Randomly amplified polymorphic DNA linkage relationships in different Norway spruce populations

2001 ◽  
Vol 31 (8) ◽  
pp. 1456-1461
Author(s):  
M Troggio ◽  
T L Kubisiak ◽  
G Bucci ◽  
P Menozzi
Keyword(s):  
Rapd Markers ◽  
Rapd Marker ◽  
Population Based ◽  
Italian Population ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Consensus Map ◽  
Norwegian Population ◽  
Marker Loci ◽  
Linkage Relationships

We tested the constancy of linkage relationships of randomly amplified polymorphic DNA (RAPD) marker loci used to construct a population-based consensus map in material from an Italian stand of Picea abies (L.) Karst. in 29 individuals from three Norwegian populations. Thirteen marker loci linked in the Italian stand did show a consistent locus ordering in the Norwegian population. The remaining 16 unlinked marker loci were spread over different linkage groups and (or) too far apart both in the population map and in this study. The limited validity of RAPD markers as genomic "hallmarks" resilient across populations is discussed. We also investigated the reliability of RAPD markers; only 58% of the RAPD markers previously used to construct the consensus map in the Italian population were repeatable in the same material. Of the repeatable ones 76.3% were amplified and found polymorphic in 29 megagametophyte sibships from three Norwegian populations.

scholarly journals Autopolyploidy versus Allopolyploidy and Low-density Randomly Amplified Polymorphic DNA Linkage Maps of Sweetpotato

1997 ◽  
Vol 122 (6) ◽  
pp. 822-828 ◽  
Author(s):  
Kittipat Ukoskit ◽  
Paul G. Thompson
Keyword(s):  
Genetic Analysis ◽  
Genome Size ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Chromosome Length ◽  
Low Density ◽  
Linkage Maps ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Genome Coverage

Low-density randomly amplified polymorphic DNA (RAPD) markers of sweetpotato [Ipomoea batatus (L.) Lam.; 2n = 6x = 90] were constructed from 76 pseudotestcross progenies obtained from `Vardaman' × `Regal'. Of 460 primers, 84 generating 196 well-resolved repeatable markers were selected for genetic analysis. `Vardaman' and `Regal' testcross progenies were analyzed for segregation and linkages of RAPD markers. Type of polyploidy, autopolyploidy, or allopolyploidy is uncertain in sweetpotato and was examined in this study using the ratio of nonsimplex to simplex RAPD markers and the ratio of simplex RAPD marker pairs linked in repulsion to coupling. Both measures indicated autopolyploidy. Low-density RAPD linkage maps of `Vardaman' and `Regal' were constructed from simplex RAPD marker linkage analysis. Duplex and triplex markers were then mapped manually into the simplex marker map. Homologous linkage groups were identified using nonsimplex RAPD markers and three homologous groups were found in each of the parent maps. Use of nonsimplex markers increased mapping efficiency. The `Vardaman' map had a predicted coverage of 10.5% at a 25-cM interval of the genome size of 5024 cM. In `Regal', genome coverage was estimated to be 5.6% at a 25-cM interval of the genome size of 6560 cM. Therefore, average chromosome length was ≈56 to 73 cM.

Segregation of random amplified polymorphic DNA markers and strategies for molecular mapping in tetraploid alfalfa

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 844-851 ◽  
Author(s):  
K. F. Yu ◽  
K. P. Pauls
Keyword(s):  
Chromosome Segregation ◽  
Dna Markers ◽  
Rapd Markers ◽  
Molecular Mapping ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Female Parent ◽  
Linkage Groups ◽  
Double Reduction ◽  
Chromatid Segregation

An F1 population was used to analyze the inheritance of random amplified polymorphic DNA (RAPD) markers in tetraploid alfalfa. Of the 32 RAPD markers that were used for a segregation analysis in this study, 27 gave ratios that are consistent with random chromosome and random chromatid segregation at meiosis. However, among all of the RAPD markers (121) that were screened in this study, only one example of a double reduction, that is typical of chromatid segregation, was observed. These results indicate that random chromosome segregation is likely the predominant but not the exclusive mode of inheritance for tetraploid alfalfa. χ2 analyses of cosegregation for RAPD marker pairs derived from the female parent revealed nine linkages that fell into four linkage groups. The recombination fractions among linked marker pairs ranged from 1 to 37%. These are the first molecular linkage groups reported in tetraploid alfalfa. In addition, various strategies for molecular mapping in the tetraploid alfalfa genome are proposed that should be of interest to plant breeders who are planning to use molecular markers for alfalfa or other tetraploid species.Key words: RAPD markers, tetraploid alfalfa, segregation, linkage groups.

scholarly journals Linkage Mapping in a Watermelon Population Segregating for Fusarium Wilt Resistance

2001 ◽  
Vol 126 (3) ◽  
pp. 344-350 ◽  
Author(s):  
Leigh K. Hawkins ◽  
Fenny Dane ◽  
Thomas L. Kubisiak ◽  
Billy B. Rhodes ◽  
Robert L. Jarret
Keyword(s):  
Ssr Markers ◽  
Fusarium Wilt ◽  
Rapd Markers ◽  
Bulked Segregant Analysis ◽  
Citrullus Lanatus ◽  
Linkage Groups ◽  
Mendelian Segregation ◽  
Marker Loci ◽  
Resistance Trait ◽  
Effective Use

Isozyme, randomly amplified polymorphic DNA (RAPD), and simple sequence repeats (SSR) markers were used to generate a linkage map in an F2 and F3 watermelon [Citrullus lanatus (Thumb.) Matsum. & Nakai] population derived from a cross between the fusarium wilt (Fusarium oxysporum f. sp. niveum) susceptible `New Hampshire Midget' and resistant PI 296341-FR. A 112.9 cM RAPD-based map consisting of 26 markers spanning two linkage groups was generated with F2 data. With F3 data, a 139 cM RAPD-based map consisting of 13 markers covering five linkage groups was constructed. Isozyme and SSR markers were unlinked. About 40% to 48% of the RAPD markers were significantly skewed from expected Mendelian segregation ratios in both generations. Bulked segregant analysis and single-factor analysis of variance were employed to identify RAPD markers linked to fusarium wilt caused by races 1 and 2 of F. oxysporum f. sp. niveum. Current linkage estimates between the resistance trait and the marker loci were too large for effective use in a marker-assisted selection program.

scholarly journals A Genetic Linkage Map for Watermelon Based on Randomly Amplified Polymorphic DNA Markers

2001 ◽  
Vol 126 (6) ◽  
pp. 730-737 ◽  
Author(s):  
Amnon Levi ◽  
Claude E. Thomas ◽  
Xingping Zhang ◽  
Tarek Joobeur ◽  
Ralph A. Dean ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
New Hampshire ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Citrullus Lanatus ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Rapd Primer ◽  
Race 1 ◽  
Linkage Distance

A genetic linkage [randomly amplified polymorphic DNA (RAPD)-based] map was constructed for watermelon [Citrullus lanatus (Thunb.) Matsum and Nakai] using a BC1 population [PI 296341-fusarium wilt resistant × New Hampshire Midget (fusarium susceptible)] × `New Hampshire Midget'. The map contains 155 RAPD markers, and a 700-base pair sequenced characterized amplified region (SCAR) marker that corresponds to a fragment produced by the RAPD primer GTAGCACTCC. This marker was reported previously as linked (1.6 cM) to race 1 fusarium wilt resistance in watermelon. The markers segregated to 17 linkage groups. Of these, 10 groups included nine to 19 markers, and seven groups included two to four markers. The map covers a genetic linkage distance of 1295 cM. Nine of the 10 large linkage groups contained segments with low (or no) level of recombination (0 to 2.6 cM) among markers, indicating that the watermelon genome may contain large chromosomal regions that are deficient in recombination events. The map should be useful for identification of markers linked closely to genes that control fruit quality and fusarium wilt (races 1 and 2) resistance in watermelon.

scholarly journals Randomly Amplified Polymorphic DNA Loci from a Walnut Backcross [(Juglans hindsii × J. regia) × J. regia]

1996 ◽  
Vol 121 (3) ◽  
pp. 358-361 ◽  
Author(s):  
Keith Woeste ◽  
Gale H. McGranahan ◽  
Robert Bernatzky
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Rapd Markers ◽  
Fragment Length Polymorphism ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Backcross Population ◽  
Persian Walnut ◽  
Marker Data ◽  
Juglans Hindsii ◽  
Restriction Fragment Length

Twenty-five random decamer primers were used to evaluate the level of polymorphism between Persian walnut and the Northern California black walnut. Sixty-six randomly amplified polymorphic DNA (RAPD) markers were identified using an interspecific walnut backcross population [(Juglans hindsii × J. regia) × J. regia]. Segregation data from these polymorphisms were joined to a previously published set of restriction fragment-length polymorphism (RFLP) marker data to expand the genetic map of walnut to 107 markers in 15 linkage groups.

scholarly journals Genetic Linkage of Randomly Amplified Polymorphic DNA (RAPD) Markers in Sweetpotato

1997 ◽  
Vol 122 (1) ◽  
pp. 79-82 ◽  
Author(s):  
Paul. G. Thompson ◽  
Liang L. Hong ◽  
Kittipat Ukoskit ◽  
Zhiqiang Zhu
Keyword(s):  
Linkage Map ◽  
Linkage Mapping ◽  
Genetic Linkage ◽  
Ipomoea Batatas ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Rapd Marker ◽  
Randomly Amplified Polymorphic Dna ◽  
Genetic Linkage Mapping ◽  
Map Construction

RAPD marker analyses were completed on parents and progeny of two sweetpotato [Ipomoea batatas (L.) Lam.] crosses to determine the feasibility of genetic linkage map construction. A total of 100 primers was tested and 96 produced amplified genomic DNA fragments. The average number of polymorphisms per primer was 0.69. A total of 134 polyphorphic markers was observed and 74 (60%) segregated 1 band present : 1 band absent as needed for use in genetic linkage mapping of polyploids. The 60% of RAPD markers that segregated 1:1 shows that genetic linkage mapping of the hexaploid sweetpotato by RAPD marker analysis is feasible. Linkage was determined for all markers that segregated 1:1 and five pairs of linked markers were found. These were the first linked molecular markers found in sweetpotato and they show that construction of a genetic linkage map is feasible. A genetic linkage map will be a valuable tool to assist in genetic improvements.

scholarly journals Keragaman Genetik Beberapa Genotipe Teh Berdasarkan Penanda RAPD (Random Amplified Polymorphic DNA)

2014 ◽  
Vol 1 (1) ◽  
pp. 1 ◽  
Author(s):  
Budi Martono ◽  
Laba Udarno
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Camellia Sinensis ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Dna Marker ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Plant Breeding Program ◽  
Marker Loci

<p>Informasi keragaman genetik dan ketersediaan plasma nutfah teh (Camellia sinensis) diperlukan dalam perakitan varietas unggul. Keragaman genetik berdasarkan penanda DNA dapat memberikan hasil yang lebih konsisten karena tidak dipengaruhi lingkungan. Dalam penelitian ini sebanyak 9 genotipe teh dianalisis keragamannya menggunakan enam penanda RAPD (OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, dan OPD 08). Penelitian dilakukan mulai bulan Maret sampai Mei 2013 di Laboratorium Terpadu Biotrop Bogor. Perhitungan koefisien kesamaan genetik dan analisis gerombol dilakukan dengan menggunakan perangkat lunak NTSYSpc versi 2.02. Sebanyak 54 lokus penanda RAPD berhasil diamplifikasi menggunakan enam primer dan 47 lokus di antaranya memiliki alel yang polimorfik (87,04%). Hasil analisis gerombol berdasarkan kesamaan genetiknya mengelompokkan 9 genotipe ke dalam enam kelompok. Empat kelompok (I, II, IV, V) masing-masing terdiri atas satu genotipe, sementara dua kelompok yang lain yaitu kelompok III dan VI masing-masing beranggotakan tiga dan dua genotipe.</p><p>Kata Kunci: Camellia sinensis, diversitas genetik, penanda RAPD</p><p>The availability of diverse tea (Camellia sinensis) germplasms as well as the information about their genetic diversity is required for plant breeding program. Genetic diversity analysis based on DNA marker is known to be more effective since the markers provide more consistent results. In this study, nine tea genotypes were evaluated for their genetic diversity using six Random Amplified Polymorphic DNA (RAPD) markers (OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08). The study was conducted from March to May 2013 in the Integrated Laboratory of Biotrop Bogor. The estimation of genetic similarity and the cluster analysis were done using NTSYSpc version 2.02. Of the six RAPD markers used in this study, a total of 54 RAPD marker loci have been successfully amplified. In which, 47 loci (87.04%) were polymorphic and subsequently used for the evaluation of tea genotypes. The results of cluster analysis showed that those tea genotypes were clustered into six groups. Each of four groups (I, II, IV, V) consisted of only one genotype. Meanwhile, the other two groups (III and VI) had three and two genotypes, respectively.</p>

scholarly journals RAPD Marker Polymorphism among Saskatoon Cultivars, Clones, and Seedlings

HortScience ◽  
1997 ◽  
Vol 32 (6) ◽  
pp. 1109-1113 ◽  
Author(s):  
B.J. Weir ◽  
R.G. St. Pierre ◽  
R.N. Chibbar
Keyword(s):  
Rapd Markers ◽  
Rapd Marker ◽  
Dna Fragments ◽  
Polymorphic Markers ◽  
Randomly Amplified Polymorphic Dna ◽  
Oligonucleotide Primers ◽  
Marker Polymorphism

Randomly amplified polymorphic DNA (RAPD) markers were used to distinguish among 16 cultivars of saskatoon (Amelanchier spp.). Eight 9-base, oligonucleotide primers amplified a total of 98 DNA fragments, of which 29 were useful as reproducible polymorphic markers. Twelve cultivars and two pairs of cultivars were uniquely characterized by these 29 markers. Polymorphism was not detected among five sources of the cv. Thiessen, whereas variability was found among seedlings from self-pollinated `Thiessen'. Samples of the cvs. Regent and Parkhill were indistinguishable from one of two sources, suggesting that the cultivars were mislabelled.

scholarly journals Genetic Diversity of a Capsicum Germplasm Collection from Nepal as Determined by Randomly Amplified Polymorphic DNA Markers

2002 ◽  
Vol 127 (3) ◽  
pp. 318-324 ◽  
Author(s):  
J. Baral ◽  
P.W. Bosland
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Similarity Index ◽  
Germplasm Collection ◽  
Western Hemisphere ◽  
Randomly Amplified Polymorphic Dna ◽  
Index Value ◽  
Single Cluster

Domesticated chile (Capsicum annuum L. var. annuum) is a widely cultivated spice and vegetable crop. It originated in the Western Hemisphere, but spread rapidly throughout the globe after the voyage of Columbus. However, very little is known about the genetic diversity of chile in Asia and especially in Nepal. Thus, research was conducted to document morphological as well as molecular characterization of C. annuum var. annuum landraces collected from Nepal. Genetic diversity in C. annuum var. annuum landraces from Nepal was investigated using randomly amplified polymorphic DNA (RAPD) markers and compared with that of C. annuum var. annuum landraces from the center of diversity, Mexico. RAPD marker based cluster analysis of C. annuum var. annuum clearly separated each accession. All accessions of C. annuum var. annuum from Nepal grouped into a single cluster at a similarity index value of 0.80, whereas, accessions from Mexico grouped into eight different clusters at the same similarity level indicating greater genetic diversity in Mexican accessions. RAPD analysis indicated that the Nepalese chile population went through an additional evolutionary bottleneck or founder effect probably due to intercontinental migrations. Some Nepalese accessions had unique RAPD markers suggesting that additional sources of genetic variation are available in Nepalese germplasm.

scholarly journals Geographic Differentiation and Embryo Type Identification in Mangifera indica L. Cultivars Using RAPD Markers

HortScience ◽  
1997 ◽  
Vol 32 (6) ◽  
pp. 1105-1108 ◽  
Author(s):  
J.A. López-Valenzuela ◽  
O. Martínez ◽  
O. Paredes-López
Keyword(s):  
Bulk Segregant Analysis ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Mangifera Indica ◽  
Rapd Marker ◽  
Geographic Origin ◽  
Arbitrary Sequence ◽  
Geographic Differentiation ◽  
Randomly Amplified Polymorphic Dna ◽  
Good Agreement

Fifteen mango cultivars were examined using randomly amplified polymorphic DNA (RAPD) markers with decamer primers of arbitrary sequence. Thirteen of the 40 primers screened were informative and 109 amplified DNA bands were selected as RAPD markers. Specific RAPD markers for some mango cultivars were identified. Cluster analysis based on the 109 RAPD markers produced a dendrogram of the genetic relatedness of the 15 mango cultivars. `Manila' and `Carabao' were the most similar, which is in good agreement with their putative pedigrees. The four major bifurcations in the dendrogram separated correctly the genotypes into four groups according to their geographic origin. Bulk segregant analysis of polyembryonic and monoembryonic cultivars detected a specific RAPD marker for polyembryony. These markers may facilitate the management of mango germplasm for breeding purposes.

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