Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Thermal adaptation of net ecosystem exchange
    Yuan, W. ; Luo, Y. ; Liang, S. ; YU, G. ; Niu, S. ; Stoy, J. ; Chen, J. ; Desai, A.R. ; Lindroth, A. ; Gough, C.M. ; Ceulenmans, R. ; Arain, A. ; Bernhofer, C. ; Cook, B. ; Cook, D.R. ; Dragoni, D. ; Gielen, B. ; Janssens, I.A. ; Longdoz, B. ; Liu, H. ; Lund, M. ; Matteucci, G. ; Moors, E.J. ; Scott, R.L. ; Seufert, G. ; Varner, R. - \ 2011
    Biogeosciences 8 (2011)6. - ISSN 1726-4170 - p. 1453 - 1463.
    carbon-dioxide exchange - long-term measurements - oak-dominated forest - scots pine forest - sub-alpine forest - soil respiration - deciduous forest - interannual variability - temperate forest - european forests
    Thermal adaptation of gross primary production and ecosystem respiration has been well documented over broad thermal gradients. However, no study has examined their interaction as a function of temperature, i.e. the thermal responses of net ecosystem exchange of carbon (NEE). In this study, we constructed temperature response curves of NEE against temperature using 380 site-years of eddy covariance data at 72 forest, grassland and shrubland ecosystems located at latitudes ranging from ~29° N to 64° N. The response curves were used to define two critical temperatures: transition temperature (Tb) at which ecosystem transfer from carbon source to sink and optimal temperature (To) at which carbon uptake is maximized. Tb was strongly correlated with annual mean air temperature. To was strongly correlated with mean temperature during the net carbon uptake period across the study ecosystems. Our results imply that the net ecosystem exchange of carbon adapts to the temperature across the geographical range due to intrinsic connections between vegetation primary production and ecosystem respiration.
    Satellite repeats in the functional centromere and pericentromeric heterochromatin of Medicago truncatula
    Kulikova, O. ; Geurts, R. ; Lamine, M. ; Kim, D.J. ; Cook, D.R. ; Leunissen, J. ; Jong, J.H.S.G.M. de; Roe, B.A. ; Bisseling, T. - \ 2004
    Chromosoma 113 (2004)6. - ISSN 0009-5915 - p. 276 - 283.
    repeated dna-sequences - arabidopsis-thaliana - plant centromeres - organization - rice - chromosomes - evolution - alignment - regions - genes
    Most eukaryotic centromeres contain long arrays of tandem repeats, with unit lengths of 150 - 300 bp. We searched for such repeats in the functional centromeres of the model legume Medicago truncatula ( Medicago) accession Jemalong A17. To this end three repeats, MtR1, MtR2 and MtR3, were identified in 20 Mb of a low-pass, whole genome sequencing data set generated by a random shotgun approach. The nucleotide sequence composition, genomic organization and abundance of these repeats were characterized. Fluorescent in situ hybridization of these repeats on chromosomes at meiosis I showed that only the MtR3 repeat, encompassing stretches of 450 kb to more than 1.0 Mb, is located in the functional portion of all eight centromeres. MtR1 and MtR2 occupy distinct regions in pericentromeric heterochromatin. We also studied the presence and distribution of MtRs in Medicago accession R108-1, a genotype with a genome that is 20% smaller than that of Jemalong A17. We determined that while MtR3 is also centromeric on all pachytene bivalents in R108-1, MtR1 and MtR2 are not present in the R108 genome.
    A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa
    Choi, H.K. ; Kim, D. ; Uhm, T. ; Limpens, E.H.M. ; Lim, H. ; Mun, J.H. ; Kalo, P. ; Penmetsa, R.V. ; Seres, A. ; Kulikova, O. ; Roe, B.A. ; Bisseling, T. ; Kiss, G.B. ; Cook, D.R. - \ 2004
    Genetics 166 (2004)3. - ISSN 0016-6731 - p. 1463 - 1502.
    nod factor transduction - pcr-based markers - arabidopsis-thaliana - linkage map - expression - construction - leguminosae - mutants - model - identification
    A core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an E, population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence tags, and 67 resistance gene analogs, covering 513 cM. In the case of EST-based markers we used an intron-targeted marker strategy with primers designed to anneal in conserved exon regions and to amplify across intron regions. Polymorphisms were significantly more frequent in intron vs. exon regions, thus providing an efficient mechanism to map) transcribed genes. Genetic and cytogenetic analysis produced eight well-resolved linkage groups, which have been previously correlated with eight chromosomes by means of FISH with mapped BAC clones. We anticipated that mapping of conserved coding regions would have utility for comparative mapping among legumes: thus 60 of the EST-based printer pairs were designed to amplify orthologons sequences across a range of legume species. As an initial test of this strategy, we used primers designed against M. truncatula exon sequences to rapidly map genes in M. sativa. The resulting comparative map, which includes 68 bridging markers, indicates that the two Medicago genomes are highly similar and establishes the basis for a Medicago composite map.
    An integrated physical, genetic and cytogenetic map around the sunn locus of Medicago truncatula
    Schnabel, E. ; Kulikova, O. ; Penmetsa, R.V. ; Bisseling, T. ; Cook, D.R. ; Frugoli, J. - \ 2003
    Genome 46 (2003)4. - ISSN 0831-2796 - p. 665 - 672.
    expressed sequence tags - nod factor transduction - legume lotus-japonicus - receptor-like kinase - root-hair - model - nodulation - mutants - fish - pachytene
    The sunn mutation of Medicago truncatula is a single-gene mutation that confers a novel supernodulation phenotype in response to inoculation with Sinorhizobium meliloti. We took advantage of the publicly available codominant PCR markers, the high-density genetic map, and a linked cytogenetic map to define the physical and genetic region containing sunn. We determined that sunn is located at the bottom of linkage group 4, where a fine-structure genetic map was used to place the locus within a similar to400-kb contig of bacterial artificial chromosome (BAC) clones. Genetic analyses of the sunn contig, as well as of a second, closely linked BAC contig designated NUM1, indicate that the physical to genetic distance within this chromosome region is in the range of 1000 -1100 kb.cM(-1). The ratio of genetic to cytogenetic distance determined across the entire region is 0.3 cM-mum(-1). These estimates are in good agreement with the empirically determined value of similar to300 kb-mum(-1) measured for the NUM1 contig. The assignment of sunn to a defined physical interval should provide a basis for sequencing and ultimately cloning the responsible gene.
    Genetic and cytogenetic mapping of DMI1, DMI2, and DMI3 genes of Medicago truncatula involved in Nod factor transduction, nodulation, and mycorrhization
    Ané, J.M. ; Lévy, J. ; Thoquet, P. ; Kulikova, O. ; Billy, F. de; Penmetsa, V. ; Kim, D.J. ; Debellé, F. ; Rosenberg, C. ; Cook, D.R. ; Bisseling, T. ; Huguet, T. ; Dénarié, J. - \ 2002
    Molecular Plant-Microbe Interactions 15 (2002)11. - ISSN 0894-0282 - p. 1108 - 1118.
    in-situ hybridization - extended dna fibers - pachytene chromosomes - arabidopsis-thaliana - pea mutants - alfalfa - fish - identification - resistance - markers
    The DMI1, DMI2, and DMI3 genes of Medicago truncatula, which are required for both nodulation and mycorrhization, control early steps of Nod factor signal transduction. Here, we have used diverse approaches to pave the way for the map-based cloning of these genes. Molecular amplification fragment length polymorphism markers linked to the three genes were identified by bulked segregant analysis. Integration of these markers into the general genetic map of M. truncatula revealed that DMI1, DMI2, and DMI3 are located on linkage groups 2, 5, and 8, respectively. Cytogenetic studies using fluorescent in situ hybridization (FISH) on mitotic and pachytene chromThe DMI1, DMI2, and DMI3 genes of Medicago truncatula, which are required for both nodulation and mycorrhization, control early steps of Nod factor signal transduction. Here, we have used diverse approaches to pave the way for the map-based cloning of these genes. Molecular amplification fragment length polymorphism markers linked to the three genes were identified by bulked segregant analysis. Integration of these markers into the general genetic map of M. truncatula revealed that DMI1, DMI2, and DMI3 are located on linkage groups 2, 5, and 8, respectively. Cytogenetic studies using fluorescent in situ hybridization (FISH) on mitotic and pachytene chromosomes confirmed the location of DMI1, DMI2, and DMI3 on chromosomes 2, 5, and 8. FISH-pachytene studies revealed that the three genes are in euchromatic regions of the genome, with a ratio of genetic to cytogenetic distances between 0.8 and 1.6 cM per ¿m in the DMI1, DMI2, and DMI3 regions. Through grafting experiments, we showed that the genetic control of the dmi1, dmi2, and dmi3 nodulation phenotypes is determined at the root level. This means that mutants can be transformed by Agrobacterium rhizogenes to accelerate the complementation step of map-based cloning projects for DMI1, DMI2, and DMI3.
    Microsynteny between pea and Medicago truncatula in the SYM2 region
    Gualtieri, G. ; Kulikova, O. ; Limpens, E. ; Kim, D.J. ; Cook, D.R. ; Bisseling, T. ; Geurts, R. - \ 2002
    Plant Molecular Biology 50 (2002)2. - ISSN 0167-4412 - p. 225 - 235.
    The crop legume pea (Pisum sativum) is genetically well characterized. However, due to its large genome it is not amenable to efficient positional cloning strategies. The purpose of this study was to determine if the model legume Medicago truncatula, which is a close relative of pea, could be used as a reference genome to facilitate the cloning of genes identified based on phenotypic and genetic criteria in pea. To this end, we studied the level of microsynteny between the SYM2 region of pea and the orthologous region in M. truncatula. Initially, a marker tightly linked to SYM2 was isolated by performing differential RNA display on near-isogenic pea lines. This marker served as the starting point for construction of a BAC physical map in M. truncatula. A fine-structure genetic map, based on eight markers from the M. truncatula physical map, indicates that the two genomes in this region share a conserved gene content. Importantly, this fine structure genetic map clearly delimits the SYM2-containing region in pea and the SYM2-orthologous region in M. truncatula, and should provide the basis for cloning SYM2. The utility of the physical and genetic tools in M. truncatula to dissect the SYM2 region of pea should have important implications for other gene cloning experiments in pea, in particular where the two genomes are highly syntenic within the region of interest.
    A region on the upper arm of chromosome 5 of Medicago truncatula is highly syntenic to the sym2 region of pea
    Geurts, R. ; Gualtieri, G. ; Kulikova, O. ; Kim, D.J. ; Cook, D.R. ; Bisseling, T. - \ 2000
    In: Nitrogen fixation: from molecules to crop productivity. Proceedings of the 12th International Congress on Nitrogen Fixation, Foz do Iguaçu, Paraná, Brazil, September 12-17, 1999. - Dordrecht/Boston/London : Kluwer Academic Publishers - ISBN 9780792362333 - p. 309 - 310.
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