Study of variability of genes involved in nitrogen fixation in
red cloved (Trifolium pratense L.)

a 2019

Study of variability of genes involved in nitrogen fixation in red cloved (Trifolium pratense L.)

TRNĚNÝ, Oldřich; David VLK; Eliška MACKOVÁ; Jana ŘEPKOVÁ; Jan NEDĚLNÍK et. al.

Basic information

Original name

Study of variability of genes involved in nitrogen fixation in red cloved (Trifolium pratense L.)

Authors

TRNĚNÝ, Oldřich; David VLK; Eliška MACKOVÁ; Jana ŘEPKOVÁ; Jan NEDĚLNÍK; Hana JAKEŠOVÁ; Petr NOVOTNÝ and Ján BOROŇ

Edition

XX. setkání biochemiků a molekulárních biologů, 2019

Other information

Language

English

Type of outcome

Conference abstract

Field of Study

10603 Genetics and heredity

Country of publisher

Czech Republic

Confidentiality degree

is not subject to a state or trade secret

RIV identification code

RIV/00216224:14310/19:00108389

Organization unit

Faculty of Science

ISBN

978-80-210-9420-8

Keywords in English

Trifolium; red clover; sequencing; nitrogen fixation; polymorphism

Changed: 8/1/2020 12:15, Mgr. David Vlk, Ph.D.

Abstract

In the original language

Biological nitrogen fixation (BNF) is a process of acquisition of atmospheric nitrogen by organism having enzymes enabling reduction of nitrogen to ammonia. This ability is typical for some bacteria, and several of these bacterial taxa can form symbiosis with plants (= root nodule symbiosis). From this relationship, legume plants, such as red clover (T. pratense L.), acquire fixed nitrogen, and bacteria, situated in root nodules, are supplied by organic compounds in return. Plants enriched by fixed nitrogen can be used as natural fertilizer and hence the development of plant with high BNF has great agronomic potential. Efficacy of BNF is highly variable among genotypes due to the occurrence of polymorphisms in genes associated with interaction between plants and bacteria, nodule formation and nitrogen fixation itself. Here, we asses variability of BNF efficacy among varieties of T. pratense in context with their genomic background, describe genes with significant association with higher BNF efficacy and introduce the planned stages of this study focused on transcriptomic landscape of root nodules. Material consists of more than 1,000 genotypes of 11 varieties of red clover, which was evaluated for their BNF efficacy using acetylene reduction assay (ARA), and selected contrasting genotypes was sequenced for 2 panels including 86 genes involved in BNF. Polymorphisms (SNPs, Indels) were identified in these genes using computational analysis, and their association with high BNF efficacy was assessed via statistical methods. Polymorphisms with higher association were acquired from both gene panels, and they will be used for SNP chip construction for rapid and massive genotyping. Next stage comprises transcriptome research of root nodule using RNA sequencing. Acquired sequencing data will lead to study of differential gene expression between genotypes contrasting in BNF efficacy, this information will be put into context with the results obtained from targeted sequencing and will enable comprehensive view to the BNF variability from genomic point of view on the two levels of gene expression.

Links

MUNI/A/0824/2017, interní kód MU

Name: Podpora výzkumné činnosti studentů molekulární biologie a genetiky 6 (Acronym: MolBiolGen)

Investor: Masaryk University, Category A

TH02010351, research and development project

Name: Efektivní biotechnologie pro syntézu populačních čipů a její ověření na pilotní matrici rostlinného materiálu

Investor: Technology Agency of the Czech Republic

Cite

TRNĚNÝ, Oldřich; David VLK; Eliška MACKOVÁ; Jana ŘEPKOVÁ; Jan NEDĚLNÍK; Hana JAKEŠOVÁ; Petr NOVOTNÝ and Ján BOROŇ. Study of variability of genes involved in nitrogen fixation in red cloved (Trifolium pratense L.). In XX. setkání biochemiků a molekulárních biologů. 2019. ISBN 978-80-210-9420-8.

@proceedings{1600296,
   author = {Trněný, Oldřich and Vlk, David and Macková, Eliška and Řepková, Jana and Nedělník, Jan and Jakešová, Hana and Novotný, Petr and Boroň, Ján},
   booktitle = {XX. setkání biochemiků a molekulárních biologů},
   keywords = {Trifolium; red clover; sequencing; nitrogen fixation; polymorphism},
   language = {eng},
   isbn = {978-80-210-9420-8},
   title = {Study of variability of genes involved in nitrogen fixation in red cloved (Trifolium pratense L.)},
   year = {2019}
}

TY  - CONF
ID  - 1600296
AU  - Trněný, Oldřich - Vlk, David - Macková, Eliška - Řepková, Jana - Nedělník, Jan - Jakešová, Hana - Novotný, Petr - Boroň, Ján
PY  - 2019
TI  - Study of variability of genes involved in nitrogen fixation in red cloved (Trifolium pratense L.)
SN  - 9788021094208
KW  - Trifolium
KW  - red clover
KW  - sequencing
KW  - nitrogen fixation
KW  - polymorphism
N2  - Biological nitrogen fixation (BNF) is a process of acquisition of atmospheric nitrogen by organism having enzymes enabling reduction of nitrogen to ammonia. This ability is typical for some bacteria, and several of these bacterial taxa can form symbiosis with plants (= root nodule symbiosis). From this relationship, legume plants, such as red clover (T. pratense L.), acquire fixed nitrogen, and bacteria, situated in root nodules, are supplied by organic compounds in return. Plants enriched by fixed nitrogen can be used as natural fertilizer and hence the development of plant with high BNF has great agronomic potential. Efficacy of BNF is highly variable among genotypes due to the occurrence of polymorphisms in genes associated with interaction between plants and bacteria, nodule formation and nitrogen fixation itself. Here, we asses variability of BNF efficacy among varieties of T. pratense in context with their genomic background, describe genes with significant association with higher BNF efficacy and introduce the planned stages of this study focused on transcriptomic landscape of root nodules. Material consists of more than 1,000 genotypes of 11 varieties of red clover, which was evaluated for their BNF efficacy using acetylene reduction assay (ARA), and selected contrasting genotypes was sequenced for 2 panels including 86 genes involved in BNF. Polymorphisms (SNPs, Indels) were identified in these genes using computational analysis, and their association with high BNF efficacy was assessed via statistical methods. Polymorphisms with higher association were acquired from both gene panels, and they will be used for SNP chip construction for rapid and massive genotyping. Next stage comprises transcriptome research of root nodule using RNA sequencing. Acquired sequencing data will lead to study of differential gene expression between genotypes contrasting in BNF efficacy, this information will be put into context with the results obtained from targeted sequencing and will enable comprehensive view to the BNF variability from genomic point of view on the two levels of gene expression.
ER  -

TRNĚNÝ, Oldřich; David VLK; Eliška MACKOVÁ; Jana ŘEPKOVÁ; Jan NEDĚLNÍK; Hana JAKEŠOVÁ; Petr NOVOTNÝ and Ján BOROŇ. Study of variability of genes involved in nitrogen fixation in red cloved (Trifolium pratense L.). In \textit{XX. setkání biochemiků a molekulárních biologů}. 2019. ISBN~978-80-210-9420-8.

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