On the lattice ground state of densely packed hard ellipses

Among lattice configurations of densely packed hard ellipses, Monte Carlo simulations are used to identify the so-called parallel and diagonal lattices as the two favorable states. The free energies of these two states are computed for several system sizes employing the Einstein crystal method. An accurate calculation of the free energy difference between the two states reveals the parallel lattice as the state with the lowest free energy. The origin of the entropic difference between the two states is further elucidated by assessing the roles of the translational and rotational degrees of freedom.

Direct Correlation Function of a Crystalline Solid

Direct correlation functions (DCFs), linked to the second functional derivative of the free energy with respect to the one-particle density, play a fundamental role in a statistical mechanics description of matter. This holds, in particular, for the ordered phases: DCFs contain information about the local structure including defects and encode the thermodynamic properties of crystalline solids; they open a route to the elastic constants beyond low temperature expansions. Via a demanding numerical approach, we have explicitly calculated for the first time the DCF of a solid: based on the fundamental measure concept, we provide results for the DCF of a hard sphere crystal. We demonstrate that this function differs at coexistence significantly from its liquid counterpart-both in shape as well as in its order of magnitude-because it is dominated by vacancies. We provide evidence that the traditional use of liquid DCFs in functional Taylor expansions of the free energy is conceptually wrong and show that the emergent elastic constants are in good agreement with simulation-based results.

Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination

Background

Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop.

Results

To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage.

Conclusions

Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-017-0419-x) contains supplementary material, which is available to authorized users.

Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer

Background

Previous studies identified microRNAs (miRNAs) and messenger RNAs with significantly different expression between normal pancreas and pancreatic cancer (PDAC) tissues. Due to technological limitations of microarrays and real-time PCR systems these studies focused on a fixed set of targets. Expression of other RNA classes such as long intergenic non-coding RNAs or sno-derived RNAs has rarely been examined in pancreatic cancer. Here, we analysed the coding and non-coding transcriptome of six PDAC and five control tissues using next-generation sequencing.

Results

Besides the confirmation of several deregulated mRNAs and miRNAs, miRNAs without previous implication in PDAC were detected: miR-802, miR-2114 or miR-561. SnoRNA-derived RNAs (e.g. sno-HBII-296B) and piR-017061, a piwi-interacting RNA, were found to be differentially expressed between PDAC and control tissues. In silico target analysis of miR-802 revealed potential binding sites in the 3′ UTR of TCF4, encoding a transcription factor that controls Wnt signalling genes. Overexpression of miR-802 in MiaPaCa pancreatic cancer cells reduced TCF4 protein levels. Using Massive Analysis of cDNA Ends (MACE) we identified differential expression of 43 lincRNAs, long intergenic non-coding RNAs, e.g. LINC00261 and LINC00152 as well as several natural antisense transcripts like HNF1A-AS1 and AFAP1-AS1. Differential expression was confirmed by qPCR on the mRNA/miRNA/lincRNA level and by immunohistochemistry on the protein level.

Conclusions

Here, we report a novel lncRNA, sncRNA and mRNA signature of PDAC. In silico prediction of ncRNA targets allowed for assigning potential functions to differentially regulated RNAs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12943-015-0358-5) contains supplementary material, which is available to authorized users.

Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells

Background

The interaction of eukaryotic host and prokaryotic pathogen cells is linked to specific changes in the cellular proteome, and consequently to infection-related gene expression patterns of the involved cells. To simultaneously assess the transcriptomes of both organisms during their interaction we developed dual 3’Seq, a tag-based sequencing protocol that allows for exact quantification of differentially expressed transcripts in interacting pro- and eukaryotic cells without prior fixation or physical disruption of the interaction.

Results

Human epithelial cells were infected with Salmonella enterica Typhimurium as a model system for invasion of the intestinal epithelium, and the transcriptional response of the infected host cells together with the differential expression of invading and intracellular pathogen cells was determined by dual 3’Seq coupled with the next-generation sequencing-based transcriptome profiling technique deepSuperSAGE (deep Serial Analysis of Gene Expression). Annotation to reference transcriptomes comprising the operon structure of the employed S. enterica Typhimurium strain allowed for in silico separation of the interacting cells including quantification of polycistronic RNAs. Eighty-nine percent of the known loci are found to be transcribed in prokaryotic cells prior or subsequent to infection of the host, while 75% of all protein-coding loci are represented in the polyadenylated transcriptomes of human host cells.

Conclusions

Dual 3’Seq was alternatively coupled to MACE (Massive Analysis of cDNA ends) to assess the advantages and drawbacks of a library preparation procedure that allows for sequencing of longer fragments. Additionally, the identified expression patterns of both organisms were validated by qRT-PCR using three independent biological replicates, which confirmed that RELB along with NFKB1 and NFKB2 are involved in the initial immune response of epithelial cells after infection with S. enterica Typhimurium.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1489-1) contains supplementary material, which is available to authorized users.

SuperSAGE as an analytical tool for host and viral gene expression

SuperSAGE is a tag-based transcript profiling method, which allows to analyze the expression of thousands of genes at a time. In SuperSAGE, 26 bp tags are extracted from cDNA using the type III restriction enzyme, EcoP15I. In SuperSAGE, the amount of transcripts was represented by tag counts. Taking advantage of uniqueness of the 26 bp tags, host and virus transcripts can be monitored in virus-infected cells. Combining next generation sequencing technology, we established High-throughput SuperSAGE (Ht-SuperSAGE), which allows the analysis of multiple samples with reduced time and cost. In this chapter, we present the protocol of Ht-SuperSAGE involving a recently available benchtop type next generation sequencer.

APADB: a database for alternative polyadenylation and microRNA regulation events

Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3′ untranslated region (3′UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3′UTR shortening accelerates disease progression, dedifferentiation and proliferation. Here we present APADB, a database of vertebrate PA sites determined by 3′ end sequencing, using massive analysis of complementary DNA ends. APADB provides (A)PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser. The database tables can either be browsed according to organism and tissue or alternatively searched for a gene of interest. APADB is the largest database of APA in human, chicken and mouse. The stored information provides experimental evidence for thousands of PA sites and APA events. APADB combines 3′ end sequencing data with prediction algorithms of miRNA binding sites, allowing to further improve prediction algorithms. Current databases lack correct information about 3′UTR lengths, especially for chicken, and APADB provides necessary information to close this gap.

Database URL:http://tools.genxpro.net/apadb/

Regulation glykolytischen Umsatzes durch Synthese und Abbau von Enzymen Regulation of Glycolysis by the Synthesis and Degradation of Enzymes

Differential derepression of the genome of potato tuber cells causes the onset of a vigorous metabolic activity, which is initiated by rapid synthesis of different RNA species, various proteins and phospholipids. Consequently enhanced respiration and the build up of cell compartments such as ribosomes and mitochondria as well as the performance of cell divisions and suberization of new-formed cell walls occur. Although there is an activation of metabolism in general with a concomitant rise in concentration of most glycolytic metabolites — as was proved for fructose-1.6-diphosphate, dihydroxyacetone, glyceraldehade-3-phosphate, phosphoenolepyruvate and pyruvate — the activities of the corresponding enzymes do not reflect these uniform metabolic changes. Aldolase and in a pronounced manner enolase and glutamate — pyruvate — transaminase lower their activities suddenly after derepression. The activity of triosephosphateisomerase remains constant. In contrast phosphoglyceromutase, pyruvate kinase and to a lower extent malic enzyme enhance their action during the same time.

Without doubt, differential lowering and enhancing the activity of glycolytic chain constituents at the same time is an important regulatory mechanism of the cell. The activation represents de novo synthesis of the protein concerned whereas the inactivation depends largely on protein synthesis. This is clearly shown by experiments with inhibitors of protein synthesis.

It is proposed that this differential synthesis and degradation represent a “long-time-regulation” of enzymatic activity of the cell in contrast to the known “short-time-regulation” by feedback or competition.

Diosgenin Contents and DNA Fingerprint Screening of Various Yam (Dioscorea sp.) Genotypes

In addition to the importance of many Dioscorea species (yams) as starchy staple food, some representatives are known and still used as a source for the steroidal sapogenin diosgenin, which, besides phytosterols derived from tall-oil, is an important precursor for partial synthesis of steroids for pharmaceutical research and applications. While in edible yams the diosgenin content should be as low as possible, a high yield of the compound is preferable for cultivars which are grown for the extraction of sterols. In the past, miscalculations and insufficiently precise techniques for quantification of diosgenin prevailed. Therefore we set out to re-evaluate the steroid content of a world collection of Dioscorea species, using leaves as sample material. We optimized diosgenin quantification techniques and fingerprinted the whole collection with the DNA amplification fingerprinting (DAF) technique. Total diosgenin contents ranged from 0.04 to 0.93% of dry weight within the collection. Several Dioscorea cultivars can be characterized via their DAF fingerprint patterns.

Molecular marker technologies for plant improvement

The exploitation of DNA polymorphisms by an ever-increasing number of molecular marker technologies has begun to have an impact on plant genome research and breeding. Restriction fragment length polymorphisms, micro- and mini-satellites and PCR-based approaches are used to determine inter- and intra-specific genetic diversity and construct molecular maps of crops using specially designed mapping populations. Resistance genes and other agronomically important loci are tagged with tightly linked DNA markers and the genes isolated by magabase DNA technology and cloning into yeast artificial chromosomes (YAC). This review discusses some recent developments and results in this field.

Plant genetic engineering for crop improvement

Plant genetic engineering has long since left its experimental stage: transgenic plants with resistance to viruses, bacteria, fungi, various pests and abiotic stresses have already been released in their hundreds. Transgenic plants can produce better fruits and food of higher quality than wild-types, and can be used as bioreactors for the synthesis of pharmaceutically important compounds. This review portrays some of the achievements in this field of plant molecular biology.

Genome-based analysis of the transcriptome from mature chickpea root nodules

Symbiotic nitrogen fixation (SNF) in root nodules of grain legumes such as chickpea is a highly complex process that drastically affects the gene expression patterns of both the prokaryotic as well as eukaryotic interacting cells. A successfully established symbiotic relationship requires mutual signaling mechanisms and a continuous adaptation of the metabolism of the involved cells to varying environmental conditions. Although some of these processes are well understood today many of the molecular mechanisms underlying SNF, especially in chickpea, remain unclear. Here, we reannotated our previously published transcriptome data generated by deepSuperSAGE (Serial Analysis of Gene Expression) to the recently published draft genome of chickpea to assess the root- and nodule-specific transcriptomes of the eukaryotic host cells. The identified gene expression patterns comprise up to 71 significantly differentially expressed genes and the expression of twenty of these was validated by quantitative real-time PCR with the tissues from five independent biological replicates. Many of the differentially expressed transcripts were found to encode proteins implicated in sugar metabolism, antioxidant defense as well as biotic and abiotic stress responses of the host cells, and some of them were already known to contribute to SNF in other legumes. The differentially expressed genes identified in this study represent candidates that can be used for further characterization of the complex molecular mechanisms underlying SNF in chickpea.

Genomic variation and relationships in aerial yam (Dioscorea bulbifera L.) detected by random amplified polymorphic DNA

Random amplified polymorphic DNA (RAPD) markers were used to assess intraspecific variability and relationships in aerial yam (Dioscorea bulbifera L.). A total of 23 accessions from different geographic locations in Africa, Asia, and Polynesia were analyzed by 10 arbitrarily chosen GC-rich decamer primers. Using cesium chloride purified genomic template DNA, highly reproducible polymorphic fingerprints were generated by all 10 primers, resulting in a total of 375 informative characters. Only eight bands were monomorphic among all investigated accessions. A binary character matrix was generated by scoring for presence/absence of a band at a particular position, transformed into a matrix of pairwise distances using either the Jaccard or a simple matching coefficient, and analyzed by neighbour joining, UPGMA (unweighted pair group method with arithmetic averaging) cluster analysis, or split decomposition. All methods of data evaluation resulted in similar groupings that reflected the geographical origin of the samples. The African accessions formed a distinct isolated group, whereas Asian and Polynesian accessions proved to be more heterogeneous. With two exceptions (var. suavior and var. sativa), the RAPD data supported previous varietal classification based on morphological characters. Stepwise reduction of the number of evaluated characters did not affect branching patterns of the trees above a minimum threshold of 150. Key words : Dioscorea bulbifera, random amplified polymorphic DNA (RAPD), genetic variation, genetic relatedness.

Identification of plant protein kinases in response to abiotic and biotic stresses using SuperSAGE

Plants are sessile organisms subjected to many environmental adversities. For their survival they must sense and respond to biotic and abiotic stresses efficiently. During this process, protein kinases are essential in the perception of environmental stimuli, triggering signaling cascades. Kinases are among the largest and most important gene families for biotechnological purposes, bringing many challenges to the bioinformaticians due to the combination of conserved domains besides diversified regions. Cowpea [Vigna unguiculata (L.) Walp.] is an important legume that is adapted to different agroclimatic conditions, including drought, humidity and a range of temperatures. For this crop, the association of the SuperSAGE method with high-throughput sequencing technology would generate reliable transcriptome profiles with millions of tags counted and statistically analyzed. An approach evaluating biotic and abiotic stresses was carried out generating over 13 million cowpea SuperSAGE tags available from leaves/roots of plants under abiotic (mechanical injury and salinity) or biotic (CABMV, Cowpea aphid born mosaic virus) stresses. The annotation and identification of tags linked by BlastN to previously well described ESTs, allowed the posterior identification of kinases. The annotation efficiency depended on the database used, with the KEGG figuring as a good source for annotated ESTs especially when complemented by an independent Gene Ontology categorization, as well as the Gene Index using selected species. The use of different approaches allowed the identification of 1,350 kinase candidates considering biotic libraries and 2,268 regarding abiotic libraries, based on a combination of both, adequate descriptions and GO terms. Additional searches in kinase specific databases allowed the identification of a relatively low number of additional kinases, uncovering the lack of kinase databases for non-model organisms, especially plants. Concerning the kinase families, a total of 713 potential kinases were classified into 13 families of the CMGC and STE groups. Concerning the differentially expressed kinases, 169 of the 713 potential kinases were identified (p < 0.05), 100 up- and 69 down-regulated when comparing distinct libraries, allowing the generation of a comprehensive panel of the differentially expressed kinases under biotic and abiotic stresses in a non-model plant as cowpea.

SuperSAGE: powerful serial analysis of gene expression

SuperSAGE is a variant of the Serial Analysis of Gene Expression (SAGE) technology, based on counting transcripts by sequencing analysis of short sequence tags. In SuperSAGE, 26 bp tags are extracted from cDNA using the Type III restriction endonuclease EcoP15I. The use of a longer tag size in SuperSAGE allows a secure tag-to-gene annotation in any eukaryotic organism. We have succeeded in combining SuperSAGE and high-throughput sequencing technology (Now- or Next-Generation Sequencing, NGS) in an approach we call High-throughput SuperSAGE (HT-SuperSAGE). This approach allows deep transcriptome analysis and multiplexing, while reducing time, cost, and effort for the analysis. In this chapter, we present the detailed HT-SuperSAGE protocol for both the Illumina Genome Analyzer and also the AppliedBiosystems SOLiD sequencer.

Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.

Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes

Cultivated chickpea is the third most important legume after field bean and garden pea worldwide. Despite considerable breeding towards improved yield and resistance to biotic and abiotic stresses, the production of chickpea remained stagnant, but molecular tools are expected to increase the impact of current improvement programs. As a first step towards this goal, various genetic linkage maps have been established and markers linked to resistance genes been identified. However, until now, only one linkage group (LG) has been assigned to a specific chromosome. In the present work, mitotic chromosomes were sorted using flow cytometry and used as template for PCR with primers designed for genomic regions flanking microsatellites. These primers amplify sequence-tagged microsatellite site markers. This approach confirmed the assignment of LG8 to the smallest chromosome H. For the first time, LG5 was linked to the largest chromosome A, LG4 to a medium-sized chromosome E, while LG3 was anchored to the second largest chromosome B. Chromosomes C and D could not be flow-sorted separately and were jointly associated to LG6 and LG7. By the same token, chromosomes F and G were anchored to LG1 and LG2. To establish a set of preferably diagnostic cytogenetic markers, the genomic distribution of various probes was verified using FISH. Moreover, a partial genomic bacterial artificial chromosome (BAC) library was constructed and putative single/low-copy BAC clones were mapped cytogenetically. As a result, two clones were identified localizing specifically to chromosomes E and H, for which no cytogenetic markers were yet available.

Assembling a puzzle of dispersed retrotransposable sequences in the genome of chickpea (Cicer arietinum L.)

Several repetitive elements are known to be present in the genome of chickpea (Cicer arietinum L.) including satellite DNA and En/Spm transposons as well as two dispersed, highly repetitive elements, CaRep1 and CaRep2. PCR was used to prove that CaRep1, CaRep2, and previously isolated CaRep3 of C. arietinum represent different segments of a highly repetitive Ty3-gypsy-like retrotransposon (Metaviridae) designated CaRep that makes up large parts of the intercalary heterochromatin. The full sequence of this element including the LTRs and untranslated internal regions was isolated by selective amplification. The restriction pattern of CaRep was different within the annual species of the genus Cicer, suggesting its rearrangement during the evolution of the genus during the last 100 000 years. In addition to CaRep, another LTR and a non-LTR retrotransposon family were isolated, and their restriction patterns and physical localization in the chickpea genome were characterized. The LINE-like element CaLin is only of comparatively low abundance and reveals a considerable heterogeneity. The Ty1-copia-like element (Pseudoviridae) CaTy is located in the distal parts of the intercalary heterochromatin and adjacent euchromatic regions, but it is absent from the centromeric regions. These results together with earlier findings allow to depict the distribution of retroelements on chickpea chromosomes, which extensively resembles the retroelement landscape of the genome of the model legume Medicago truncatula Gaertn.

The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE

BACKGROUND

The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level.

RESULTS

We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress.Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available.

CONCLUSIONS

This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 x C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM-ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2-21 alleles and polymorphic information content value 0.04-0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.

Simulating pesticide transport from a sloped tropical soil to an adjacent stream

Preferential flow from stream banks is an important component of pesticide transport in the mountainous areas of northern Thailand. Models can help evaluate and interpret field data and help identify the most important transport processes. We developed a simple model to simulate the loss of pesticides from a sloped litchi (Litchi chinensis Sonn.) orchard to an adjacent stream. The water regime was modeled with a two-domain reservoir model, which accounts for rapid preferential flow simultaneously with slow flow processes in the soil matrix. Preferential flow is triggered when the topsoil matrix is saturated or the infiltration capacity exceeded. In addition, close to matrix saturation, rainfall events induce water release to the fractures and lead to desorption of pesticides from fracture walls and outflow to the stream. Pesticides undergo first order degradation and equilibrium sorption to soil matrix and fracture walls. The model was able to reproduce the dynamics of the discharge reasonably well (model efficiency [EF] = 0.56). The cumulative pesticide mass (EF = 0.91) and the pesticide concentration in the stream were slightly underestimated, but the deviation from measurement data is acceptable. Shape and timing of the simulated concentration peaks occurred in the same pattern as observed data. While the effect of surface runoff and preferential interflow on pesticide mass transport could not be absolutely clarified, according to our simulations, most concentration peaks in the stream are caused by preferential interflow pointing to the important role of this flow path in the hilly areas of northern Thailand.

SuperSAGE: a modern platform for genome-wide quantitative transcript profiling

SuperSAGE is a variant of SAGE (Serial Analysis of Gene Expression) technology, which allows making transcript profiling by 26-bp tags extracted from cDNA employing the typeIII restriction enzyme EcoP15I. Its tag length is the longest among all the versions of SAGE, and is advantageous in tag-to-gene annotation, thereby allowing the technique to applicable to any eukaryotic life organisms. For model organisms with genome or cDNA sequences available, genes corresponding to 26-bp tags are uniquely defined by simple BLAST search. For non-model organisms without these sequence information, the 26-bp tag sequence is directly applicable to design PCR primer for amplifying cDNA of corresponding genes by 3'- or 5'-RACE. Furthermore, SuperSAGE allows various applications including "interaction transcriptome" and "SuperSAGE array". Emerging "Next Generation Sequencing" technologies perfectly complement SuperSAGE, and their combination has generated a novel transcriptome platform, that is superior to all the different microarray variants in terms of throughput, data quality and cost of analysis.

SuperSAGE: the drought stress-responsive transcriptome of chickpea roots

BACKGROUND

Drought is the major constraint to increase yield in chickpea (Cicer arietinum). Improving drought tolerance is therefore of outmost importance for breeding. However, the complexity of the trait allowed only marginal progress. A solution to the current stagnation is expected from innovative molecular tools such as transcriptome analyses providing insight into stress-related gene activity, which combined with molecular markers and expression (e)QTL mapping, may accelerate knowledge-based breeding. SuperSAGE, an improved version of the serial analysis of gene expression (SAGE) technique, generating genome-wide, high-quality transcription profiles from any eukaryote, has been employed in the present study. The method produces 26 bp long fragments (26 bp tags) from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs. Further, SuperSAGE tags may be immediately used to produce microarrays and probes for real-time-PCR, thereby overcoming the lack of genomic tools in non-model organisms.

RESULTS

We applied SuperSAGE to the analysis of gene expression in chickpea roots in response to drought. To this end, we sequenced 80,238 26 bp tags representing 17,493 unique transcripts (UniTags) from drought-stressed and non-stressed control roots. A total of 7,532 (43%) UniTags were more than 2.7-fold differentially expressed, and 880 (5.0%) were regulated more than 8-fold upon stress. Their large size enabled the unambiguous annotation of 3,858 (22%) UniTags to genes or proteins in public data bases and thus to stress-response processes. We designed a microarray carrying 3,000 of these 26 bp tags. The chip data confirmed 79% of the tag-based results, whereas RT-PCR confirmed the SuperSAGE data in all cases.

CONCLUSION

This study represents the most comprehensive analysis of the drought-response transcriptome of chickpea available to date. It demonstrates that--inter alias--signal transduction, transcription regulation, osmolyte accumulation, and ROS scavenging undergo strong transcriptional remodelling in chickpea roots already 6 h after drought stress. Certain transcript isoforms characterizing these processes are potential targets for breeding for drought tolerance. We demonstrate that these can be easily accessed by micro-arrays and RT-PCR assays readily produced downstream of SuperSAGE. Our study proves that SuperSAGE owns potential for molecular breeding also in non-model crops.

SuperSAGE

As a tool for high-throughput, quantitative gene expression analysis, serial analysis of gene expression (SAGE) is one of the most powerful techniques. However, the short size of tags (14 bp) has hindered the application of SAGE to a vast majority of eukaryotes without sufficient genomic resources, including expressed sequence tag and genome sequences. To overcome this problem, we developed SuperSAGE, which is based on 26-bp tags from complementary DNA (cDNA), using EcoP15I as a tagging enzyme. Because longer cDNA fragments can easily be recovered by 3'-rapid amplification of cDNA ends (RACE) PCR using primers corresponding to the 26-bp tag sequences in non-model organisms, SuperSAGE allows the identification of novel genes in all eukaryotic organisms, and recommends itself as a useful platform in various fields of biological studies. Here, we present an updated SuperSAGE protocol, which incorporates several modifications and some recommendations to avoid total failure, particularly in the EcoP15I digestion step.

Mining microsatellites in eukaryotic genomes

During recent decades, microsatellites have become the most popular source of genetic markers. More recently, the availability of enormous sequence data for a large number of eukaryotic genomes has accelerated research aimed at understanding the origin and functions of microsatellites and searching for new applications. This review presents recent developments of in silico mining of microsatellites to reveal various facets of the distribution and dynamics of microsatellites in eukaryotic genomes. Two aspects of microsatellite search strategies--using a suitable search tool and accessing a relevant microsatellite database--have been explored. Judicious microsatellite mining not only helps in addressing biological questions but also facilitates better exploitation of microsatellites for diverse applications.

Micro-trench experiments on interflow and lateral pesticide transport in a sloped soil in northern Thailand

During recent decades, a change in land use in the mountainous regions of Northern Thailand has been accompanied by an increased input of agrochemicals. We identified lateral water flow and pesticide transport pathways and mechanisms in a Hapludult on a sloped litchi orchard in Northern Thailand. During two rainy seasons, two micro-trench experiments were performed at the plot scale (2 by 3 m). The first experiment was performed at the footslope of the orchard; the second was performed at a midslope position. Two salt tracers (bromide and chloride) and two pesticides {methomyl [S-methyl-N-(methylcarbamoyloxy)thioacetimidate] and chlorothalonil (2,4,5,6-Tetrachlor-1,3-benzdicarbonitril)} were applied in stripes parallel to the slope 150 and 300 cm away from the trench. At the trench, soil water was collected by wick samplers. Tensiometers and time-domain reflectometry probes were installed. At the end of the experiment, soil samples were taken and analyzed for residual concentrations of tracers and pesticides. Lateral subsurface flow of water occurred exclusively along preferential flow paths and was mainly observed at 0- to 30- and 60- to 90-cm depth. Lateral transport of pesticides was negligible, but both pesticides were found beneath the application area at 90 cm depth. Therefore, they may pose a groundwater contamination risk. The amount of wick flow and the location of interflow were mainly a function of rain amount and antecedent soil water suction. During dry periods, water flow was restricted to the topsoil. After heavy rain events and wet periods, interflow was mainly observed in the subsoil. The cumulative rain amount between samplings necessary to induce interflow was 20 mm. At the footslope, the interflow was seven times higher, and the network of water-bearing pores increased compared with the midslope position.

Genetic diversity and phylogenetic relationships in Vigna Savi germplasm revealed by DNA amplification fingerprinting

The pantropical genus Vigna (Leguminosae) comprises 7 cultivated species that are adapted to a wide range of extreme agroclimatic conditions. Few data are available on the relationships among these cultivated species or on their importance as sources of resistance against biotic and abiotic stresses. Therefore, we optimized DNA amplification fingerprinting (DAF) to estimate the genetic diversity within, and genetic relationships among, a representative core collection of cowpea, as compared with 16 accessions representing cultivars from 6 Vigna species. A set of 26 primers was selected from 262 tested random primers and used for the characterization of 85 Vigna accessions (6 V. angularis , 4 each of V. mungo and V. radiata , 2 V. umbellata , 1 V. aconitifolia , and 68 V. unguiculata ), with Phaseolus vulgaris subsp. vulgaris as outgroup. A total of 212 polymorphic bands were used for maximum parsimony analysis. Our results clearly distinguished Brazilian from African V. unguiculata genotypes. At the species level, V. angularis was the most related and V. radiata the most divergent species relative to V. unguiculata. DAF markers were also informative at the intraspecific level, detecting a large diversity between cowpea cultivars. The implications of the presented results for cowpea breeding programs are discussed.

SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays

We developed a new platform for genome-wide gene expression analysis in any eukaryotic organism, which we called SuperSAGE array. The SuperSAGE array is a microarray onto which 26-bp oligonucleotides corresponding to SuperSAGE tag sequences are directly synthesized. A SuperSAGE array combines the advantages of the highly quantitative SuperSAGE expression analysis with the high-throughput microarray technology. We demonstrated highly reproducible gene expression profiling by the SuperSAGE array for 1,000 genes (tags) in rice. We also applied this technology to the detailed study of expressed genes identified by SuperSAGE in Nicotiana benthamiana, an organism for which sufficient genome sequence information is not available. We propose that the SuperSAGE array system represents a new paradigm for microarray construction, as no genomic or cDNA sequence data are required for its preparation.

SuperSAGE

The application of transcriptomics to study host-pathogen interactions has already brought important insights into the mechanisms of pathogenesis, and is expanding further keeping pace with the accumulation of genomic sequences of host organisms (human and economically important organisms such as food crops) and their pathogens (viruses, bacteria, fungi and protozoa). In this review, we introduce SuperSAGE, a substantially improved variant of serial analysis of gene expression (SAGE), as a potent tool for the transcriptomics of host-pathogen interactions. Notably, the generation of 26 bp tags in the SuperSAGE procedure allows to decipher the 'interaction transcriptome', i.e. the simultaneous monitoring of quantitative gene expression, of both a host and one of its eukaryotic pathogens. The potential of SuperSAGE tags for a rapid functional analysis of target genes is also discussed.

Quantitative trait loci governing carotenoid concentration and weight in seeds of chickpea (Cicer arietinum L.)

Chickpea is a staple protein source in many Asian and Middle Eastern countries. The seeds contain carotenoids such as beta-carotene, cryptoxanthin, lutein and zeaxanthin in amounts above the engineered beta-carotene-containing "golden rice" level. Thus, breeding for high carotenoid concentration in seeds is of nutritional, socio-economic, and economic importance. To study the genetics governing seed carotenoids in chickpea, we studied the relationship between seed weight and concentrations of beta-carotene and lutein by means of high-performance liquid chromatography in segregating progeny from a cross between an Israeli cultivar and wild Cicer reticulatum Ladiz. Seeds of the cross progeny varied with respect to their carotenoid concentration (heritability estimates ranged from 0.5 to 0.9), and a negative genetic correlation was found between mean seed weight and carotenoid concentration in the F(3). To determine the loci responsible for the genetic variation observed, the population was genotyped using 91 sequence tagged microsatellite site markers and two CytP450 markers to generate a genetic map consisting of nine linkage groups and a total length of 344.6 cM. Using quantitative data collected for beta-carotene and lutein concentration and seed weight of the seeds of the F(2) population, we were able to identify quantitative trait loci (QTLs) by interval mapping. At a LOD score of 2, four QTLs for beta-carotene concentration, a single QTL for lutein concentration and three QTLs for seed weight were detected. The results of this investigation may assist in improving the nutritional quality of chickpea.

Ionic microgels as model systems for colloids with an ultrasoft electrosteric repulsion: Structure and thermodynamics

We present a theoretical analysis of the structural properties and phase behavior of spherical, loosely cross-linked ionic microgels that possess a low monomer concentration. The analysis is based on the recently derived effective interaction potential between such particles [A. R. Denton, Phys. Rev. E 67, 011804 (2003)]. By employing standard tools from the theory of the liquid state, we quantitatively analyze the pair correlations in the fluid and find anomalous behavior above the overlap concentration, similar to the cases of star-branched neutral and charged polymers. We also employ an evolutionary algorithm in order to predict the crystalline phases of the system without any a priori assumptions regarding their symmetry class. A very rich phase diagram is obtained, featuring two reentrant melting transitions and a number of unusual crystal structures. At high densities, both the Hansen-Verlet freezing criterion [J.-P. Hansen and L. Verlet, Phys. Rev. 184, 151 (1969)] and the Lindemann melting criterion [F. A. Lindemann, Phys. Z. 11, 609 (1910)] lose their validity. The topology of the phase diagram is altered when the steric interactions between the polymer segments become strong enough, in which case the lower-density reentrant melting disappears and the region of stability of the fluid is split into two disconnected domains, separated by intervening fcc and bcc regions.

Molecular mapping of Fusarium oxysporum f. sp. ciceris race 3 resistance gene in chickpea

Sequence-tagged microsatellite site (STMS) and sequence-tagged site (STS) markers linked closely to Fusarium oxysporum f. sp. ciceris race 3 resistance gene in chickpea were identified, and linkage between three wilt resistance genes was elucidated. The resistance to race 3 in chickpea germplasm accession WR-315 was inherited as a single gene, designated foc-3, in 100 F(7) recombinant inbred lines derived from the cross of WR-315 (resistant) x C-104 (susceptible). The foc-3 gene was mapped 0.6 cM from STMS markers TA96 and TA27 and STS marker CS27A. Another STMS marker, TA194, at 14.3 cM, flanked the gene on the other side. Linkage between foc-3 and two other chickpea wilt resistance genes, foc-1 (syn. h(1)) and foc-4, was established. foc-3 was mapped 9.8 cM from foc-1 and 8.7 cM from foc-4, whereas foc-1 and foc-4 are closely linked at 1.1 cM. The identification of closely linked markers to resistance genes will facilitate marker-assisted selection for introgression of the race 3 resistance gene to susceptible chickpea lines.

Phase behavior of ionic microgels

We employ effective interaction potentials between spherical polyelectrolyte microgels in order to investigate theoretically the structure, thermodynamics, and phase behavior of ionic microgel solutions. Combining a genetic algorithm with accurate free energy calculations we are able to perform an unrestricted search of candidate crystal structures. Hexagonal, body-centered orthogonal, and trigonal crystals are found to be stable at high concentrations and charges of the microgels, accompanied by reentrant melting behavior and fluid-fcc-bcc transitions below the overlap concentration.

Theoretical description of phase coexistence in model C60

We have investigated the phase diagram of a pair interaction model of C60 fullerene [L. A. Girifalco, J. Phys. Chem. 96, 858 (1992)], in the framework provided by two integral equation theories of the liquid state, namely, the modified hypernetted chain (MHNC) implemented under a global thermodynamic consistency constraint, and the self-consistent Ornstein-Zernike approximation (SCOZA), and by a perturbation theory (PT) with various degrees of refinement, for the free energy of the solid phase. We present an extended assessment of such theories as set against a recent Monte Carlo study of the same model [D. Costa, G. Pellicane, C. Caccamo, and M. C. Abramo, J. Chem. Phys. 118, 304 (2003)]. We have compared the theoretical predictions with the corresponding simulation results for several thermodynamic properties such as the free energy, the pressure, and the internal energy. Then we have determined the phase diagram of the model, by using either the SCOZA, the MHNC, or the PT predictions for one of the coexisting phases, and the simulation data for the other phase, in order to separately ascertain the accuracy of each theory. It turns out that the overall appearance of the phase portrait is reproduced fairly well by all theories, with remarkable accuracy as for the melting line and the solid-vapor equilibrium. All theories show a more or less pronounced discrepancy with the simulated fluid-solid coexistence pressure, above the triple point. The MHNC and SCOZA results for the liquid-vapor coexistence, as well as for the corresponding critical points, are quite accurate; the SCOZA tends to underestimate the density corresponding to the freezing line. All results are discussed in terms of the basic assumptions underlying each theory. We have then selected the MHNC for the fluid and the first-order PT for the solid phase, as the most accurate tools to investigate the phase behavior of the model in terms of purely theoretical approaches. It emerges that the use of different procedures to characterize the fluid and the solid phases provides a semiquantitative reproduction of the thermodynamic properties of the C60 model at issue. The overall results appear as a robust benchmark for further theoretical investigations on higher order C(n>60) fullerenes, as well as on other fullerene-related materials, whose description can be based on a modelization similar to that adopted in this work.

Development of flow cytogenetics and physical genome mapping in chickpea (Cicer arietinum L.)

Procedures for flow cytometric analysis and sorting of mitotic chromosomes (flow cytogenetics) have been developed for chickpea (Cicer arietinum). Suspensions of intact chromosomes were prepared from root tips treated to achieve a high degree of metaphase synchrony. The optimal protocol consisted of a treatment of roots with 2 mmol/L hydroxyurea for 18 h, a 4.5-h recovery in hydroxyurea-free medium, 2 h incubation with 10 micromol/L oryzalin, and ice-water treatment overnight. This procedure resulted in an average metaphase index of 47%. Synchronized root tips were fixed in 2% formaldehyde for 20 min, and chromosome suspensions prepared by mechanical homogenization of fixed root tips. More than 4 x 10(5) morphologically intact chromosomes could be isolated from 15 root tips. Flow cytometric analysis of DAPI-stained chromosomes resulted in histograms of relative fluorescence intensity (flow karyotypes) containing eight peaks, representing individual chromosomes and/or groups of chromosomes with a similar relative DNA content. Five peaks could be assigned to individual chromosomes (A, B, C, G, H). The parity of sorted chromosome fractions was high, and chromosomes B and H could be sorted with 100% purity. PCR on flow-sorted chromosome fractions with primers for sequence-tagged microsatellite site (STMS) markers permitted assignment of the genetic linkage group LG8 to the smallest chickpea chromosome H. This study extends the number of legume species for which flow cytogenetics is available, and demonstrates the potential of flow cytogenetics for genome mapping in chickpea.

Molecular markers closely linked to fusarium resistance genes in chickpea show significant alignments to pathogenesis-related genes located on Arabidopsis chromosomes 1 and 5

A population of 131 recombinant inbred lines from a wide cross between chickpea ( Cicer arietinum L., resistant parent) and Cicer reticulatum (susceptible parent) segregating for the closely linked resistances against Fusarium oxysporum f.sp. ciceri races 4 and 5 was used to develop DNA amplification fingerprinting markers linked to both resistance loci. Bulked segregant analysis revealed 19 new markers on linkage group 2 of the genetic map on which the resistance genes are located. Closest linkage (2.0 cM) was observed between marker R-2609-1 and the race 4 resistance locus. Seven other markers flanked this locus in a range from 4.1 to 9.0 cM. These are the most closely linked markers available for this locus up to date. The sequences of the linked markers were highly similar to genes encoding proteins involved in plant pathogen response, such as a PR-5 thaumatin-like protein and an important regulator of the phytoalexin pathway, anthranilate N-hydroxycinnamoyl-benzoyltransferase. Others showed significant alignments to genes encoding housekeeping enzymes such as the MutS2 DNA-mismatch repair protein. In the Arabidopsis genome, similar genes are located on short segments of chromosome 1 and 5, respectively, suggesting synteny between the fusarium resistance gene cluster of chickpea and the corresponding regions in the Arabidopsis genome. Three marker sequences were similar to retrotransposon-derived and/or satellite DNA sequences. The markers developed here provide a starting point for physical mapping and map-based cloning of the fusarium resistance genes and exploration of synteny in this highly interesting region of the chickpea genome.

Mapping of gene-specific markers on the genetic map of chickpea (Cicer arietinum L.)

With the exception of the fact that it is made up of eight different chromosomes, the physical organization of the 738-Mb genome of the important legume crop chickpea (Cicer arietinum L.) is unknown. In an attempt to increase our knowledge of the basic structure of this genome, we determined the map positions of a series of genes involved in plant defence responses (DR) by genetic linkage analysis. Exploiting the sequence data available in GenBank, we selected genes known to be induced in chickpea and other plants by pathogen attack. Gene-specific primers were designed based on conserved regions, and used to detect the corresponding gene sequences in a segregating population derived from an interspecific cross between Cicer arietinum and C. reticulatum. Forty-seven gene-specific markers were integrated into an existing map based on STMS, AFLP, DAF and other anonymous markers. The potential of this approach is discussed.

Electrophoretic identification of new genomic profiles with a modified selective amplification of microsatellite polymorphic loci technique based on AT/AAT polymorphic repeats

The present paper introduces improvements of the conventional selective amplification of microsatellite polymorphic loci (SAMPL) technique, that exploit AT-rich microsatellite primers. Generally, AT/AAT microsatellites are frequent components of eukaryotic genomes, but their ubiquity and polymorphic information content (PIC) could not be exploited yet, because standard SAMPL conditions did not allow amplifications. Here we report (i) on the design of new versatile AT-rich microsatellite primers, that are combined with (ii) a modified SAMPL adapter primer (called EcoRI-Short), and (iii) special polymerase chain reaction (PCR) amplification regimes. The novel SAMPL procedure expands the range of useful microsatellite primers to AT-rich sequences and produces a high number of bands and a clear banding pattern, and detects polymorphisms in otherwise nonpolymorphic genomes of plants (Dioscorea alata, D. rotundata) and a fungus (Mycosphaerella fijiensis).

A PCR-based assay to detect En/Spm-like transposon sequences in plants

Degenerate primers deduced from the TPase region of plant En/Spm-like transposons allowed the amplification of similar sequences from various plant species including sugar beet, wheat and pea. These primers are efficient tools for the detection of this family of transposons in many plant genomes irrespective of sequence knowledge or phenotypic pecularities. An efficient PCR assay was therefore developed for these class II transposons, similar to assays already available for Ty1-copia-, Ty3-gypsy- or LINEs. This approach allowed us not only to show the widespread almost-ubiquitous presence of En/Spm-elements in plant genomes, but also to characterize their genomic organization and chromosomal distribution in the genome of chickpea (Cicer arietinum L.) and its abundance in related Cicer species. This approach can be used for the detection and characterization of endogenous DNA transposable elements in plant species, their complete isolation and evaluation of their use for genome analysis.

Resistance gene analogues of chickpea ( Cicer arietinum L.): isolation, genetic mapping and association with a Fusarium resistance gene cluster

Resistance gene analogues (RGAs) of Cicer were isolated by different PCR approaches and mapped in an inter-specific cross segregating for fusarium wilt by RFLP and CAPS analysis. Initially, two pairs of degenerate primers targeting sequences encoded at nucleotide-binding sites (NBS), which are conserved in plant disease resistance genes such as RPS2, L6 and N, were selected for amplification. Cloning and sequence analysis of amplified products from C. arietinum DNA revealed eight different RGAs. Additionally, five RGAs were identified after characterisation of the presumptive RGA alleles from C. reticulatum. Therefore, a total of 13 different RGAs were isolated from Cicer and classified through pair-wise comparison into nine distinct classes with sequence similarities below a 68% amino acid identity threshold. Sequence comparison of seven RGA alleles of C. arietinum and C. reticulatum revealed polymorphisms in four RGAs with identical numbers of synonymous and non-synonymous substitutions. An NlaIII site, unique in the RGA-A allele of C. arietinum, was exploited for CAPS analysis. Genomic organisation and map position of the NBS-LRR candidate resistance genes was probed by RFLP analysis. Both single-copy as well as multi-copy sequence families were present for the selected RGAs, which represented eight different classes. Five RGAs were mapped in an inter-specific population segregating for three race-specific Fusarium resistances. All RGAs mapped to four of the previously established eight linkage groups for chickpea. Two NBS-LRR clusters were identified that could not be resolved in our mapping population. One of these clusters, which is characterised by RFLP probe CaRGA-D, mapped to the linkage group harbouring two of three Fusarium resistance genes characterised in the inter-specific population. Our study provides a starting point for the characterisation and genetic mapping of candidate resistance genes in Cicer that is useful for marker-assisted selection and as a pool for resistance genes of Cicer.

Thermodynamic properties of a polydisperse system

We use the virial theorem to derive a closed analytic form of the Helmholtz free energy for a polydisperse system of sticky hard spheres (SHS) within the mean spherical model (MSM). To this end we calculate the free energy of the MSM for an N-component mixture of SHS via the virial route and apply to it-after imposing a Lorentz-Berthelot type rule on the interactions-the stochastic (i.e., polydisperse) limit. The resulting excess free energy of this polydisperse system is of the truncatable moment free energy format. We also discuss the compressibility and the energy routes.