scholarly journals Development of Randomly Amplified Polymorphic DNA Based SCAR Marker for Identification ofIpomoea mauritianaJacq (Convolvulaceae)

2011 ◽  
Vol 2011 ◽  
pp. 1-6 ◽  
Author(s):  
Kambiranda Devaiah ◽  
Subramani Paranthaman Balasubramani ◽  
Padma Venkatasubramanian
Keyword(s):  
Scar Marker ◽  
The Other ◽  
Herbal Drug ◽  
Randomly Amplified Polymorphic Dna ◽  
Pueraria Tuberosa ◽  
Sequence Characterized Amplified Region ◽  
Cycas Circinalis ◽  
Scar Primers

Vidari is an Ayurvedic herbal drug used as aphrodisiac, galactagogue and is also used in the preparation ofChyavanaprash. Tubers ofIpomoea mauritianaJacq. (Convolvulaceae),Pueraria tuberosa(Roxb. ex Willd.) DC (Fabaceae),Adenia hondala(Gaertn.) de Wilde (Passifloraceae) and pith ofCycas circinalisL. (Cycadaceae) are all traded in the name of Vidari, creating issues of botanical authenticity of the Ayurvedic raw drug. DNA-based markers have been developed to distinguishI. mauritianafrom the other Vidari candidates. A putative 600-bp polymorphic sequence, specific toI. mauritianawas identified using randomly amplified polymorphic DNA (RAPD) technique. Furthermore, sequence characterized amplified region (SCAR) primers (IM1F and IM1R) were designed from the unique RAPD amplicon. The SCAR primers produced a specific 323-bp amplicon in authenticI. mauritianaand not in the allied species.

scholarly journals Authentication of Herbal Medicines Dipsacus asper and Phlomoides umbrosa Using DNA Barcodes, Chloroplast Genome, and Sequence Characterized Amplified Region (SCAR) Marker

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1748 ◽  
Author(s):  
Inkyu Park ◽  
Sungyu Yang ◽  
Wook Kim ◽  
Pureum Noh ◽  
Hyun Lee ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Scar Marker ◽  
Herbal Medicines ◽  
The Other ◽  
Evolutionary Information ◽  
Scar Markers ◽  
Dna Barcodes ◽  
Genomic Information ◽  
Sequence Characterized Amplified Region ◽  
Dipsacus Asper

Dried roots of Dipsacus asper (Caprifoliaceae) are used as important traditional herbal medicines in Korea. However, the roots are often used as a mixture or contaminated with Dipsacus japonicus in Korean herbal markets. Furthermore, the dried roots of Phlomoides umbrosa (Lamiaceae) are used indiscriminately with those of D. asper, with the confusing Korean names of Sok-Dan and Han-Sok-Dan for D. asper and P. umbrosa, respectively. Although D. asper and P. umbrosa are important herbal medicines, the molecular marker and genomic information available for these species are limited. In this study, we analysed DNA barcodes to distinguish among D. asper, D. japonicus, and P. umbrosa and sequenced the chloroplast (CP) genomes of D. asper and D. japonicus. The CP genomes of D. asper and D. japonicus were 160,530 and 160,371 bp in length, respectively, and were highly divergent from those of the other Caprifoliaceae species. Phylogenetic analysis revealed a monophyletic group within Caprifoliaceae. We also developed a novel sequence characterised amplified region (SCAR) markers to distinguish among D. asper, D. japonicus, and P. umbrosa. Our results provide important taxonomic, phylogenetic, and evolutionary information on the Dipsacus species. The SCAR markers developed here will be useful for the authentication of herbal medicines.

Development of SCAR markers for sex determination in the dioecious shrub Aucuba japonica (Cornaceae)

Genome ◽  
2009 ◽  
Vol 52 (3) ◽  
pp. 231-237 ◽  
Author(s):  
Masayuki Maki
Keyword(s):  
Sex Identification ◽  
The Other ◽  
Scar Markers ◽  
Specific Sequence ◽  
Sequence Characterized Amplified Region ◽  
Annealing Temperatures ◽  
Aucuba Japonica ◽  
Males And Females ◽  
Male Specific ◽  
Scar Primers

Two sex-linked fragments were identified by RAPD analyses in the dioecious diploid shrub Aucuba japonica var. ovoidea and were converted into markers of male-specific sequence characterized amplified region (SCAR) markers. PCRs using the primers designed in this study correctly discriminated 24 flowering males and 24 flowering females at higher annealing temperatures (SCAR markers OPA10-424 at 55 °C and OPN11-1095 at 65 °C), although at relatively low annealing temperatures, the fragments were amplified in both males and females. These SCAR primers were also tested to see whether they were applicable to sex identification in the conspecific tetraploid Aucuba japonica var. japonica. One set pf SCAR primers could be used for sex identification even in this tetraploid variety, although the other failed. The SCAR markers developed in this study will provide a powerful tool in identifying the sex of immature plants of dioecious A. japonica, which is a commercially valuable shrub due to its conspicuous fruits.

Genetic diversity of root-knot nematodes from Brazil and development of SCAR markers specific for the coffee-damaging species

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 862-870 ◽  
Author(s):  
Onivaldo Randig ◽  
Michel Bongiovanni ◽  
Regina M.D.G Carneiro ◽  
Philippe Castagnone-Sereno
Keyword(s):  
Genetic Diversity ◽  
Multiplex Pcr ◽  
Rapd Markers ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Scar Markers ◽  
Meloidogyne Hapla ◽  
Root Knot Nematodes ◽  
Sequence Characterized Amplified Region ◽  
Scar Primers

RAPD markers were used to characterize the genetic diversity and relationships of root-knot nematodes (RKN) (Meloidogyne spp.) in Brazil. A high level of infraspecific polymorphism was detected in Meloidogyne arenaria, Meloidogyne exigua, and Meloidogyne hapla compared with the other species tested. Phylogenetic analyses showed that M. hapla and M. exigua are more closely related to one another than they are to the other species, and illustrated the early divergence of these meiotically reproducing species from the mitotic ones. To develop a PCR-based assay to specifically identify RKN associated with coffee, three RAPD markers were further transformed into sequence-characterized amplified region (SCAR) markers specific for M. exigua, Meloigogyne incognita and Meloidogyne paranaensis, respectively. After PCR using the SCAR primers, the initial polymorphism was retained as the presence or absence of amplification. Moreover, multiplex PCR using the three pairs of SCAR primers in a single reaction enabled the unambiguous identification of each species, even in mixtures. Therefore, it is concluded that the method developed here has potential for application in routine diagnostic procedures.Key words: diagnostic, multiplex PCR, phylogeny, RAPD, root-knot nematodes.

scholarly journals Characterization of a Resistance Locus (Pfs-1) to the Spinach Downy Mildew Pathogen (Peronospora farinosa f. sp. spinaciae) and Development of a Molecular Marker Linked to Pfs-1

2008 ◽  
Vol 98 (8) ◽  
pp. 894-900 ◽  
Author(s):  
B. M. Irish ◽  
J. C. Correll ◽  
C. Feng ◽  
T. Bentley ◽  
B. G. de los Reyes
Keyword(s):  
Disease Resistance ◽  
Downy Mildew ◽  
Scar Marker ◽  
Mapping Population ◽  
Dominant Gene ◽  
Resistance Locus ◽  
Sequence Characterized Amplified Region ◽  
Wide Range ◽  
Spinach Downy Mildew ◽  
Homozygous Resistant

Downy mildew is a destructive disease of spinach worldwide. There have been 10 races described since 1824, six of which have been identified in the past 10 years. Race identification is based on qualitative disease reactions on a set of diverse host differentials which include open-pollinated cultivars, contemporary hybrid cultivars, and older hybrid cultivars that are no longer produced. The development of a set of near-isogenic open-pollinated spinach lines (NILs), having different resistance loci in a susceptible and otherwise common genetic background, would facilitate identification of races of the downy mildew pathogen, provide a tool to better understand the genetics of resistance, and expedite the development of molecular markers linked to these disease resistance loci. To achieve this objective, the spinach cv. Viroflay, susceptible to race 6 of Peronospora farinosa f. sp. spinaciae, was used as the recurrent susceptible parent in crosses with the hybrid spinach cv. Lion, resistant to race 6. Resistant F1 progeny were subsequently backcrossed to Viroflay four times with selection for race 6 resistance each time. Analysis of the segregation data showed that resistance was controlled by a single dominant gene, and the resistance locus was designated Pfs-1. By bulk segregant analysis, an amplified fragment length polymorphism (AFLP) marker (E-ACT/M-CTG) linked to Pfs-1 was identified and used to develop a co-dominant Sequence characterized amplified region (SCAR) marker. This SCAR marker, designated Dm-1, was closely linked (≈1.7 cM) to the Pfs-1 locus and could discriminate among spinach genotypes that were homozygous resistant (Pfs-1Pfs-1), heterozygous resistant (Pfs-1pfs-1), or homozygous susceptible (pfs-1pfs-1) to race 6 within the original mapping population. Evaluation of a wide range of commercial spinach lines outside of the mapping population indicated that Dm-1 could effectively identify Pfs-1 resistant genotypes; the Dm-1 marker correctly predicted the disease resistance phenotype in 120 out of 123 lines tested. In addition, the NIL containing the Pfs-1 locus (Pfs-1Pfs-1) was resistant to multiple races of the downy mildew pathogen indicating Pfs-1 locus may contain a cluster of resistance genes.

scholarly journals Genetic Relationships among 11 Nonheading Chinese Cabbage Accessions and the SCAR Marker Specific for ‘Suzhouqing’

HortScience ◽  
2018 ◽  
Vol 53 (9) ◽  
pp. 1288-1293
Author(s):  
Xuelin Shen ◽  
Yanmei Zhang ◽  
Zhao Lei ◽  
Yibo Lin ◽  
Minxu Cao ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Genetic Relationship ◽  
Yangtze River ◽  
Scar Marker ◽  
Yangtze River Delta ◽  
River Delta ◽  
The Other ◽  
The Yangtze River ◽  
Relationship Analysis ◽  
The Yangtze River Delta

‘Suzhouqing’ is a unique landrace of nonheading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] with a long history of cultivation in Suzhou of Jiangsu Province, China. However, transitional and overlapped morphologic traits make it difficult to authenticate this accession from other nonheading Chinese cabbages. Genetic relationship between ‘Suzhouqing’ and the related 10 popular accessions in the Yangtze River Delta were analyzed using two well-studied single-copy nuclear genes—ARGONAUTES 7 (AGO7) and BcMF15; the molecular identification of ‘Suzhouqing’ was determined based on the intersimple sequence repeat–sequence-characterized amplified region (ISSR-SCAR) marker. The results indicated that ‘Suzhouqing’ could be identified specifically from the other 10 accessions based on 21 specific nucleotide variations of the AGO7 gene. Sequence variations show a strong correlation with leaf morphology, suggestive of partial causal links between the two. Genetic relationship analysis showed that five accessions with close geographic locations had a very close genetic relationship, whereas the genetic relationship of the other five accessions was related to their morphologic similarity. One exception, ‘AJH’, might undergo a special evolutionary process. Furthermore, ISSR-880 was screened as the specific primer to identify accession ‘Suzhouqing’, and a specific discrimination ISSR-SCAR marker was explored, which amplified no target band in any other accessions. The development of molecular markers for the specific identification of ‘Suzhouqing’ in 11 popular accessions in the Yangtze River Delta could provide a theoretical basis for the protective identification of other agricultural crops.

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