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

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.

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

Genome ◽

10.1139/g93-112 ◽

1993 ◽

Vol 36 (5) ◽

pp. 844-851 ◽

Cited By ~ 23

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.

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Evidence for Colinearity among Genetic Linkage Maps in Cucumber

HortScience ◽

10.21273/hortsci.42.1.20 ◽

2007 ◽

Vol 42 (1) ◽

pp. 20-27 ◽

Cited By ~ 9

Author(s):

Jack E. Staub ◽

Zhanyong Sun ◽

Sang-Min Chung ◽

Richard L. Lower

Keyword(s):

Quantitative Trait Loci ◽

Fragment Length ◽

Quantitative Trait ◽

Yield Component ◽

Genetic Maps ◽

Linkage Groups ◽

Length Polymorphisms ◽

Trait Loci ◽

Processing Line ◽

Simple Sequence

Cucumber (Cucumis sativus L. var. sativus; 2n = 2x = 14), has a narrow genetic base (3% to 8% polymorphism). Nevertheless, several genetic maps exist for this species. It is important to know the degree of colinearity among these maps. Thus, the positions of random amplified polymorphic DNAs, sequenced characterized amplified regions, simple sequence repeat, restriction fragment length polymorphisms, and fluorescent amplified fragment length polymorphism markers were compared in four maps. A previously unreported map was constructed in a narrow cross (processing line 2A × Gy8; C. s. var. sativus; ≈7% polymorphism) and compared with the three published maps [two narrow-based (processing type; C. s. var. sativus; 8% to 12% polymorphism) and a broad-based (C. s. var. sativus × C. s. var. hardwickii (R.) Alef. ≈12%)]. Common makers were identified in seven linkage groups, providing evidence for microsynteny. These common markers were used as anchor markers for map position comparisons of yield component quantitative trait loci. The relative order of anchor markers in each of six linkage groups (linkage groups 1, 2, and 4–7) that had two or more anchor markers within each group was colinear, and instances of microsynteny were detected. Commonalities in the position of some yield component quantitative trait loci exist in linkage groups 1 and 4 of the maps examined, and the general synteny among these maps indicates that identification and mapping of additional anchor markers would lead to successful map merging to increase cucumber map saturation for use in cucumber breeding.

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

Genome ◽

10.1139/g99-136 ◽

2000 ◽

Vol 43 (2) ◽

pp. 333-340 ◽

Cited By ~ 88

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.

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

Genetics ◽

10.1093/genetics/150.1.275 ◽

1998 ◽

Vol 150 (1) ◽

pp. 275-282 ◽

Cited By ~ 3

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.

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

Genetics ◽

10.1093/genetics/136.4.1435 ◽

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.

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

Silvae Genetica ◽

10.1515/sg-2012-0031 ◽

2012 ◽

Vol 61 (1-6) ◽

pp. 247-255 ◽

Cited By ~ 5

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.

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

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.128.4.0515 ◽

2003 ◽

Vol 128 (4) ◽

pp. 515-520 ◽

Cited By ~ 40

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.

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A genetic linkage map for the domesticated silkworm, Bombyx mori, based on restriction fragment length polymorphisms

Genetics Research ◽

10.1017/s0016672300034467 ◽

1995 ◽

Vol 66 (2) ◽

pp. 109-126 ◽

Cited By ~ 48

Author(s):

Jinrui Shi ◽

David G. Heckel ◽

Marian R. Goldsmith

Keyword(s):

Linkage Map ◽

Bombyx Mori ◽

Restriction Fragment ◽

Fragment Length ◽

Restriction Fragment Length Polymorphisms ◽

Genetic Maps ◽

Crossing Over ◽

Linkage Groups ◽

Length Polymorphisms ◽

Restriction Fragment Length

SummaryWe present data for the initial construction of a molecular linkage map for the domesticated silkworm, Bombyx mori, based on 52 progeny from an F2 cross from a pair mating of inbred strains p50 and C108, using restriction fragment length polymorphisms (RFLPs). The map contains 15 characterized single copy sequences, 36 anonymous sequences derived from a follicular cDNA library, and 10 loci corresponding to a low copy number retrotransposon, mag. The 15 linkage groups and 8 ungrouped loci account for 23 of the 28 chromosomes and span a total recombination length of 413 cM; 10 linkage groups were correlated with established classic genetic maps. Scoring data from Southern blots were analysed using two Pascal programs written specifically to analyse linkage data in Lepidoptera, where females are the heterogametic sex and have achiasmatic meiosis (no crossing-over). These first examine evidence for linkage by calculating the maximum lod score under the hypothesis that the two loci are linked over the likelihood under the hypothesis that the two loci assort independently, and then determine multilocus linkage maps for groups of putatively syntenic loci by calculating the maximum likelihood estimate of the recombination fractions and the log likelihood using the EM algorithm for a specified order of loci along the chromosome. In addition, the possibility of spurious linkage was exhaustively tested by searching for genotypes forbidden by the absence of crossing-over in one sex.

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

Indonesian Journal of Biotechnology ◽

10.22146/ijbiotech.25798 ◽

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.

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Mapping of digested and undigested random amplified microsatellite polymorphisms in barley

Genome ◽

10.1139/g95-130 ◽

1995 ◽

Vol 38 (5) ◽

pp. 991-998 ◽

Cited By ~ 26

Author(s):

Jörg Becker ◽

Manfred Heun

Keyword(s):

Simple Sequence Repeats ◽

Dna Markers ◽

Simple Sequence Repeat ◽

Sequence Data ◽

Linkage Maps ◽

Sequence Repeat ◽

Rflp Map ◽

Alternative Approach ◽

Microsatellite Mapping ◽

Simple Sequence

The broad use of microsatellites as a tool for constructing linkage maps in plants has been limited by the need for sequence data to detect the underlying simple sequence repeats. Therefore, random amplified microsatellite polymorphisms (RAMPs) were studied as an alternative approach for barley mapping. Labelled (GA)n simple sequence repeat primers were combined with RAPD primers of different length and sequence to generate RAMPs. To get additional polymorphisms (called dRAMPs), the obtained products were also analysed after digestion with MseI. There were 0–11 polymorphisms found per primer combination. Sixty RAMPs/dRAMPs identifying 40 new loci were mapped onto a barley RFLP map. The new DNA markers are found on all chromosomes and they increased the length of the barley map by 174 cM to a total of 1270 cM. Interestingly, the RAMPs/dRAMPs caused stretching effects in genome areas where stretching was also observed for AFLPs.Key words: barley, microsatellite, mapping, RAMP, RFLP.

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