RESUMEN
Cytokinins (CKs) are a group of phytohormones that are involved in plant growth, development, and disease resistance. The isopentenyl transferase (IPT) and cytokinin oxidase/dehydrogenase (CKX) families comprise key enzymes controlling CK biosynthesis and degradation. However, an integrated analysis of these two gene families in radish has not yet been explored. In this study, 13 RsIPT and 12 RsCKX genes were identified and characterized, most of which had four copies in Brassica napus and two copies in radish and other diploid Brassica species. Promoter analysis indicated that the genes contained at least one phytohormone or defense and stress responsiveness cis-acting element. RsIPTs and RsCKXs were expanded through segmental duplication. Moreover, strong purifying selection drove the evolution of the two gene families. The expression of the RsIPT and RsCKX genes distinctly showed diversity in different tissues and developmental stages of the root. Expression profiling showed that RsCKX1-1/1-2/1-3 was significantly upregulated in club-resistant materials during primary infection, suggesting their vital function in clubroot resistance. The interaction network of CKX proteins with similar 3D structures also reflected the important role of RsCKX genes in disease resistance. This study provides a foundation for further functional study on the IPT and CKX genes for clubroot resistance improvement in Raphanus.
Asunto(s)
Resistencia a la Enfermedad , Regulación de la Expresión Génica de las Plantas , Familia de Multigenes , Oxidorreductasas , Enfermedades de las Plantas , Proteínas de Plantas , Raphanus , Raphanus/genética , Resistencia a la Enfermedad/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/parasitología , Transferasas Alquil y Aril/genética , Transferasas Alquil y Aril/metabolismo , Filogenia , Raíces de Plantas/genética , Raíces de Plantas/metabolismo , Regiones Promotoras Genéticas , Perfilación de la Expresión GénicaRESUMEN
Polyploids are essential in plant evolution and species formation, providing a rich genetic reservoir and increasing species diversity. Complex polyploids with higher ploidy levels often have a dosage effect on the phenotype, which can be highly detrimental to gametes, making them rare. In this study, offspring plants resulting from an autoallotetraploid (RRRC) derived from the interspecific hybridization between allotetraploid Raphanobrassica (RRCC, 2n = 36) and diploid radish (RR, 2n = 18) were obtained. Fluorescence in situ hybridization (FISH) using C-genome-specific repeats as probes revealed two main genome configurations in these offspring plants: RRRCC (2n = 43, 44, 45) and RRRRCC (2n = 54, 55), showing more complex genome configurations and higher ploidy levels compared to the parental plants. These offspring plants exhibited extensive variation in phenotypic characteristics, including leaf type and flower type and color, as well as seed and pollen fertility. Analysis of chromosome behavior showed that homoeologous chromosome pairing events are widely observed at the diakinesis stage in the pollen mother cells (PMCs) of these allopolyploids, with a range of 58.73% to 78.33%. Moreover, the unreduced C subgenome at meiosis anaphase II in PMCs was observed, which provides compelling evidence for the formation of complex allopolyploid offspring. These complex allopolyploids serve as valuable genetic resources for further analysis and contribute to our understanding of the mechanisms underlying the formation of complex allopolyploids.
Asunto(s)
Aneuploidia , Cromosomas de las Plantas , Poliploidía , Raphanus , Raphanus/genética , Cromosomas de las Plantas/genética , Hibridación Fluorescente in Situ , Brassica/genética , Hibridación Genética , Meiosis/genética , Genoma de Planta , Polen/genética , FenotipoRESUMEN
The green radish (Raphanus sativus L.) contains abundant chlorophyll (Chl). DOF-type transcription factor OBF BINDING PROTEIN (OBP) plays crucial functions in plant growth, development, maturation and responses to various abiotic stresses. However, the metabolism by which OBP transcription factors regulate light-induced Chl metabolism in green radish is not well understood. In this study, six OBP genes were identified from the radish genome, distributed unevenly across five chromosomes. Among these genes, RsOBP2a showed significantly higher expression in the green flesh compared to the white flesh of green radish. Analysis of promoter elements suggested that RsOBPs might be involved in stress responses, particularly in light-related processes. Overexpression of RsOBP2a led to increase Chl levels in cotyledons and adventitious roots of radish, while silencing RsOBP2a expression through TYMV-induced gene silencing accelerated leaf senescence. Further investigations revealed that RsOBP2a was localized in the nucleus and served as a transcriptional repressor. RsOBP2a was induced by light and directly suppressed the expression of STAYGREEN (SGR) and RED CHLOROPHYLL CATABOLITE REDUCTASE (RCCR), thereby delaying senescence in radish. Overall, a novel regulatory model involving RsOBP2a, RsSGR, and RsRCCR was proposed to govern Chl metabolism in response to light, offering insights for the enhancement of green radish germplasm.
Asunto(s)
Clorofila , Regulación de la Expresión Génica de las Plantas , Proteínas de Plantas , Raphanus , Factores de Transcripción , Raphanus/genética , Raphanus/metabolismo , Clorofila/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Regiones Promotoras Genéticas , Filogenia , LuzRESUMEN
Radish exhibits significant variation in color, particularly in sprouts, leaves, petals, fleshy roots, and other tissues, displaying a range of hues such as green, white, red, purple, and black. Although extensive research has been conducted on the color variation of radish, the underlying mechanism behind the variation in radish flower color remains unclear. To date, there is a lack of comprehensive research investigating the variation mechanism of radish sprouts, leaves, fleshy roots, and flower organs. This study aims to address this gap by utilizing transcriptome sequencing to acquire transcriptome data for white and purple radish flowers. Additionally, the published transcriptome data of sprouts, leaves, and fleshy roots were incorporated to conduct a systematic analysis of the regulatory mechanisms underlying anthocyanin biosynthesis in these four radish tissues. The comparative transcriptome analysis revealed differential expression of the anthocyanin biosynthetic pathway genes DFR, UGT78D2, TT12 and CPC in the four radish tissues. Additionally, the WGCNA results identified RsDFR.9c and RsUGT78D2.2c as hub genes responsible for regulating anthocyanin biosynthesis. By integrating the findings from the comparative transcriptome analysis, WGCNA, and anthocyanin biosynthetic pathway-related gene expression patterns, it is hypothesized that genes RsDFR.9c and RsUGT78D2.2c may serve as pivotal regulators of anthocyanins in the four radish tissues. Furthermore, the tissue-specific expression of the four copies of RsPAP1 is deemed crucial in governing anthocyanin synthesis and accumulation. Our results provide new insights into the molecular mechanism of anthocyanin biosynthesis and accumulation in different tissues of radish.
Asunto(s)
Antocianinas , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Raphanus , Raphanus/genética , Raphanus/metabolismo , Antocianinas/biosíntesis , Antocianinas/genética , Transcriptoma , Vías Biosintéticas/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Flores/genética , Flores/metabolismoRESUMEN
Spontaneous tumour formation in higher plants can occur in the absence of pathogen invasion, depending on the plant genotype. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this paper, using Oxford Nanopore and Illumina technologies, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We identified a large number of single nucleotide variants (amino acid substitutions, insertions or deletions, SNVs) that are likely to be associated with the spontaneous tumour formation. Among the genes involved in the trait, we have identified those that regulate the cell cycle, meristem activity, gene expression, and metabolism and signalling of phytohormones. After identifying the SNVs, we performed Sanger sequencing of amplicons corresponding to SNV-containing regions to validate our results. We then checked for the presence of SNVs in other tumour lines of the radish genetic collection and found the ERF118 gene, which had the SNVs in the majority of tumour lines. Furthermore, we performed the identification of the CLAVATA3/ESR (CLE) and WUSCHEL (WOX) genes and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.
Asunto(s)
Genoma de Planta , Raphanus , Secuenciación Completa del Genoma , Raphanus/genética , Secuenciación Completa del Genoma/métodos , Tumores de Planta/genética , Polimorfismo de Nucleótido Simple , Proteínas de Plantas/genéticaRESUMEN
Melanins are dark-brown to black-colored biomacromolecules which have been thoroughly studied in animals and microorganisms. However, the biochemical and molecular basis of plant melanins are poorly understood. We first characterized melanin from the black radish (Raphanus sativus var. niger) 'HLB' through spectroscopic techniques. p-Coumaric acid was identified as the main precursor of radish melanin. Moreover, a joint analysis of transcriptome and coexpression network was performed for the two radish accessions with black and white cortexes, 'HLB' and '55'. A set of R2R3-type RsMYBs and enzyme-coding genes exhibited a coexpression pattern, and were strongly correlated with melanin formation in radish. Transient overexpression of two phenol oxidases RsLAC7 (laccase 7) or RsPOD22-1 (peroxidase 22-1) resulted in a deeper brown color around the infiltration sites and a significant increase in the total phenol content. Furthermore, co-injection of the transcriptional activator RsMYB48/RsMYB97 with RsLAC7 and/or RsPOD22-1, markedly increased the yield of black extracts. Spectroscopic analyses revealed that these extracts are similar to the melanin found in 'HLB'. Our findings advance the understanding of structural information and the transcriptional regulatory mechanism underlying melanin formation in radish.
Asunto(s)
Regulación de la Expresión Génica de las Plantas , Melaninas , Monofenol Monooxigenasa , Raphanus , Raphanus/genética , Raphanus/metabolismo , Melaninas/metabolismo , Monofenol Monooxigenasa/genética , Monofenol Monooxigenasa/metabolismo , Transcriptoma , Perfilación de la Expresión Génica , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteínas de Plantas/química , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/química , Ácidos Cumáricos/metabolismoRESUMEN
KEY MESSAGE: This study found that three paralogous R2R3-MYB transcription factors exhibit functional divergence among different subspecies and cultivated types in radish. Cultivated radish taproots exhibit a wide range of color variations due to unique anthocyanin accumulation patterns in various tissues. This study investigated the universal principles of taproot color regulation that developed during domestication of different subspecies and cultivated types. The key candidate genes RsMYB1 and RsMYB2, which control anthocyanin accumulation in radish taproots, were identified using bulked segregant analysis in two genetic populations. We introduced the RsMYB1-RsF3'H-RsMYB1Met genetic model to elucidate the complex and unstable genetic regulation of taproot flesh color in Xinlimei radish. Furthermore, we analyzed the expression patterns of three R2R3-MYB transcription factors in lines with different taproot colors and investigated the relationship between RsMYB haplotypes and anthocyanin accumulation in a natural population of 56 germplasms. The results revealed that three paralogous RsMYBs underwent functional divergence during radish domestication, with RsMYB1 regulating the red flesh of Xinlimei radish, and RsMYB2 and RsMYB3 regulating the red skin of East Asian big long radish (R. sativus var. hortensis) and European small radish (R. sativus var. sativus), respectively. Moreover, RsMYB1-H1, RsMYB2-H10, and RsMYB3-H6 were identified as the primary haplotypes exerting regulatory functions on anthocyanin synthesis. These findings provide an understanding of the genetic mechanisms regulating anthocyanin synthesis in radish and offer a potential strategy for early prediction of color variations in breeding programs.
Asunto(s)
Pigmentación , Proteínas de Plantas , Raphanus , Factores de Transcripción , Antocianinas/metabolismo , Antocianinas/biosíntesis , Epigénesis Genética , Regulación de la Expresión Génica de las Plantas , Haplotipos , Fenotipo , Pigmentación/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raíces de Plantas/genética , Raíces de Plantas/metabolismo , Raphanus/genética , Raphanus/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismoRESUMEN
Cauliflower mosaic virus (CaMV) has a double-stranded DNA genome and is globally distributed. The phylogeny tree of 121 CaMV isolates was categorized into two primary groups, with Iranian isolates showing the greatest genetic variations. Nucleotide A demonstrated the highest percentage (36.95%) in the CaMV genome and the dinucleotide odds ratio analysis revealed that TC dinucleotide (1.34 ≥ 1.23) and CG dinucleotide (0.63 ≤ 0.78) are overrepresented and underrepresented, respectively. Relative synonymous codon usage (RSCU) analysis confirmed codon usage bias in CaMV and its hosts. Brassica oleracea and Brassica rapa, among the susceptible hosts of CaMV, showed a codon adaptation index (CAI) value above 0.8. Additionally, relative codon deoptimization index (RCDI) results exhibited the highest degree of deoptimization in Raphanus sativus. These findings suggest that the genes of CaMV underwent codon adaptation with its hosts. Among the CaMV open reading frames (ORFs), genes that produce reverse transcriptase and virus coat proteins showed the highest CAI value of 0.83. These genes are crucial for the creation of new virion particles. The results confirm that CaMV co-evolved with its host to ensure the optimal expression of its genes in the hosts, allowing for easy infection and effective spread. To detect the force behind codon usage bias, an effective number of codons (ENC)-plot and neutrality plot were conducted. The results indicated that natural selection is the primary factor influencing CaMV codon usage bias.
Asunto(s)
Caulimovirus , Uso de Codones , Evolución Molecular , Genoma Viral , Filogenia , Enfermedades de las Plantas , Genoma Viral/genética , Caulimovirus/genética , Enfermedades de las Plantas/virología , Sistemas de Lectura Abierta/genética , Codón/genética , Variación Genética , Brassica rapa/genética , Brassica rapa/virología , Interacciones Huésped-Patógeno/genética , Brassica/genética , Brassica/virología , Raphanus/genética , Raphanus/virología , IránRESUMEN
BACKGROUND: This study introduces a wild radish population collected from Yelbeni in the Western Australian grainbelt that evolved an early silique abscission (shedding) trait to persist despite long-term harvest weed seed control (HWSC) use. In 2017, field-collected seed (known herein as Yelbeni) was compared to surrounding ruderal and field-collected populations in a fully randomized common garden study. RESULTS: The Yelbeni population exhibited a higher rate of silique abscission when compared to the ruderal populations collected from the site before wheat (Triticum aestivum L.) harvest (assessed at soft dough stage, Zadoks 83). A similar common garden study was conducted in the subsequent season (2018) using progeny reproduced on a single site without stress. The HWSC-selected progeny (Yelbeni P) shed 1048 (±288) siliques before wheat maturity at the soft dough stage (Zadoks 83) compared to 25 (±7) siliques from the pooled control populations. The Yelbeni P population only flowered 6 days earlier (FT50 as determined by log-logistic analysis) than pooled control populations, which is unlikely to fully account for the increased rate of silique abscission. The Yelbeni P population also located its lowest siliques below the lowest height for harvest interception (10 cm), which is likely to increase HWSC evasion. The mechanism inducing early silique-shedding is yet to be determined; however, wild radish is known for its significant genetic variability and has demonstrated its capacity to adapt to environmental and management stresses. CONCLUSION: This study demonstrates that the repeated use of HWSC can lead to the selection of HWSC-avoidance traits including early silique-shedding before harvest and/or locating siliques below the harvest cutting height for interception. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Asunto(s)
Fenotipo , Raphanus , Semillas , Control de Malezas , Raphanus/crecimiento & desarrollo , Raphanus/genética , Raphanus/fisiología , Australia Occidental , Semillas/crecimiento & desarrollo , Control de Malezas/métodos , Flores/crecimiento & desarrolloRESUMEN
Glycosyltransferases (GTs), crucial enzymes in plants, alter natural substances through glycosylation, a process with extensive applications in pharmaceuticals, food, and cosmetics. This study narrows its focus to GT family 1, specifically UDP-glycosyltransferases (UGTs), which are known for glycosylating small phenolic compounds, especially hydroxybenzoates. We delve into the workings of Raphanus sativus glucosyltransferase (Rs89B1), a homolog of Arabidopsis thaliana UGT89B1, and its mutant to explore their glycosyltransferase activities toward hydroxybenzoates. Our findings reveal that Rs89B1 glycosylates primarily the para-position of mono-, di-, trihydroxy benzoic acids, and its substrate affinity is swayed by the presence and position of the hydroxyl group on the benzene ring of hydroxybenzoate. Moreover, mutations in the loop region of Rs89B1 impact both substrate affinity and catalytic activity. The study demonstrates that insertional/deletional mutations in non-conserved regions, which are distant from the UGT's recognition site, can have an effect on the UGT's substrate recognition site, which in turn affects acceptor substrate selectivity and glycosyltransferase activity. This research uncovers new insights suggesting that mutations in the loop region could potentially fine-tune enzyme properties and enhance its catalytic activity. These findings not only have significant implications for enzyme engineering in biotechnological applications but also contribute to a more profound understanding of this field.
Asunto(s)
Arabidopsis , Raphanus , Glicosiltransferasas/genética , Raphanus/genética , Arabidopsis/genética , Uridina Difosfato , Hidroxibenzoatos , MutaciónRESUMEN
The 70 kD heat shock proteins (HSP70s) represent a class of molecular chaperones that are widely distributed in all kingdoms of life, which play important biological roles in plant growth, development, and stress resistance. However, this family has not been systematically characterized in radish (Raphanus sativus L.). In this study, we identified 34 RsHSP70 genes unevenly distributed within nine chromosomes of R. sativus. Phylogenetic and multiple sequence alignment analyses classified the RsHSP70 proteins into six distinct groups (Group A-F). The characteristics of gene structures, motif distributions, and corresponding cellular compartments were more similar in closely linked groups. Duplication analysis revealed that segmental duplication was the major driving force for the expansion of RsHSP70s in radish, particularly in Group C. Synteny analysis identified eight paralogs (Rs-Rs) in the radish genome and 19 orthologs (Rs-At) between radish and Arabidopsis, and 23 orthologs (Rs-Br) between radish and Chinese cabbage. RNA-seq analysis showed that the expression change of some RsHSP70s were related to responses to heat, drought, cadmium, chilling, and salt stresses and Plasmodiophora brassicae infection, and the expression patterns of these RsHSP70s were significantly different among 14 tissues. Furthermore, we targeted a candidate gene, RsHSP70-23, the product of which is localized in the cytoplasm and involved in the responses to certain abiotic stresses and P. brassicae infection. These findings provide a reference for further molecular studies to improve yield and stress tolerance of radish.
Asunto(s)
Arabidopsis , Raphanus , Raphanus/genética , Raphanus/metabolismo , Filogenia , Proteínas HSP70 de Choque Térmico/genética , Proteínas HSP70 de Choque Térmico/metabolismo , Sintenía , Estrés Fisiológico/genética , Arabidopsis/genética , Arabidopsis/metabolismo , Regulación de la Expresión Génica de las Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Genoma de PlantaRESUMEN
Floral transition is accelerated by exposure to long-term cold like winter in plants, which is called as vernalization. Acceleration of floral transition by vernalization is observed in a diversity of biennial and perennial plants including Brassicaceae family plants. Scientific efforts to understand molecular mechanism underlying vernalization-mediated floral transition have been intensively focused in model plant Arabidopsis thaliana. To get a better understanding on floral transition by vernalization in radish (Raphanus sativus L.), we investigated transcriptomic changes taking place during vernalization in radish. Thousands of genes were differentially regulated along time course of vernalization compared to non-vernalization (NV) sample. Twelve major clusters of DEGs were identified based on distinctive expression profiles during vernalization. Radish FLC homologs were shown to exert an inhibition of floral transition when transformed into Arabidopsis plants. In addition, DNA region containing RY motifs located within a Raphanus sativus FLC homolog, RsFLC1 was found to be required for repression of RsFLC1 by vernalization. Transgenic plants harboring disrupted RY motifs were impaired in the enrichment of H3K27me3 on RsFLC1 chromatin, thus resulting in the delayed flowering in Arabidopsis. Taken together, we report transcriptomic profiles of radish during vernalization and demonstrate the requirement of RY motif for vernalization-mediated repression of RsFLC homologs in radish (Raphanus sativus L.).
Asunto(s)
Arabidopsis , Brassicaceae , Raphanus , Raphanus/genética , Arabidopsis/genética , Vernalización , CromatinaRESUMEN
KEY MESSAGE: Two major QTLs for bolting time in radish were mapped to chromosome 02 and 07 in a 0.37 Mb and 0. 52 Mb interval, RsFLC1 and RsFLC2 is the critical genes. Radish (Raphanus sativus L.) is an important vegetable crop of Cruciferae. The premature bolting and flowering reduces the yield and quality of the fleshy root of radish. However, the molecular mechanism underlying bolting and flowering in radish remains unknown. In YZH (early bolting) × XHT (late bolting) F2 population, a high-density genetic linkage map was constructed with genetic distance of 2497.74 cM and an average interval of 2.31 cM. A total of nine QTLs for bolting time and two QTLs for flowering time were detected. Three QTLs associated with bolting time in radish were identified by QTL-seq using radish GDE (early bolting) × GDL (late bolting) F2 population. Fine mapping narrowed down qBT2 and qBT7.2 to an 0.37 Mb and 0.52 Mb region on chromosome 02 and 07, respectively. RNA-seq and qRT-PCR analysis showed that RsFLC1 and RsFLC2 were the candidate gene for qBT7.2 and qBT2 locus, respectively. Subcellular localization exhibited that RsFLC1 and RsFLC2 were mainly expressed in the nucleus. A 1856-bp insertion in the first intron of RsFLC1 was responsible for bolting time. Overexpression of RsFLC2 in Arabidopsis was significantly delayed flowering. These findings will provide new insights into the exploring the molecular mechanism of late bolting and promote the marker-assisted selection for breeding late-bolting varieties in radish.
Asunto(s)
Arabidopsis , Raphanus , Raphanus/genética , Mapeo Cromosómico , Fitomejoramiento , Sitios de Carácter Cuantitativo , Arabidopsis/genéticaRESUMEN
Radish (Raphanus sativus L.) is one of the most vital root vegetable crops worldwide. Cadmium (Cd), a non-essential and toxic heavy metal, can dramatically restrict radish taproot quality and safety. Although the Peiotrpic Drug Resistance (PDR) genes play crucial roles in heavy metal accumulation and transport in plants, the systematic identification and functional characterization of RsPDRs remain largely unexplored in radish. Herein, a total of 19 RsPDR genes were identified from the radish genome. A few RsPDRs, including RsPDR1, RsPDR8 and RsPDR12, showed significant differential expression under Cd and lead (Pb) stress in the 'NAU-YH' genotype. Interestingly, the plasma membrane-localized RsPDR8 exhibited significantly up-regulated expression and enhanced promoter activity under Cd exposure. Ectopic expression of RsPDR8 conferred Cd tolerance via reducing Cd accumulation in yeast cells. Moreover, the transient transformation of RsPDR8 revealed that it positively regulated Cd tolerance by promoting ROS scavenging and enhancing membrane permeability in radish. In addition, overexpression of RsPDR8 increased root elongation but deceased Cd accumulation compared with the WT plants in Arabidopsis, demonstrating that it could play a positive role in mediating Cd efflux and tolerance in plants. Together, these results would facilitate deciphering the molecular mechanism underlying RsPDR8-mediated Cd tolerance and detoxification in radish.
Asunto(s)
Arabidopsis , Raphanus , Raphanus/genética , Raphanus/metabolismo , Cadmio/toxicidad , Cadmio/metabolismo , Arabidopsis/genética , Arabidopsis/metabolismoRESUMEN
Anthocyanin biosynthesis in plants is influenced by a wide range of environmental factors, such as light, temperature and nutrient availability. In this study, we revealed that the potassium-repressed anthocyanin accumulation in radish hypocotyls was associated with altered sugar distribution and sugar signaling pathways rather than changes in oxidative stress status. Sugar-feeding experiments suggested a hexokinase-independent glucose signal acted as a major contributor in regulating anthocyanin biosynthesis, transport and regulatory genes at the transcriptional level. Several R2R3-MYBs were identified as anthocyanin-related MYBs. Phylogenetic and protein sequence analyses suggested that RsMYB75 met the criteria of subgroup 6 MYB activator, while RsMYB39 and RsMYB82 seemed to be a non-canonical MYB anthocyanin activator and repressor, respectively. Through yeast-one-hybrid, dual-luciferase and transient expression assays, we confirmed that RsMYB39 strongly induced the promoter activity of anthocyanin transport-related gene RsGSTF12, while RsMYB82 significantly reduced anthocyanin biosynthesis gene RsANS1 expression. Molecular models are proposed in the discussion, allowing speculation on how these novel RsMYBs may regulate the expression levels of anthocyanin-related structural genes. Together, our data evidenced the strong impacts of potassium on sugar metabolism and signaling and its regulation of anthocyanin accumulation through different sugar signals and R2R3-MYBs in a hierarchical regulatory system.
Asunto(s)
Antocianinas , Raphanus , Factores de Transcripción/metabolismo , Raphanus/genética , Raphanus/metabolismo , Azúcares , Filogenia , Proteínas de Plantas/metabolismo , Regulación de la Expresión Génica de las PlantasRESUMEN
Radish (Raphanus sativus) roots exhibit various colors that reflect their anthocyanin compositions and contents. However, the details of the mechanism linking the expression of anthocyanin biosynthesis and their transcriptional regulators to anthocyanin composition in radish roots remained unknown. Here, we characterized the role of the anthocyanin biosynthetic enzyme flavonoid 3'-hydroxylase (RsF3'H), together with the R2R3 MYB transcription factor (TF) RsMYB1 and the basic helix-loop-helix (bHLH) TF TRANSPARENT TESTA 8 (RsTT8), in four radish plants with different root colors: white (W), deep red (DR), dark purple (DP), and dark greyish purple (DGP). The DR plant contained heterozygous for RsF3'H with low expression level and accumulated a large amount of pelargonidin, resulting in deep red color. While, the DP and DGP plants accumulated the cyanidin due to the higher expression level of functional RsF3'H. Notably, RsMYB1 and RsTT8 transcripts were abundant in all pigmented roots, but not in white roots. To investigate the differential expression of RsMYB1 and RsTT8, we compared the sequences of their promoter regions among the four radish plants, revealing variations in the numbers of cis-elements and in promoter architecture. Promoter activation assays demonstrated that variation in the RsMYB1 and RsTT8 promoters may contribute to the expression level of these genes, and RsMYB1 can activate its own expression as well as promote the RsTT8 expression. These results suggested that RsF3'H plays a vital role in anthocyanin composition and the expression level of both RsMYB1 and RsTT8 are crucial determinants for anthocyanin content in radish roots. Overall, these findings provide insight into the molecular basis of anthocyanin composition and level in radish roots.
Asunto(s)
Raphanus , Raphanus/genética , Raphanus/metabolismo , Antocianinas/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Regulación de la Expresión Génica de las PlantasRESUMEN
To understand the coloring mechanism in black radish, the integrated metabolome and transcriptome analyses of root skin from a black recombinant inbred line (RIL 1901) and a white RIL (RIL 1911) were carried out. A total of 172 flavonoids were detected, and the analysis results revealed that there were 12 flavonoid metabolites in radish root skin, including flavonols, flavones, and anthocyanins. The relative concentrations of most flavonoids in RIL 1901 were higher than those in RIL 1911. Meanwhile, the radish root skin also contained 16 types of anthocyanins, 12 of which were cyanidin and its derivatives, and the concentration of cyanidin 3-o-glucoside was very high at different development stages of black radish. Therefore, the accumulation of cyanidin and its derivatives resulted in the black root skin of radish. In addition, a module positively related to anthocyanin accumulation and candidate genes that regulate anthocyanin synthesis was identified by the weighted gene co-expression network analysis (WGCNA). Among them, structural genes (RsCHS, RsCHI, RsDFR, and RsUGT75C1) and transcription factors (TFs) (RsTT8, RsWRKY44L, RsMYB114, and RsMYB308L) may be crucial for the anthocyanin synthesis in the root skin of black radish. The anthocyanin biosynthesis pathway in the root skin of black radish was constructed based on the expression of genes related to flavonoid and anthocyanin biosynthesis pathways (Ko00941 and Ko00942) and the relative expressions of metabolites. In conclusion, this study not only casts new light on the synthesis and accumulation of anthocyanins in the root skin of black radish but also provides a molecular basis for accelerating the cultivation of new black radish varieties.
Asunto(s)
Antocianinas , Raphanus , Antocianinas/genética , Transcriptoma , Raphanus/genética , Flavonoides , Perfilación de la Expresión GénicaRESUMEN
BACKGROUND: Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativus L.). RESULTS: In this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome resequencing between 'YZH' and 'XHT'. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome sequencing. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. The 100 polymorphic InDels markers generated 207 alleles among 200 Chinese radish germplasm, with an average 2.07 of the number of alleles (Na) and with an average 0.33 of the polymorphism information content (PIC). Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 11,003 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained. CONCLUSIONS: The large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The SNPs and InDels within flowering time-related DGEs provide fundamental insight into for dissecting molecular mechanism of bolting and flowering in radish.
Asunto(s)
Raphanus , Raphanus/genética , Transcriptoma , Polimorfismo de Nucleótido Simple , Filogenia , Análisis de Secuencia de ADN , Genoma de Planta , Mutación INDELRESUMEN
BACKGROUND: Sugars produced by photosynthesis provide energy for biological activities and the skeletons for macromolecules; they also perform multiple physiological functions in plants. Sugar transport across plasma membranes mediated by the Sugar Will Eventually be Exported Transporter (SWEET) genes substantially affects these processes. However, the evolutionary dynamics and function of the SWEET genes are largely unknown in radish, an important Brassicaceae species. METHODS AND RESULTS: Genome-wide identification and analysis of the RsSWEET genes from the recently updated radish reference genome was conducted using bioinformatics methods. The tissue-specific expression was analyzed using public RNA-seq data, and the expression levels in the bud, stamens, pistils, pericarps and seeds at 15 and 30 days after flowering (DAF) were determined by RTâqPCR. Thirty-seven RsSWEET genes were identified and named according to their Arabidopsis homologous. They are unevenly distributed across the nine radish chromosomes and were further divided into four clades by phylogenetic analysis. There are 5-7 transmembrane domains and at least one MtN3_slv domain in the RsSWEETs. RNA-seq and RTâqPCR revealed that the RsSWEETs exhibit higher expression levels in the reproductive organs, indicating that these genes might play vital roles in reproductive organ development. RsSWEET15.1 was found to be especially expressed in siliques according to the RNA-seq data, and the RTâqPCR results further confirmed that it was most highly expressed levels in the seeds at 30 DAF, followed by the pericarp at 15 DAF, indicating that it is involved in seed growth and development. CONCLUSIONS: This study suggests that the RsSWEET genes play vital roles in reproductive organ development and provides a theoretical basis for the future functional analysis of RsSWEETs in radish.
Asunto(s)
Arabidopsis , Raphanus , Filogenia , Raphanus/genética , Genes de Plantas , Evolución Biológica , Arabidopsis/genética , Azúcares , Proteínas de Plantas/metabolismo , Regulación de la Expresión Génica de las Plantas/genéticaRESUMEN
The mechanisms underlying trait conservation over long evolutionary time scales are poorly known. These mechanisms fall into the two broad and nonmutually exclusive categories of constraint and selection. A variety of factors have been hypothesized to constrain trait evolution. Alternatively, selection can maintain similar trait values across many species if the causes of selection are also relatively conserved, while many sources of constraint may be overcome over longer periods of evolutionary divergence. An example of deep trait conservation is tetradynamy in the large family Brassicaceae, where the four medial stamens are longer than the two lateral stamens. Previous work has found selection to maintain this difference in lengths, which we call anther separation, in wild radish, Raphanus raphanistrum. Here, we test the constraint hypothesis using five generations of artificial selection to reduce anther separation in wild radish. We found a rapid linear response to this selection, with no evidence for depletion of genetic variation and correlated responses to this selection in only four of 15 other traits, suggesting a lack of strong constraint. Taken together, available evidence suggests that tetradynamy is likely to be conserved due to selection, but the function of this trait remains unclear.