Development of Randomly Amplified Polymorphic DNA-Sequence Characterized Amplified Region Marker for Identification of Apocynum venetum LINN. from A. pictum SCHRENK

Resistance to begomoviruses tomato mottle virus (ToMoV) and tomato yellow leaf curl virus (TYLCV) has been introgressed to tomato (Lycopersicon esculentum) from L. chilense accessions LA 1932, LA 2779, and LA 1938. Resistance genes have been mapped to three regions on chromosome 6 using randomly amplified polymorphic DNA (RAPD) markers. We call these regions 1, 2, and 3. To facilitate breeding by marker assisted selection, advanced breeding lines with resistance from the above sources were assayed for the presence of RAPD markers to determine which were most tightly linked to begomovirus resistance. The best RAPD markers were then converted to sequence characterized amplified region (SCAR) markers or cleaved amplified polymorphic sequence (CAPS) markers. In addition, selected restriction fragment length polymorphism (RFLP) markers near the three regions were converted into CAPS markers, which were tested for association with the advanced breeding lines. Only LA 2779 derivatives have the L. chilense introgression in region 1, which is near the location of the Ty-1 gene and spans across CAPS markers 32.5Cla and TG118. Two region 1 RAPD markers UBC197 and UBC621 were converted co-dominant SCAR or CAPS markers, which were present in all 16 resistant breeding lines tested. Derivatives from all three accessions have introgressions in region 2. Further assays with more markers in this region are under way to determine the lengths and locations of the introgressions. No tightly linked RAPD markers have been found for the resistance gene from LA 1932 in region 3. RFLP and CAPS markers are being used to more precisely locate the region 3 gene.

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Development of Sequence-characterized Amplified Region Markers for the Identification of Grapevine Cultivars

HortScience ◽

10.21273/hortsci.50.12.1744 ◽

2015 ◽

Vol 50 (12) ◽

pp. 1744-1750

Author(s):

Kang Hee Cho ◽

Jung Ho Noh ◽

Seo Jun Park ◽

Se Hee Kim ◽

Dae-Hyun Kim ◽

...

Keyword(s):

Rapd Markers ◽

Morphological Characteristics ◽

Polymorphic Band ◽

Group Method ◽

Scar Markers ◽

Randomly Amplified Polymorphic Dna ◽

Genetic Fingerprinting ◽

Sequence Characterized Amplified Region ◽

Pair Group ◽

Average Similarity

Grapevine cultivars have traditionally been identified based on the morphological characteristics, but the identification of closely related cultivars has been difficult because of their similar pedigree backgrounds. In this study, we developed DNA markers for genetic fingerprinting in 37 grapevine cultivars, including 20 cultivars bred in Korea. A total of 180 randomly amplified polymorphic DNA (RAPD) markers were obtained using 30 different primers. The number of polymorphic bands ranged from three (OPG-08 and OPU-19) to nine (OPV-01 and UBC116), with an average of six. RAPD markers were used in cluster analysis performed with the unweighted pair-group method of arithmetic averages (UPGMA). The average similarity value was 0.69 and the dendrogram clustered the 37 grapevine cultivars into five clusters. The relationships among the grapevine cultivars were consistent with the known pedigrees of the cultivars. The 50 RAPD fragments selected were sequenced for the development of sequence-characterized amplified region (SCAR) markers. As a result, 16 of 50 fragments were successfully converted into SCAR markers. A single polymorphic band, the same size as the RAPD fragments or smaller, was amplified depending on the primer combinations in the 14 SCAR markers, and codominant polymorphisms were detected using the SCAR markers G119_412 and GB17_732. Among these markers, combination of 11 SCAR markers, GG05_281, G116_319, G146_365, G119_412, GW04_463, G169_515, G116_539, GV04_618, GV01_678, GG05_689, and GB17_732, provided sufficient polymorphisms to distinguish the grapevine cultivars investigated in this study. These newly developed markers could be a fast and reliable tool for identifying grapevine cultivars.

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Molecular authentication of Gynostemma pentaphyllum through development and application of random amplification polymorphic DNA sequence-characterized amplified region marker

Genetics and Molecular Research ◽

10.4238/2015.december.8.10 ◽

2015 ◽

Vol 14 (4) ◽

pp. 16204-16214 ◽

Cited By ~ 4

Author(s):

J. Zhou ◽

Y.S. Wu ◽

R.Q. Zhao ◽

J.F. Jiang ◽

Y. Luo ◽

...

Keyword(s):

Dna Sequence ◽

Gynostemma Pentaphyllum ◽

Molecular Authentication ◽

Sequence Characterized Amplified Region ◽

Random Amplification

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

Evidence-based Complementary and Alternative Medicine ◽

10.1093/ecam/neq023 ◽

2011 ◽

Vol 2011 ◽

pp. 1-6 ◽

Cited By ~ 7

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.

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Study of specific random amplification of polymorphic DNA- sequence characterized amplified region (RAPD-SCAR) marker for the endangered Chinese endemic herb Atractylodes lancea

Journal of Medicinal Plants Research ◽

10.5897/jmpr12.327 ◽

2012 ◽

Vol 6 (21) ◽

Author(s):

Xiaoqin Sun

Keyword(s):

Dna Sequence ◽

Scar Marker ◽

Sequence Characterized Amplified Region ◽

Atractylodes Lancea ◽

Random Amplification

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Sequence characterized amplified region markers tightly linked to the mating factors ofLentinula edodes

Genome ◽

10.1139/g03-131 ◽

2004 ◽

Vol 47 (1) ◽

pp. 156-162 ◽

Cited By ~ 12

Author(s):

Ayako Tanaka ◽

Kazuhiro Miyazaki ◽

Haruki Murakami ◽

Susumu Shiraishi

Keyword(s):

Mating Type ◽

Lentinula Edodes ◽

Mating Types ◽

Randomly Amplified Polymorphic Dna ◽

Chain Reaction ◽

Identification Procedure ◽

Polymerase Chain Reaction Condition ◽

Sequence Characterized Amplified Region ◽

Polymerase Chain ◽

Mating Factor

Detecting the mating types in shiitake, Lentinula edodes (Berk.) Pegler, is important for making progress in the breeding of this mushroom and determining the compatibility of the pair to cross. Shiitake is a tetrapolar fungus with two unlinking mating factors, A factor and B factor. We screened molecular markers linked to the mating factors using the randomly amplified polymorphic DNA (RAPD) method to develop the mating type identification procedure. Using 147 oligonucleotide primers, a total of 6 linkage markers for the shiitake mating factors, 4 markers for the A factor and 2 markers for the B factor, were discovered with a logarithm of the odds threshold of 3.0 for linkage. Two RAPDs that perfectly segregated with each mating factor among 72 basidiospore strains were detected. Both of these RAPDs were cloned and sequenced to convert them to the sequence characterized amplified region (SCAR) markers. Four primers, two sets of primers, were designed according to the internal sequences of two RAPDs tightly linking to the A factor or B factor. Consequently, we determined the polymerase chain reaction condition for multiplex analyses of these SCAR markers.Key words: Lentinula edodes, SCAR, diagnostic, mating type.

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DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100122885 ◽

1992 ◽

Vol 50 (1) ◽

pp. 496-497

Author(s):

Barbara Trask ◽

Susan Allen ◽

Anne Bergmann ◽

Mari Christensen ◽

Anne Fertitta ◽

...

Keyword(s):

In Situ Hybridization ◽

Dna Sequence ◽

Dna Sequences ◽

Dual Band ◽

Nick Translation ◽

Metaphase Chromosomes ◽

Band Pass ◽

Texas Red ◽

Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

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