In-silico mining,type and frequency analysis of genic microsatellites of finger millet (Eleusine coracana (L.) Gaertn.): a comparative genomic analysis of NBS–LRR regions of finger millet with rice

In recent years, the increased availability of the DNA sequences has given the possibility to develop and explore the expressed sequence tags (ESTs) derived SSR markers. In the present study, a total of 1956 ESTs of finger millet were used to find the microsatellite type, distribution, frequency and developed a total of 545 primer pairs from the ESTs of finger millet. Thirty-two EST sequences had more than two microsatellites and 1357 sequences did not have any SSR repeats. The most frequent type of repeats was trimeric motif, however the second place was occupied by dimeric motif followed by tetra-, hexa- and penta repeat motifs. The most common dimer repeat motif was GA and in case of trimeric SSRs, it was CGG. The EST sequences of NBS-LRR region of finger millet and rice showed higher synteny and were found on nearly same positions on the rice chromosome map. A total of eight, out of 15 EST based SSR primers were polymorphic among the selected resistant and susceptible finger millet genotypes. The primer FMBLEST5 could able to differentiate them into resistant and susceptible genotypes. The alleles specific to the resistant and susceptible genotypes were sequenced using the ABI 3130XL genetic analyzer and found similarity to NBS–LRR regions of rice and finger millet and contained the characteristic kinase-2 and kinase 3a motifs of plant R-genes belonged to NBS–LRR region. The In-silico and comparative analysis showed that the genes responsible for blast resistance can be identified, mapped and further introgressed through molecular breeding approaches for enhancing the blast resistance in finger millet.     

Farmers’ Management of Finger Millet (Eleusine coracana L.) diversity in Tigray, Ethiopia and Implications for on-Farm Conservation

Tigray (region) is one of the major finger millet growing regions in Ethiopia and an important site from an archeobotanical point of view. Three zones of Tigray (east, central and west) were identified as representative sites in the region and a total of 14 districts/ ‘Woreda’ were surveyed. Thirty-seven landraces/farmers’ varieties of finger millet were identified/recorded. Farmers in Tigray undertake pre and post harvest selection in finger millet and sometimes they also select seeds from storage based on a number of attributes. Farmers maintain diversity as a way to ensure harvest security or stability of production, to promote diversity of diet and income sources, minimize crop failure risk, reduce insect and disease incidences and ensure efficient use of labour. The traditional management of finger millet in the entire study area is generally found to be demand driven, showing the existence of potential sites for on-farm conservation. The high morphological diversity (H =0.76 ± 0.09) found in the gene bank collections of Tigrayan origin also reveals the importance of linking ex situ with in situ conservation activities. Furthermore, the enhancement and conservation significance of the crop is discussed.     

Identification and characterization of RAPD–SCAR markers linked to glyphosate-susceptible and -resistant biotypes of Eleusine indica (L.) Gaertn

Eleusine indica is one of the most common weed species found in agricultural land worldwide. Although herbicide-glyphosate provides good control of the weed, its frequent uses has led to abundant reported cases of resistance. Hence, the development of genetic markers for quick detection of glyphosate-resistance in E. indica population is imperative for the control and management of the weed. In this study, a total of 14 specific random amplified polymorphic DNA (RAPD) markers were identified and two of the markers, namely S4R727 and S26R₆976 were further sequence characterized. Sequence alignment revealed that marker S4R727 showing a 12-bp nucleotides deletion in resistant biotypes, while marker S26R₆976 contained a 167-bp nucleotides insertion in the resistant biotypes. Based on these sequence differences, three pairs of new sequence characterized amplified region (SCAR) primers were developed. The specificity of these primer pairs were further validated with genomic DNA extracted from ten individual plants of one glyphosate-susceptible and five glyphosate-resistant (R2, R4, R6, R8 and R11) populations. The resulting RAPD–SCAR markers provided the basis for assessing genetic diversity between glyphosate-susceptible and -resistant E. indica biotypes, as well for the identification of genetic locus link to glyphosate-resistance event in the species.     

Antifeedants of Finger Millet,Eleusine coracana GAERTN,Against Brown Planthopper,Nilaparvata lugens (STÅL)

Nine compounds isolated from finger millet as antifeedants for brown planthopper have been identified as known compounds, l-malic acid, isocitric acid, 4-hydroxybenzoic acid, vanillic acid, 4-hydroxy- benzaldehyde, and vitexin, and new constituents, 2-O-[4-hydroxy-(Z and E)-cinnamoyl]glyceric acid and 8-C-β-d-[6″-O-(3-hydroxy-3-methyl)glutaroyl]glucopyranosylapigenin.     

Agrobacterium tumefaciens-mediated transformation of safflower (Carthamus tinctorius L.) cv. ‘Centennial’

Efficient callus formation was achieved from cotyledon, stem, and leaf expiants of the domestic safflower cultivar Centennial on MS salts medium containing 1 mg/L BAP and 1 mg/L NAA. Shoot buds were regenerated from 26% of leaf-derived calli on callus induction medium, although attempts to root regenerated shoots were not successful. Centennial expiants inoculated with Agrobacterium tumefaciens containing NPT II and GUS genes produced kanamycin-resistant calli from which buds were regenerated. Transformation and stable integration of transgenes was confirmed by GUS assay and DNA hybridization in kanamycin-resistant calli, and GUS assay in regenerated shoots.Abbreviations BAP 6-benzylaminopurine - NAA 1-naphthaleneacetic acid - 2,4-D 2,4-dichlorophenoxyacetic acid - MS Murashige and Skoog (1962) - GUS -glucuronidase - IAA indole-3-acetic acid - NPT II neomycin phosphotransferase II     

The Draft Genome Sequence of European Pear (Pyrus communis L. ‘Bartlett’)

We present a draft assembly of the genome of European pear (Pyrus communis) ‘Bartlett’. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of ‘Louise Bonne de Jersey’ and ‘Old Home’. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus×domestica). The ‘Bartlett’ genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development.     

The Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L. cv. ‘Aseel’)

Date palm (Phoenix dactylifera L.) is an economically important and widely cultivated palm of the family Arecaceae. We sequenced the complete date palm chloroplast genome (cpDNA) from Pakistani cv. ??Aseel??, using a combination of Sanger-based and next-generation sequencing technologies. Being very similar to a sequence from a Saudi Arabian date palm cultivar ??Khalas?? published recently, the size of the genome was 158,458?bp with a pair of inverted repeat (IR) regions of 27,276?bp that were separated by a large single-copy (LSC) region of 86,195?bp and a small single-copy (SSC) region of 17,711?bp. Genome annotation demonstrated a total of 138 genes, of which 89 were protein coding, 39 were tRNA, and eight were rRNA genes. Comparison of cpDNA sequences of cultivars ??Aseel?? and ??Khalas?? showed following intervarietal variations in the LSC region; (a) two SNPs in intergenic spacers and one SNP in the rpoc1 gene, (b) polymorphism in two mono-nucleotide simple sequence repeats (SSR), and (c) a 4-bp indel in the accD-psaI intergenic spacer. The SSC region has a polymorphic site in the mono-nucleotide SSR located at position 120,710. We also compared cv. ??Aseel?? cpDNA sequence with partial P. dactylifera cpDNA sequence entries deposited in Genbank and identified a number of potentially useful polymorphisms in this species. Analysis of date palm cpDNA sequences revealed a close relationship with Typha latifolia. Occurrence of small numbers of forward and inverted repeats in date palm cpDNA indicated conserved genome arrangement.     

Volatile constituents of Erodium cicutarium (L.) L’ Hérit. (Geraniaceae)

Essential oils from Erodium cicutarium were obtained by hydrodistillation (samples consisting of entire plants (ec1), leaves and stems (ec2)) and analyzed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC/MS), resulting in a total of 177 components being identified. The essential oils were of a very similar chemical composition and consisted mainly of aliphatic compounds and their derivatives. Fatty acids and fatty acid derived compounds were the most common, 51.3% (ec1) and 60.1% (ec2), followed by carotenoid derived compounds, 12.6% (ec1) and 20.2% (ec2), and then terpenoids, 14.9% (ec1) and 14.2% (ec2). The main constituents in the oils were hexadecanoic acid, 22.8% (ec2) and 35.9% (ec1) and hexahydrofarnesyl acetone, 10.8% (ec2) and 11.6% (ec1). The results obtained differ markedly from those previously reported for the same species.     

Organelle genome stability in anther-derived doubled haploids of wheat (Triticum aestivum L., cv. ‘Moisson’)

Summary Chloroplast and mitochondrial compartments of a parental line of wheat (Triticum aestivum L., cv. Moisson) and its anther-derived doubled haploid lines have been analyzed and compared on the basis of their DNA restriction patterns. The results obtained show that no noticeable difference can be detected between doubled haploid lines and parental line at the level of ctDNA and mtDNA organization. It may be concluded that in vitro culture by itself does not systematically generate a cytoplasmic variation in germ cells.     

The use of green fluorescent protein (GFP) improves Agrobacterium-mediated transformation of ‘Spadona’ pear (Pyrus communis L.)

An efficient and reproducible system for Agrobacterium-mediated transformation of the pear (Pyrus communis L.) cultivar Spadona was developed. Leaf explants of in vitro propagated plants were cocultivated with the disarmed Agrobacterium strain EHA105 harboring the plasmid pME504, carrying the uidA-intron and nptII genes. Under selective conditions, 5% of the plantlets regenerated and were positively stained for GUS. However, most of the GUS-positive plants re-callused and subsequently died, leaving only 0.3–0.8% of these plantlets to reach maturity. In order to identify transformed shoots at early stages of regeneration, we introduced the green fluorescent protein (GFP) into the pear cultivar Spadona using the plasmid PZP carrying the nuclear-targeted GFP and nptII genes. High expression levels of GFP were detected in transgenic cells as early as 7 days after transformation. GFP marked-callii and transformed plants were observed after 14 and 24 days, respectively. Fluorescence microscopy screening of transformed plant material, under the selection of kanamycin, increased the transformation frequency to 3.0–4.0%. We conclude that the introduction of GFP improves the selection of transformed plants of Spadona pear.     

Survey of microfungi on Alnus glutinosa (L.) Gaertn. from Münsterland, Germany

During our investigation on microfungi in Antoniusheim, Fleissenbach und Merfelderbruch near Dülmen in Münsterland in the years 2005 and 2006 we were able to collect and identify 25 microfungi on Alnus glutinosa (L.) GAERTN. Among them are some which are very rare in Germany linke Phragmoporthe conformis (Berkley & Broome) Petrak, Cryptosporiopsis alnea (Rostr.) Petr., Prosthecium auctum (Berk. & Broome) Petr., Taphrina alni-incanae (Kun.) Magn. [= T. Amentorum (Sadeback) Rostrup], Cryptodiaporthe oxystoma (Rehm.) Z. Urb., Cladosporium alnicola Bub. & Vleug. [= C. Herbarum (Pers.)], Erysiphe penicillata (Wallr.) Link, Melampsoridium betulinum Kleb., Bacterodesmium longisporum M.B. Ellis, Marssonina alni Karak. Asteroma alneum (Pers.: Fr.) Sutton . All collected species can be found in the text.     

The isolation of tissue culture ofPopulus alba L. ‘Pyramidalis’

Tissue culture was isolated from the stem ofPopulus alba L. ‘pyramidalis’. Callus formation was observed since November till March (1974),i.e. till the formation of calluses suitable for further subeultivation. The most vigorous growth was obtained with the callus culture cultivated on the nutrient medium of DIAZ-COLONet al. (1972) on which more than 11 g of fresh matter was produced after 30 d at the end of the first year of cultivation in darkness, with inoculum weight 1.5-1.8 g. A mild decrease in growth rate of the tissue culture was observed after the first year of cultivation. When illuminated, the originally yellow calluses turned green. The morphological and anatomical structure of the callus culture is also described and cell shape and cell size evaluated.     

The nutritional status of Picea abies (L.) Karst. across Europe,and implications for ‘forest decline’

Summary During the summer of 1986, three year-classes of foliage were sampled from approximately 30-year-old Norway spruce [Picea abies (L.) Karst.] trees at 12 sites from S. W. Germany to N. Scotland. At sites in Germany, where trees were showing symptoms of decline, samples were taken from trees with good crown condition and poor crown conditon. The distinction between good and poor was made on the basis of international protocols for defining crown density and foliar discoloration. There was a wide range in nutrient content (percent dry weight) in apparently healthy trees. Current year foliage had ranges of mean values per site: S(0.07–0.13%), N(0.9–1.4%), K(0.5–0.9%), Ca(0.2–0.7%), and Mg (0.05–0.1%). Ranges were greater for 2-year-old foliage: S(0.09–0.18%), N(1.0–1.8%), K(0.4–0.7%), Ca(0.2–1.4%), and Mg(0.03–0.09%). At sites with trees having poor crown condition, there were significantly smaller concentrations of Mg and Ca, and larger concentrations of K in 2-year-old foliage from poor trees, compared with adjacent good trees. Ratios of nutrient content were more significantly related to crown condition within sites than individual nutrients, especially in older needles. Poor crowns were associated with larger ratios of NMg, KMg, SMg, KCa and smaller ratios of SK and NK. A risk index is defined for trees showing no visible decline symptoms, based upon nutrient content and nutrient ratios, which may be useful in identifying sites liable to experience deterioration in crown condition.With the exception of one German site, where few poor trees were observed, the index increases from Scottish sites to English sites to Dutch sites to German sites. The index is empirical, and not necessarily related to potential effects of air pollution. The time dependence of foliar nutrient content may also be useful in diagnosis. At sites with trees having poor crown condition, even apparently healthy trees showed a lack of increase in calcium content with needle age, decreases in nitrogen content and very large decreases in magnesium content with needle age. The results show the importance of sampling several year classes of foliage from Norway spruce trees in determining the nutrient status of the tree.     

The systematic value of nuclear genome size for “all” species of Tulipa L. (Liliaceae)

Nuclear genome size, as measured by flow cytometry with propidium iodide, was used to investigate the relationships within the genus Tulipa L. (Liliaceae). More than 400 accessions representing 123 taxa from mainly wild-collected plants were investigated. Most species of Tulipa have the same basic chromosome number, 2n = 2x = 24. However, the somatic DNA 2C value (2C) is shown to range from 32 to 69 pg for the diploids. The largest genome contains roughly 3.4 × 10¹⁰ more base pairs than the smallest and has chromosomes that are more than twice as large. These large differences in the amount of nuclear DNA predict that the hybrids, if any arise, are usually sterile. Depending on the size of the total genome, 1 pg amounts to several thousand genes. Moreover, genome sizes are evaluated here in combination with available morphological, geographical, and molecular data. Therefore, the taxonomy proposed here is not a single-character taxonomy based on genome size alone. The genus Tulipa, as here determined, has 87 species, 29 more than accepted by van Raamsdonk et al. [Acta Hort (ISHS) 430:821–828, 1997], but including 25 species that were not available to them. Of these 87 species, 28 were not seen by Hall (The genus Tulipa, The Royal Horticultural Society, London, 1940) in a living state and placed by him in an addendum. Species of the subgenus Clusianae (Baker) Zonn. differ strongly in nuclear DNA content (DNA 2C value), 32 versus 40–68 pg for all other tulips, and are placed here in a separate subgenus. Also Orithyia, the only group with a style and with only 38–39 pg is placed in a separate subgenus. Therefore, all tulips are attributed to four subgenera, Clusianae (Baker) Zonn., Tulipa, Eriostemones Raamsd., and Orithyia (D. Don) Baker and divided further into 12 sections. Seven of the eight series of section Eichleres (A.D. Hall) Raamsd. are now placed in four sections: (1) section Lanatae (Raamsd.) Zonn., mainly confined to species from the Pamir-Alay and including series Lanatae Raamsd., (2) section Multiflorae (Raamsd.) Zonn. (including series Glabrae Raamsd.), (3) section Vinistriatae (Raamsd.) Zonn. (including series Undulatae Raamsd.), and (4) section Spiranthera Vved. ex Zonn. and Veldk. Triploids, tetraploids, and pentaploids were found in several species. DNA content confirmed the close relationships of the species within the different sections. The rather similar looking and therefore often confused T. armena Boiss. (51.8 pg), T. systola Stapf (56.3 pg), and T. julia K., Koch (61.6 pg) could be clearly distinguished. The same is true for T. biebersteiniana Schult. f. (56.9 pg), T. sylvestris ssp. australis (Link) Pamp. (62.0 pg), and T. primulina Baker (64.6 pg). T. doerfleri Gand. and T. whittalli (Dykes) Hall could be placed as polyploid forms of T. orphanidea Boiss. ex Heldr. On the basis of DNA content, a systematic association between T. julia K. Koch and the triploid T. aleppensis Boiss. and between T. systola Stapf and the triploid T. praecox Tenore was suggested. The new species T. lemmersii Zonn., Peterse, and de Groot is described, and four possible new species are indicated. Genome size as measured by using flow cytometry may conveniently be used to produce systematic data. It is applicable even in the case of dormant bulbs or sterile plants for monitoring the trade in bulbous species.     

The wall structure of the ‘reticulate’ cells of Conocephalum conicum (L.) Dum., observed by SEM

Abstract

SEM observations on the thallus of Conocephalum conicum after treatment with sodium hypochlorite show that the walls of the ‘reticulate’ cells constituting the hyaline parenchyma have thickenings (the ‘bars’) and large primary pit fields with a huge number of plasmodesmata-derived pores, on the unthickened areas of the walls. By contrast the parenchymatous cells constituting the nerve have plasmodesmata-derived pores, grouped in small sparse fields, especially on the transverse and oblique walls. It is suggested that the reticulate cells playa role in lateral distribution by symplastic and apoplastic conduction of solutes carried by the midrib.     

Micropropagation of fig (Ficus carica L.) ‘Roxo de Valinhos’ plants

Summary An in vitro protocol for Ficus carica cv. ‘Roxo de Valinhos’ was optimized. Nodal explants containing two buds were excised from field-grown mature plants, and transferred to different proliferation media consisting of combinations of distinct concentrations of activated charcoal with benzyladenine (BA), kinetin with gibberellic acid (GA₃), and WPM (woody plant medium) with kinetin. The regular strength of WPM in combination with 0.5 mgl⁻¹ kinetin was the best condition for shoot proliferation of Ficus carica ‘Roxo de Valinhos’ plants. The addition of activated charcoal in the medium completely inhibited shoot proliferation. The inclusion of BA in the medium induced excessive callus formation as well as small and vitrified shoots, while GA₃ induced excessive elongation associated with vitrification, chlorosis, and tip-burned shoots.