A genetic map of 1,000 SSR and DArT markers in a wide barley cross

A high-density genetic map was developed from an F1-derived doubled haploid population generated from a cross between cultivated barley (Hordeum vulgare) and the subspecies H. vulgare ssp. spontaneum. The map comprises 1,000 loci, amplified using 536 SSR (558 loci) and 442 DArT markers. Of the SSRs, 149 markers (153 loci) were derived from barley ESTs, and 7 from wheat ESTs. A high level of polymorphism (∼70%) was observed, which facilitated the mapping of 197 SSRs for which genetic assignments had not been previously reported. Comparison with a published composite map showed a high level of co-linearity and telomeric coverage on all seven chromosomes. This map provides access to previously unmapped SSRs, improved genome coverage due to the integration of DArT and EST-SSRs and overcomes locus order issues of composite maps constructed from the alignment of several genetic maps. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Low temperature stress-induced biochemical changes affect stubble bud sprouting in sugarcane (<Emphasis Type="Italic">Saccharum</Emphasis> spp. hybrid)

A laboratory experiment was conducted to study the effect of low temperature stress on stubble bud sprouting and associated biochemical changes in sugarcane (Saccharum spp. hybrid). At 25°C, stubble bud sprouting was about 80%, whereas at 15 and 6°C, it was 56% and 23%, respectively. In stubble buds, the levels of reducing sugars and acid invertase were low, while IAA, total phenols and proline contents were high at low temperatures, as compared to normal temperature (25°C). Similarly, the specific activities of antioxidant enzymes, viz., catalase and peroxidase in stubble buds were higher at low temperatures than at normal temperature. The results indicate that poor sprouting of stubble buds at low temperatures appears to be due to a reduced availability of reducing sugars concomitant with a lower activity of acid invertase. An increased level of IAA together with toxicity build-up in situ due to an accumulation of total phenols may be responsible for the maintenance of dormancy in stubble buds at low temperatures. On the other hand, higher activities of catalase and peroxidase enzymes may protect stubble buds from an oxidative damage, while proline accumulates to act as an osmoprotectant under low temperature stress.     

Volatiles of bacterial antagonists inhibit mycelial growth of the plant pathogen <Emphasis Type="Italic">Rhizoctonia solani</Emphasis>

Bacterial antagonists are bacteria that negatively affect the growth of other organisms. Many antagonists inhibit the growth of fungi by various mechanisms, e.g., secretion of lytic enzymes, siderophores and antibiotics. Such inhibition of fungal growth may indirectly support plant growth. Here, we demonstrate that small organic volatile compounds (VOCs) emitted from bacterial antagonists negatively influence the mycelial growth of the soil-borne phytopathogenic fungus Rhizoctonia solani Kühn. Strong inhibitions (99–80%) under the test conditions were observed with Stenotrophomonas maltophilia R3089, Serratia plymuthica HRO-C48, Stenotrophomonas rhizophila P69, Serratia odorifera 4Rx13, Pseudomonas trivialis 3Re2-7, S. plymuthica 3Re4-18 and Bacillus subtilis B2g. Pseudomonas fluorescens L13-6-12 and Burkholderia cepacia 1S18 achieved 30% growth reduction. The VOC profiles of these antagonists, obtained through headspace collection and analysis on GC-MS, show different compositions and complexities ranging from 1 to almost 30 compounds. Most volatiles are species-specific, but overlapping volatile patterns were found for Serratia spp. and Pseudomonas spp. Many of the bacterial VOCs could not be identified for lack of match with mass-spectra of volatiles in the databases.     

Cladistic and phenetic analyses of relationships among Fusarium spp. in Dongtan wetland by morphology and isozymes

Variations of 12 morphological characters and 78 isozymic bands among 78 isolates of five Fusarium spp. from Dongtan wetland were described and analysed with cladistic parsimony and phenetic UPGMA methods. Hierarchical cluster analysis of 12 morphological characters grouped 78 strains into five defined species with a high overlap between isolates. Hierarchical cluster analysis of isozyme patterns showed a higher degree of relationship among five Fusarium spp., in which Fusarium nivale, Fusarium semitectum and Fusarium oxysporum clustered as one group, and F. semitectum was closer to F. nivale than to F. oxysporum; Fusarium graminearum and Fusarium moniliforme formed one group and showed clearly distinct from the first group. Groups of individual isolates indicated by a plot of principal component analysis were consistent with these findings. The comparison of two different data sets revealed that isozyme patterns showed higher variations between species and among individual isolates than morphological characters. Parsimony analysis of morphological characters yielded unresolved cladograms. Parsimony analysis of isozymes as presence/absence characters revealed the same five species in general as the results indicated by phenetic analysis, differing in the relative position of species in subclusters.     

Flow cytometric analysis reveals different nuclear DNA contents in cultivated Fonio (Digitaria spp.) and some wild relatives from West-Africa

Nuclear DNA amounts of 118 cultivated fonio accessions representing 94 landraces collected from the major growing areas of West-Africa (Benin, Burkina Faso, Guinea, Mali and Togo) and eight accessions of four wild relatives were investigated by Laser flow cytometry. In cultivated species, average 2C-values ranged from 1.848 ± 0.031 pg for Digitaria iburua to 1.956 ± 0.004 pg for D. exilis. In D. exilis landraces the chromosome number was determined at 2n = 36. The closely related wild species D. longiflora and D. ternata showed similar 2C DNA contents of 1.869 ± 0.035 pg and 1.775 ± 0.070 pg, respectively. Distinctly larger genomes were identified for more distant species D. lecardii and D. ciliaris with 2.660 ± 0.070 pg and 2.576 ± 0.030 pg per 2C nucleus, respectively. Intra-specific variations were found to be slight and insignificant, suggesting genome size stability mainly within the cultivated gene pool. These results support the distance of cultivated fonio species D. exilis and D. iburua from D. lecardii and D. ciliaris as well as their close relationships with D. longiflora and D. ternata. Relevance of the results for ploidy level considerations in fonio millets is discussed.     

Multi-locus real-time PCR for quantitation of bacteria in the environment reveals Exiguobacterium to be prevalent in permafrost

We developed a multi-locus quantitative PCR approach to minimize problems of precision, sensitivity and primer specificity for quantifying a targeted microbial group in nature. This approach also avoids a systematic error in population quantitation when 16S rRNA genes are used because of copy number heterogeneity. Specific primers were designed to assess the abundance of psychrotrophic and mesophilic Exiguobacterium spp. that excluded the thermophilic members of the genus. The chosen primers targeted genes for DNA gyrase B (gyrB), the beta subunit of the RNA polymerase gene (rpoB) and a hypothetical gene so far found only in this group. The results demonstrate that the multiple primer approach provides a more reliable estimate of population density; that the targeted Exiguobacterium group is found at a median density of 50,000 gene copies per mug of total community DNA in 27 of 29 permafrost soils but was found in only one of the four temperate and tropical soils tested.     

Growth response of Vibrio cholerae and other Vibrio spp. to cyanobacterial dissolved organic matter and temperature in brackish water

Environmental control of growth and persistence of vibrios in aquatic environments is poorly understood even though members of the genus Vibrio are globally important pathogens. To study how algal-derived organic matter and temperature influenced the abundance of different Vibrio spp., Baltic Sea microcosms inoculated with Vibrio cholerae, Vibrio vulnificus, Vibrio parahaemolyticus, Vibrio alginolyticus and native bacterioplankton, were exposed to different temperatures (12-25 degrees C) and amended with dissolved organic matter from Nodularia spumigena (0-4.2 mg C L(-1)). Vibrio abundance was monitored by culture-dependent and molecular methods. Results suggested that Vibrio populations entered a viable but nonculturable state during the incubations. Abundance of Vibrio spp. and total bacterioplankton were orders of magnitude higher in microcosms amended with organic matter compared with reference microcosms. Vibrio cholerae abundances ranged from 0.9 to 1.9 x 10(5) cells mL(-1) in treatments amended with 4.2 mg C L(-1). Vibrio cholerae abundance relative to total bacterioplankton and other Vibrio spp. also increased >10-fold. In addition, V. vulnificus abundance increased in mesocosms with the highest organic matter addition (0.9-1.8 x 10(4) cells mL(-1)). Temperature alone did not significantly affect abundances of total bacterioplankton, total Vibrio spp. or individual Vibrio populations. By contrast, cyanobacterial-derived organic matter represented an important factor regulating growth and abundance of V. cholerae and V. vulnificus in brackish waters.     

Effect of<Emphasis Type="Italic">Trichoderma</Emphasis> species on growth of Fusarium<Emphasis Type="Italic">proliferatiom</Emphasis> and production of fumonisins,fusaproliferin and beauvericin

Trichoderma species has been suggested as potential biocontrol agent forFusarium verticillioides on maize. In this cereal,F. verticillioides and F. proliferatum contributed to fumonisin accumulation. In addition,F. proliferatum could produce beauvericin and fusaproliferin. The aim of this work was to evaluate the effect ofTrichoderma spp. on growth and fumonisin B¹ fusaproliferin and beauvericin production byF. proliferatum. Dual cultures of F.proliferatum andT. harzianum ITEM 3636 andT. longibrachiatum ITEM 3635 on maize meal agar at 0.995 aw were done. The effect ofTrichoderma spp. on the lineal growth ofF. proliferatum was determined. The effect ofTrichoderma species on fumonisin B¹, fusaproliferin and beauvericin production byF. proliferatum was determined on co-inoculated maize kernels by HPLC.T. harzianum suppressedF. proliferatum growth once contact between the colonies occurred.T. longibrachiatum showed a less antagonistic effect againstF. proliferatum. A reduction on fumonisin B¹ production of 98% and 88% was observed in the co-incubation ofF. proliferatum withT. harzianum andT. longibrachiatum, respectively. The decrease of FB¹ production was significant even in maize kernels on whichF. proliferatum had been growing 7 days prior to the addition ofTrichoderma spp. The concentration of beauvericin and fusaproliferin produced during 30 days coincubation ofF. proliferatum with bothTrichoderma spp. did not differ to those produced byF. proliferatum alone. These mycotoxins might enter the food chain causing so far unknown consequences to the health of domestic animals and humans. For this reason it is important, when a potential biocontrol agent is under study, to test the effect on the fungal growth and on the putative mycotoxin produced. Part of the information was presented at the Mycotoxin Prevention Cluster Dissemination Day and Mycoglobe Launch Conference, Brussels, Belgium, Oct 20–21, 2004 Financial support: Agenda Córdoba Ciencia, grant N^o 0279–000431/00     

Call diversity of wild male orangutans: a phylogenetic approach

Over the past 20 years several studies have attempted to clarify orangutan systematics based on DNA sequences and karyological and morphological data; however, the systematic and phylogenetic relationships among orangutan taxa remain controversial. Surprisingly, few systematic studies have used data from wild-living orangutans of exactly known provenance. Furthermore, most of these studies pooled data from huge geographic areas in their analyses, thus ignoring possibly distinct subpopulations. This study represents a new approach to orangutan systematics that uses orangutan long calls. Long calls are species-specific vocalizations used by many nonhuman primates, and data on their acoustical and temporal structures have been used to assess the relationships among, and phylogenies of, several primate taxa. Altogether, 78 long calls from wild-living orangutans from five populations in Borneo and five in Sumatra were included in the analyses. Aside from the chiefly paraphyletic topology of cladistic results, which neither support nor reject a Borneo-Sumatra dichotomy, bootstrap values support three monophyletic clades (northwest Borneo, northeast-east Borneo, and Ketambe) that corroborate geographic groups. The shortest trees and multivariate analyses provide some support for a closer relationship between Sumatran and specific Bornean demes than between particular Bornean demes themselves, indicating that conservation management should be based on orangutans from different populations rather than on just the two island-specific groups.     

Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium)

Genome sizes vary by several orders of magnitude, driven by mechanisms such as illegitimate recombination and transposable element proliferation. Prior analysis of the CesA region in two cotton genomes that diverged 5–10 million years ago (Ma), and acquired a twofold difference in genome size, revealed extensive local conservation of genic and intergenic regions, with no evidence of the global genome size difference. The present study extends the comparison to include BAC sequences surrounding the gene encoding alcohol dehydrogenase A ( AdhA ) from four cotton genomes: the two co-resident genomes (A_T and D_T) of the allotetraploid, Gossypium hirsutum , as well as the model diploid progenitors, Gossypium arboreum (A) and Gossypium raimondii (D). In contrast to earlier work, evolution in the AdhA region reflects, in a microcosm, the overall difference in genome size, with a nearly twofold difference in aligned sequence length. Most size differences may be attributed to differential accumulation of retroelements during divergence of the genome diploids from their common ancestor, but in addition there has been a biased accumulation of small deletions, such that those in the smaller D genome are on average twice as large as those in the larger A genome. The data also provide evidence for the global phenomenon of 'genomic downsizing' in polyploids shortly after formation. This in part reflects a higher frequency of small deletions post-polyploidization, and increased illegitimate recombination. In conjunction with previous work, the data here confirm the conclusion that genome size evolution reflects many forces that collectively operate heterogeneously among genomic regions.