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.
- MeSH
- Alleles MeSH
- Phenotype MeSH
- Nitrogen Fixation genetics MeSH
- Genotype MeSH
- Host Microbial Interactions MeSH
- Plant Roots genetics microbiology MeSH
- Polymorphism, Genetic * MeSH
- Rhizobium physiology MeSH
- Genes, Plant genetics MeSH
- Sequence Analysis, DNA methods MeSH
- Symbiosis genetics MeSH
- Trifolium genetics microbiology MeSH
- Publication type
- Journal Article MeSH
KEY MESSAGE: Vanadium compounds increased the content and release of distinct isoflavones in a Trifolium pratense suspension culture. Regarding transport-mechanism inhibitors, the process was mostly facilitated by ABC proteins and vesicular transport. The transport of isoflavones and other secondary metabolites is an important part of metabolism within plants and cultures in vitro regarding their role in defence against various abiotic and biotic stressors. This research focuses on the way how to increase production and exudation of isoflavones by application of chemical elicitor and the basic identification of their transport mechanisms across cell membranes. The release of five isoflavones (genistin, genistein, biochanin A, daidzein, and formononetin) into a nutrient medium was determined in a Trifolium pratense var. DO-8 suspension culture after two vanadium compound treatments and cultivation for 24 and 48 h. The NH4VO3 solution caused a higher concentration of isoflavones in the medium after 24 h. This increased content of secondary metabolites was subsequently suppressed by distinct transport-mechanism inhibitors. The transport of isoflavones in T. pratense was mostly affected by ABC inhibitors from the multidrug-resistance-associated protein subfamily, but the genistein concentration in the medium was lower after treatment with multidrug-resistance protein subfamily inhibitors. Brefeldin A, which blocks vesicular transport, also decreased the concentration of some isoflavones in the nutrient medium.
Using high-throughput sequencing, a novel waikavirus was identified in a mixed virus infection of red clover (Trifolium pratense L.). Its complete genomic sequence was determined and characterized. The virus, tentatively named red clover associated virus 1 (RCaV1), is phylogenetically related to members of the genus Waikavirus (family Secoviridae, order Picornavirales).
- MeSH
- Phylogeny MeSH
- Genome, Viral * MeSH
- Molecular Sequence Data MeSH
- Plant Diseases virology MeSH
- Open Reading Frames MeSH
- Satellite Viruses classification genetics isolation & purification MeSH
- Base Sequence MeSH
- Sequence Analysis, DNA MeSH
- Trifolium virology MeSH
- Waikavirus classification genetics isolation & purification MeSH
- Publication type
- Journal Article MeSH
This study reports the complete genomic sequence of a novel virus isolated from red clover. According to its genomic organization, its similarity to luteoviruses, and a greater than 10% difference in all genes, this virus isolate likely represents a new luteovirus species. As seen in nectarine stem pitting-associated virus (NSPaV) and NSPaV-South Korea (SK) luteoviruses, it differs from typical luteoviruses through the absence of ORF3a and ORF4 encoding movement proteins. Furthermore, its P5 protein (responsible for aphid transmission) is more similar to the P5 of enamoviruses than that of luteoviruses. The virus isolate has been named red clover-associated luteovirus (RCaV).
During aetiological study of diseased red clover (Trifolium pratense L.) using high throughput sequencing, a novel virus with a 10 kb genome divided into two segments was discovered. The virus, tentatively named red clover associated varicosavirus (RCaVV), is phylogenetically related to classifiable members of the genus Varicosavirus (family Rhabdoviridae, order Mononegavirales). Analysis of mRNA levels from the individual RCaVV genes suggested possible differences in transcription regulation between rhabdoviruses with divided and undivided genomes.
- MeSH
- DNA Viruses classification genetics isolation & purification MeSH
- Phylogeny MeSH
- Genome, Viral MeSH
- Plant Diseases virology MeSH
- Plant Viruses classification genetics isolation & purification MeSH
- Sequence Analysis, DNA MeSH
- Trifolium virology MeSH
- Viral Proteins genetics MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Publication type
- Journal Article MeSH
During high throughput sequencing (HTS) of leaves from a symptomatic red clover plant, a new RNA virus, tentatively named red clover nepovirus A (RCNVA), was discovered. The complete genomic sequence was determined and characterized. Particularly noteworthy was that RCNVA shares high sequence identities in RNA1 with a group of phylogenetically related nepoviruses while homologies in the RNA2 segments are markedly lower. Based on the genomic organization and phylogenetic attributes, RCNVA should be classified as a novel virus of the genus Nepovirus (subfamily Comovirinae, family Secoviridae, order Picornavirales).
In the production of fermented feed, each crop can be contaminated with a variety of microorganisms that may produce natural pollutants. Biogenic amines, mycotoxins, and undesirable organic acids can decrease health feed safety. The aim of this study was to compare the counts of microorganisms, levels of biogenic amines, and the mycotoxins in forage legumes, and also to compare the occurrence of microorganisms and levels of mycotoxins in green fodder and subsequently produced silage and the influence of additives on the content of natural harmful substances in silage. The experimental plot was located in Troubsko and Vatín, in the Czech Republic. Two varieties of Medicago sativa and one variety of Trifolium pratense were compared. Green fodder and subsequently produced silage reaching up to 23% of dry matter were evaluated and prepared using a bio-enzymatic additive and a chemical additive. Green fodder of Medicago sativa was more contaminated by Enterococci than Trifolium pratense fodder. The obvious difference was determined by the quality of silage leachate. The silage prepared from Medicago sativa fodder was more contaminated with butyric acid. Fungi were present in higher counts in the anaerobic environment of green fodder and contaminated it with zearalenone and deoxynivalenol. Lower counts of fungi were found in silage, although the zearalenone content did not change. Lower content of deoxynivalenol was detected in silage, compared with green fodder. Silages treated with a chemical additive were found not to contain butyric acid. Lower ethanol content was determined, and the tendency to reduce the risk of biogenic amines occurrence was evident. The additives proved to have no influence on the content of mycotoxins.
- MeSH
- Biogenic Amines chemistry MeSH
- Fermentation MeSH
- Food Contamination prevention & control MeSH
- Animal Feed microbiology MeSH
- Medicago sativa chemistry microbiology MeSH
- Mycotoxins chemistry MeSH
- Food Additives pharmacology MeSH
- Silage analysis microbiology MeSH
- Trifolium chemistry microbiology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
Subterranean clover is an important annual forage legume, whose diploidy and inbreeding nature make it an ideal model for genomic analysis in Trifolium. We reported a draft genome assembly of the subterranean clover TSUd_r1.1. Here we evaluate genome mapping on nanochannel arrays and generation of a transcriptome atlas across tissues to advance the assembly and gene annotation. Using a BioNano-based assembly spanning 512 Mb (93% genome coverage), we validated the draft assembly, anchored unplaced contigs and resolved misassemblies. Multiple contigs (264) from the draft assembly coalesced into 97 super-scaffolds (43% of genome). Sequences longer than >1 Mb increased from 40 to 189 Mb giving 1.4-fold increase in N50 with total genome in pseudomolecules improved from 73 to 80%. The advanced assembly was re-annotated using transcriptome atlas data to contain 31 272 protein-coding genes capturing >96% of the gene content. Functional characterization and GO enrichment confirmed gene expression for response to water deprivation, flavonoid biosynthesis and embryo development ending in seed dormancy, reflecting adaptation to the harsh Mediterranean environment. Comparative analyses across Papilionoideae identified 24 893 Trifolium-specific and 6325 subterranean-clover-specific genes that could be mined further for traits such as geocarpy and grazing tolerance. Eight key traits, including persistence, improved livestock health by isoflavonoid production in addition to important agro-morphological traits, were fine-mapped on the high-density SNP linkage map anchored to the assembly. This new genomic information is crucial to identify loci governing traits allowing marker-assisted breeding, comparative mapping and identification of tissue-specific gene promoters for biotechnological improvement of forage legumes.
- MeSH
- Genome, Plant genetics MeSH
- Genomics methods MeSH
- Sequence Analysis, DNA methods MeSH
- Trifolium genetics MeSH
- Publication type
- Journal Article MeSH
- MeSH
- Angelica sinensis MeSH
- Dioscorea MeSH
- Phytotherapy methods MeSH
- Hormone Replacement Therapy MeSH
- Climacteric * physiology drug effects MeSH
- Complementary Therapies methods MeSH
- Quality of Life MeSH
- Humans MeSH
- Menopause * physiology drug effects MeSH
- Trifolium MeSH
- Check Tag
- Humans MeSH
- Female MeSH
- Keywords
- isoflavonoid daidzein na fytoestrogen S-equol, účinný S-equol - stanovení v moči,
- MeSH
- Diet, Vegetarian * MeSH
- Adult MeSH
- Endocrine Disruptors * adverse effects MeSH
- Estrogens * physiology MeSH
- Flavonoids * administration & dosage pharmacology physiology therapeutic use MeSH
- Phytoestrogens * administration & dosage pharmacology chemistry urine standards adverse effects therapeutic use MeSH
- Glycine max * standards adverse effects MeSH
- Climacteric * MeSH
- Infant MeSH
- Middle Aged MeSH
- Humans MeSH
- Dietary Supplements * MeSH
- Soy Foods * MeSH
- Thyroid Gland * physiology drug effects MeSH
- Pregnancy MeSH
- Trifolium * physiology MeSH
- Check Tag
- Adult MeSH
- Infant MeSH
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Pregnancy MeSH
- Female MeSH
