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1.
J Agric Food Chem ; 68(49): 14463-14470, 2020 Dec 09.
Article in English | MEDLINE | ID: mdl-33216541

ABSTRACT

Radish (Raphanus sativus) is an important worldwide vegetable with a wide variety of colors that affect its appearance and nutritional quality. However, the large-scale detection, identification, and quantification of flavonoids in multicolor radish have rarely been studied. To uncover the diversity and accession-specific flavonoids in radish, liquid chromatography electrospray ionization-tandem mass spectrometry was used to analyze the metabolic profiles in the skin and flesh of six colored radish accessions: light-red Manshenhong, dark-red Touxinhong (TXH), purple Zijinling (ZJL), Xinlimei with red flesh (XLMF) and green skin, white Shizhuangbai (SZB), and black radish. In total, 133 flavonoids, including 16 dihydroflavones, 44 flavones, 14 flavonoids, 9 anthocyanins, and 28 flavonols, were characterized. The flavonoid metabolic profiles differed among the different colored radishes. Red and purple radishes contained similar anthocyanin compounds responsible for color pigmentation, including red cyanidin, callistephin, and pelargonin. Purple ZJL was most enriched with cyanidin o-syringic acid and cyanin, whereas callistephin and pelargonin were more abundant in dark-red TXH. Additionally, the black and white radishes shared similar anthocyanin and flavonoid profiles, suggesting that the color of black radishes was not caused by anthocyanin but by other metabolites. The metabolites in colored radishes that differed from SZB were mainly involved in the biosynthesis of plant secondary metabolites, such as flavonoid, flavone, flavonol, isoflavonoid, and phenylpropanoid biosynthesis. This study provides new insights into the differences in metabolite profiles among radishes with different skin and flesh colors. The results will be useful for aiding the cultivation of valuable new radish varieties.


Subject(s)
Flavonoids/metabolism , Pigments, Biological/metabolism , Raphanus/chemistry , Color , Flavonoids/chemistry , Metabolomics , Pigments, Biological/chemistry , Plant Roots/chemistry , Plant Roots/classification , Plant Roots/metabolism , Raphanus/classification , Raphanus/metabolism
2.
Int J Mol Sci ; 21(21)2020 Nov 04.
Article in English | MEDLINE | ID: mdl-33158201

ABSTRACT

The CPA (cation proton antiporter) family plays an essential role during plant stress tolerance by regulating ionic and pH homeostasis of the cell. Radish fleshy roots are susceptible to abiotic stress during growth and development, especially salt stress. To date, CPA family genes have not yet been identified in radish and the biological functions remain unclear. In this study, 60 CPA candidate genes in radish were identified on the whole genome level, which were divided into three subfamilies including the Na+/H+ exchanger (NHX), K+ efflux antiporter (KEA), and cation/H+ exchanger (CHX) families. In total, 58 of the 60 RsCPA genes were localized to the nine chromosomes. RNA-seq. data showed that 60 RsCPA genes had various expression levels in the leaves, roots, cortex, cambium, and xylem at different development stages, as well as under different abiotic stresses. RT-qPCR analysis indicated that all nine RsNHXs genes showed up regulated trends after 250 mM NaCl exposure at 3, 6, 12, and 24h. The RsCPA31 (RsNHX1) gene, which might be the most important members of the RsNHX subfamily, exhibited obvious increased expression levels during 24h salt stress treatment. Heterologous over-and inhibited-expression of RsNHX1 in Arabidopsis showed that RsNHX1 had a positive function in salt tolerance. Furthermore, a turnip yellow mosaic virus (TYMV)-induced gene silence (VIGS) system was firstly used to functionally characterize the candidate gene in radish, which showed that plant with the silence of endogenous RsNHX1 was more susceptible to the salt stress. According to our results we provide insights into the complexity of the RsCPA gene family and a valuable resource to explore the potential functions of RsCPA genes in radish.


Subject(s)
Antiporters/genetics , Plant Proteins/genetics , Proton Pumps/genetics , Raphanus/genetics , Salt Stress/genetics , Antiporters/metabolism , Arabidopsis/genetics , Cations/metabolism , Chromosomes, Plant , Evolution, Molecular , Gene Expression Regulation, Plant , Genome-Wide Association Study , Multigene Family , Phylogeny , Plant Proteins/metabolism , Plants, Genetically Modified , Proton Pumps/metabolism , Protons , Raphanus/classification , Raphanus/metabolism , Salt Tolerance/genetics , Stress, Physiological/genetics , Transcriptome/physiology
3.
DNA Res ; 27(1)2020 Feb 01.
Article in English | MEDLINE | ID: mdl-32065621

ABSTRACT

Radish (Raphanus sativus L.) is cultivated around the world as a vegetable crop and exhibits diverse morphological and physiological features. DNA polymorphisms are responsible for differences in traits among cultivars. In this study, we determined genome-wide single-nucleotide polymorphisms (SNPs) among geographically diverse radish accessions using the double-digest restriction site-associated DNA sequencing (ddRAD-Seq) method. A total of 52,559 SNPs was identified in a collection of over 500 radish accessions (cultivated and wild) from East Asia, South and Southeast Asia, and the Occident and Near East. In addition, 2,624 SNP sites without missing data (referred to as common SNP sites) were identified among 510 accessions. Genetic diversity analyses, based on the common SNP sites, divided the cultivated radish accessions into four main groups, each derived from four geographical areas (Japan, East Asia, South and Southeast Asia, and the Occident and Near East). Furthermore, we discuss the origin of cultivated radish and its migration from the West to East Asia. SNP data generated in this work will facilitate further genetic studies on the radish breeding and production of DNA markers.


Subject(s)
Polymorphism, Restriction Fragment Length , Polymorphism, Single Nucleotide , Raphanus/genetics , Asia , Asia, Southeastern , Asia, Eastern , Genetic Markers , Genome, Plant , Japan , Phylogeny , Raphanus/classification , Sequence Analysis, DNA
4.
Gene ; 731: 144340, 2020 Mar 20.
Article in English | MEDLINE | ID: mdl-31923575

ABSTRACT

As a member of the large Brassicaceae family, yellow mustard (Sinapis alba L.) has been used as an important gene pool for the genetic improvement of cash crops in Brassicaceae. Understanding the phylogenetic relationship between Sinapis alba (S. alba) and other Brassicaceae crops can provide guidance on the introgression of its favorable alleles into related species. The chloroplast (cp) genome is an ideal model for assessing genome evolution and the phylogenetic relationships of complex angiosperm families. Herein, we de novo assembled the complete cp genome of S. alba by integrating the PacBio and Illumina sequencing platforms. A 153,760 bp quadripartite cycle without any gap was obtained, including a pair of inverted repeats (IRa and IRb) of 26,221 bp, separated by a large single copy (LSC) region of 83,506 bp and a small single copy (SSC) region of 17,821 bp. A total of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes were identified in this cp genome, as were 89 simple sequence repeat (SSR) loci of 18 types. The codon usage analysis revealed a preferential use of the Leu codon with the A/U ending. The phylogenetic analysis using 82 Brassicaceae species demonstrated that S. alba had a close relationship with important Brassica and Raphanus species; moreover, it likely originated from a separate evolutionary pathway compared with the congeneric Sinapis arvensis. The synonymous (Ks) and non-synonymous (Ks) substitution rate analysis showed that genes encoding "Subunits of cytochrome b/f complex" were under the lowest purifying selection pressure, whereas those associated with "Maturase", "Subunit of acetyl-CoA", and "Subunits of NADH-dehydrogenase" underwent relatively higher purifying selection pressures. Our results provide valuable information for fully utilizing the S. alba cp genome as a potential genetic resource for the genetic improvement of Brassica and Raphanus species.


Subject(s)
Brassicaceae/classification , Brassicaceae/genetics , Genome, Chloroplast/genetics , Mustard Plant/genetics , Sinapis/genetics , Chloroplasts/genetics , Evolution, Molecular , High-Throughput Nucleotide Sequencing , Mustard Plant/classification , Mustard Plant/cytology , Phylogeny , Raphanus/classification , Raphanus/cytology , Raphanus/genetics , Sequence Analysis, DNA/methods , Sinapis/classification , Sinapis/cytology , Whole Genome Sequencing
5.
J Agric Food Chem ; 66(33): 8714-8721, 2018 Aug 22.
Article in English | MEDLINE | ID: mdl-30037222

ABSTRACT

Vascular diseases, such as myocardial and cerebral infarctions, are the leading causes of death. Some vascular diseases occur as the result of decreases in vascular endothelial function. The innermost layer of the vasculature is formed by vascular endothelial cells (VECs), which are critical for nitric oxide (NO) synthesis. In our search for active constituents in farm products with the potential for improving the vascular system, we examined the effect of Raphanus sativus cv. Sakurajima Daikon on NO production in VECs. In this study, we found that the underlying mechanism for stimulating NO production by Sakurajima Daikon extract involves endothelial-NO-synthase (eNOS) activation by the phosphorylation of Ser1177 and the dephosphorylation of Thr495, which are triggered by elevated concentrations of cytoplasmic Ca2+ resulting from the activation of Ca2+ channels in VECs. We observed that trigonelline, an active constituent of Sakurajima Daikon, improves NO production in VEC cultures.


Subject(s)
Endothelial Cells/drug effects , Endothelium, Vascular/drug effects , Plant Extracts/pharmacology , Raphanus/chemistry , Animals , Calcium/metabolism , Endothelial Cells/metabolism , Endothelium, Vascular/metabolism , Humans , Nitric Oxide/metabolism , Nitric Oxide Synthase Type III/metabolism , Plant Extracts/chemistry , Raphanus/classification , Swine
6.
Bull Environ Contam Toxicol ; 98(2): 290-295, 2017 Feb.
Article in English | MEDLINE | ID: mdl-27933329

ABSTRACT

The effects of increasing Cd additions on plant growth and Cd fractionation and enzyme activities in rhizosphere soil of two radish cultivars were investigated. The results showed that Cd concentrations in shoot and root of cultivar 4 were both higher than for cultivar 19 under different Cd levels. Compared with cultivar 19, the total, shoot and root biomasses of cultivar 4 were significantly reduced with increasing Cd levels. A decrease in soil pH was observed for cultivar 4. The exchangeable Cd concentration of soil from cultivar 4 was significantly higher than for soil from cultivar 19, while the carbonate-bound Cd concentration of soil from cultivar 4 was significantly lower than for cultivar 19. Enzyme activities, especially acid phosphatase activity, were more susceptible to Cd in soil from cultivar 4. These results indicated that cultivar 19 exhibits a stronger ability to adapt to Cd stress than cultivar 4.


Subject(s)
Acid Phosphatase/metabolism , Cadmium/isolation & purification , Cadmium/toxicity , Raphanus/drug effects , Raphanus/enzymology , Rhizosphere , Soil Pollutants/toxicity , Biomass , Hydrogen-Ion Concentration , Plant Roots/drug effects , Raphanus/chemistry , Raphanus/classification , Soil/chemistry , Soil Pollutants/isolation & purification
7.
PLoS One ; 11(12): e0166802, 2016.
Article in English | MEDLINE | ID: mdl-27936159

ABSTRACT

Since plant mating choices are flexible and responsive to the environment, rates of spontaneous hybridization may vary across ecological clines. Developing a robust and predictive framework for rates of plant gene flow requires assessing the role of environmental sensitivity on plant reproductive traits, relative abundance, and pollen vectors. Therefore, across a soil moisture gradient, we quantified pollinator movement, life-history trait variation, and unidirectional hybridization rates from crop (Raphanus sativus) to wild (Raphanus raphanistrum) radish populations. Both radish species were grown together in relatively dry (no rain), relatively wet (double rain), or control soil moisture conditions in Ohio, USA. We measured wild and crop radish life-history, phenology and pollinator visitation patterns. To quantify hybridization rates from crop-to-wild species, we used a simply inherited morphological marker to detect F1 hybrid progeny. Although crop-to-wild hybridization did not respond to watering treatments, the abundance of hybrid offspring was higher in fruits produced late in the period of phenological overlap, when both species had roughly equal numbers of open flowers. Therefore, the timing of fruit production and its relationship to flowering overlap may be more important to hybrid zone formation in Raphanus spp. than soil moisture or pollen vector movements.


Subject(s)
Crops, Agricultural/genetics , Hybridization, Genetic , Raphanus/genetics , Soil/chemistry , Water/metabolism , Ecosystem , Flowers/genetics , Gene Flow , Genes, Plant/genetics , Phenotype , Pollen/genetics , Pollination/genetics , Rain , Raphanus/classification , Reproduction/genetics , Species Specificity
8.
Molecules ; 21(2): 157, 2016 Jan 28.
Article in English | MEDLINE | ID: mdl-26828471

ABSTRACT

A total of 13 anthocyanins and 33 metabolites; including organic acids, phenolic acids, amino acids, organic compounds, sugar acids, sugar alcohols, and sugars, were profiled in three radish cultivars by using high-performance liquid chromatography (HPLC) and gas chromatography time-of-flight mass spectrometry (GC-TOFMS)-based metabolite profiling. Total phenolics and flavonoids and their in vitro antioxidant activities were assessed. Pelargonidins were found to be the major anthocyanin in the cultivars studied. The cultivar Man Tang Hong showed the highest level of anthocyanins (1.89 ± 0.07 mg/g), phenolics (0.0664 ± 0.0033 mg/g) and flavonoids (0.0096 ± 0.0004 mg/g). Here; the variation of secondary metabolites in the radishes is described, as well as their association with primary metabolites. The low-molecular-weight hydrophilic metabolite profiles were subjected to principal component analysis (PCA), hierarchical clustering analysis (HCA), Pearson's correlation analysis. PCA fully distinguished the three radish cultivars tested. The polar metabolites were strongly correlated between metabolites that participate in the TCA cycle. The chemometrics results revealed that TCA cycle intermediates and free phenolic acids as well as anthocyanins were higher in the cultivar Man Tang Hong than in the others. Furthermore; superoxide radical scavenging activities and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging were investigated to elucidate the antioxidant activity of secondary metabolites in the cultivars. Man Tang Hong showed the highest superoxide radical scavenging activity (68.87%) at 1000 µg/mL, and DPPH activity (20.78%), followed by Seo Ho and then Hong Feng No. 1. The results demonstrate that GC-TOFMS-based metabolite profiling, integrated with chemometrics, is an applicable method for distinguishing phenotypic variation and determining biochemical reactions connecting primary and secondary metabolism. Therefore; this study might provide information on the relationship between primary and secondary metabolites and a synergistic antioxidant ability derived from the secondary metabolites in the radish cultivars.


Subject(s)
Antioxidants/isolation & purification , Antioxidants/pharmacology , Metabolomics/methods , Raphanus/chemistry , Anthocyanins/isolation & purification , Anthocyanins/pharmacology , Antioxidants/chemistry , Chromatography, High Pressure Liquid/methods , Flavonoids/chemistry , Flavonoids/isolation & purification , Flavonoids/pharmacology , Oxidative Stress/drug effects , Phenols/chemistry , Phenols/isolation & purification , Phenols/pharmacology , Plant Extracts/analysis , Principal Component Analysis , Raphanus/classification
9.
J Agric Food Chem ; 64(1): 61-70, 2016 Jan 13.
Article in English | MEDLINE | ID: mdl-26672790

ABSTRACT

Radish (Raphanus sativus L.), a root vegetable, is rich in glucosinolates (GLs), which are beneficial secondary metabolites for human health. To investigate the genetic variations in GL content in radish roots and the relationship with other root phenotypes, we analyzed 71 accessions from 23 different countries for GLs using HPLC. The most abundant GL in radish roots was glucoraphasatin, a GL with four-carbon aliphatic side chain. The content of glucoraphasatin represented at least 84.5% of the total GL content. Indolyl GL represented only 3.1% of the total GL at its maximum. The principal component analysis of GL profiles with various root phenotypes showed that four different genotypes exist in the 71 accessions. Although no strong correlation with GL content and root phenotype was observed, the varied GL content levels demonstrate the genetic diversity of GL content, and the amount that GLs could be potentially improved by breeding in radishes.


Subject(s)
Glucosinolates/chemistry , Plant Extracts/chemistry , Raphanus/chemistry , Vegetables/chemistry , Chromatography, High Pressure Liquid , Humans , Plant Roots/chemistry , Plant Roots/classification , Plant Roots/genetics , Raphanus/classification , Raphanus/genetics , Vegetables/classification , Vegetables/genetics
10.
PLoS One ; 10(8): e0135132, 2015.
Article in English | MEDLINE | ID: mdl-26247202

ABSTRACT

Coastal plants with simple linear distribution ranges along coastlines provide a suitable system for improving our understanding of patterns of intra-specific distributional history and genetic variation. Due to the combination of high seed longevity and high dispersibility of seeds via seawater, we hypothesized that wild radish would poorly represent phylogeographic structure at the local scale. On the other hand, we also hypothesized that wild radish populations might be geographically differentiated, as has been exhibited by their considerable phenotypic variations along the islands of Japan. We conducted nuclear DNA microsatellite loci and chloroplast DNA haplotype analyses for 486 samples and 144 samples, respectively, from 18 populations to investigate the phylogeographic structure of wild radish in Japan. Cluster analysis supported the existence of differential genetic structures between the Ryukyu Islands and mainland Japan populations. A significant strong pattern of isolation by distance and significant evidence of a recent bottleneck were detected. The chloroplast marker analysis resulted in the generation of eight haplotypes, of which two haplotypes (A and B) were broadly distributed in most wild radish populations. High levels of variation in microsatellite loci were identified, whereas cpDNA displayed low levels of genetic diversity within populations. Our results indicate that the Kuroshio Current would have contributed to the sculpting of the phylogeographic structure by shaping genetic gaps between isolated populations. In addition, the Tokara Strait would have created a geographic barrier between the Ryukyu Islands and mainland Japan. Finally, extant habitat disturbances (coastal erosion), migration patterns (linear expansion), and geographic characteristics (small islands and sea currents) have influenced the expansion and historical population dynamics of wild radish. Our study is the first to record the robust phylogeographic structure in wild radish between the Ryukyu Islands and mainland Japan, and might provide new insight into the genetic differentiation of coastal plants across islands.


Subject(s)
DNA, Chloroplast/genetics , Phylogeny , Plant Dispersal/physiology , Raphanus/genetics , Seeds/genetics , Cluster Analysis , Ecosystem , Genetic Drift , Genetic Variation , Haplotypes , Japan , Microsatellite Repeats , Phylogeography , Raphanus/classification , Reproductive Isolation
11.
Environ Toxicol Chem ; 33(9): 1950-5, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24839227

ABSTRACT

Genetic diversity has supplied effective ways to improve crop yields and disease resistance. Therefore, crop uptake of heavy metals may be reduced by collecting germplasm resources. In the present study, cadmium accumulation and nutrients in radish were investigated by intercropping 3 genotypes (red, green, and white radish) in different combinations. Both pot and field experiments showed that cadmium content in radish was increased by intercropping 2 or 3 genotypes, except when white radish was intercropped with green radish. The biomass of red radish was improved by a mixture of all 3 genotypes, green radish biomass was improved by intercropping with the other 2 varieties, and white radish biomass was improved by intercropping with red radish in both pot and field experiments. The pot experiment indicated that the soil exchangeable cadmium concentration of red radish grown with green radish was lower than that of monoculture, whereas red radish intercropped with white radish was between the respective monocultures; the soil exchangeable cadmium concentrations of green radish grown with white radish and with all 3 genotypes grown together were greater than those of the monocultures. Some intercropping modes also improved potassium and phosphorus contents in the edible parts of radish in the pot experiment.


Subject(s)
Cadmium/analysis , Raphanus/genetics , Raphanus/metabolism , Soil Pollutants/analysis , Biomass , Cadmium/metabolism , Genotype , Phosphorus/analysis , Phosphorus/metabolism , Raphanus/chemistry , Raphanus/classification , Soil/chemistry , Soil Pollutants/metabolism
12.
PLoS One ; 8(11): e80350, 2013.
Article in English | MEDLINE | ID: mdl-24265813

ABSTRACT

Raphanus sativus is not only a popular edible vegetable but also an important source of medicinal compounds. However, the paucity of knowledge about the transcriptome of R. sativus greatly impedes better understanding of the functional genomics and medicinal potential of R. sativus. In this study, the transcriptome sequencing of leaf tissues in R. sativus was performed for the first time. Approximately 22 million clean reads were generated and used for transcriptome assembly. The generated unigenes were subsequently annotated against gene ontology (GO) database. KEGG analysis further revealed two important pathways in the bolting stage of R.sativus including spliceosome assembly and alkaloid synthesis. In addition, a total of 6,295 simple sequence repeats (SSRs) with various motifs were identified in the unigene library of R. sativus. Finally, four unigenes of R. sativus were selected for alignment with their homologs from other plants, and phylogenetic trees for each of the genes were constructed. Taken together, this study will provide a platform to facilitate gene discovery and advance functional genomic research of R. sativus.


Subject(s)
Plant Leaves , Raphanus/genetics , Transcriptome , Computational Biology/methods , Gene Expression Profiling , Gene Regulatory Networks , Microsatellite Repeats , Molecular Sequence Annotation , Phylogeny , Raphanus/classification , Sequence Analysis, RNA , Species Specificity
13.
BMC Genomics ; 14: 721, 2013 Oct 21.
Article in English | MEDLINE | ID: mdl-24144082

ABSTRACT

BACKGROUND: Radish (Raphanus sativus L., 2n = 2× = 18) is an economically important vegetable crop worldwide. A large collection of radish expressed sequence tags (ESTs) has been generated but remains largely uncharacterized. RESULTS: In this study, approximately 315,000 ESTs derived from 22 Raphanus cDNA libraries from 18 different genotypes were analyzed, for the purpose of gene and marker discovery and to evaluate large-scale genome duplication and phylogenetic relationships among Raphanus spp. The ESTs were assembled into 85,083 unigenes, of which 90%, 65%, 89% and 89% had homologous sequences in the GenBank nr, SwissProt, TrEMBL and Arabidopsis protein databases, respectively. A total of 66,194 (78%) could be assigned at least one gene ontology (GO) term. Comparative analysis identified 5,595 gene families unique to radish that were significantly enriched with genes related to small molecule metabolism, as well as 12,899 specific to the Brassicaceae that were enriched with genes related to seed oil body biogenesis and responses to phytohormones. The analysis further indicated that the divergence of radish and Brassica rapa occurred approximately 8.9-14.9 million years ago (MYA), following a whole-genome duplication event (12.8-21.4 MYA) in their common ancestor. An additional whole-genome duplication event in radish occurred at 5.1-8.4 MYA, after its divergence from B. rapa. A total of 13,570 simple sequence repeats (SSRs) and 28,758 high-quality single nucleotide polymorphisms (SNPs) were also identified. Using a subset of SNPs, the phylogenetic relationships of eight different accessions of Raphanus was inferred. CONCLUSION: Comprehensive analysis of radish ESTs provided new insights into radish genome evolution and the phylogenetic relationships of different radish accessions. Moreover, the radish EST sequences and the associated SSR and SNP markers described in this study represent a valuable resource for radish functional genomics studies and breeding.


Subject(s)
Expressed Sequence Tags , Genome, Plant , Raphanus/genetics , Arabidopsis/metabolism , Databases, Protein , Gene Library , Genotype , Microsatellite Repeats , Phylogeny , Polymorphism, Single Nucleotide , Raphanus/classification
14.
J Genet Genomics ; 40(3): 117-26, 2013 Mar 20.
Article in English | MEDLINE | ID: mdl-23522384

ABSTRACT

To explore the mitochondrial genes of the Cruciferae family, the mitochondrial genome of Raphanus sativus (sat) was sequenced and annotated. The circular mitochondrial genome of sat is 239,723 bp and includes 33 protein-coding genes, three rRNA genes and 17 tRNA genes. The mitochondrial genome also contains a pair of large repeat sequences 5.9 kb in length, which may mediate genome reorganization into two sub-genomic circles, with predicted sizes of 124.8 kb and 115.0 kb, respectively. Furthermore, gene evolution of mitochondrial genomes within the Cruciferae family was analyzed using sat mitochondrial type (mitotype), together with six other reported mitotypes. The cruciferous mitochondrial genomes have maintained almost the same set of functional genes. Compared with Cycas taitungensis (a representative gymnosperm), the mitochondrial genomes of the Cruciferae have lost nine protein-coding genes and seven mitochondrial-like tRNA genes, but acquired six chloroplast-like tRNAs. Among the Cruciferae, to maintain the same set of genes that are necessary for mitochondrial function, the exons of the genes have changed at the lowest rates, as indicated by the numbers of single nucleotide polymorphisms. The open reading frames (ORFs) of unknown function in the cruciferous genomes are not conserved. Evolutionary events, such as mutations, genome reorganizations and sequence insertions or deletions (indels), have resulted in the non-conserved ORFs in the cruciferous mitochondrial genomes, which is becoming significantly different among mitotypes. This work represents the first phylogenic explanation of the evolution of genes of known function in the Cruciferae family. It revealed significant variation in ORFs and the causes of such variation.


Subject(s)
Evolution, Molecular , Genes, Mitochondrial , Genes, Plant , Genome, Mitochondrial , RNA, Plant/metabolism , Raphanus/genetics , Base Sequence , Mitochondria/genetics , Open Reading Frames , Phylogeny , Polymorphism, Single Nucleotide , RNA, Plant/genetics , RNA, Transfer/genetics , RNA, Transfer/metabolism , Raphanus/classification , Repetitive Sequences, Nucleic Acid , Species Specificity
15.
Theor Appl Genet ; 119(1): 189-98, 2009 Jun.
Article in English | MEDLINE | ID: mdl-19363601

ABSTRACT

Four types of cytoplasms (Ogura, DCGMS, DBRMF1, and DBRMF2) were identified in the previous studies using molecular markers based on mitochondrial genome variations in radish (Raphanus sativus L.). However, mtDNA markers have limitations in obtaining clear results due to complexity of radish mitochondrial genomes. To improve fidelity, molecular markers based on variation of chloroplast genome sequences were developed in this study. We searched for the sequence variations of chloroplast genome among the four cytoplasm types in 11 noncoding intergenic regions of ~8.7 kb. Highly variable intergenic regions between trnK and rps16 were identified, and a couple of 4-34 bp indels were used to develop a simple PCR-based marker that distinguished the four cytoplasm types based on the PCR product length polymorphism. Two additional cpDNA markers were developed by using a single nucleotide polymorphism and 17-bp insertion. Analysis of 90 accessions using both mtDNA and cpDNA markers showed the perfect match of results of both the markers, suggesting strict co-transmission of mitochondria and chloroplast in radish. Phylogenetic trees showed that two male-sterility inducing cytoplasms, Ogura and DCGMS, were closely related to DBRMF1 and DBRMF2, respectively. Analysis of 120 radish germplasms introduced from diverse countries showed that the frequency of male-sterility inducing mitotypes of Ogura and DCGMS was very low, and DCGMS was predominately detected in eastern European countries. Majority of accessions from Europe and Asia were shown to contain DBRMF2 and DBRMF1 mitotypes, respectively.


Subject(s)
Base Sequence , Chloroplasts/genetics , DNA, Plant , Genetic Markers , Raphanus/cytology , Raphanus/genetics , Animals , DNA, Plant/analysis , DNA, Plant/genetics , Genetic Variation , Genome , Genome, Mitochondrial/genetics , Molecular Sequence Data , Phylogeny , Raphanus/classification , Sequence Alignment
16.
Genetika ; 43(10): 1411-23, 2007 Oct.
Article in Russian | MEDLINE | ID: mdl-18069346

ABSTRACT

The characteristics of a unique genetic collection of radish inbred lines and the history of its creation and study are presented. The possible research prospects are discussed.


Subject(s)
Inbreeding , Raphanus/classification , Raphanus/genetics , History, 20th Century , History, 21st Century , Russia
17.
Theor Appl Genet ; 115(8): 1137-45, 2007 Nov.
Article in English | MEDLINE | ID: mdl-17828522

ABSTRACT

Plant mitochondrial genomes have complex configurations resulting from the multipartite structures and highly rearranged substoichiometric molecules created by repetitive sequences. To expedite the reliable classification of the diverse radish (Raphanus sativus L.) cytoplasmic types, we have developed consistent molecular markers within their complex mitochondrial genomes. orf138, a gene responsible for Ogura male-sterility, was detected in normal cultivars in the form of low-copy-number substoichiometric molecules. In addition to the dominant orf138-atp8 Ogura mitochondrial DNA (mtDNA) organization, three novel substoichiometric organizations linked to the atp8 gene were identified in this study. PCR amplification profiles of seven atp8- and atp6-linked sequences were divided into three groups. Interestingly, the normal cytoplasm type, which had previously been considered a single group, showed two patterns by PCR amplification. The most prominent difference between the two normal mtDNAs was size variation within four short-repeat sequences linked to the atp6 gene. This variation appeared to be the result of a double crossover, mediated by these homologous, short-repeat sequences. Specific PCR amplification profiles reflecting the stoichiometry of different mtDNA fragments were conserved within cultivars and across generations. Therefore, the specific sequences detected in these profiles were used as molecular markers for the classification of diverse radish germplasm. Using this classification system, a total of 90 radish cultivars, or accessions, were successfully assigned to three different mitotypes.


Subject(s)
Cytoplasm/genetics , Genome, Mitochondrial , Raphanus/classification , Raphanus/genetics , Base Sequence , DNA, Mitochondrial/genetics , Gene Rearrangement , Genetic Markers , Mitochondrial Proteins/genetics , Molecular Sequence Data , Plant Proteins/genetics
18.
Evolution ; 57(3): 480-6, 2003 Mar.
Article in English | MEDLINE | ID: mdl-12703937

ABSTRACT

Plant traits that show little variation across higher taxa are often used as diagnostic traits, but the reason for the stasis of such traits remains unclear. Wild radish, Raphanus raphanistrum, exhibits tetradynamous stamens (four long and two short, producing a dimorphism in anther height within each flower), as do the vast majority of the more than 3,000 species in the Brassicaceae. Here we examine the hypothesis that selection maintains the stasis of dimorphic anther height by investigating the effects of this trait on pollen removal, seed siring success, and seed set in R. raphanistrum using both experimental and observational methods. Observational selection gradient analysis based on lifetime seed siring success provided evidence for an optimum dimorphism that was greater than zero in one of three years. In both experimentally manipulated and unmanipulated flowers, more pollen was removed in single visits from flowers with less dimorphism. There was no significant effect of anther dimorphism on female fitness (seed set). Therefore, there is some evidence to suggest that selection is maintaining anther dimorphism in wild radish, and that higher male fitness might result from restriction of single-visit pollen removal. We discuss these results in light of pollen presentation theory.


Subject(s)
Raphanus/genetics , Selection, Genetic , Flowers/physiology , Pollen , Raphanus/classification , Raphanus/physiology , Species Specificity
19.
Evolution ; 57(3): 487-95, 2003 Mar.
Article in English | MEDLINE | ID: mdl-12703938

ABSTRACT

Measurements of the genetic variation and covariation underlying quantitative traits are crucial to our understanding of current evolutionary change and the mechanisms causing this evolution. This fact has spurred a large number of studies estimating heritabilities and genetic correlations in a variety of organisms. Most of these studies have been done in laboratory or greenhouse settings, but it is not well known how accurately these measurements estimate genetic variance and covariance expressed in the field. We conducted a quantitative genetic half-sibling analysis on six floral traits in wild radish. Plants were grown from seed in the field and were exposed to natural environmental variation throughout their lives, including herbivory and intra- and interspecific competition. The estimates of heritabilities and the additive genetic variance-covariance matrix (G) obtained from this analysis were then compared to previous greenhouse estimates of the same floral traits from the same natural population. Heritabilities were much lower in the field for all traits, and this was due to both large increases in environmental variance and decreases in additive genetic variance. Additive genetic covariance expressed was also much lower in the field. These differences resulted in highly significant differences in the G matrix between the greenhouse and field environments using two complementary testing methods. Although the G matrices shared some principal components in common, they were not simply proportional to each other. Therefore, the greenhouse results did not accurately depict how the floral traits would respond to natural selection in the field.


Subject(s)
Environment , Flowers/genetics , Genetic Variation , Raphanus/classification , Raphanus/genetics , Flowers/growth & development , Raphanus/growth & development , Species Specificity
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