Open Access

Genes, volume 12, issue 7, pages 952

Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis

Grigoreva Elizaveta ^{1, 2, 3}

Tkachenko Alexander ¹

Arkhimandritova Serafima ⁴

Beatovic Aleksandar ¹

Ulianich Pavel ⁵

Volkov Vladimir ^{2, 3}

Karzhaev Dmitry ³

Ben Cecile ⁶

Gentzbittel Laurent ⁶

Potokina Elena ^{2, 3}

Hide authors affiliations Show authors affiliations: 6 affiliations

Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia |

Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia

Peter the Great St. Petersburg Polytechnic University

Saint-Petersburg State Forest Technical University

Sirius University of Science and Technology, 354340 Sochi, Russia |

⁴

Vavilov All-Russian Institute of Plant Genetic Resources, 190000 St. Petersburg, Russia |

⁵

All-Russian Research Institute of Agricultural Microbiology, 196608 St. Petersburg, Russia |

⁶

Skolkovo Institute of Science and Technology, 121205 Moscow, Russia |

Publication type: Journal Article

Publication date: 2021-06-22

Multidisciplinary Digital Publishing Institute (MDPI)

Journal: Genes

Quartile SCImago

Quartile WOS

Impact factor: 3.5

ISSN: 20734425

DOI: 10.3390/genes12070952

Copy DOI

PubMed ID: 34206279

Genetics

Genetics (clinical)

Abstract

Guar (Cyamopsis tetragonoloba (L.) Taub.) is an annual legume crop native to India and Pakistan. Seeds of the plant serve as a source of galactomannan polysaccharide (guar gum) used in the food industry as a stabilizer (E412) and as a gelling agent in oil and gas fracturing fluids. There were several attempts to introduce this crop to countries of more northern latitudes. However, guar is a plant of a short photoperiod, therefore, its introduction, for example, to Russia is complicated by a long day length during the growing season. Breeding of new guar varieties insensitive to photoperiod slowed down due to the lack of information on functional molecular markers, which, in turn, requires information on guar genome. Modern breeding strategies, e.g., genomic predictions, benefit from integration of multi-omics approaches such as transcriptome, proteome and metabolome assays. Here we present an attempt to use transcriptome-metabolome integration to understand the genetic determination of flowering time variation among guar plants that differ in their photoperiod sensitivity. This study was performed on nine early- and six delayed-flowering guar varieties with the goal to find a connection between 63 metabolites and 1,067 differentially expressed transcripts using Shiny GAM approach. For the key biomarker of flowering in guar myo-inositol we also evaluated the KEGG biochemical pathway maps available for Arabidopsis thaliana. We found that the phosphatidylinositol signaling pathway is initiated in guar plants that are ready for flowering through the activation of the phospholipase C (PLC) gene, resulting in an exponential increase in the amount of myo-inositol in its free form observed on GC-MS chromatograms. The signaling pathway is performed by suppression of myo-inositol phosphate kinases (phosphorylation) and alternative overexpression of phosphatases (dephosphorylation). Our study suggests that metabolome and transcriptome information taken together, provide valuable information about biomarkers that can be used as a tool for marker-assisted breeding, metabolomics and functional genomics of this important legume crop.

By date By citations

Citations by journals

	1 2
Plants	Plants, 2, 40% Plants 2 publications, 40%
Frontiers in Genetics	Frontiers in Genetics, 1, 20% Frontiers in Genetics 1 publication, 20%
Genetic Resources and Crop Evolution	Genetic Resources and Crop Evolution, 1, 20% Genetic Resources and Crop Evolution 1 publication, 20%
Scientia Horticulturae	Scientia Horticulturae, 1, 20% Scientia Horticulturae 1 publication, 20%
	1 2

Citations by publishers

	1 2
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 2, 40% Multidisciplinary Digital Publishing Institute (MDPI) 2 publications, 40%
Frontiers Media S.A.	Frontiers Media S.A., 1, 20% Frontiers Media S.A. 1 publication, 20%
Springer Nature	Springer Nature, 1, 20% Springer Nature 1 publication, 20%
Elsevier	Elsevier, 1, 20% Elsevier 1 publication, 20%
	1 2

We do not take into account publications that without a DOI.
Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
Statistics recalculated weekly.

{"yearsCitations":{"type":"bar","data":{"show":true,"labels":[2021,2022,2023,2024],"ids":[0,0,0,0],"codes":[0,0,0,0],"imageUrls":["","","",""],"datasets":[{"label":"Citations number","data":[1,2,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":["20","40","20","20"],"barThickness":null}]},"options":{"indexAxis":"x","maintainAspectRatio":true,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":1,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Citations per year","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"journals":{"type":"bar","data":{"show":true,"labels":["Plants","Frontiers in Genetics","Genetic Resources and Crop Evolution","Scientia Horticulturae"],"ids":[17251,13242,21766,20595],"codes":[0,0,0,0],"imageUrls":["\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/4QWA67eqfcfyOiA8Wk7YnqroHFqQbTsmDJUYTCTg_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp"],"datasets":[{"label":"","data":[2,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[40,20,20,20],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Journals","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"publishers":{"type":"bar","data":{"show":true,"labels":["Multidisciplinary Digital Publishing Institute (MDPI)","Frontiers Media S.A.","Springer Nature","Elsevier"],"ids":[202,208,8,17],"codes":[0,0,0,0],"imageUrls":["\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/4QWA67eqfcfyOiA8Wk7YnqroHFqQbTsmDJUYTCTg_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp"],"datasets":[{"label":"","data":[2,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[40,20,20,20],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Publishers","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}}}

Publication PDF

Metrics

Cite this

GOST |

Cite this

GOST Copy

Grigoreva E. et al. Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis // Genes. 2021. Vol. 12. No. 7. p. 952.

GOST all authors (up to 50) Copy

Grigoreva E., Tkachenko A., Arkhimandritova S., Beatovic A., Ulianich P., Volkov V., Karzhaev D., Ben C., Gentzbittel L., Potokina E. Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis // Genes. 2021. Vol. 12. No. 7. p. 952.

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.3390/genes12070952

UR - https://doi.org/10.3390%2Fgenes12070952

TI - Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis

T2 - Genes

AU - Tkachenko, Alexander

AU - Beatovic, Aleksandar

AU - Karzhaev, Dmitry

AU - Potokina, Elena

AU - Grigoreva, Elizaveta

AU - Arkhimandritova, Serafima

AU - Ulianich, Pavel

AU - Volkov, Vladimir

AU - Ben, Cecile

AU - Gentzbittel, Laurent

PY - 2021

DA - 2021/06/22 00:00:00

PB - Multidisciplinary Digital Publishing Institute (MDPI)

SP - 952

IS - 7

VL - 12

PMID - 34206279

SN - 2073-4425

ER -

BibTex |

Cite this

BibTex Copy

@article{2021_Grigoreva,

author = {Alexander Tkachenko and Aleksandar Beatovic and Dmitry Karzhaev and Elena Potokina and Elizaveta Grigoreva and Serafima Arkhimandritova and Pavel Ulianich and Vladimir Volkov and Cecile Ben and Laurent Gentzbittel},

title = {Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis},

journal = {Genes},

year = {2021},

volume = {12},

publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},

month = {jun},

url = {https://doi.org/10.3390%2Fgenes12070952},

number = {7},

pages = {952},

doi = {10.3390/genes12070952}

}

MLA

Cite this

MLA Copy

Grigoreva, Elizaveta, et al. “Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis.” Genes, vol. 12, no. 7, Jun. 2021, p. 952. https://doi.org/10.3390%2Fgenes12070952.

Found error?

Publisher

Multidisciplinary Digital Publishing Institute (MDPI)

Journal

Genes

Quartile SCImago

Quartile WOS

Impact factor

3.5

ISSN

20734425 (Print)

Labs

Center for Bioinformatics and Genomic Research

Profiles