Construction of a framework map in Pinus contorta subsp. latifolia using random amplified polymorphic DNA markers

Genome ◽  
2001 ◽  
Vol 44 (2) ◽  
pp. 147-153 ◽  
Author(s):  
Changxi Li ◽  
Francis C Yeh
Keyword(s):  
Pinus Contorta ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Lod Score ◽  
Chain Reaction ◽  
Base Pairs ◽  
Oligonucleotide Primers ◽  
Polymerase Chain ◽  
Genomic Map

We report on the construction of the first random amplified polymorphic DNA (RAPD) framework map in Pinus contorta subsp. latifolia. Genomic DNA of haploid megagametophytes from 90 open-pollinated seeds originating from a single tree were amplified with 840 random decamer oligonucleotide primers by the polymerase chain reaction. Three-hundred twenty-eight RAPD markers with fragment sizes that ranged between 260 and 3080 base pairs were found segregating at 110 random decamer oligonucleotide primers. Of these 328 RAPD markers, 148 were mapped to 16 framework linkage groups and 77 were mapped as accessory markers onto the framework linkage groups, on a support interval of minimal LOD score of 3. The 16 framework maps cover a distance of 2287 cM. The estimate of genome size was 2407 cM with a 95% confidence interval of 2304–2459 cM.Key words: framework genomic map, RAPD, Pinus contorta subsp. latifolia.

Inheritance of random amplified polymorphic DNA markers in an interspecific cross in the genus Stylosanthes

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 50-56 ◽  
Author(s):  
Kemal Kazan ◽  
John M. Manners ◽  
Don F. Cameron
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Interspecific Cross ◽  
Parental Origin ◽  
Chain Reaction ◽  
Stylosanthes Hamata ◽  
Polymerase Chain

The inheritance of random amplified polymorphic DNA (RAPD) markers generated via the polymerase chain reaction amplification of genomic DNA sequences in an F2 family of an interspecific cross between Stylosanthes hamata and S. scabra was investigated. An initial comparison between the parental species, S. hamata cv. Verano and S. scabra cv. Fitzroy, demonstrated that 34% of detected RAPD bands were polymorphic. Of 90 primers tested, 35 showed relatively simple and reliably scorable polymorphisms and were used for segregation analysis. Sixty F2 individuals were scored for the segregation of 73 RAPD markers and 55 of these markers fit a 3:1 ratio. Segregation of eight other RAPD markers deviated significantly from a 3:1 ratio. There was no bias in the inheritance of RAPD markers regarding parental origin of the segregating RAPD markers. Linkage analysis revealed 10 linkage groups containing a total of 44 RAPD loci. Another 10 RAPD markers (7 of maternal origin) that were polymorphic between the parents did not segregate in the F2 population. One of the maternally inherited RAPD bands hybridized to chloroplast DNA. Analysis of RAPD loci by DNA hybridization indicated that mainly repeated sequences were amplified. These data indicate that RAPDs are useful genetic markers in Stylosanthes spp. and they may be suitable for genetic mapping.Key words: genetic mapping, molecular markers, polymerase chain reaction, Stylosanthes hamata, Stylosanthes scabra.

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.

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.

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 663 PB 101 IDENTIFICATION OF POINSETTIA CULTIVARS USING RAPD MARKERS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 527g-528
Author(s):  
Jing-Tian Ling ◽  
Roger Sauve ◽  
Nick Gawel
Keyword(s):  
Polymerase Chain Reaction ◽  
Rapd Markers ◽  
Patent Protection ◽  
Cultivar Identification ◽  
Randomly Amplified Polymorphic Dna ◽  
Chain Reaction ◽  
Base Pairs ◽  
Ctab Method ◽  
Leaf Tissues ◽  
Polymerase Chain

The development of scoreable genetic markers in poinsettia will be valuable for cultivar identification and for use in patent protection. In this study, polymerase chain reaction (PCR) and randomly amplified polymorphic DNA (RAPD) techniques were investigated for their feasibility in the identification of poinsettia cultivars. DNA was extracted from leaf tissues using the CTAB method. Thirty-six out of 39 (92.4%) primers amplified poinsettia DNA. The size of the amplified DNA fragments ranged from 140 to 2,000 base pairs. On average, 5.4 bands (range 1 - 13) were obtained per primer. A total of 195 bands were obtained; 49 (25.1%) bands were polymorphic in the 9 tested poinsettia cultivars. All tested cultivars could be discriminated with the banding profiles generated from 2 primers. RADP markers provide a consistently reliable and efficient technique for the identification of poinsettia cultivar.

scholarly journals Identification of Citrus Chimeras by RAPD Markers

HortScience ◽  
1995 ◽  
Vol 30 (6) ◽  
pp. 1276-1278 ◽  
Author(s):  
Kuniaki Sugawara ◽  
Atsushi Oowada ◽  
Takaya Moriguchi ◽  
Mitsuo Omura
Keyword(s):  
Polymerase Chain Reaction ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Chain Reaction ◽  
Reaction Conditions ◽  
Polymerase Chain

Random amplified polymorphic DNA (RAPD) markers were used to detect chimerism of citrus cultivars. Polymerase chain reaction conditions suitable for discriminating citrus chimeras were determined. Primers that produced consistent and repeatable bands that differed between the parental cultivars were chosen to create discriminating band patterns. Our results show that selected 12-mer primers can be useful for identifying the four citrus chimeras tested using RAPD technology.

scholarly journals Genetic diversity analysis of endemic species, Garcinia cambogia Gaertn using randomly amplified Polymorphic DNA markers

2017 ◽  
Vol 7 ◽  
Author(s):  
Santosh P ◽  
Suresh B. Arakera
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Consumer Preference ◽  
Randomly Amplified Polymorphic Dna ◽  
Chain Reaction ◽  
Garcinia Cambogia ◽  
Polymerase Chain ◽  
Polymorphic Bands ◽  
Dna Pcr

<p><strong>Polymerase chain reaction based random amplified polymorphic DNA (PCR-RAPD) markers were employed to assess genetic diversity in eight <em>Garcinia  cambogia</em>  genotypes. Among the 20 random primers used in the present investigation, 9 primers showed polymorphism. A total number of 227 bands were obtained from 9 primers, out of which 225 were polymorphic, showing 99.11% polymorphism. An average of 25.22 bands per primer was scored and average number of polymorphic bands found to be 25. The eight accessions fall into two major clusters. Cluster analysis showed that the red and yellow accessions cannot be regarded as two different varieties. The use of red and yellow fruits for commercial and medicinal purposes, respectively, is purely based on consumer preference. </strong></p>

Detection of the Glanzmann's Thrombasthenia Mutations in Arab and Iraqi-Jewish Patients by Polymerase Chain Reaction and Restriction Analysis of Blood or Urine Samples

1991 ◽  
Vol 66 (04) ◽  
pp. 500-504 ◽  
Author(s):  
H Peretz ◽  
U Seligsohn ◽  
E Zwang ◽  
B S Coller ◽  
P J Newman
Keyword(s):  
Polymerase Chain Reaction ◽  
Base Pair ◽  
Restriction Analysis ◽  
Urine Samples ◽  
Chain Reaction ◽  
Base Pairs ◽  
Glanzmann’S Thrombasthenia ◽  
Glanzmann's Thrombasthenia ◽  
Base Pair Deletion ◽  
Polymerase Chain

SummarySevere Glanzmann's thrombasthenia is relatively frequent in Iraqi-Jews and Arabs residing in Israel. We have recently described the mutations responsible for the disease in Iraqi-Jews – an 11 base pair deletion in exon 12 of the glycoprotein IIIa gene, and in Arabs – a 13 base pair deletion at the AG acceptor splice site of exon 4 on the glycoprotein IIb gene. In this communication we show that the Iraqi-Jewish mutation can be identified directly by polymerase chain reaction and gel electrophoresis. With specially designed oligonucleotide primers encompassing the mutation site, an 80 base pair segment amplified in healthy controls was clearly distinguished from the 69 base pair segment produced in patients. Patients from 11 unrelated Iraqi-Jewish families had the same mutation. The Arab mutation was identified by first amplifying a DNA segment consisting of 312 base pairs in controls and of 299 base pairs in patients, and then digestion by a restriction enzyme Stu-1, which recognizes a site that is absent in the mutant gene. In controls the 312 bp segment was digested into 235 and 77 bp fragments, while in patients there was no change in the size of the amplified 299 bp segment. The mutation was found in patients from 3 out of 5 unrelated Arab families. Both Iraqi-Jewish and Arab mutations were detectable in DNA extracted from blood and urine samples. The described simple methods of identifying the mutations should be useful for detection of the numerous potential carriers among the affected kindreds and for prenatal diagnosis using DNA extracted from chorionic villi samples.

scholarly journals Characterization of Xanthomonas axonopodis pv. phaseoli isolates

2008 ◽  
Vol 34 (3) ◽  
pp. 228-231 ◽  
Author(s):  
Willian Mário de Carvalho Nunes ◽  
Maria Júlia Corazza ◽  
Silvana Aparecida Crestes Dias de Souza ◽  
Siu Mui Tsai ◽  
Eiko Eurya Kuramae
Keyword(s):  
Xanthomonas Campestris ◽  
Random Amplified Polymorphic Dna ◽  
Hypersensitive Reaction ◽  
Chain Reaction ◽  
Xanthomonas Axonopodis ◽  
Paulo State ◽  
Total Dna ◽  
Polymerase Chain ◽  
Bacterial Plant Pathogen

A simple, quick and easy protocol was standardized for extraction of total DNA of the bacteria Xanthomonas axonopodis pv. phaseoli. The DNA obtained by this method had high quality and the quantity was enough for the Random Amplified Polymorphic DNA (RAPD) reactions with random primers, and Polymerase Chain Reaction (PCR) with primers of the hypersensitivity and pathogenicity gene (hrp). The DNA obtained was free of contamination by proteins or carbohydrates. The ratio 260nm/380nm of the DNA extracted ranged from 1.7 to 1.8. The hrp gene cluster is required by bacterial plant pathogen to produce symptoms on susceptible hosts and hypersensitive reaction on resistant hosts. This gene has been found in different bacteria as well as in Xanthomonas campestris pv. vesicatoria (9). The primers RST21 and RST22 (9) were used to amplify the hrp gene of nine different isolates of Xanthomonas axonopodis pv. phaseoli from Botucatu, São Paulo State, Brazil, and one isolate, "Davis". PCR amplified products were obtained in all isolates pathogenic to beans.

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