Inter- and intra-specific variation among five Erythroxylum taxa assessed by AFLP

BACKGROUND: and Aims The four cultivated Erythroxylum taxa (E. coca var. coca, E. novogranatense var. novogranatense, E. coca var. ipadu and E. novogranatense var. truxillense) are indigenous to the Andean region of South America and have been cultivated for folk-medicine and, within the last century, for illicit cocaine production. The objective of this research was to assess the structure of genetic diversity within and among the four cultivated alkaloid-bearing taxa of Erythroxylum in the living collection at Beltsville Agricultural Research Center. METHODS: Amplified fragment length polymorphism (AFLP) fingerprinting was performed in 86 Erythroxylum accessions using a capillary genotyping system. Cluster analysis, multidimensional scaling (MDS) and analysis of molecular variance (AMOVA) were used to assess the pattern and level of genetic variation among and within the taxa. KEY RESULTS: A clear distinction was revealed between E. coca and E. novogranatense. At the intra-specific level, significant differentiation was observed between E. c. var. coca and E. c. var. ipadu, but the differentiation between E. n. var. novogranatense and E. n. var. truxillense was negligible. Erythroxylum c. var. ipadu had a significantly lower amount of diversity than the E. c. var. coca and is genetically different from the E. c. var. ipadu currently under cultivation in Colombia, South America. CONCLUSIONS: There is a heterogeneous genetic structure among the cultivated Erythroxylum taxa where E. coca and E. novogranatense are two independent species. Erythroxylum coca var. coca is most likely the ancestral taxon of E. c. var. ipadu and a founder effect may have occurred as E. c. var. ipadu moved from the eastern Andes in Peru and Bolivia into the lowland Amazonian basin. There is an indication of artificial hybridization in coca grown in Colombia.     

Molecular diversity and allergenic profiles of Alternaria spp. from desert environments in Arizona

This study examined the genetic diversity of small-spored Alternaria species in the southwest desert of the USA by sampling 552 isolates from different habitats (soil and plant debris) in different locations (urban and an undisturbed desert). To estimate the genetic diversity, Amplified Fragment Length Polymorphism (AFLP) fingerprinting analysis was performed for all isolates. Strains representative of the sampled genotypic diversity (n = 125) were further characterized according their sporulation pattern and the capability to produce allergens. Morphological characterization assigned the majority of the strains to the Alternaria alternata and Alternaria tenuissima morpho-groups with only two isolates assigned to the Alternaria arborescens morpho-group. AFLP fingerprinting differentiated the A. arborescens morpho-groups, but could not distinguish between the A. alternata and A. tenuissima morpho-groups. Western blot analysis showed that a large number of allergenic proteins were produced by strains. These proteins were not specific for any morpho-group nor source of isolation. A hierarchical analysis of molecular variance was performed on the AFLP data to quantify molecular variation and partition this variation among sampled locations and habitat. No statistically significant differentiation among locations and habitat was detected indicating a lack of population structure across environments.     

洋桔梗品种遗传多样性的AFLP分析

该研究以洋桔梗(Eustoma grandiflorum)2个品种‘玛丽艾基粉色’和‘圣剑白底紫边’为试材,提取叶片DNA,经过EcoRⅠ/MseⅠ双酶切、连接、预扩增、选择性扩增,建立了洋桔梗的AFLP最佳反应体系;并以64个常用引物组合进行扩增,得到154个多态性条带,从中筛选出扩增条带较多且多态性较好的4个引物组合(E-ACA/M-CTC,E-ACC/M-CAC,E-AGC/M-CTT,E-ACT/M-CAG),其多态位点百分率均值为24.36%。利用上述4个引物组合,以最佳反应体系为基础,构建了7个常见洋桔梗品种的AFLP指纹图谱,统计7个品种各4个引物组合在1 000~300bp区间7个区段的扩增条带,并将各个品种的AFLP指纹图谱转换成各品种4组7位数构成的28位特异数字指纹,极大地方便了种质比较及鉴定;7个品种间的遗传相似系数介于0.683 5~0.860 8之间,平均值为0.774 6。研究结果为进一步进行洋桔梗的种质研究及利用奠定了基础。     

Genotypic variation and chromosomal location of QTLs for somatic embryogenesis revealed by epidermal layers culture of recombinant inbred lines in the sunflower (Helianthus annuus L.)

The present study was conducted to identify the genetic factors controlling somatic embryogenesis in the sunflower. Two traits, the number of embryogenic explants per 40 explants plated (EE/40 E) and the number of embryos per 40 explants (E/40 E), were scored in 74 recombinant inbred lines (RILs) from a cross between ’PAC-2’ and ’RHA-266’. The experiment was designed as a randomized complete block with 76 genotypes (74 recombinant inbred lines and two parents) and three replications. Each replication consisted of three Erlenmeyer flasks with 40 epidermal layers (explants). Analyses of variance indicated the existence of highly significant differences among parental genotypes and their RILs. Heritabilities for the somatic embryogenesis traits studied, EE/40 E and E/40 E, were high (0.64 and 0.77 respectively) and the genetic gain, in percentage of the best parent for 10% of selected RILs, was significant. Four QTLs for EE/40 E (tee) and seven for E/40 E (ete) were detected using composite interval mapping and AFLP mapping. The QTLs for EE/40 E explained 48% of the phenotypic variation while the QTLs for E/40 E explained about 89% of the variation. Received:14 December 1999 / Accepted:18 May 2000     

Genome wide AFLP markers support cryptic species in Coniophora (Boletales)

Numerous fungal morphospecies include cryptic species that routinely are detected by sequencing a few unlinked DNA loci. However, whether the patterns observed by multi-locus sequencing are compatible with genome wide data, such as amplified fragment length polymorphisms (AFLPs), is not well known for fungi. In this study we compared the ability of three DNA loci and AFLP data to discern between cryptic fungal lineages in the three morphospecies Coniophora olivacea, Coniophora arida, and Coniophora puteana. The sequences and the AFLP data were highly congruent in delimiting the morphotaxa into multiple cryptic species. However, while the DNA sequences indicated introgression or hybridization between some of the cryptic lineages the AFLP data did not. We conclude that as few as three polymorphic DNA loci was sufficient to recognize cryptic lineages within the studied Coniophora taxa. However, based on analyses of a few (three) sequenced loci the hybridization could not easily be distinguished from incomplete lineage sorting. Hence, great caution should be taken when concluding about hybridization based on data from just a few loci.     

Advances in the systematics and evolution of western Mediterranean representative species of the Pentanema conyzae clade through genetic fingerprinting

Forty-five populations of Pentanema corresponding to seven species included in the Pentanema conyzae clade have been studied using AFLP fingerprinting. The results show that allopolyploidization could have been involved in the diversification of this group, specifically in species P. langeanum and P. maletii. Molecular data confirm the presence of P. britannicum in the Iberian Peninsula and key steps are provided to identify the species that are morphologically the most challenging.     

利用SPSS与AFLP方法对双丰甜菜品种（系）间亲缘关系与系谱分析比较

作物育种必须调查植物学性状和生物学特征指标数据,来建立种质资源库,利用SPSS多元分析方法克服了传统植物学性状和生物学特征指标难以综合评价的缺陷,探讨利用SPSS统计分析软件对双丰系列甜菜品种（系）间亲缘关系与系谱进行准确性分析,除双丰2号品种块根产量、产糖量和株高三个主成分具有极值影响外,结果基本与亲本分析一致,可以作为亲缘关系与系谱分析的一种辅助工具;通过AFLP获得不同基因型品种的特征带和特征缺失带,表明AFLP技术在甜菜品种鉴定上的应用潜力。但AFLP也具有缺点,主要是标记是共显性的,不能完全区分某一位点是杂合体和纯合体,因而不能更好地估算种群遗传的变异,对种群遗传结构的分析不能提供更多的统计信息,相信随着AFLP分子标记技术的不断完善与发展,将与SPSS统计分析软件一起越来越广泛地利用在种群遗传和系谱分析中。     

Diversity of Vibrios associated with reared clams in Galicia (NW Spain)

The aim of the present study was to characterize and identify vibrios isolated from cultured clams in Galicia (NW Spain). A total of 759 isolates were obtained, phenotypically characterized, grouped and assigned to the genus Vibrio. Subsequently, the genomic diversity of 145 representative strains was analyzed by means of amplified fragment length polymorphism (AFLP), which revealed a high genetic diversity amongst these isolates. Only 57 out of 145 strains could be identified to the species level, and they were distributed in 13 AFLP clusters. V. cyclitrophicus, V. splendidus and V. alginolyticus were the most abundantly represented species. Eighty-eight isolates remained unidentified, 59 were distributed over 16 clusters, while 29 were unclustered. Sequencing of the 16S rRNA and two house-keeping genes (rpoA and recA) from representative strains belonging to eight unidentified clusters with the highest number of isolates confirmed their assignation to the Vibrionaceae family, and some of these probably represent new species within the genus. The present study confirmed that the phenotypic characterization of vibrios is not sufficient to identify them at the species level. A wide diversity of vibrios was found in cultured clams from all four geographic locations analyzed. In total, more than 12 Vibrio species and at least three potential new species in this genus were identified.     

Unexpectedly high genetic variation in large unisexual clumps of the subdioecious plant Honckenya peploides (Caryophyllaceae)

Honckenya peploides is a subdioecious dune plant that reproduces both sexually and by clonal growth. In northwest Spain this species was found to exhibit an extreme spatial segregation of the sexes, and our objective was to investigate genetic variation in unisexual clumps. Genetic variation was studied in six unisexual clumps of H. peploides, three of them exclusively composed of males and three exclusively female. In total, 193 samples were analysed using isozyme analysis and 80 samples were analysed using two AFLP primer combinations. Both techniques revealed considerably high genetic diversity (average proportion of distinguishable genotypes: 0.22 for isozymes and 0.36 for AFLP; average Simpson’s D: 0.65 for isozymes and 0.68 for AFLP). Our results show that, in spite of clonal growth, each unisexual clump consists of different genotypes. Genetic diversity within clumps is similar for both sexual morphs. Reasons for unisexuality of the clumps are discussed.     

Contrasting phylogeographies inferred for the two alpine sister species Cardamine resedifolia and C. alpina (Brassicaceae)

Aim We use Cardamine alpina and C. resedifolia as models to address the detailed history of disjunctions in the European alpine system. These species grow on siliceous bedrock: C. alpina in the Alps and Pyrenees, and C. resedifolia in several mountain ranges from the Sierra Nevada to the Balkans. We explore differentiation among their disjunct populations as well as within the contiguous Alpine and Pyrenean ranges, and compare the phylogeographical histories of these diploid sister species. We also include samples of the closely related, arctic diploid C. bellidifolia in order to explore its origin and post‐glacial establishment. Location European alpine system, Norway and Iceland. Methods We employed amplified fragment length polymorphisms (AFLPs). AFLP data were analysed using principal coordinates analysis, neighbour joining and Bayesian clustering, and measures of diversity and differentiation were computed. Results For the snow‐bed species C. alpina (27 populations, 203 plants) we resolved two strongly divergent lineages, corresponding to the Alps and the Pyrenees. Although multiple glacial refugia were invoked in the Pyrenees, we inferred only a single one in the Maritime Alps – from which rapid post‐glacial colonization of the entire Alps occurred, accompanied by a strong founder effect. For C. resedifolia (33 populations, 247 plants), which has a broader ecological amplitude and a wider distribution, the genetic structuring was rather weak and did not correspond to the main geographical disjunctions. This species consists of two widespread and largely sympatric main genetic groups (one of them subdivided into four geographically more restricted groups), and frequent secondary contacts exist between them. Main conclusions The conspicuously different histories of these two sister species are likely to be associated with their different ecologies. The more abundant habitats available for C. resedifolia may have increased the probability of its gradual migration during colder periods and also of successful establishment after long‐distance dispersal, whereas C. alpina has been restricted by its dependence on snow‐beds. Surprisingly, the arctic C. bellidifolia formed a very divergent lineage with little variation, contradicting a scenario of recent, post‐glacial migration from the Alps or Pyrenees.