useful for studies of population genetics, reproductive ecology and regeneration dynamics of D. aromatica.     

草鱼EST-SSR标记及5个不同地域群体的遗传结构分析

以草鱼(Ctenopharyngodon idella)脑、肌肉、肝等组织构建cDNA文库,经测序获得unigenes序列45 318个,从中筛选微卫星序列共5 556个,据此设计EST-SSR引物118对,其中19对引物能够扩增出带型清晰且多态性较高的谱带。用这19个EST-SSR标记研究3个长江水系群体(石首、监利和长沙)和2个珠江水系群体(清远和肇庆)草鱼的遗传结构。结果表明,5个群体的平均多态信息含量(PIC)为0.415 4～0.460 4,显示草鱼群体的遗传多样性偏低;平均观测杂合度(Ho)为0.415 8～0.501 3,平均期望杂合度为(He)0.450 6～0.502 8,其中,长沙群体平均期望杂合度最高,为0.502 8,监利群体的平均观察杂合度和平均期望杂合度均最低,分别为0.415 8和0.450 6,即长沙群体的遗传多样性最高,监利群体的遗传多样性最低;对数据进行F-检验,结果表明,群体间的遗传分化程度低。Hardy-Weinberg平衡的卡方检验结果表明,5个群体均一定程度上偏离了平衡;聚类分析显示长沙群体、石首群体与监利群体聚成一支;肇庆群体与清远群体聚成一支,这与草鱼群体的流域分布一致。     

基于SSR标记探讨三种金花茶植物的遗传多样性和遗传结构

薄叶金花茶、小花金花茶和小瓣金花茶是三种濒危金花茶植物,为了解珍稀濒危植物遗传多样性和遗传结构,该研究利用微卫星标记对他们的7个种群共184个个体进行了遗传多样性和遗传结构分析。结果表明:11个位点共检测到等位基因92个。在物种水平上,小瓣金花茶平均等位基因数(N_A)为3.9、有效等位基因数(N_E)为2.328、观测杂合度(H_o)为0.520、期望杂合度(H_e)为0.501,高于薄叶金花茶和小花金花茶。在种群水平上,有效等位基因数(N_E)在1.788～2.466之间,期望杂合度(H_e)在0.379～0.543之间;种群间遗传分化系数(FST)在0.143 7～0.453 3之间,种群间基因流(N_m)在0.301 5～1.488 9之间。AMOVA分子变异分析显示65.72%的变异存在于种群内。三种金花茶具有较低水平的遗传多样性和高水平的种群间遗传分化。STRUCTURE和PCoA种群遗传结构分析结果将取样种群分为2组,即薄叶金花茶和小花金花茶大部分个体分为一组,小瓣金花茶大部分个体分为一组。现存所有种群应根据实际情况尽快采取就地保护或迁地保护措施。     

细叶云南松天然种源林遗传多样性的SSR分析

利用12对SSR引物对三个不同种源的细叶云南松群体遗传多样性进行研究。结果表明:共检测到13个位点37个等位基因,每个位点平均观察等位基因数(A)为2.85,多态率为100%;平均有效等位基因数(Ne)1.45。各群体内的有效等位基因数平均为1.447,观察杂合度平均为0.341,期望杂合度平均为0.281。三个群体的Nei’s基因多样度指标的变化范围为0.256~0.297,Shannon多样性指数变化范围为0.448~0.484,各群体间的多态性水平差异不大。细叶云南松群体间的基因分化系数(Gst)为0.089,群体间的遗传分化水平较低,大部分变异均存在群体内。细叶云南松群体间的基因流(Nm)在不同位点的变化范围从4.693~122.189,平均为11.17。说明细叶云南松群体间存在比较充分的基因交流。     

Isolation and characterization of microsatellite loci of Lycopodium fordii Bak. (Lycopodiaceae, Pteridophyta)

Lycopodium fordii Bak. (Lycopodiaceae, Pteridophyta) is a gardening plant with a native, fragmentary distribution in Taiwan. In this study, we described the development of eleven microsatellite loci in L. fordii for genetic studies. These new markers were tested in 16 individuals of three populations. The number of alleles ranged from 1 to 5 and the expected heterozygosity from 0.41746 to 0.72222. Four of the nine polymorphic loci were significantly deviated from Hardy-Weinberg expectations due to the heterozygote deficiency. The microsatellite markers have also been proved as informative genetic markers for other 15 Lycopodium species.     

木棉的SSR引物开发

木棉是分布于热带地区的重要经济树种。通过磁珠富集方法开发了木棉的SSR引物,并在采自于西南干热河谷的32个木棉个体中进行了多态性验证。结果表明:这些位点等位基因数量为2～6个,期望杂合度和观测杂合度范围分别为0～0.525和0.121～0.561。仅有一个位点显示Hardy-Weinberg平衡的偏离。这些微卫星标记的开发在木棉属中尚属首次,对于木棉的野生种群遗传多样性研究和木棉遗传资源利用上有很高的潜在价值。     

Effects of reforestation methods on genetic diversity of lodgepole pine: an assessment using microsatellite and randomly amplified polymorphic DNA markers

 We examined the effects of different methods of forest regeneration on the genetic diversity of lodgepole pine (Pinus contorta var ‘latifolia’) using two different DNA-based molecular markers [randomly amplified polymorphic DNA (RAPDs) and microsatellites or simple sequence repeats (SSRs)]. Genetic diversity was estimated for 30 individuals in each of four populations for the following three stand types: (1) mature lodgepole pine (>100 years); (2) 20- to 30-year-old harvested stands left for natural regeneration; (3) 20- to 30-year-old planted stands (4 stands of each type); and one group of 30 operationally produced seedlings. There was no significant effect of stand type on expected heterozygosity, although allelic richness and diversity were much higher for SSRs than for RAPDs. Expected heterozygosity ranged from 0.39 to 0.47 based on RAPDs and from 0.67 to 0.77 based on SSRs. The number of alleles per locus for SSRs ranged from 3 to 34 (mean 21.0), and there was a significant relationship between sequence repeat length and the number of alleles at a locus. Both marker types showed that over 94% of the variation was contained within the populations and that the naturally regenerated stands sampled had lower (not significant) expected heterozygosity than the planted or unharvested stands. The group of seedlings (assessed by RAPDs only) had expected heterozygosity and allele frequencies similar to those of the unharvested stands. Genetic distance measures were higher than obtained previously in the species using isozyme markers. There was no correlation between the two marker types for pair-wise genetic distances based on populations analyzed by both methods. Pair-wise genetic distance measures and an ordination of allele frequencies for both marker types showed little effect of geographic location or stand type on genetic similarity. Received: 18 August 1998 / Accepted: 17 September 1998     

基于SSR标记的大明松天然群体遗传多样性分析

大明松是广西和贵州特有的高山松类,具有很高的经济价值和生态价值,其自然种群长期没有得到充分的保护和利用,不利于该树种长期稳定发展。为了合理保护和开发利用大明松天然遗传资源,该文利用12个SSR分子标记对大明松3个天然群体进行遗传多样性研究,分析其群体间的遗传分化和基因流,为该物种的保护策略提供参考。研究结果表明:(1)12对引物共检测到37 个等位基因,多态位点百分率为100%。每个位点平均观察等位基因数(Na)为3.08,平均有效等位基因数(Ne)为1.68, 不同位点间有效等位基因数差异较大; 每个位点平均观察杂合度(Ho)为0.35,平均期望杂合度(He)为0.40,平均多态信息含量(PIC)为0.31。(2)3 个群体的Shannon''s多样性指数变化范围为0.48～0.65,Nei''s基因多样度的变化范围为0.27～0.39,与其他近缘种松类相比遗传多样性偏低。群体平均观察杂合度为0.40,平均期望杂合度为0.33,平均有效等位基因数为1.58。群体间基因分化系数(Gst)为0.10,群体间的遗传分化水平较低,大部分变异均存在群体内。群体间的基因流(Nm)为2.74,说明大明松群体间的基因交流比较充分。该研究可为大明松生物多样性保护提供重要参考依据,为科学利用大明松资源打下基础。     

Development and characterization of microsatellite markers for <Emphasis Type="Italic">Prunus verecunda</Emphasis> and <Emphasis Type="Italic">Prunus grayana</Emphasis> (Rosaceae)

Simple sequence repeat (SSR) markers were developed for Prunus verecunda and Prunus grayana to help understand the seed dispersal pattern of each species. We isolated and characterized nine microsatellite loci (four from P. verecunda and five from P. grayana). In P. verecunda, the number of alleles detected and the expected heterozygosity of five loci ranged from 11 to 24 and 0.59 to 0.92, respectively. In P. grayana, the number of alleles detected and the expected heterozygosity of five loci ranged from 4 to 14 and 0.62 to 0.86, respectively. These results show that the markers described here will be useful in studying the seed dispersal pattern of Prunus species.     

Isolation and characterization of eight polymorphic microsatellite loci for the critically endangered Arenaria nevadensis (Caryophyllaceae)

We report on the isolation and characterization of eight microsatellite markers from enriched libraries for Arenaria nevadensis, one of the most critically endangered plant species in the Iberian Peninsula. These are the first microsatellite loci reported for Arenaria species. The number of alleles ranged from two to eight, and the expected heterozygosity from 0.067 to 0.873. These markers will be useful for characterizing the genetic diversity in A. nevadensis and understanding its population structure, and will provide important genetic data for the conservation and recovery of this species.     

Development and characterization of microsatellite markers in Eucommia ulmoides Oliver (Eucommiaceae)

Twenty‐three microsatellite markers were developed from an AC‐enriched genomic library of Eucommia ulmoides, an economically important tree species for both herbal medicine and organic chemical industry in China. Nineteen microsatellite loci were found polymorphic by testing 36 individuals from 10 populations, with two to 14 alleles per locus. The expected heterozygosity ranged from 0.054 to 0.874. This set of microsatellite markers has provided a useful tool for the ongoing efforts in studying population genetic structure of E. ulmoides.     

Genetic characterization of four strains of Nile tilapia (Oreochromis niloticus L.) using microsatellite markers

Four domesticated strains of Nile tilapia (Oreochromis niloticus L.) were genetically characterized using 14 microsatellite markers and 64 animals per strain. Two strains, Chitralada (AIT) and International Development Research Centers (IDRC) were obtained from the AIT institute, Bangkok, Thailand. The GIFT strain (5th generation) came from NAGRI, Thailand, and the GÖTT strain was supplied by the University of Göttingen, Germany. The average numbers of alleles per marker were 5.0 (GÖTT), 5.4 (AIT), 5.6 (IDRC) and 7.5 (GIFT). Private alleles were found at all markers with the exception of two. No fixation of alleles was found at any marker. Population differentiation, F_ST, was 0.178 (great genetic differentiation) and confirmed grouping of the animals in strains. The expected level of heterozygosity ranged from 0.624 to 0.711, but the observed level of heterozygosity significantly deviated from the expected level in three strains. This was probably because of small population size. Moderate to great genetic differentiation was found between strains. A phylogenetic tree reflected the strains known histories. Application of the Weitzman approach showed that all strains have added value for the total genetic diversity and thus should be retained.     

Isolation and characterization of microsatellite loci in the endangered tree Berchemiella wilsonii var. pubipetiolata and cross-species amplification in closely related taxa

Twenty-eight polymorphic microsatellite loci were developed and characterized for the endangered tree Berchemiella wilsonii var. pubipetiolata. The observed number of allele ranged from two to seven. The ranges of observed and expected heterozygosity were 0.039–1.000 and 0.038–0.816, respectively. In addition, this set of microsatellites produced robust cross-species amplification in other two endangered taxa: Berchemiella berchemiaefolia and Berchemiella wilsonii, suggesting these microsatellite markers should provide a useful tool for genetic and conservation studies of the globally endangered genus Berchemiella.     

Polymorphic microsatellites identified by cross-species amplifications in the European Coot Fulica atra

We tested the cross-amplification of 26 microsatellites developed for passerines and an additional three developed for Gallinula species in eight European Coots from two populations. Sixteen microsatellite markers successfully amplified, of which nine were polymorphic with 2–6 alleles (mean 3.7 alleles) and an expected heterozygosity (H _e) ranging from 0.375 to 0.805 (mean H _e = 0.589). On average, we found 2.22 alleles/locus and a mean H _e of 0.440 in one nest, and 2.56 alleles/locus and a mean H _e of 0.494 in the other one. These nine polymorphic markers could be of potential use in studies of genetic variability, population structure and reproductive strategy of European Coots.     

Microsatellite markers for Ceiba pentandra (Bombacaceae), an endangered tree species of the Amazon forest

From a genomic library enriched for AG/TC repeats, eight polymorphic microsatellite markers were developed for Ceiba pentandra, a pan‐tropical forest tree. Polymorphism was evaluated using a panel of 74 adult trees. Using automated fluorescence detection, a total of 112 alleles was detected with an average of 14 alleles per locus. All microsatellite loci showed very high levels of genetic information content, with expected heterozygosity ranging from 0.814 to 0.895. These microsatellite markers represent a powerful tool to investigate refined questions of mating systems, gene flow, family structure and population dynamics in natural populations of C. pentandra.     

The use of microsatellite polymorphism in genetic mapping of the ostrich (<Emphasis Type="Italic">Struthio camelus</Emphasis>)

The aim of this study was to determine microsatellite polymorphism in ostriches and using it in creation the genetic map of the ostrich. The polymorphism analysis covered 30 microsatellite markers characteristic of ostrich, for the CAU (China Agricultural University) group. The material consisted of 150 ostriches (Struthio camelus). The 30 microsatellite loci was examined and a total of 343 alleles was identified. The number of alleles at a single locus ranged from 5 at locus CAU78 to 34 at locus CAU85. The values for the observed heterozygosity H_o ranged from 0.467 (locus CAU78) to 0.993 (locus CAU16), whereas for the expected heterozygosity H_e - from 0.510 (locus CAU78) to 0.953 (locus CAU85). Analyzing the individual loci, the highest PIC value, more than 0.7 was observed for: loci CAU85 (0.932), CAU64 (0.861) and CAU32, 75 (0.852), respectively. It should be noted, that the microsatellite markers used in our study were very polymorphic as evidenced by the large number of detected alleles and high rates of heterozygosity, PIC and PE as well. The analysed microsatellite markers may be used in genetic linkage mapping of ostrich, the construction of a comparative genetic map with other ratites, such as emu and rhea, and population genetics studies or phylogenetic studies of these birds.     

Development of ten microsatellite markers for <Emphasis Type="Italic">Quercus mongolica</Emphasis> var. <Emphasis Type="Italic">crispula</Emphasis> by database mining

Simple sequence repeats (SSRs) in the NCBI dbEST database were surveyed to identify potential SSR markers for Quercus mongolica. In total, 2,691 gene sequences, mainly from expressed sequence tags (ESTs) for Q. robur and Q. petraea had been registered. Twenty-two PCR primers were designed for SSRs in these sequences and screened for polymorphisms in 16 Q. mongolica trees. Ten loci were easily genotyped and showed polymorphism, with numbers of alleles and expected heterozygosity ranging from 3 to 15 and 0.28 to 0.94, respectively. These EST-SSR markers should be useful for studying the genetic diversity of Quercus species.     

Development of thirty new polymorphic microsatellite primers for <Emphasis Type="Italic">Paeonia suffruticosa</Emphasis>

Four new microsatellite primer pairs were developed in tree peony (Paeonia suffruticosa) based on the database mining and other twenty-six primer pairs by fast isolation by AFLP of sequences containing repeats (FIASCO) method. The polymorphism of each locus was further evaluated in 40 individuals of one population plus 5 tree peony related species. The number of alleles per locus ranged from 3 to 7 and the expected (H_e) and observed (H_o) heterozygosity at each locus ranged from 0.42 to 0.78 and 0.28 to 0.59, respectively. These microsatellite markers will be useful for investigating genetic diversity and studies of population genetic structure of tree peony.