Polyploidisation and Geographic Differentiation Drive Diversification in a European High Mountain Plant Group (Doronicum clusii Aggregate,Asteraceae)

Range shifts (especially during the Pleistocene), polyploidisation and hybridization are major factors affecting high-mountain biodiversity. A good system to study their role in the European high mountains is the Doronicum clusii aggregate (Asteraceae), whose four taxa (D. clusii s.s., D. stiriacum, D. glaciale subsp. glaciale and D. glaciale subsp. calcareum) are differentiated geographically, ecologically (basiphilous versus silicicolous) and/or via their ploidy levels (diploid versus tetraploid). Here, we use DNA sequences (three plastid and one nuclear spacer) and AFLP fingerprinting data generated for 58 populations to infer phylogenetic relationships, origin of polyploids—whose ploidy level was confirmed by chromosomally calibrated DNA ploidy level estimates—and phylogeographic history. Taxonomic conclusions were informed, among others, by a Gaussian clustering method for species delimitation using dominant multilocus data. Based on molecular data we identified three lineages: (i) silicicolous diploid D. clusii s.s. in the Alps, (ii) silicicolous tetraploid D. stiriacum in the eastern Alps (outside the range of D. clusii s.s.) and the Carpathians and (iii) the basiphilous diploids D. glaciale subsp. glaciale (eastern Alps) and D. glaciale subsp. calcareum (northeastern Alps); each taxon was identified as distinct by the Gaussian clustering, but the separation of D. glaciale subsp. calcareum and D. glaciale subsp. glaciale was not stable, supporting their taxonomic treatment as subspecies. Carpathian and Alpine populations of D. stiriacum were genetically differentiated suggesting phases of vicariance, probably during the Pleistocene. The origin (autopolyploid versus allopolyploid) of D. stiriacum remained unclear. Doronicum glaciale subsp. calcareum was genetically and morphologically weakly separated from D. glaciale subsp. glaciale but exhibited significantly higher genetic diversity and rarity. This suggests that the more widespread D. glaciale subsp. glaciale originated from D. glaciale subsp. calcareum, which is restricted to a prominent Pleistocene refugium previously identified in other alpine plant species.     

Reticulate evolution in the apogamous Dryopteris varia complex (Dryopteridaceae,subg. Erythrovariae,sect. Variae) and its related sexual species in Japan

Apogamous fern species are often difficult to distinguish from related species because of their continuous morphological variations. To clarify the genetic relationships among the members of the Dryopteris varia complex, we analyzed the nucleotide sequences of the plastid gene rbcL and the nuclear gene PgiC. We also analyzed the diploid sexual species D. caudipinna and D. chinensis, which have not been included in the complex, but were recently shown to be closely related to the complex in a molecular phylogenetic study. The PgiC sequences of the diploid sexual species, D. varia, D. saxifraga, D. sp. ‘protobissetiana’ (undescribed diploid sexual species), D. caudipinna, and D. chinensis, were well differentiated and hence designated A, B, C, D, and E, respectively. Thus, the PgiC constitution of apogamous species in the complex was as follows: D. bissetiana, B + C; D. kobayashii, B + C + E); D. pacifica, A + C, A + B + C, or A + C + D; D. sacrosancta, A + C + E; and D. saxifragivaria, B + C. These results suggest that these apogamous species are formed by hybridizations of species including not only the three diploid sexual species of the D. varia complex (A, B, and C) but also the two diploid sexual species D. caudipinna (D) and D. chinensis (E), which do not belong to the complex.     

Aucubinartige glucoside als systematische merkmale bei labiaten — I. Lamiastrum

Lamiastrum (Lamium) galeobdolon occurs in Europe with the two diploid taxa subsp. galeobdolon and subsp. flavidum and with one tetraploid taxon, subsp, montanum. The latter is supposed to have had an allopolyploid origin. Chromosome counts demonstrated that subsp, montanum is by far the most common taxon in the Netherlands. Leaves of many plants of several countries of Europe were investigated for aucubin-like glycosides. Subspecies galeobdolon contains harpagide, acetylharpagide and an unknown aucubinoid constituent. Many plants of subsp, montanum contained galiridoside in addition. Galiridoside is also present in small amounts in subsp, flavidum; in this taxon, however, the unknown compound seems to be lacking. It seems likely, in the light of leaf aucubinoids, that subsp, montanum is of allopolyploid origin with the two diploid taxa as parents. The distribution and systematic meaning of iridoid constituents in Labiatae is discussed. Lamiastrum differs from Lamium by accumulating predominantly aucubin-like glycosides of the C-9-aglycon group.     

Investigations into the evolutionary history of the polyploid complexAntennaria neodioica (Asteraceae: Inuleae)

TheAntennaria neodioica polyploid agamic complex is a polymorphic species occurring across North America mainly north of the terminal margin of the Wisconsin glacier. This taxonomically difficult group has recently been treated as consisting of the four subspeciesA. neodioica subsp.canadensis, subsp.howellii, subsp.neodioica, and subsp.petaloidea. TheA. neodioica agamic complex has been considered of hybrid origin with several sexual diploid species constituting its parentage. Crosses were made among five sexual diploid species ofAntennaria, morphologically similar toA. neodioica s.l., in an attempt to discover its origins. Representative specimens of the five diploid species,A. neodioica s. l., and the synthetic interspecific F₁ hybrids were subjected to various analyses including PCA, cluster (UPGMA), and discriminant analyses. Results suggest that theA. neodioica complex is of multiple hybrid origin involving the four diploid speciesA. neglecta, A. plantaginifolia, A. racemosa, andA. virginica. BecauseA. neodioica is the result of diverse origin it is more desirable to consider the agamic complex as a separate, distinct species from its sexual diploid relatives. Several morphological characters in the diploid species were determined to be polygenically inherited.Investigations into the Evolutionary History of the Polyploid Complexes inAntennaria (Asteraceae: Inuleae). I.     

Selected chromosome counts of the Czechoslovak flora II

Chromosome numbers are presented in the following 16 Phanerogams of the Czechoslovak flora:Amaranthus blitoides S. Watson,Anthoxanthum alpinum Á. Löve etD. Löve Acter amellus L.,Bistorta major S. F. Gray,Cardamine hirsuta L.,Cardamine parviflora L.,Chrysosplenium oppositifolium L.,Dactylis glomerata L.subsp. aschersoniana (Graebner) Thell.,Elatine hydropiper L. s. l.,Geranium phaeum L.,Hieracium lachenalii C. C. Gmel.,Jovibarba sobolifera (Sims) Opiz,Kickxia spuria (L.)Dum.,Persicaria hydropiper (L.)Spach,Sedum alpestre Vill. andTephroseris crispa (Jacq.) Schur. Six of them are reported for the first time from Czechoslovakia, the others are mostly first reports of chromosome numbers from the Bohemian and Moravian regions. A new diploid number of 2n=36 is given inElatine hydropiper L. s. l. All results are compared with as yet published data.     

Evidence of 2n microspore production in a natural diploid population of Turnera sidoides subsp. carnea and its relevance in the evolution of the T. sidoides (Turneraceae) autopolyploid complex

Turnera sidoides is a complex of distylous perennial rhizomatous herbs that includes five subspecies. Since polyploidy has played a prominent role within this species (x?=?7), ongoing studies in T. sidoides are focused on the understanding of the mechanisms involved in the origin and the establishment of polyploids. Therefore, aiming to contribute to the understanding of the mode of polyploid formation, in this study we investigated the frequency of unreduced microspores in a natural diploid population of T. sidoides subsp. carnea by analyzing the size range of pollen and the constitution of the sporads. The results showed that some of the individuals studied produced 2n and 4n microspores, both in short- and long-styled floral morphs. The analysis performed documents the production of unreduced microspores in T. sidoides subsp. carnea and provides evidence that support the hypothesis of sexual polyploidization as one of the most probable mechanisms involved in the origin of polyploids within this species complex. The role of unreduced pollen in the establishment and persistence of newly formed polyploids in diploid populations of T. sidoides is also discussed.     

Dopamine Receptors Antagonistically Regulate Behavioral Choice between Conflicting Alternatives in C. elegans

Caenorhabditis elegans is a useful model to study the neuronal or molecular basis for behavioral choice, a specific form of decision-making. Although it has been implied that both D1-like and D2-like dopamine receptors may contribute to the control of decision-making in mammals, the genetic interactions between D1-like and D2-like dopamine receptors in regulating decision-making are still largely unclear. In the present study, we investigated the molecular control of behavioral choice between conflicting alternatives (diacetyl and Cu²⁺) by D1-like and D2-like dopamine receptors and their possible genetic interactions with C. elegans as the assay system. In the behavioral choice assay system, mutation of dop-1 gene encoding D1-like dopamine receptor resulted in the enhanced tendency to cross the Cu²⁺ barrier compared with wild-type. In contrast, mutations of dop-2 or dop-3 gene encoding D2-like dopamine receptor caused the weak tendency to cross the Cu²⁺ barrier compared with wild-type. During the control of behavioral choice, DOP-3 antagonistically regulated the function of DOP-1. The behavioral choice phenotype of dop-2; dop-1dop-3 triple mutant further confirmed the possible antagonistic function of D2-like dopamine receptor on D1-like dopamine receptor in regulating behavioral choice. The genetic assays further demonstrate that DOP-3 might act through Gα_o signaling pathway encoded by GOA-1 and EGL-10, and DOP-1 might act through Gα_q signaling pathway encoded by EGL-30 and EAT-16 to regulate the behavioral choice. DOP-1 might function in cholinergic neurons to regulate the behavioral choice, whereas DOP-3 might function in GABAergic neurons, RIC, and SIA neurons to regulate the behavioral choice. In this study, we provide the genetic evidence to indicate the antagonistic relationship between D1-like dopamine receptor and D2-like dopamine receptor in regulating the decision-making of animals. Our data will be useful for understanding the complex functions of dopamine receptors in regulating decision-making in animals.     

Antichemotactic and Antifungal Action of the Essential Oils from Cryptocarya aschersoniana,Schinus terebinthifolia,and Cinnamomum amoenum

The purpose of this work was to determine the chemical composition and evaluate the antichemotactic, antioxidant, and antifungal activities of the essential oil obtained from the species Cryptocarya aschersoniana Mez , Cinnamomum amoenum (Ness & Mart .) Kosterm. , and Schinus terebinthifolia Raddi , as well as the combination of C. aschersoniana essential oil and terbinafine against isolates of dermatophytes. Allo‐aromadendrene, bicyclogermacrene, and germacrene B were identified as major compounds in essential oils. The essential oil of C. aschersoniana shown 100 % inhibitory effect on leukocyte migration at the concentration of 10 μg/mL while S. terebinthifolia oil presented 80.1 % inhibitory effect at the same concentration. Only S. terebinthifolia oil possessed free‐radical‐scavenging activity which indicates its antioxidant capacity. The essential oils were also tested against fungal isolates of dermatophyte species (Trichophyton rubrum, Trichophyton mentagrophytes, Microsporum canis and Microsporum gypseum), resulting in MIC ranging from 125 μg/mL to over 500 μg/mL. C. aschersoniana oil combined with terbinafine resulted in an additive interaction effect. In this case, the essential oil may act as a complement to conventional therapy for the topical treatment of superficial fungal infections, mainly because it is associated with an anti‐inflammatory effect.     

Intraspecific phylogenetic relationships in Ixeridium dentatum (Compositae) complex based on genetic and morphological evidence

Ixeridium dentatum (I. dentatum; family Compositae) forms a complex species through intraspecific differentiation. In this study, intraspecific taxa of I. dentatum were analyzed by counting chromosome numbers, sequencing internal transcribed spacer (ITS), and detecting amplified fragment length polymorphisms (AFLP) to explore phylogenetic relationships within I. dentatum. Analysis of ploidy levels showed that I. dentatum subsp. kitayamense and subsp. nipponicum were diploid (2n = 2x = 14), I. dentatum subsp. kimuranum was tetraploid (2n = 4x = 28), and other intraspecific taxa of I. dentatum were triploid (2n = 3x = 21). The ITS sequences contained only 13 variable sites (2.7 %) among intraspecific taxa, suggesting that the I. dentatum complex originated by autoploidy. Our AFLP-based analysis separated these taxa into five groups: (1) I. dentatum subsp. kimuranum and subsp. kitayamense; (2) subsp. nipponicum and var. albiflorum; (3) two types of subsp. dentatum and f. atropurpureum; (4) f. amplifolium; (5) subsp. ozense and new taxa, which were discovered in this study. The identified clusters significantly differed from morphological classifications. For example, morphologically similar variety and forms of I. dentatum subsp. nipponicum were separated into different groups. Taken together with the ploidy data, this study proposes a possible evolutionary history generating the current taxonomic combinations of the I. dentatum complex. The proposed model suggests that diverse taxa recently emerged during migration to lowlands.     

Phylogenetic analysis in some Hordeum species (Triticeae; Poaceae) based on two single-copy nuclear genes encoding acetyl-CoA carboxylase

We investigate the phylogenetic relationship, and evolutionary history of 18 diploid and polyploid Hordeum species including 22 taxa based on two single-copy nuclear ACC1 and ACC2 genes using maximum parsimony, maximum likelihood, and Bayesian inference. The results of molecular phylogenetic analysis demonstrated genetic relationships among taxa and origin of polyploids. Our phylogenetic analyses revealed a clear alloploid origin of Hordeum capense, with Eurasian Hordeum marinum subsp. gussoneanum as the Xa genome donor and diploid Asian Hordeum roshevitzii as the H genome donor. The formation of hexaploid Hordeum lechleri likely involves hybridization between tetraploid Hordeum brachyantherum subsp. brachyantherum and a diploid possessing the I genome. The Acc1 and Acc2 gene data analyses suggested that Siberian Hordeum bogdanii might have be the common ancestor of the diploid New World Hordeum species. Perennial diploid South American species, Hordeum comosum was the first-diverging group within the clade of diploid American species in the analyses.     

Dynamics of polyploid formation and establishment in the allotetraploid rock fern Asplenium majoricum

Background and Aims

Successful establishment of newly formed polyploid species depends on several interlinked genetic and ecological factors. These include genetic diversity within and among individuals, chromosome behaviour and fertility, novel phenotypes resulting from novel genomic make-up and expression, intercytotypic and interspecific competition, and adaptation to distinct habitats. The allotetraploid rock fern Asplenium majoricum is known from one small population in Valencia, Spain, and several larger populations on the Balearic island of Majorca. In Valencia, it occurs sympatrically with its diploid parents, A. fontanum subsp. fontanum and A. petrarchae subsp. bivalens, and their diploid hybrid A. × protomajoricum. This highly unusual situation allowed the study of polyploid genetic diversity and its relationship to the formation and establishment of nascent polyploid lineages.

Methods

Genetic variation for isozyme and chloroplast DNA markers was determined for A. majoricum and A. × protomajoricum sampled thoroughly from known sites in Majorca and Valencia. Results were compared with variation determined previously for the diploid parent taxa.

Key Results

A highly dynamic system with recurring diploid hybrid and allotetraploid formation was discovered. High diversity in the small Valencian A. majoricum population indicates multiple de novo origins from diverse parental genotypes, but most of these lineages become extinct without becoming established. The populations on Majorca most probably represent colonization(s) from Valencia rather than an in situ origin. Low genetic diversity suggests that this colonization may have occurred only once.

Conclusions

There is a striking contrast in success of establishment of the Majorcan and Valencian populations of A. majoricum. Chance founding of populations in a habitat where neither A. fontanum subsp. fontanum nor A. petrarchae subsp. bivalens occurs appears to have been a key factor enabling the establishment of A. majoricum on Majorca. Successful establishment of this polyploid is probably dependent on geographic isolation from diploid progenitor competition.     

Allelopathic potential of alkylphenols from Dactylis glomerata subsp. hispanica (Roth) Nyman

Eleven alkylphenols were isolated from the aerial parts of Dactylis glomerata subsp. hispanica, six of them described for the first time. The structural characterization of these compounds has been elucidated by 1D and 2D NMR techniques. The fragmentation patterns of the metabolites obtained by GC–MS analysis allowed the side chain to be elucidated. The allelopathic potential of three alkylphenols, representative of each homologous series of alkylphenols from D. glomerata subsp. hispanica, has been assayed on D. glomerata subsp. hispanica and an herbaceous coexisting species, Phleum subulatum. The bioassay results showed a high auto-stimulation values of germination and root and shoot elongation for D. glomerata subsp. hispanica at high concentrations.     

Geographical Distribution of Diploid and Tetraploid Cytotypes of Thymus sect. Mastichina (Lamiaceae) in the Iberian Peninsula, Genome Size and Evolutionary Implications

The occurrence of diploid and tetraploid cytotypes in Thymus section Mastichina (Lamiaceae) was investigated by chromosome counting and flow cytometric measurements of DNA content. To cover the entire native distribution of the section across the Iberian Peninsula, plant material was sampled from 29 populations, representing all three taxa (Thymus albicans, T. mastichina subsp. mastichina and T. mastichina subsp. donyanae). We provide first estimates of genome size for taxa of this section. Analyses revealed the existence of new cytotypes in T. mastichina subsp. mastichina (2n?=?2x?=?28, 30) and confirmed the existence of previous ones (2n?=?4x?=?56, 58, 60). We also confirmed the presence of exclusively diploid cytotypes (2n?=?2x?=?30) in the southwestern Iberian endemics T. albicans and T. mastichina subsp. donyanae. We conclude that the southwestern Iberian Peninsula acted as a Pleistocene glacial refugium that may have permitted speciation processes within this section. Several hypotheses concerning these processes and the origin and distribution of the studied taxa are discussed.     

Identification of Bacillus thuringiensis subsp. kurstaki Strain HD1-Like Bacteria from Environmental and Human Samples after Aerial Spraying of Victoria, British Columbia, Canada, with Foray 48B

Aerial applications of Foray 48B, which contains Bacillus thuringiensis strain HD1, were carried out on 9 to 10 May, 19 to 21 May, and 8 to 9 June 1999 to control European gypsy moth (Lymantria dispar) populations in Victoria, British Columbia, Canada. A major assessment of the health impact of B. thuringiensis subsp. kurstaki was conducted by the Office of the Medical Health Officer of the Capital Health Region during this period. Environmental (air and water) and human (nasal swab) samples, collected before and after aerial applications of Foray 48B, both in the spray zone and outside of the spray zone, were analyzed for the presence of strain HD1-like bacteria. Random amplified polymorphic DNA analysis, cry gene-specific PCR, and dot blot DNA hybridization techniques were used to screen over 11,000 isolates of bacteria. We identified bacteria with genetic patterns consistent with those of B. thuringiensis subsp. kurstaki HD1 in 9,102 of 10,659 (85.4%) isolates obtained from the air samples, 13 of 440 (2.9%) isolates obtained from the water samples, and 131 of 171 (76.6%) isolates from the nasal swab samples. These analyses suggest that B. thuringiensis subsp. kurstaki HD1-like bacteria were present both in the environment and in the human population of Victoria prior to aerial applications of Foray 48B. The presence of B. thuringiensis subsp. kurstaki HD1-like bacteria in human nasal passages increased significantly after the application of Foray 48B, both inside and outside the spray zone.     

Cytogenetics, geographical distribution, pollen stainability and fecundity of five diploid taxa of Santolina rosmarinifolia L. aggregate (Asteraceae: Anthemideae)

The chromosome analysis of Santolina rosmarinifolia subsp. rosmarinifolia, S. oblongifolia, S. semidentata subsp. semidentata, S. semidentata subsp. melidensis, S. canescens and the hybrid complex (S. rosmarinifolia subsp. rosmarinifolia, S. oblongifolia and their putative hybrids) shows that all the taxa are diploids (2n = 2x = 18; 18 + 1 or more B chromosomes, with 2n = 19, 20 only in the hybrid complex). The results show a conserved general structure of the karyotype (14m + 2sm + 2st), but in S. semidentata subsp. melidensis it is variable, with 14m + 2sm + 2st in ten individuals, 14m + (1m ? 1sm) + (1 m ? 1st) in nine individuals and 12m + (1m ? 1sm) + (1m ? 1st) + 2st + 1B in five individuals. Tetraploid individuals occurred in the diploid populations of S. rosmarinifolia subsp. rosmarinifolia and S. canescens, and their autopolyploid origin is discussed. Multivalent configurations at diakinesis, simple and double chromosome bridges and delayed disjunction of homologous and non-homologous chromosomes at anaphase I have negative effects on pollen stainability. The mean fructification percentage is moderate. The results suggest that the complex is a mosaic of introgressive hybrids.     

Morphological evaluation of the Pinus kesiya complex (Pinaceae)

The main aim of this study is to compare all taxa from the Pinus kesiya complex and related P. tabuliformis using statistical, ordination and discrimination techniques focusing on ten most discriminating morphological traits. Special emphasis was placed on the recently described taxa Pinus densata subsp. tibetica and P. × naxiorum (=P. yunnanensis × P. densata). Population comparisons of the particular main geographic distribution areas of Pinus kesiya, P. densata subsp. tibetica and P. yunnanensis were also conducted separately within each mentioned taxon using the same data. Pinus densata subsp. tibetica proved to be sufficiently morphologically differentiated from subsp. densata as well as from other species of the P. kesiya complex and P. tabuliformis. The recently originating hybrid P. × naxiorum appears to be intermediate between its parents. The unique shrubby taxon P. densata var. pygmaea is clearly closer to P. densata than to P. yunnanensis, to which it has been classified in Chinese floras. Populations of four distant Pinus kesiya geographic distribution areas lack substantial differences that would support the recognition of infraspecific taxa such as subsp. insularis or var. langbianensis. Pinus yunnanensis is very similar to P. kesiya, with only one trait, leaf length, being significantly different.     

Phylogenetic Analysis and Polyphasic Characterization of Clavibacter michiganensis Strains Isolated from Tomato Seeds Reveal that Nonpathogenic Strains Are Distinct from C. michiganensis subsp. michiganensis

The genus Clavibacter comprises one species and five subspecies of plant-pathogenic bacteria, four of which are classified as quarantine organisms due to the high economic threat they pose. Clavibacter michiganensis subsp. michiganensis is one of the most important pathogens of tomato, but the recommended diagnostic tools are not satisfactory due to false-negative and/or -positive results. To provide a robust analysis of the genetic relatedness among a worldwide collection of C. michiganensis subsp. michiganensis strains, relatives (strains from the four other C. michiganensis subspecies), and nonpathogenic Clavibacter-like strains isolated from tomato, we performed multilocus sequence-based analysis and typing (MLSA and MLST) based on six housekeeping genes (atpD, dnaK, gyrB, ppK, recA, and rpoB). We compared this “framework” with phenotypic and genotypic characteristics such as pathogenicity on tomato, reaction to two antisera by immunofluorescence and to five PCR identification tests, and the presence of four genes encoding the main C. michiganensis subsp. michiganensis pathogenicity determinants. We showed that C. michiganensis subsp. michiganensis is monophyletic and is distinct from its closest taxonomic neighbors. The nonpathogenic Clavibacter-like strains were identified as C. michiganensis using 16S rRNA gene sequencing. These strains, while cross-reacting with C. michiganensis subsp. michiganensis identification tools, are phylogenetically distinct from the pathogenic strains but belong to the C. michiganensis clade. C. michiganensis subsp. michiganensis clonal complexes linked strains from highly diverse geographical origins and also strains isolated over long periods of time in the same location. This illustrates the importance of seed transmission in the worldwide dispersion of this pathogen and its survival and adaptation abilities in a new environment once introduced.     

Phytochemical diversity of Origanum vulgare L. subsp. vulgare (Lamiaceae) from Austria

This investigation was aiming at the phytochemical characterisation of Origanum vulgare subsp. vulgare from Austria. To study the qualitative and quantitative composition of essential oil compounds 374 individual plants were analysed via GC. The volatiles of Austrian O. vulgare subsp. vulgare were found to be complex mixtures of 53 mono- and sesquiterpenes. Among the sesquiterpenes β-caryophyllene, germacrene D, E-E-α-farnesene, germacrene D-4-ol and caryophyllene oxide were frequently present in higher amounts. The monoterpenes were mainly made up of sabinyl-compounds [mainly sabinene (up to 48.4%) and cis-sabinene hydrate (up to 57.8%)] and/or cymyl-compounds [mainly p-cymene (up to 49.7%), γ-terpinene (up to 21.5%) and carvacrol (up to 32.9%)] that were accompanied by usually smaller amounts of bornyl-compounds and acyclic compounds. Some exceptional (in O. vulgare rare) chemotypes were detected. The essential oil content of Austrian O. vulgare subsp. vulgare ranged between 0.1 and 1.8%. The content of rosmarinic acid was analysed by HPLC and ranged from 0.6 mg/g dry mass up to 37.2 mg/g dry mass. No arbutin could be detected in the analysed populations.     

Population Structure and Diversity in Finger Millet (Eleusine coracana) Germplasm

A genotypic analysis of 79 finger millet accessions (E. coracana subsp. coracana) from 11 African and five Asian countries, plus 14 wild E. coracana subsp. africana lines collected in Uganda and Kenya was conducted with 45 SSR markers distributed across the finger millet genome. Phylogenetic and population structure analyses showed that the E. coracana germplasm formed three largely distinct subpopulations, representing subsp. africana, subsp. coracana originating from Africa and subsp. coracana originating from Asia. A few lines showed admixture between the African and Asian cultivated germplasm pools and were the result of either targeted or accidental intercrossing. Evidence of gene flow was also seen between the African wild and cultivated subpopulations, indicating that hybridizations among subspecies occur naturally where both species are sympatric. The genotyping, combined with phylogenetic and population structure analyses proved to be very powerful in predicting the origin of breeding materials. The genotypic study was complemented by a phenotypic evaluation. The wild and cultivated accessions differed by a range of domestication-related characters, such as tiller number, plant height, peduncle length, seed color and grain yield. Significant differences in plant architecture and yield were also identified between the Asian and African subpopulations. The observed population structure within cultivated finger millet is consistent with the theory that, after the introduction of finger millet from Africa into India via the trade routes some 3000 years ago, the two germplasm pools remained largely isolated until recent times. The significantly lower diversity present within the Asian subpopulation also suggests that it arose from a relatively small number of founder plants.     

Isolation of a new retrotransposon-like DNA sequence and its use in analysis of diversity within the Oryza officinalis

To better understand the genetic diversity of the wild relatives of rice (Oryza sativa L.) in the O. officinalis species complex repetitive DNA markers were obtained from the diploid species of this complex. One cloned sequence from O. eichingeri gave intense hybridization signals with all species of the O. officinalis complex. This 242 bp clone, named pOe.49, has a copy number from 0.9 to 4.0 × 10⁴ in diploid species of this complex. Analysis of the primary structure and database searches revealed homology of pOe.49 to a number of sequences representing part of the integrase coding domain of retroviruses and gypsy-like retrotransposons. Sequencing of specific PCR products confirmed that pOe.49 is part of a gypsy-like retrotransposon. RFLP analysis was used to study the genomic organisation of pOe.49 among 30 accessions of the O. officinalis complex using 10 restriction enzymes. Diversity analysis based on 120 polymorphic fragments obtained from the RFLP assay grouped the O. officinalis complex accessions by genome, species and eco-geographic groups. The results suggest that, with further characterization, this retrotransposon-like DNA sequence may be useful for phylogenetic analysis of species in the O. officinalis complex. This revised version was published online in August 2006 with corrections to the Cover Date.