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.

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.

Development of a second generation linkage map for almond using RAPD and SSR markers

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 649-655 ◽  
Author(s):  
T Joobeur ◽  
N Periam ◽  
M C de Vicente ◽  
G J King ◽  
P Arús
Keyword(s):  
Simple Sequence Repeats ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Prunus Amygdalus ◽  
Total Size ◽  
Length Polymorphisms ◽  
Simple Sequence

Fifty-four RAPD (random amplified polymorphic DNA) markers and 6 SSRs (simple sequence repeats) were included in a molecular marker map with 120 RFLPs (restriction fragment length polymorphisms) and 7 isozyme genes previously constructed using the offspring of a cross between the almond (Prunus amygdalus) cultivars 'Ferragnès' and 'Tuono'. Only highly reproducible RAPDs segregating 1:1 were used. To identify these markers, a total of 325 primers were screened, from which 41 produced RAPDs useful for mapping. Polymorphism was detected in six of the eight Prunus SSRs (simple sequence repeats) studied, thus enabling these to be mapped. All markers were placed on the 8 linkage groups previously identified. The number of new markers included in the map of 'Ferragnès' was 33 for a total of 126, and 30 in the map of 'Tuono' for a total of 99. The sizes of the maps of 'Ferragnès' (415 cM) and 'Tuono' (416 cM) were similar, representing a 5% increase over the maps constructed solely with isozymes and RFLPs. The estimated total size of the almond map was of 457 cM. Some markers were placed in zones with low density of markers and others in the extreme of linkage groups. The use of RAPD markers to complete genetic maps constructed with transferable markers is discussed.Key words: almond, Prunus amygdalus, RAPD, SSR, mapping.

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.

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.

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.

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.

A gene controlling sex in grapevines placed on a molecular marker-based genetic map

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 333-340 ◽  
Author(s):  
M A Dalbó ◽  
G N Ye ◽  
N F Weeden ◽  
H Steinkellner ◽  
K M Sefc ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Dna Markers ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Basic Number ◽  
Genetic Maps ◽  
Hybrid Population ◽  
Linkage Groups ◽  
Starting Point ◽  
Map Distance

Genetic maps of Vitis (2n = 38) have been constructed from an interspecific hybrid population of 58 seedlings of the cross 'Horizon' ('Seyval' × 'Schuyler') × Illinois 547-1 (V. cinerea B9 × V. rupestris B38). The maps were initially constructed based on 277 RAPD (random amplified polymorphic DNA) markers using a double-pseudotestcross strategy. Subsequently, 25 microsatellites, 4 CAPS (cleaved amplified polymorphic sequence), and 12 AFLP (amplified fragment length polymorphism) markers were added to the maps. Another 120 markers, mostly those segregating 3:1, were also assigned but not positioned on the linkage groups in the two maps. The 'Horizon' map consisted of 153 markers covering 1199 cM, with an average map distance of 7.6 cM between markers. The Illinois 547-1 map had 179 markers covering 1470 cM, with an average map distance of 8.1 cM. There were 20 linkage groups in each map, one more than the basic number of chromosomes in grapes. Ten linkage groups in each map were identified as homologous using 16 microsatellite and 2 CAPS markers polymorphic in both parents. A single locus controlling sex in grapes mapped close to a microsatellite marker. These maps provide enough coverage of the genome for QTL (quantitative trait loci) analysis and as a starting point for positional gene cloning in grapes. Key words: Vitis, RAPD, microsatellite, SSR, CAPS.

Functional genomic resources for potato

2008 ◽  
Vol 88 (4) ◽  
pp. 573-581 ◽  
Author(s):  
Xiu-Qing Li ◽  
Rebecca Griffiths ◽  
David De Koeyer ◽  
Charlotte Rothwell ◽  
Vicki Gustafson ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Genetic Maps ◽  
Genomic Research ◽  
Functional Genomic ◽  
Entire Genome ◽  
Future Directions ◽  
Genomic Resources ◽  
Expressed Sequence ◽  
Selection Of ◽  
Made In

Considerable functional genomic resources have been developed by the potato research community in the past decade, including expressed sequence tag (EST) libraries, SAGE libraries, microarrays, molecular-function maps, and mutant populations. This article reviews the types, characteristics, strengths, limitations, and appropriate applications of these resources for genomic research and discusses perspectives on future directions. This wide selection of resources available to potato researchers complements efforts to sequence the entire genome and advances made in the development of saturated genetic maps. Key words: Solanum, potato, genomics, expressed sequence tag, microarray, longSAGE, data mining

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