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Open AccessArticle

Allelic Variants for Candidate Nitrogen Fixation Genes Revealed by Sequencing in Red Clover (Trifolium pratense L.)

1
Agricultural Research, Ltd., Zahradní 1, 664 41 Troubsko, Czech Republic
2
Department of Experimental Biology, Masaryk University, 625 00 Brno, Czech Republic
3
Red Clover and Grass Breeding, 724 47 Hladké Životice, Czech Republic
4
Institute of Microbiology of the Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
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Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
6
Research Institute for Fodder Crops, Ltd., 664 41 Troubsko, Czech Republic
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(21), 5470; https://doi.org/10.3390/ijms20215470
Received: 26 September 2019 / Revised: 25 October 2019 / Accepted: 30 October 2019 / Published: 2 November 2019
(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)
Plant–rhizobia symbiosis can activate key genes involved in regulating nodulation associated with biological nitrogen fixation (BNF). Although the general molecular basis of the BNF process is frequently studied, little is known about its intraspecific variability and the characteristics of its allelic variants. This study’s main goals were to describe phenotypic and genotypic variation in the context of nitrogen fixation in red clover (Trifolium pretense L.) and identify variants in BNF candidate genes associated with BNF efficiency. Acetylene reduction assay validation was the criterion for selecting individual plants with particular BNF rates. Sequences in 86 key candidate genes were obtained by hybridization-based sequence capture target enrichment of plants with alternative phenotypes for nitrogen fixation. Two genes associated with BNF were identified: ethylene response factor required for nodule differentiation (EFD) and molybdate transporter 1 (MOT1). In addition, whole-genome population genotyping by double-digest restriction-site-associated sequencing (ddRADseq) was performed, and BNF was evaluated by the natural 15N abundance method. Polymorphisms associated with BNF and reflecting phenotype variability were identified. The genetic structure of plant accessions was not linked to BNF rate of measured plants. Knowledge of the genetic variation within BNF candidate genes and the characteristics of genetic variants will be beneficial in molecular diagnostics and breeding of red clover. View Full-Text
Keywords: associated genes; associated polymorphisms; genome-wide association; biological nitrogen fixation; red clover associated genes; associated polymorphisms; genome-wide association; biological nitrogen fixation; red clover
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Trněný, O.; Vlk, D.; Macková, E.; Matoušková, M.; Řepková, J.; Nedělník, J.; Hofbauer, J.; Vejražka, K.; Jakešová, H.; Jansa, J.; Piálek, L.; Knotová, D. Allelic Variants for Candidate Nitrogen Fixation Genes Revealed by Sequencing in Red Clover (Trifolium pratense L.). Int. J. Mol. Sci. 2019, 20, 5470.

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