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 linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers.

Genetics ◽  
1994 ◽  
Vol 137 (4) ◽  
pp. 1121-1137 ◽  
Author(s):  
D Grattapaglia ◽  
R Sederoff
Keyword(s):  
Genetic Linkage ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Eucalyptus Grandis ◽  
Single Individual ◽  
Linkage Maps ◽  
Eucalyptus Urophylla ◽  
Linkage Groups ◽  
Mapping Strategy ◽  
Genetic Linkage Maps

Abstract We have used a "two-way pseudo-testcross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F1 progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, theta = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support > or = 1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organisms. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the paradigm of a species index map to the heterodox proposal of constructing several maps for individual trees of a population, therefore mitigating the problem of linkage equilibrium between marker and trait loci for the application of marker assisted strategies in tree breeding.

scholarly journals A Composite Genetic Map of the Parasitoid Wasp Trichogramma brassicae Based on RAPD Markers

Genetics ◽  
1998 ◽  
Vol 150 (1) ◽  
pp. 275-282 ◽  
Author(s):  
Valérie Laurent ◽  
Eric Wajnberg ◽  
Brigitte Mangin ◽  
Thomas Schiex ◽  
Christine Gaspin ◽  
...  
Keyword(s):  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Parasitoid Wasp ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Trichogramma Brassicae ◽  
Haploid Male ◽  
The Mean ◽  
Mapping Populations

Abstract Three linkage maps of the genome of the microhymenopteran Trichogramma brassicae were constructed from the analysis of segregation of random amplified polymorphic DNA markers in three F2 populations. These populations were composed of the haploid male progeny of several virgin F1 females, which resulted from the breeding of four parental lines that were nearly fixed for different random amplified polymorphic DNA markers and that were polymorphic for longevity and fecundity characters. As the order of markers common to the three mapping populations was found to be well conserved, a composite linkage map was constructed. Eighty-four markers were organized into five linkage groups and two pairs. The mean interval between two markers was 17.7 cM, and the map spanned 1330 cM.

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.

scholarly journals Integration of EST-CAPS markers into genetic maps of Eucalyptus urophylla and E. tereticornis and their alignment with E. grandis genome sequence

2012 ◽  
Vol 61 (1-6) ◽  
pp. 247-255 ◽  
Author(s):  
X. Yu ◽  
Y. Guo ◽  
X. Zhang ◽  
F. Li ◽  
Q. Weng ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Rapd Markers ◽  
Expressed Sequence Tag ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Maps ◽  
Eucalyptus Urophylla ◽  
Linkage Groups ◽  
Caps Markers ◽  
Expressed Sequence ◽  
Genus Eucalyptus

AbstractA suite of 91 expressed sequence tag (EST) derived cleaved amplified polymorphic sequence (CAPS) markers were developed and used for enriching the genetic maps of Eucalyptus urophylla and E. tereticornis built previously based on random amplified polymorphic DNA (RAPD) markers. The EST-CAPS markers were highly similar to original ESTs, with sequence identity ranging from 92.5% to 100.0%. In linkage analysis, 48 and 42 EST-CAPSs were integrated into the genetic maps of E. urophylla and E. tereticornis, respectively, including 13 shared by both maps, while 14 were unmapped. For E. urophylla, the final map had a total length of 1789.5 cM and a mean interval between markers of 9.7 cM, being 284.9 cM larger and 1.3 cM less than those of the prior RAPD map, respectively. For E. tereticornis, the final map had a length of 1488.1 cM and a mean interval of 10.3 cM, being 452.4 and 0.2 cM more than the prior map, respectively. All the 77 newly mapped EST-CAPSs found each at least one homologue in the E. grandis genome sequence released recently, and conserved synteny and colinearity were observed between E. grandis genome and our linkage groups. The enriched maps would provide a set of useful markers for genome analysis, comparative mapping and fine-mapping of important genes located in conserved regions for the important tree genus Eucalyptus.

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.

scholarly journals Mapping and Evaluation of Malus ×domestica Microsatellites in Apple and Pear

2003 ◽  
Vol 128 (4) ◽  
pp. 515-520 ◽  
Author(s):  
Minou Hemmat ◽  
Norman F. Weeden ◽  
Susan K. Brown
Keyword(s):  
Simple Sequence Repeat ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Dna Polymorphisms ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Malus Sylvestris ◽  
Ssr Primers ◽  
Primer Sets ◽  
Simple Sequence

We mapped DNA polymorphisms generated by 41 sets of Simple Sequence Repeat (SSR) primers, developed independently in four laboratories. All primer sets gave polymorphisms that could be located on our `White Angel' x `Rome Beauty' map for apple [Malus sylvestris (L.) Mill. Var. domestica (Borkh.) Mansf.]. The SSR primers were used to identify homologous linkage groups in `Wijcik McIntosh', NY 75441-58, `Golden Delicious', and `Liberty' cultivars for which relatively complete linkage maps have been constructed from isozyme and Random Amplified Polymorphic DNA (RAPD) markers. In several instances, two or more SSRs were syntenic, and except for an apparent translocation involving linkage group (LG) 6, these linkages were conserved throughout the six maps. Twenty-four SSR primers were consistently polymorphic, and these are recommended as standard anchor markers for apple maps. Experiments on a pear (Pyrus communis L.) population indicated that many of the apple SSRs would be useful for mapping in pear. However some of the primers produced fragments in pear significantly different in size than those in apple.

Genetic Linkage Maps of the Guppy ( Poecilia reticulata ): Assignment of RAPD Markers to Multipoint Linkage Groups

2003 ◽  
Vol 5 (3) ◽  
pp. 279-293 ◽  
Author(s):  
Gideon Khoo ◽  
Meng Huat Lim ◽  
Haridas Suresh ◽  
Damien K. Y. Gan ◽  
Kok Fang Lim ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Rapd Markers ◽  
Poecilia Reticulata ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Multipoint Linkage ◽  
Genetic Linkage Maps

scholarly journals Assessment of genetic diversity among surian Toona sinensis Roem in progenies test using random amplified polymorphic DNA markers

2018 ◽  
Vol 22 (1) ◽  
pp. 22
Author(s):  
Jayusman Jayusman ◽  
Muhammad Na’iem ◽  
Sapto Indrioko ◽  
Eko Bhakti Hardiyanto ◽  
ILG Nurcahyaningsih
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Management Strategies ◽  
Genetic Distances ◽  
Sampled Data ◽  
Toona Sinensis ◽  
The Mean ◽  
Individual Trees

Surian Toona sinensis Roem is one of the most widely planted species in Indonesia. This study aimed to estimate the genetic diversity between a number of surian populations in a progeny test using RAPD markers, with the goal of proposing management strategies for a surian breeding program. Ninety-six individual trees from 8 populations of surian were chosen as samples for analysis. Eleven polymorphic primers (OP-B3, OP-B4, OP-B10, OP-H3, OP-Y6, OP-Y7, OP-Y8, OP-Y10, OP-Y11, OP-Y14, and OP-06) producing reproducible bands were analyzed for the 96 trees, with six trees per family sampled. Data were analyzed using GenAlEx 6.3, NTSYS 2.02. The observed percentage of polymorphic loci ranged from 18.2% to 50%. The mean level of genetic diversity among the surian populations was considered to be moderate (He 0.304). Cluster analysis grouped the genotypes into two main clusters, at similarity levels of 0.68 and 0.46. The first two axes of the PCoA explained 46.16% and 25.54% of the total variation, respectively. The grouping of samples into clusters and subclusters did not correspond with family and their distances, but the grouping was in line with the genetic distances of the samples.

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.

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.

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