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Search Results: 1 - 10 of 191274 matches for " D Hoisington "
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Genetic relationships among seven sections of genus Arachis studied by using SSR markers
Ravi Koppolu, Hari D Upadhyaya, Sangam L Dwivedi, David A Hoisington, Rajeev K Varshney
BMC Plant Biology , 2010, DOI: 10.1186/1471-2229-10-15
Abstract: The average transferability rate of 101 SSR markers tested to section Arachis and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, Arachis pusilla exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (A. duranensis) and the B-genome accession ICG 8206 (A. ipa?nsis) were found most closely related to A. hypogaea.A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of Arachis, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of A. monticola and A. hypogaea as well as on the most probable donor of A and B-genomes of cultivated groundnut.The genus Arachis has its origin in South America where the species of this genus are widespread [1]. This genus includes 80 species, 69 species described by Krapovickas and Gregory [1] and 11 species described by Valls and Simpson [2]. Arachis is divided into 9 sections (Arachis, Erectoides, Heteranthae, Caulorrhizae, Rhizomatosae, Extranervosae, Triseminatae, Procumbentes and Trierectoides) based on morphology, geographic distribution and cross compatibility relationships [1]. Species present in sections Erectoides, Extranervosae and Triseminatae and diploid species of section Rhizomatosae are believed to be basal in their divergence when compared to the species in other sections [3,4].
Genetic diversity in Indian isolates of Fusarium oxysporum f. sp. ciceris, chickpea wilt pathogen
M Sharma, RK Varshney, JN Rao, S Kannan, D Hoisington, S Pande
African Journal of Biotechnology , 2009,
Abstract: Forty-eight isolates of FOC collected from different chickpea growing regions in India were evaluated for genetic variations using amplified fragment length polymorphism (AFLP). Out of 48 isolates, 41 were found pathogenic and seven non-pathogenic. Pathogenic isolates differ in their virulence however; there was no apparent correlation between geographical origin and virulence of the isolates. The genetic variation was evaluated by the AFLP analysis. A total 339 fragments were scored following selective amplification with five EcoR1 and Mse1 primer combinations E-TC/M-CAT, E-TC/M-CAC, EAC/ M-CAG, E-TA/MCAG, E-TA/M-CAG, out of which 331 fragments were polymorphic. UPGMA cluster analysis and principle coordinate analysis distinctly classified 48 isolates into two major groups; pathogenic and non-pathogenic. The pathogenic isolates could be further clustered into six major groups at 0.77 genetic similarities. Region specific grouping was observed with in few isolates. The results of the present study provide evidence of the high discriminatory power of AFLP analysis, suggesting the applicability of this method to the molecular characterization of Fusarium oxysporum f.sp. ciceris.
Evaluation of the shoot regeneration response in tissue culture of pigeonpea (Cajanus cajan [L.] Millsp.) varieties adapted to eastern and southern Africa
S de Villiers, Q Emongor, R Njeri, E Gwata, D Hoisington, I Njagi, S Silim, K Sharma
African Journal of Biotechnology , 2008,
Abstract: Seven varieties of pigeonpea (Cajanus cajan [L.] Millsp.) of varying growth durations and adapted to a wide range of environments across eastern and southern Africa were evaluated for their shoot regeneration response in tissue culture. On a standardized shoot regeneration medium, the short duration varieties (ICPV 88091 and ICPV 86012) generally responded faster and better than the medium duration (ICEAP 00554 and ICEAP 00557) and long duration (ICEAP 00020, ICEAP 00040 and ICEAP 00053) varieties. However, all the tested varieties produced healthy rooted plants in vitro that could be transferred to the greenhouse where they exhibited normal growth, flowering and viable seed set. This study established the basis for genetic engineering of African pigeonpea varieties.
Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)
Hari D Upadhyaya, Sangam L Dwivedi, Michael Baum, Rajeev K Varshney, Sripada M Udupa, Cholenahalli LL Gowda, David Hoisington, Sube Singh
BMC Plant Biology , 2008, DOI: 10.1186/1471-2229-8-106
Abstract: The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection.The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.Chickpea (Cicer arietinum L.) is the 4th most important grain-legume crop after soybean, bean, and pea, but contributes only 3.1% to the world grain legumes production (based on 2001 to 2006 average production of 266.5 million tons of soybean, beans, peas, chickpea, broad beans, cowpea, lentil, and pigeonpea) http://faostat.fao.org/site/408/DesktopDefault.aspx?PageID=408 webcite, assessed on 27th Jan
A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.)
Rajeev K Varshney, Pavana J Hiremath, Pazhamala Lekha, Junichi Kashiwagi, Jayashree Balaji, Amit A Deokar, Vincent Vadez, Yongli Xiao, Ramamurthy Srinivasan, Pooran M Gaur, Kadambot HM Siddique, Christopher D Town, David A Hoisington
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-523
Abstract: A total of 20,162 (18,435 high quality) drought- and salinity- responsive ESTs were generated from ten different root tissue cDNA libraries of chickpea. Sequence editing, clustering and assembly analysis resulted in 6,404 unigenes (1,590 contigs and 4,814 singletons). Functional annotation of unigenes based on BLASTX analysis showed that 46.3% (2,965) had significant similarity (≤1E-05) to sequences in the non-redundant UniProt database. BLASTN analysis of unique sequences with ESTs of four legume species (Medicago, Lotus, soybean and groundnut) and three model plant species (rice, Arabidopsis and poplar) provided insights on conserved genes across legumes as well as novel transcripts for chickpea. Of 2,965 (46.3%) significant unigenes, only 2,071 (32.3%) unigenes could be functionally categorised according to Gene Ontology (GO) descriptions. A total of 2,029 sequences containing 3,728 simple sequence repeats (SSRs) were identified and 177 new EST-SSR markers were developed. Experimental validation of a set of 77 SSR markers on 24 genotypes revealed 230 alleles with an average of 4.6 alleles per marker and average polymorphism information content (PIC) value of 0.43. Besides SSR markers, 21,405 high confidence single nucleotide polymorphisms (SNPs) in 742 contigs (with ≥ 5 ESTs) were also identified. Recognition sites for restriction enzymes were identified for 7,884 SNPs in 240 contigs. Hierarchical clustering of 105 selected contigs provided clues about stress- responsive candidate genes and their expression profile showed predominance in specific stress-challenged libraries.Generated set of chickpea ESTs serves as a resource of high quality transcripts for gene discovery and development of functional markers associated with abiotic stress tolerance that will be helpful to facilitate chickpea breeding. Mapping of gene-based markers in chickpea will also add more anchoring points to align genomes of chickpea and other legume species.Chickpea is a member of the Legu
A database of annotated tentative orthologs from crop abiotic stress transcripts
Jayashree Balaji,Jonathan H Crouch,Prasad VNS Petite,David A Hoisington
Bioinformation , 2006,
Abstract: A minimal requirement to initiate a comparative genomics study on plant responses to abiotic stresses is a dataset of orthologous sequences. The availability of a large amount of sequence information, including those derived from stress cDNA libraries allow for the identification of stress related genes and orthologs associated with the stress response. Orthologous sequences serve as tools to explore genes and their relationships across species. For this purpose, ESTs from stress cDNA libraries across 16 crop species including 6 important cereal crops and 10 dicots were systematically collated and subjected to bioinformatics analysis such as clustering, grouping of tentative orthologous sets, identification of protein motifs/patterns in the predicted protein sequence, and annotation with stress conditions, tissue/library source and putative function. All data are available to the scientific community at http://intranet.icrisat.org/gt1/tog/homepage.htm. We believe that the availability of annotated plant abiotic stress ortholog sets will be a valuable resource for researchers studying the biology of environmental stresses in plant systems, molecular evolution and genomics.
An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms
B. Jayashree,Manindra S. Hanspal,Rajgopal Srinivasan,R. Vigneshwaran,Rajeev K. Varshney,N. Spurthi,K. Eshwar,N. Ramesh,S. Chandra,David A. Hoisington
Comparative and Functional Genomics , 2007, DOI: 10.1155/2007/35604
Abstract: The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.
An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (Arachis hypogaea L.)
Bhimana Gautami, Daniel Foncéka, Manish K. Pandey, Márcio C. Moretzsohn, Venkataswamy Sujay, Hongde Qin, Yanbin Hong, Issa Faye, Xiaoping Chen, Amindala BhanuPrakash, Trushar M. Shah, Makanahally V. C. Gowda, Shyam N. Nigam, Xuanqiang Liang, Dave A. Hoisington, Baozhu Guo, David J. Bertioli, Jean-Francois Rami, Rajeev K. Varshney
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0041213
Abstract: Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01–a10 and b01–b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut.
Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping
B Jayashree, Praveen T Reddy, Y Leeladevi, Jonathan H Crouch, V Mahalakshmi, Hutokshi K Buhariwalla, KE Eshwar, Emma Mace, Rolf Folksterma, S Senthilvel, Rajeev K Varshney, K Seetha, R Rajalakshmi, VP Prasanth, Subhash Chandra, L Swarupa, P SriKalyani, David A Hoisington
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-383
Abstract: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics.A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp webcite.Plant genotyping is a technology that has widespread applications in the fields of breeding, research and commerce. With the increasing availability of sequence information, more and more molecular markers are becoming available for use in plant genotyping; for example SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms) [1]. These markers are widely used in screening genebank collections of cultivated and wild germplasm, genome mapping for traits of interest and marker assisted selectio
Electrical Conductivity of Collapsed Multilayer Graphene Tubes  [PDF]
D. Mendoza
World Journal of Nano Science and Engineering (WJNSE) , 2012, DOI: 10.4236/wjnse.2012.22009
Abstract: Synthesis of multilayer graphene on copper wires by a chemical vapor deposition method is reported. After copper etching, the multilayer tube collapses forming stripes of graphitic films, their electrical conductance as a function of temperature indicate a semiconductor-like behavior. Using the multilayer graphene stripes, a cross junction is built and owing to its electrical behavior we propose that a tunneling process exists in the device.
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