The genomes of many plants, animals, and fungi frequently comprise dispensable B chromosomes that rely upon various chromosomal drive mechanisms to counteract the tendency of non-essential genetic elements to be purged over time. The B chromosome of rye - a model system for nearly a century - undergoes targeted nondisjunction during first pollen mitosis, favouring segregation into the generative nucleus, thus increasing their numbers over generations. However, the genetic mechanisms underlying this process are poorly understood. Here, using a newly-assembled, ~430 Mb-long rye B chromosome pseudomolecule, we identify five candidate genes whose role as trans-acting moderators of the chromosomal drive is supported by karyotyping, chromosome drive analysis and comparative RNA-seq. Among them, we identify DCR28, coding a microtubule-associated protein related to cell division, and detect this gene also in the B chromosome of Aegilops speltoides. The DCR28 gene family is neo-functionalised and serially-duplicated with 15 B chromosome-located copies that are uniquely highly expressed in the first pollen mitosis of rye.
- MeSH
- Aegilops genetika metabolismus MeSH
- chromozomy rostlin * genetika MeSH
- karyotypizace MeSH
- mitóza * genetika MeSH
- nondisjunkce genetická MeSH
- pyl genetika MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné geny MeSH
- rostlinné proteiny genetika metabolismus MeSH
- žito * genetika MeSH
- Publikační typ
- časopisecké články MeSH
The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gene family members were identified from a genome-wide search against Arabidopsis thaliana in the genome data of 18 dicots and seven monocots. The phylogenetic and sequence alignment analyses divided NGA genes into different clusters and revealed that the numbers of genes varied depending on the species. The phylogeny was followed by the characterization of the Solanaceae (tomato, potato, capsicum, tobacco) and Poaceae (Brachypodium distachyon, Oryza sativa L. japonica, and Sorghum bicolor) family members in comparison with A. thaliana. The gene and protein structures revealed a similar pattern for NGA and NGA-like sequences, suggesting that both are conserved during evolution. Promoter cis-element analysis showed that phytohormones such as abscisic acid, auxin, and gibberellins play a crucial role in regulating the NGA gene family. Gene ontology analysis revealed that the NGA gene family participates in diverse biological processes such as flower development, leaf morphogenesis, and the regulation of transcription. The gene duplication analysis indicates that most of the genes are evolved due to segmental duplications and have undergone purifying selection pressure. Finally, the gene expression analysis implicated that the NGA genes are abundantly expressed in lateral organs and flowers. This analysis has presented a detailed and comprehensive study of the NGA gene family, providing basic knowledge of the gene, protein structure, function, and evolution. These results will lay the foundation for further understanding of the role of the NGA gene family in various plant developmental processes.
- MeSH
- Arabidopsis * genetika metabolismus MeSH
- Brachypodium * genetika MeSH
- fylogeneze MeSH
- genom rostlinný MeSH
- multigenová rodina MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné proteiny genetika metabolismus MeSH
- rýže (rod) * genetika metabolismus MeSH
- transkripční faktory genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- MeSH
- mitochondriální proteiny metabolismus MeSH
- oxidoreduktasy * biosyntéza genetika MeSH
- RNA * MeSH
- rostlinné proteiny genetika metabolismus MeSH
- savci genetika metabolismus MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- komentáře MeSH
Cells sense a variety of extracellular signals balancing their metabolism and physiology according to changing growth conditions. Plasma membranes are the outermost informational barriers that render cells sensitive to regulatory inputs. Membranes are composed of different types of lipids that play not only structural but also informational roles. Hormones and other regulators are sensed by specific receptors leading to the activation of lipid metabolizing enzymes. These enzymes generate lipid second messengers. Among them, phosphatidic acid (PA) is a well-known intracellular messenger that regulates various cellular processes. This lipid affects the functional properties of cell membranes and binds to specific target proteins leading to either genomic (affecting transcriptome) or non-genomic responses. The subsequent biochemical, cellular and physiological reactions regulate plant growth, development and stress tolerance. In the present review, we focus on primary (genome-independent) signaling events triggered by rapid PA accumulation in plant cells and describe the functional role of PA in mediating response to hormones and hormone-like regulators. The contributions of individual lipid signaling enzymes to the formation of PA by specific stimuli are also discussed. We provide an overview of the current state of knowledge and future perspectives needed to decipher the mode of action of PA in the regulation of cell functions.
- MeSH
- fosfolipasa D * metabolismus MeSH
- hormony metabolismus MeSH
- kyseliny fosfatidové * metabolismus MeSH
- proteiny metabolismus MeSH
- rostlinné proteiny genetika MeSH
- rostliny metabolismus MeSH
- signální transdukce fyziologie MeSH
- vývoj rostlin MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
The root is the below-ground organ of a plant, and it has evolved multiple signaling pathways that allow adaptation of architecture, growth rate, and direction to an ever-changing environment. Roots grow along the gravitropic vector towards beneficial areas in the soil to provide the plant with proper nutrients to ensure its survival and productivity. In addition, roots have developed escape mechanisms to avoid adverse environments, which include direct illumination. Standard laboratory growth conditions for basic research of plant development and stress adaptation include growing seedlings in Petri dishes on medium with roots exposed to light. Several studies have shown that direct illumination of roots alters their morphology, cellular and biochemical responses, which results in reduced nutrient uptake and adaptability upon additive stress stimuli. In this review, we summarize recent methods that allow the study of shaded roots under controlled laboratory conditions and discuss the observed changes in the results depending on the root illumination status.
- MeSH
- fyziologická adaptace * MeSH
- kořeny rostlin metabolismus účinky záření MeSH
- regulace genové exprese u rostlin účinky záření MeSH
- rostlinné proteiny genetika metabolismus MeSH
- rostliny metabolismus účinky záření MeSH
- semenáček metabolismus účinky záření MeSH
- světlo * MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
KEY MESSAGE: Multiple origins of Indian dwarf wheat were due to two mutations targeting the same TREE domain of a GSK3-like kinase, and these mutations confer to enhanced drought tolerance and increased phosphate and nitrogen accumulation for adaptation to the dry climate of Indian and Pakistan. Indian dwarf wheat, featured by the short stature, erect leaves, dense spikes, and small, spherical grains, was a staple crop in India and Pakistan from the Bronze Age until the early 1900s. These morphological features are controlled by a single locus Sphaerococcum 1 (S1), but the genetic identity of the locus and molecular mechanisms underlying the selection of this wheat type are unknown. In this study, we showed that the origin of Indian dwarf wheat was due to two independent missense mutations targeting the conserved TREE domain of a GSK3-like kinase, which is homologous to the Arabidopsis BIN2 protein, a negative regulator in brassinosteroid signaling. The S1 protein is involved in brassinosteroid signaling by physical interaction with the wheat BES1/BZR1 proteins. The dwarf alleles are insensitive to brassinosteroid, upregulates brassinosteroid biosynthetic genes, significantly enhanced drought tolerance, facilitated phosphate accumulation, and increased high molecular weight glutenins. It is the enhanced drought tolerance and accumulation of nitrogen and phosphate that contributed to the adaptation of such a small-grain form of wheat to the dry climate of India and Pakistan. Thus, our research not only identified the genetic events underlying the origin of the Indian dwarf wheat, but also revealed the function of brassinosteroid in the regulation of drought tolerance, phosphate homeostasis, and grain quality.
- MeSH
- fenotyp MeSH
- fosfáty metabolismus MeSH
- fosforylace MeSH
- geneticky modifikované rostliny genetika fyziologie MeSH
- kinasa 3 glykogensynthasy genetika metabolismus MeSH
- mutace * MeSH
- období sucha * MeSH
- pšenice genetika fyziologie MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné proteiny genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
Structural knowledge of biological macromolecules is essential for understanding their function and for modifying that function by engineering. Protein crystallography is a powerful method for elucidating molecular structures of proteins, but it is essential that the investigator has a basic knowledge of good practices and of the major pitfalls in the technique. Here we describe issues specific for the case of structural studies of strigolactone (SL) receptor structure and function, and in particular the difficulties associated with capturing complexes of SL receptors with the SL hormone ligand in the crystal.
- MeSH
- heterocyklické sloučeniny tricyklické metabolismus MeSH
- konformace proteinů MeSH
- krystalografie rentgenová MeSH
- laktony metabolismus MeSH
- ligandy MeSH
- molekulární modely MeSH
- receptory buněčného povrchu genetika metabolismus MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné proteiny genetika metabolismus MeSH
- signální transdukce MeSH
- vazba proteinů MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
KEY MESSAGE: The new 4.2-kb transposable insertion in the intron of ZmCCT reversely responded relative to the known 5.1-kb transposable insertion to photoperiods between low- and high-latitude regions. Flowering time is a key trait for cereal adaptation that is controlled by a complex genetic background in maize. The effect of multiple alleles from a quantitative trait locus (QTL) on flowering time remains largely unknown. Here, we fine-mapped a major QTL for flowering time on maize chromosome 10 corresponding to ZmCCT, where a new allele with a 4.2-kilobase (kb) transposable insertion was present in the intron. The known allele with a 5.1-kb transposon insertion in the promoter of ZmCCT enhances flowering in high-latitude regions, but has no effect on flowering time in low-latitude regions in comparison with the null allele lacking this insertion. However, our new allele with a 4.2-kb insertion reduced flowering in the low-latitude region, but produced unchanged flowering time in the high-latitude region relative to the 5.1-kb transposable insertion. Transcription analysis revealed that the new allele with 4.2-kb insertion versus the 5.1-kb insertion repressed and unchanged the transcription of ZmCCT in the low- and high-latitude regions, respectively. Thus, the allele with the 4.2-kb transposable insertion showed a completely opposite response to photoperiods between these two regions. Phylogenetic analysis revealed that the 4.2-kb transposable insertion in the two Northern flint corns originated from tropical maize. RNA-seq analysis and dual-luciferase transient expression assays further identified a conserved gene regulation network of ZmCCT between maize and rice, in which ZmCCT directly repressed the transcription of the florigen gene ZCN8 via ZmEhd1. Our results suggest that transposable elements play an important role in maize adaptation.
- MeSH
- chromozomy rostlin genetika MeSH
- fenotyp MeSH
- fotoperioda * MeSH
- fyziologická adaptace MeSH
- kukuřice setá genetika růst a vývoj účinky záření MeSH
- květy genetika růst a vývoj účinky záření MeSH
- lokus kvantitativního znaku MeSH
- mapování chromozomů metody MeSH
- promotorové oblasti (genetika) MeSH
- regulace genové exprese u rostlin * MeSH
- rostlinné proteiny genetika metabolismus MeSH
- transpozibilní elementy DNA * MeSH
- Publikační typ
- časopisecké články MeSH
Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.
- MeSH
- délka genomu MeSH
- duplikace genu MeSH
- genetické lokusy MeSH
- genom rostlinný * MeSH
- kontigové mapování metody MeSH
- kvantitativní znak dědičný * MeSH
- pšenice genetika MeSH
- regulace genové exprese u rostlin MeSH
- retroelementy MeSH
- rostlinné proteiny genetika metabolismus MeSH
- škrob biosyntéza MeSH
- šlechtění rostlin MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- zemědělské plodiny genetika MeSH
- žito genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.
- MeSH
- fyziologická adaptace genetika MeSH
- fyziologický stres MeSH
- genom rostlinný * MeSH
- genová introgrese MeSH
- imunita rostlin genetika MeSH
- karyotyp MeSH
- mapování chromozomů metody MeSH
- pšenice genetika MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné proteiny genetika metabolismus MeSH
- šlechtění rostlin metody MeSH
- zemědělské plodiny genetika imunologie MeSH
- žito genetika imunologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
