LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 34

Search options

  1. Article ; Online: Over-expression of a YUCCA-Like Gene Results in Altered Shoot and Stolon Branching and Reduced Potato Tuber Size

    Roumeliotis, Efstathios / Kloosterman, Bjorn / Oortwijn, Marian / Kohlen, Wouter / Bouwmeester, Harro J. / Bachem, Christian W. B. / Visser, Richard G. F.

    Potato Res.. 2023 Mar., v. 66, no. 1 p.67-84

    2023  

    Abstract: Auxin is known to be involved in various developmental processes, including meristem identity, shoot branching and initiation of potato tubers. The previously identified StYUCCA8 gene in potato that exhibits a peak in gene expression after tuber ... ...

    Abstract Auxin is known to be involved in various developmental processes, including meristem identity, shoot branching and initiation of potato tubers. The previously identified StYUCCA8 gene in potato that exhibits a peak in gene expression after tuber induction and prior to tuber swelling was cloned and over-expressed in order to study the effects of altered auxin content on shoot and stolon architecture and tuber development. The potato plants transformed with the 35S::StYUCCA8 construct exhibited increased shoot and stolon branching, reduced leaf size, lower average tuber fresh weight and enhanced adventitious and lateral root formation. Investigation of the IAA content revealed that the concentration of auxin was not altered in the shoot apex but was significantly lower in the basal part of the stem despite the several 100-fold increase of expression of the StYUCCA8 gene in three independent transgenic clones. This is the first time a potato YUCCA gene is used in an experiment in order to identify the role of endogenous auxin biosynthesis in potato plant development. Our research helps elucidate the importance of small changes of auxin content on several developmental events of the potato plant, such as shoot, stolon and root architecture.
    Keywords auxins ; biosynthesis ; gene expression ; genes ; genetically modified organisms ; lateral roots ; leaf area ; meristems ; plant development ; potatoes
    Language English
    Dates of publication 2023-03
    Size p. 67-84.
    Publishing place Springer Netherlands
    Document type Article ; Online
    ZDB-ID 407680-1
    ISSN 1871-4528 ; 0014-3065
    ISSN (online) 1871-4528
    ISSN 0014-3065
    DOI 10.1007/s11540-022-09572-x
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 1214: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: Over-expression of a YUCCA-Like Gene Results in Altered Shoot and Stolon Branching and Reduced Potato Tuber Size

    Roumeliotis, Efstathios / Kloosterman, Bjorn / Oortwijn, Marian / Kohlen, Wouter / Bouwmeester, Harro J. / Bachem, Christian W.B. / Visser, Richard G.F.

    Potato Research

    2023  Volume 66, Issue 1

    Abstract: Auxin is known to be involved in various developmental processes, including meristem identity, shoot branching and initiation of potato tubers. The previously identified StYUCCA8 gene in potato that exhibits a peak in gene expression after tuber ... ...

    Abstract Auxin is known to be involved in various developmental processes, including meristem identity, shoot branching and initiation of potato tubers. The previously identified StYUCCA8 gene in potato that exhibits a peak in gene expression after tuber induction and prior to tuber swelling was cloned and over-expressed in order to study the effects of altered auxin content on shoot and stolon architecture and tuber development. The potato plants transformed with the 35S::StYUCCA8 construct exhibited increased shoot and stolon branching, reduced leaf size, lower average tuber fresh weight and enhanced adventitious and lateral root formation. Investigation of the IAA content revealed that the concentration of auxin was not altered in the shoot apex but was significantly lower in the basal part of the stem despite the several 100-fold increase of expression of the StYUCCA8 gene in three independent transgenic clones. This is the first time a potato YUCCA gene is used in an experiment in order to identify the role of endogenous auxin biosynthesis in potato plant development. Our research helps elucidate the importance of small changes of auxin content on several developmental events of the potato plant, such as shoot, stolon and root architecture.
    Keywords Auxin ; Plant development ; Potato ; StYUCCA ; Stolons
    Subject code 580
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 407680-1
    ISSN 1871-4528 ; 0014-3065
    ISSN (online) 1871-4528
    ISSN 0014-3065
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 1214: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Book ; Online: Transcription profiling of Solanum tuberosum for tuber quality traits - Flesh color and Cooking type

    Kloosterman, Bjorn

    2009  

    Abstract: BSA expression profiling for tuber flesh color. Extreme individuals segregating for tuber flesh color are selected and RNA is pooled together. Gene expression is profiled using microarray technology. Genes displaying differential expression between the ... ...

    Abstract BSA expression profiling for tuber flesh color. Extreme individuals segregating for tuber flesh color are selected and RNA is pooled together. Gene expression is profiled using microarray technology. Genes displaying differential expression between the constrasting bulks are considered as candidate genes responsible for the targeted trait and further analyzed using the individual genotypes.
    Keywords Solanum tuberosum
    Publisher Wageningen UR
    Publishing country nl
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Book ; Online: Transcription profiling of potato tubers for the investigation of methionine content

    Kloosterman, Bjorn

    2009  

    Abstract: BSA pooling experiment for methionine content in a segrating diploid potato population (CxE). RNA of constrasting individuals for methionine content are pooled together based on their tuber methionine content and marker association with either or both of ...

    Abstract BSA pooling experiment for methionine content in a segrating diploid potato population (CxE). RNA of constrasting individuals for methionine content are pooled together based on their tuber methionine content and marker association with either or both of the identified QTLs for methionine content.
    Keywords Solanum tuberosum
    Publisher Wageningen UR
    Publishing country nl
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Book ; Thesis: Transcriptomic analysis of potato tuber development and tuber quality traits using microarray technology

    Kloosterman, Bjorn

    2006  

    Author's details Bjorn Kloosterman
    Language English
    Size 128 p. :, ill. (some col.) ;, 24 cm.
    Publisher s.n
    Publishing place Wageningen
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Thesis (doctoral)--Wageningen Universiteit, 2006
    Note Summary in Dutch. ; "Stellingen" inserted. ; Vita.
    ISBN 9085044545 ; 9789085044543
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Book ; Thesis: Transcriptomic analysis of potato tuber development and tuber quality traits using microarray technology

    Kloosterman, Bjorn

    in search of candidate genes

    2006  

    Author's details Bjorn Kloosterman
    Language English
    Size 128 S., Ill., graph. Darst.
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Wageningen, 2006
    ISBN 9085044545 ; 9789085044543
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: Integration of multi-omics data for prediction of phenotypic traits using random forest.

    Acharjee, Animesh / Kloosterman, Bjorn / Visser, Richard G F / Maliepaard, Chris

    BMC bioinformatics

    2016  Volume 17 Suppl 5, Page(s) 180

    Abstract: Background: In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of tuber quality phenotypic data ... ...

    Abstract Background: In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of tuber quality phenotypic data from a diploid segregating mapping population of potato. In this study we present an approach to integrate these ~ omics data sets for the purpose of predicting phenotypic traits. This gives us networks of relatively small sets of interrelated ~ omics variables that can predict, with higher accuracy, a quality trait of interest.
    Results: We used Random Forest regression for integrating multiple ~ omics data for prediction of four quality traits of potato: tuber flesh colour, DSC onset, tuber shape and enzymatic discoloration. For tuber flesh colour beta-carotene hydroxylase and zeaxanthin epoxidase were ranked first and forty-fourth respectively both of which have previously been associated with flesh colour in potato tubers. Combining all the significant genes, LC-peaks, GC-peaks and proteins, the variation explained was 75 %, only slightly more than what gene expression or LC-MS data explain by themselves which indicates that there are correlations among the variables across data sets. For tuber shape regressed on the gene expression, LC-MS, GC-MS and proteomics data sets separately, only gene expression data was found to explain significant variation. For DSC onset, we found 12 significant gene expression, 5 metabolite levels (GC) and 2 proteins that are associated with the trait. Using those 19 significant variables, the variation explained was 45 %. Expression QTL (eQTL) analyses showed many associations with genomic regions in chromosome 2 with also the highest explained variation compared to other chromosomes. Transcriptomics and metabolomics analysis on enzymatic discoloration after 5 min resulted in 420 significant genes and 8 significant LC metabolites, among which two were putatively identified as caffeoylquinic acid methyl ester and tyrosine.
    Conclusions: In this study, we made a strategy for selecting and integrating multiple ~ omics data using random forest method and selected representative individual peaks for networks based on eQTL, mQTL or pQTL information. Network analysis was done to interpret how a particular trait is associated with gene expression, metabolite and protein data.
    MeSH term(s) Chromatography, High Pressure Liquid ; Chromosomes, Plant/genetics ; Chromosomes, Plant/metabolism ; Gas Chromatography-Mass Spectrometry ; Gene Expression Regulation, Plant ; Genomics ; Mass Spectrometry ; Metabolomics ; Phenotype ; Plant Proteins/analysis ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plant Tubers/chemistry ; Plant Tubers/genetics ; Plant Tubers/metabolism ; Proteomics ; Quantitative Trait Loci ; Solanum tuberosum/genetics ; Solanum tuberosum/metabolism
    Chemical Substances Plant Proteins
    Language English
    Publishing date 2016-06-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-016-1043-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article ; Online: Genetical genomics of quality related traits in potato tubers using proteomics.

    Acharjee, Animesh / Chibon, Pierre-Yves / Kloosterman, Bjorn / America, Twan / Renaut, Jenny / Maliepaard, Chris / Visser, Richard G F

    BMC plant biology

    2018  Volume 18, Issue 1, Page(s) 20

    Abstract: Background: Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. To get more ... ...

    Abstract Background: Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. To get more insight into the genetic factors underlying variation in quality traits related to carbohydrate and starch metabolism and cold sweetening, we determined the protein content and composition in potato tubers using 2D-gel electrophoresis in a diploid potato mapping population. Upon analyzing we made sure that the proteins from the patatin family were excluded to ensure a better representation of the other proteins.
    Results: We subsequently performed pQTL analyses for all other proteins with a sufficient representation in the population and established a relationship between proteins and 26 potato tuber quality traits (e.g. flesh colour, enzymatic discoloration) by co-localization on the genetic map and a direct correlation study of protein abundances and phenotypic traits. Over 1643 unique protein spots were detected in total over the two harvests. We were able to map pQTLs for over 300 different protein spots some of which co-localized with traits such as starch content and cold sweetening. pQTLs were observed on every chromosome although not evenly distributed over the chromosomes. The largest number of pQTLs was found for chromosome 8 and the lowest for chromosome number 10. For some 20 protein spots multiple QTLs were observed.
    Conclusions: From this analysis, hotspot areas for protein QTLs were identified on chromosomes three, five, eight and nine. The hotspot on chromosome 3 coincided with a QTL previously identified for total protein content and had more than 23 pQTLs in the region from 70 to 80 cM. Some of the co-localizing protein spots associated with some of the most interesting tuber quality traits were identified, albeit far less than we had anticipated at the onset of the experiments.
    MeSH term(s) Carbohydrate Metabolism ; Food Quality ; Genomics ; Phenotype ; Plant Tubers/genetics ; Plant Tubers/physiology ; Proteomics ; Solanum tuberosum/genetics ; Solanum tuberosum/physiology ; Starch/metabolism
    Chemical Substances Starch (9005-25-8)
    Language English
    Publishing date 2018--23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1471-2229
    ISSN (online) 1471-2229
    DOI 10.1186/s12870-018-1229-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  9. Article ; Online: Integration of multi-omics data for prediction of phenotypic traits using random forest

    Acharjee, Animesh / Kloosterman, Bjorn / Visser, Richard G.F. / Maliepaard, Chris

    BMC Bioinformatics

    2016  Volume 17, Issue 5

    Abstract: Background: In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of tuber quality phenotypic data ... ...

    Abstract Background: In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of tuber quality phenotypic data from a diploid segregating mapping population of potato. In this study we present an approach to integrate these ~ omics data sets for the purpose of predicting phenotypic traits. This gives us networks of relatively small sets of interrelated ~ omics variables that can predict, with higher accuracy, a quality trait of interest. Results: We used Random Forest regression for integrating multiple ~ omics data for prediction of four quality traits of potato: tuber flesh colour, DSC onset, tuber shape and enzymatic discoloration. For tuber flesh colour beta-carotene hydroxylase and zeaxanthin epoxidase were ranked first and forty-fourth respectively both of which have previously been associated with flesh colour in potato tubers. Combining all the significant genes, LC-peaks, GC-peaks and proteins, the variation explained was 75%, only slightly more than what gene expression or LC-MS data explain by themselves which indicates that there are correlations among the variables across data sets. For tuber shape regressed on the gene expression, LC-MS, GC-MS and proteomics data sets separately, only gene expression data was found to explain significant variation. For DSC onset, we found 12 significant gene expression, 5 metabolite levels (GC) and 2 proteins that are associated with the trait. Using those 19 significant variables, the variation explained was 45%. Expression QTL (eQTL) analyses showed many associations with genomic regions in chromosome 2 with also the highest explained variation compared to other chromosomes. Transcriptomics and metabolomics analysis on enzymatic discoloration after 5min resulted in 420 significant genes and 8 significant LC metabolites, among which two were putatively identified as caffeoylquinic acid methyl ester and tyrosine. Conclusions: ...
    Keywords Data integration ; Genetical genomics ; Networks ; Random forest
    Subject code 333
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 2041484-5
    ISSN 1471-2105
    ISSN 1471-2105
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article: The PIN family of proteins in potato and their putative role in tuberization.

    Roumeliotis, Efstathios / Kloosterman, Bjorn / Oortwijn, Marian / Visser, Richard G F / Bachem, Christian W B

    Frontiers in plant science

    2013  Volume 4, Page(s) 524

    Abstract: The PIN family of trans-membrane proteins mediates auxin efflux throughout the plant and during various phases of plant development. In Arabidopsis thaliana, the PIN family comprised of 8 members, divided into "short" and "long" PINs according to the ... ...

    Abstract The PIN family of trans-membrane proteins mediates auxin efflux throughout the plant and during various phases of plant development. In Arabidopsis thaliana, the PIN family comprised of 8 members, divided into "short" and "long" PINs according to the length of the hydrophilic domain of the protein. Based on sequence homology using the recently published potato genome sequence (Solanum tuberosum group Phureja) we identified ten annotated potato StPIN genes. Mining the publicly available gene expression data, we constructed a catalog tissue specificity of StPIN gene expression, focusing on the process of tuberization. A total of four StPIN genes exhibited increased expression 4 days after tuber induction, prior to the onset of stolon swelling. For two PIN genes, StPIN4 and StPIN2, promoter sequences were cloned and fused to the GUS reporter protein to study tissue specificity in more detail. StPIN4 promoter driven GUS staining was detected in the flower stigma, in the flower style, below the ovary and petals, in the root tips, in the vascular tissue of the stolons and in the tuber parenchyma cells. StPIN2 promoter driven GUS staining was detected in flower buds, in the vascular tissue of the swelling stolons and in the storage parenchyma of the growing tubers. Based on our results, we postulate a role for the StPINs in redistributing auxin in the swelling stolon during early events in tuber development.
    Language English
    Publishing date 2013-12-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2013.00524
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top