Development of random amplified polymorphic DNA markers for genetic mapping in Pacific yew (Taxusbrevifolia)

1996 ◽  
Vol 26 (3) ◽  
pp. 497-503 ◽  
Author(s):  
B. Göçmen ◽  
Z. Kaya ◽  
K.D. Jermstad ◽  
D.B. Neale
Keyword(s):  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
Polymorphic Locus ◽  
Single Mother ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Arbitrary Sequence ◽  
Linkage Groups ◽  
Polymerase Chain

A genetic linkage map was constructed for Pacific yew (Taxusbrevifolia Nutt.) based on random amplified polymorphic DNA (RAPD) markers. A series of optimization experiments were conducted to develop a highly repeatable protocol for Pacific yew. In these experiments, a high MgCl2 concentration (5.5 mM) together with a low primer concentration (0.2 μm) in the polymerase chain reaction (PCR) mixture yielded the best amplification products. PCR amplification products were further improved by treating the template DNAs with RNase. Experiments showed that bovine serum albumine had the same effect as RNase on PCR amplification. The segregating mapping population consisted of 39 haploid megagametophytes from a single mother tree. DNA extracted from a subset of 6 megagametophytes was screened with 345 ten-base oligonucleotide primers of arbitrary sequence. Of the screened primers, 28% revealed at least one polymorphic locus. Eighty-six of these primers revealed at least one polymorphic locus and were used with the entire set of megagametophyte DNAs. One-hundred-two loci were scored and segregated in the expected 1:1 ratio (1.19 locus per primer). Linkage analysis was conducted using MAPMAKER. Forty-one of 102 markers were distributed into 17 linkage groups and covered 305.8 centimorgans. The remaining 61 unlinked markers should be assigned to linkage groups as more markers are added to the map.

Linkage of random amplified polymorphic DNA, isozyme and morphological markers in grasspea (Lathyrus sativus)

1999 ◽  
Vol 133 (4) ◽  
pp. 389-395 ◽  
Author(s):  
M. A. CHOWDHURY ◽  
A. E. SLINKARD
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Average Distance ◽  
Random Amplified Polymorphic Dna ◽  
Lathyrus Sativus ◽  
Morphological Markers ◽  
Linkage Studies ◽  
Linkage Groups

We constructed a genetic linkage map of grasspea (Lathyrus sativus L.; 2n = 14) from 100 F2 individuals derived from a cross between PI 426891.1.3 and PI 283564c.3.2. A total of 71 RAPD, three isozyme and one morphological markers segregated in the F2 progeny. A small fraction of markers (12%) deviated significantly from the expected Mendelian ratio (1[ratio ]2[ratio ]1 or 3[ratio ]1). Out of 75 markers, 69 (one morphological, three isozyme and 65 RAPD markers) were assigned to 14 linkage groups comprising 898 cM. The average distance between two adjacent markers was 17·2 cM. The present linkage map will serve as a reference point for further linkage studies in grasspea.

scholarly journals Molecular characterization of onion (Allium cepa) using RAPD markers

1970 ◽  
Vol 35 (2) ◽  
pp. 313-322 ◽  
Author(s):  
M Maniruzzaman ◽  
ME Haque ◽  
MM Haque ◽  
MA Sayem ◽  
M Al-Amin
Keyword(s):  
Allium Cepa ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Group Method ◽  
Genetic Studies ◽  
Pair Group ◽  
Genetic Level ◽  
Polymerase Chain

A polymerase chain reaction (PCR) based approach, namely random amplified polymorphic DNA (RAPD) analysis was applied to l0 varieties of onion (Allium cepa) in order to assess the degree of polymorphism within the genes and to investigate if this approach was suitable for genetic studies of onion. For this study, ten cultivars of onion were evaluated for variability using a set of 15 random l0-mer primers. The polymorphisms in PCR amplification products were subjected to the unweighed pair group method for arithmetic averages (UPGMA) and plotted in a phenogram. The dendogram constructed from the similarity data showed that all the cultivars analyzed were related. Among them, 12 of the primers revealed scorable (168 bands) polymorphisms between cultivars of A. cepa and the rest did not show polymorphism in their genetic level. In this study, it was found that Bermis and India-2 were more dissimilar and on the other hand, Faridpuri and Bhati were the most similar in their genetic level. Keywords: RAPD; onion; genetic diversity; polymorphism. DOI: 10.3329/bjar.v35i2.5894Bangladesh J. Agril. Res. 35(2) : 313-322, June 2010

A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers

Genome ◽  
2012 ◽  
Vol 55 (4) ◽  
pp. 327-335 ◽  
Author(s):  
Xiaoxia Yu ◽  
Xiaolei Li ◽  
Yanhong Ma ◽  
Zhuo Yu ◽  
Zaozhe Li
Keyword(s):  
Molecular Markers ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
Gene Localization ◽  
Linkage Groups ◽  
Crested Wheatgrass ◽  
Map Distance

Using a population of 105 interspecific F2 hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. ‘Fairway’ as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future.

Genetic segregation of random amplified polymorphic DNA in diploid cultivated alfalfa

Genome ◽  
1992 ◽  
Vol 35 (1) ◽  
pp. 84-87 ◽  
Author(s):  
C. S. Echt ◽  
L. A. Erdahl ◽  
T. J. McCoy
Keyword(s):  
Polymerase Chain Reaction ◽  
Rapd Markers ◽  
Genome Mapping ◽  
Polymerase Chain Reaction Amplification ◽  
Random Amplified Polymorphic Dna ◽  
Rapid Development ◽  
Arbitrary Sequence ◽  
Chain Reaction ◽  
Backcross Population ◽  
Polymerase Chain

Polymerase chain reaction was used, with single 10-mer primers of arbitrary sequence, to amplify random regions of genomic DNA from a diploid cultivated alfalfa backcross population. Segregation of the random amplified polymorphic DNA (RAPD) fragments was analysed to determine if RAPD markers are suitable for use as genetic markers. Of the 19 primers tested, 13 amplified a total of 37 polymorphic fragments, of which 28 (76%) segregated as dominant Mendelian traits. RAPD markers appear useful for the rapid development of genetic information in species like alfalfa where little information currently exists or is difficult to obtain.Key words: random amplified polymorphic DNA, polymerase chain reaction amplification, genome mapping, restriction fragment length polymorphism, Medicago sativa.

scholarly journals DNA FINGERPRINTING IN RHODODENDRONS USING RANDOM AMPLIFIED POLYMORPHIC DNA

HortScience ◽  
1996 ◽  
Vol 31 (3) ◽  
pp. 323g-324
Author(s):  
Stacey M. Sakakibara ◽  
John E. Carlson
Keyword(s):  
Dna Fingerprinting ◽  
Large Scale ◽  
Rapd Markers ◽  
Dna Isolation ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Arbitrary Sequence ◽  
Agarose Gel Electrophoresis ◽  
Ethidium Bromide Staining ◽  
High Level

Random amplified polymorphic DNA (RAPD) markers were evaluated for use in DNA fingerprinting of commercial Rhododendron cultivars. DNA was isolated from Rhododendron leaves and subjected to PCR amplification with single primers, 10 nucleotides in length, and of arbitrary sequence. Amplification products were visualized by agarose gel electrophoresis and ethidium bromide staining. Fingerprints were readily identifiable for a number of cultivars, and a high level of polymorphism was observed among clones of 10 rhododendron varieties. The technique was consistently reproducible in different trials using the thermocycler, between different thermocyclers, and using different DNA isolation from the same plant. This method will be applied to large-scale fingerprinting of Rhododendron cultivars and for distinguishing material propagated in tissue culture.

scholarly journals A genetic linkage map of Saccharum spontaneum L. 'SES 208'.

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1249-1260 ◽  
Author(s):  
S M al-Janabi ◽  
R J Honeycutt ◽  
M McClelland ◽  
B W Sobral
Keyword(s):  
Single Dose ◽  
Linkage Map ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
Direct Analysis ◽  
Arbitrary Sequence ◽  
Saccharum Spontaneum ◽  
Repulsion Phase ◽  
Point Analysis ◽  
Polymerase Chain

Abstract The arbitrarily primed polymerase chain reaction was used to detect single-dose polymorphisms that, in turn, were used to generate a linkage map of a polyploid relative of cultivated sugarcane, Saccharum spontaneum 'SES 208' (2n = 64). The mapping population was composed of 88 progeny from a cross between SES 208 and a diploidized haploid derived from SES 208 by anther culture, ADP 85-0068. This cross allowed direct analysis of meiosis in SES 208 and gametic segregation ratios to be observed. One hundred twenty-seven 10-mer oligonucleotide primers of arbitrary sequence were selected from a pool of 420 primers used to screen the mapping parents. Three hundred thirty-six of the 420 primers amplified 4,540 loci or 13.5 loci per primer. The selected 127 primers revealed 2,160 loci of which 279 were present in SES 208 and absent in ADP 85-0068 and easily scored. Two hundred and eight (74.6%) of these 279 polymorphisms were single-dose polymorphisms (i.e., they displayed 1:1 segregation, chi 2 at 98% confidence level). Linkage analysis (theta = 0.25, LOD = 9.0 for two-point analysis, then theta = 0.25, LOD = 6.0 for multipoint analysis) of single-dose polymorphisms placed them into 42 linkage groups containing at least 2 markers. These single-dose markers span 1,500 contiguous centimorgans (cM) with 32 markers remaining unlinked (15.4%). From this 208-marker map we estimated the genome size of SES 208 to be 2,500 cM. The map has a predicted coverage of 85.1% at 30 cM, meaning that any new marker placed has an 85.1% chance of being within 30 cM of an existing marker. Furthermore, we show that SES 208 behaves like an autopolyploid because (i) the ratio of single-dose markers to higher dose markers fit the assumption of auto-octaploidy and (ii) the absence of repulsion phase linkages. This is the first genetic map constructed directly on a polyploid species for which no diploid relatives are known.

scholarly journals Analysis of a detailed genetic linkage map of Lactuca sativa (lettuce) constructed from RFLP and RAPD markers.

Genetics ◽  
1994 ◽  
Vol 136 (4) ◽  
pp. 1435-1446
Author(s):  
R V Kesseli ◽  
I Paran ◽  
R W Michelmore
Keyword(s):  
Lactuca Sativa ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Maps ◽  
Morphological Markers ◽  
Linkage Groups ◽  
F2 Population

Abstract A detailed genetic map has been constructed from the F2 population of a single intraspecific cross of Lactuca sativa (n = 9). It comprises 319 loci, including 152 restriction fragment length polymorphism (RFLP), 130 random amplified polymorphic DNA (RAPD), 7 isozyme, 19 disease resistance, and 11 morphological markers. Thirteen major, four minor linkage groups and several unlinked markers are identified for this genome which is estimated to be approximately 1950 cM. RFLP and RAPD markers show similar distributions throughout the genome and identified similar levels of polymorphism. RAPD loci were much quicker to identify but more difficult to order. Procedures for generating accurate genetic maps and their limitations are described.

scholarly journals Identification, Mapping and Linkage Analysis of Randomly Amplified DNA Polymorphisms in Tetrahymena thermophila

Genetics ◽  
1996 ◽  
Vol 143 (2) ◽  
pp. 811-821 ◽  
Author(s):  
Jason H Brickner ◽  
Timothy J Lynch ◽  
Dawn Zeilinger ◽  
Eduardo Orias
Keyword(s):  
Rapd Markers ◽  
Tetrahymena Thermophila ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Inbred Strains ◽  
Dna Polymorphisms ◽  
Linkage Groups ◽  
Ciliated Protozoan ◽  
Template Dna ◽  
Do So

Abstract Using the random amplified polymorphic DNA (RAPD) technique and exploiting the unique genetics of Tetrahymena themnophila, we have identified and characterized 40 DNA polymorphisms occurring between two inbred strains (B and C3) of this ciliated protozoan. These RAPD markers permit the PCR amplification of a DNA species using template DNA from SB1969 (B strain) but fail to do so using DNA from C3-368-5 (C3 strain). Polymorphisms were mapped to chromosomes using a panel of monosomic strains constructed by crossing B strainderived nullisomic strains to inbred strain C3. They map to all five chromosomes and appear to be evenly distributed throughout the genome. Chromosomal groups were then analyzed for linkage using meiotic segregants; four linkage groups were identified in chromosomes IR, 2L, 3 and 5. The RAPD method appears useful for the construction of a genetic map of the Tetrahymena genome based on DNA polymorphisms.

Genetic mapping in Eucalyptus urophylla and Eucalyptus grandis using RAPD markers

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1051-1061 ◽  
Author(s):  
Daniel Verhaegen ◽  
Christophe Plomion
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Eucalyptus Grandis ◽  
Linkage Maps ◽  
Eucalyptus Urophylla ◽  
Linkage Groups ◽  
Decamer Primer ◽  
The Mean ◽  
Polymerase Chain ◽  
Selection Of

Two single-tree linkage maps were constructed for Eucalyptus urophylla and Eucalyptus grandis, based on the segregation of 480 random amplified polymorphic DNA (RAPD) markers in a F1 interspecific progeny. A mixture of three types of single-locus segregations were observed: 244 1:1 female, 211 1:1 male, and 25 markers common to both, segregating 3:1. Markers segregating in the 1:1 ratio (testcross loci) were used to establish separate maternal and paternal maps, while markers segregating in the 3:1 ratio were used to identify homology between linkage groups of the two species maps. An average of 2.8 polymorphic loci were mapped for each arbitrary decamer primer used in the polymerase chain reaction. The mean interval size beween framework markers on the maps was 14 cM. The maps comprised 269 markers covering 1331 cM and 236 markers covering 1415 cM, in 11 linkage groups, for E. urophylla (2n = 2x = 22) and E. grandis (2n = 2x = 22), respectively. A comparative mapping analysis with two other E. urophylla and E. grandis linkage maps showed that RAPDs could be reliable markers for establishing a consensus species map. RAPD markers were automatically and quantitatively scored with an imaging analyzer. They were classified into four categories based on their optical density. A fragment intensity threshold is proposed to optimize the selection of reliable RAPD markers for future mapping experiments. Key words : genetic linkage map, Eucalyptus urophylla, Eucalyptus grandis, random amplified polymorphic DNA, RAPD, automated data collection.

scholarly journals GENETIC LINKAGES OF RAPD MARKERS IN SWEETPOTATO

HortScience ◽  
1994 ◽  
Vol 29 (7) ◽  
pp. 727d-727
Author(s):  
Liang L. Hong ◽  
Paul G. Thompson
Keyword(s):  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Random Amplified Polymorphic Dna ◽  
Mendelian Inheritance ◽  
Linkage Groups ◽  
Banding Patterns ◽  
Segregation Ratios ◽  
Genetic Linkages ◽  
Polymorphic Bands

Random amplified polymorphic DNA (RAPD) markers were analyzed in parents and progeny of four sweetpotato crosses. An average of 69 primers were tested and 23.5% produced well resolved polymorphic banding patterns. Each polymorphic primer had an average of 1.9 polymorphic bands resulting in 0.45 polymorphic fragments per primer tested. Phenotypic segregation ratios of 88% of polymorphic fragments fit those expected for hexaploid Mendelian inheritance. Numbers of linked polymorphic fragments and numbers of linkage groups were 13 and 5 for Cross A, 0 and 0 for Cross B, 23 and 3 for Cross C and 16 and 6 for Cross D. Those results indicated that RAPD markers have potential for a genetic linkage map in sweetpotato; however, many primers must be screened.

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