scholarly journals Developing RAPD Markers for Grape Breeding

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 609f-609 ◽  
Author(s):  
J. Lu ◽  
O. Lamikanra ◽  
Y. Wang ◽  
Z. Liu ◽  
D. Ramming
Keyword(s):  
Rapd Markers ◽  
Scar Marker ◽  
Bulked Segregant Analysis ◽  
Rapd Marker ◽  
Early Screening ◽  
Horticultural Crop ◽  
Pooled Dna ◽  
Rapd Primer ◽  
Breeding Selection ◽  
Grape Breeding

The grape is an important horticultural crop that is grown worldwide. Breeding a new grape cultivar by conventional means normally will take several generations of backcross, at least 15 years. The efficiency and speed of selection can be accelerated if genetic markers are available for early screening. This project is designed to generate RAPD markers linked to viticulturally important traits, including seedlessness and pistillate genes. A F1 population with 64 progenies of V. vinifera was used for the RAPD analysis. Bulked Segregant Analysis (BSA) method was used for RAPD primer screening. Three-hundred primers were screened between the two pairs of pooled DNA samples, seeded and seedlessness, pistillate and perfect flowers. At least 10 primers produced one polymorphism each between the pools. Further analysis revealed that one of these RAPDs cosegregated tightly with the seedlessness trait, while the others either had loose linkage or no linkage to the traits. To make the RAPD marker useful for breeding selection, an attempt was made to convert it into SCAR marker. The results demonstrated that the RAPD marker may be useful for grape breeding and interpreting inheritance of a particular trait in grapes.

Isolation of microsatellite and RAPD markers flanking the Yr15 gene of wheat using NILs and bulked segregant analysis

Genome ◽  
1999 ◽  
Vol 42 (6) ◽  
pp. 1050-1056 ◽  
Author(s):  
V Chagué ◽  
T Fahima ◽  
A Dahan ◽  
G L Sun ◽  
A B Korol ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Stripe Rust ◽  
Rust Resistance ◽  
Rapd Markers ◽  
Bulked Segregant Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Rust Resistance Gene ◽  
Stripe Rust Resistance ◽  
Stripe Rust Resistance Gene

Microsatellite and random amplified polymorphic DNA (RAPD) primers were used to identify molecular markers linked to the Yr15 gene which confer resistance to stripe rust (Puccina striiformis Westend) in wheat. By using near isogenic lines (NILs) for the Yr15 gene and a F2 mapping population derived from crosses of these lines and phenotyped for resistance, we identified one microsatellite marker (GWM33) and one RAPD marker (OPA19800) linked to Yr15. Then, bulked segregant analysis was used in addition to the NILs to identify RAPD markers linked to the target gene. Using this approach, two RAPD markers linked to Yr15 were identified, one in coupling (UBC199700) and one in repulsion phase (UBC2121200). After Mapmaker linkage analysis on the F2 population, the two closest markers were shown to be linked to Yr15 within a distance of about 12 cM. The recombination rates were recalculated using the maximum likelihood technique to take into account putative escaped individuals from the stripe rust resistance test and obtain unbiased distance estimates. As a result of this study, the stripe rust resistance gene Yr15 is surrounded by two flanking PCR markers, UBC199700 and GWM33, at about 5 cM from each side.Key words: wheat, Triticum dicoccoides, Yr15 stripe rust resistance gene, genetic mapping, microsatellite markers, RAPD markers.

scholarly journals Identification and Confirmation of RAPD and SCAR Markers Linked to the ms-3 Gene Controlling Male Sterility in Melon (Cucumis melo L.)

2004 ◽  
Vol 129 (6) ◽  
pp. 819-825 ◽  
Author(s):  
Soon O. Park ◽  
Kevin M. Crosby ◽  
Rongfeng Huang ◽  
T. Erik Mirkov
Keyword(s):  
Male Sterility ◽  
Seed Production ◽  
Rapd Markers ◽  
Scar Marker ◽  
Rapd Marker ◽  
Hybrid Seed ◽  
Hybrid Seed Production ◽  
Scar Markers ◽  
Male Sterile ◽  
The Cross

Male sterility is an important trait of melon in F1 hybrid seed production. Molecular markers linked to a male-sterile gene would be useful in transferring male sterility into fertile melon cultivars and breeding lines. However, markers linked to the ms-3 gene for male sterility present in melon have not been reported. Our objectives were to identify randomly amplified polymorphic DNA (RAPD) markers linked to the ms-3 gene controlling male sterility using bulked segregant analysis in an F2 population from the melon cross of line ms-3 (male-sterile) × `TAM Dulce' (male-fertile), convert the most tightly linked RAPD marker to the ms-3 gene into a sequence characterized amplified region (SCAR) marker based on a specific forward and reverse 20-mer primer pair, and confirm the linkage of the RAPD and SCAR markers with the ms-3 gene in an F2 population from the cross of line ms-3 × `Mission' (male-fertile). A single recessive gene controlling male sterility was found in F2 individuals and confirmed in F3 families. Two RAPD markers that displayed an amplified DNA fragment in the male-sterile bulk were detected to be linked to the ms-3 gene in the F2 population from the cross of line ms-3 × `TAM Dulce'. RAPD marker OAM08.650 was closely linked to the ms-3 gene at 2.1 cM. SCAR marker SOAM08.644 was developed on the basis of the specific primer pair designed from the sequence of the RAPD marker OAM08.650. The linked RAPD and SCAR markers were confirmed in the F2 population from the cross of line ms-3 × `Mission' to be consistently linked to the ms-3 gene at 5.2 cM. These markers were also present in 22 heterozygous fertile F1 plants having the ms-3 gene. The RAPD and SCAR markers linked to the ms-3 gene identified, and confirmed here could be utilized for backcrossing of male sterility into elite melon cultivars and lines for use as parents for F1 hybrid seed production.

scholarly journals Identification of RAPD Markers Linked to Major Gene for Indeterminate Growth Habit using Bulked Segregant Analysis in Common Bean Cross

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 623c-623
Author(s):  
S.O. Park ◽  
J.M. Bokosi ◽  
D.P. Coyne
Keyword(s):  
Rapd Markers ◽  
Growth Habit ◽  
Bulked Segregant Analysis ◽  
Major Gene ◽  
Indeterminate Growth ◽  
Bulked Dna ◽  
Rapd Primer ◽  
Plant Growth Habit ◽  
Indeterminate Growth Habit ◽  
Determinate Growth

Plant growth habit is an important trait. Our objective was to identify RAPD markers linked to major gene for indeterminate growth habit using bulked segregant analysis in an F2 population from a bean cross Chichara (indeterminate growth habit × PC-50 (determinate growth habit). A total of 132 RAPD primers (600 RAPD primer screened) showed polymorphisms between bulked DNA derived from indeterminate and determinate plants. All markers showed coupling linkage with indeterminate growth habit. RAPD markers of A-8, A-17, C-7, C-15, D-4, D-5, F-6, F-16, G-9, H-3, H-20, and I-7 were 2.2 cM distant from the gene for indeterminate growth habit. Markers of B-7, B-16, B-17, C-8, E-1, F-1, F-20 and H-l9 primers were 4.6 cM distant from the gene for indeterminate growth habit.

scholarly journals Identification of Random Amplified Polymorphic DNA (RAPD) Markers for Self-incompatibility Alleles in Hazelnut

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 591e-591
Author(s):  
Kirk W. Pomper ◽  
Anita N. Azarenko ◽  
Joel W. Davis ◽  
Shawn A. Mehlenbacher
Keyword(s):  
Rapd Markers ◽  
Uv Light ◽  
Bulked Segregant Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Self Incompatibility ◽  
Ethidium Bromide Staining ◽  
Young Leaves ◽  
Incompatibility Alleles ◽  
Selection Of

Random amplified polymorphic DNA (RAPD) markers were identified for self-incompatibility (SI) alleles that will allow marker-assisted selection of desired S-alleles and assist in cloning the locus responsible for the sporophytic SI displayed in hazelnut (Corylus avellana L.). DNA was extracted from young leaves collected from field-planted parents and 27 progeny of the cross OSU 23.017 (S1 S12) × VR6-28 (S2 S26). Screening of 10-base oligonucleotide RAPD primers was performed using bulked segregant analysis. DNA samples from six trees each were pooled into four “bulks,” one for each of the following: S1 S2, S1 S26, S2 S12, and S12 S26. “Super bulks” of twelve trees each for S1, S2, S12, and S26 then were created for each allele by combining the appropriate bulks. The DNA from these four super bulks and also the parents was used as a template in the PCR assays. Amplification products were electrophoresed on 2% agarose gels and photographed under UV light after ethidium bromide staining. 200 primers were screened and one RAPD marker each was identified for alleles S2 (OPI-07700) and S1 (OPJ-141700).

Identification of RAPD markers for common root rot and spot blotch (Cochliobolus sativus) resistance in barley

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 206-215 ◽  
Author(s):  
H. R. Kutcher ◽  
K. L. Bailey ◽  
B. G. Rossnagel ◽  
W. G. Legge
Keyword(s):  
Root Rot ◽  
Rapd Markers ◽  
Bulked Segregant Analysis ◽  
Rapd Marker ◽  
Spot Blotch ◽  
Cochliobolus Sativus ◽  
Common Root ◽  
Gene Manipulation ◽  
Common Root Rot ◽  
The Cross

The identification of RAPD markers associated with genes for resistance to Cochliobolus sativus in barley would increase the efficiency of gene manipulation by reducing the number of lines that must be evaluated from a resistant by susceptible cross and by allowing selection during the off season. Two barley crosses consisting of resistant and susceptible parent genotypes ('Virden' × 'Ellice' and Fr926-77 × 'Deuce', both 2 row × 6 row crosses) and more than 140 homozygous progeny lines were rated for their reactions in field nurseries to common root rot and in a controlled environment for spot blotch. Putative RAPD markers were identified using bulked segregant analysis followed by individual progeny line analyses. Polymorphisms associated with disease reaction were detected between bulked segregant samples as differences in the band intensity of DNA fragments. The bulked segregant samples were screened against 186 RAPD primers (decamers) using the polymerase chain reaction. For the cross Fr926-77 × 'Deuce', one RAPD marker was obtained that did not segregate as expected but was associated with both diseases. For the cross 'Virden' × 'Ellice', a single RAPD marker was obtained that did not have the expected segregation ratio but was associated with spot blotch reaction. One RAPD marker linked to 2-rowed and 6-rowed spike locus was obtained in each cross, and both the marker and row type were associated with common root rot and spot blotch reactions. For the cross 'Virden' × 'Ellice', a linkage group consisting of three RAPD markers was associated with common root rot and spot blotch reaction. The genes associated with these markers condition significant levels of resistance to C. sativus and may be used to increase the speed and precision of resistance gene manipulation in barley germplasm. Key words : common root rot, spot blotch, Cochliobolus sativus, molecular markers, barley.

scholarly journals 059 Molecular Markers Linked to the Ur-6 Gene Controlling Specific Rust Resistance in Common Bean

HortScience ◽  
2000 ◽  
Vol 35 (3) ◽  
pp. 398D-398 ◽  
Author(s):  
Soon O. Park ◽  
Dermot P. Coyne ◽  
James R. Steadman
Keyword(s):  
Common Bean ◽  
Rust Resistance ◽  
Rapd Markers ◽  
Specific Resistance ◽  
Bulked Segregant Analysis ◽  
Rapd Marker ◽  
Dominant Gene ◽  
Coupling Phase ◽  
Repulsion Phase ◽  
Segregating Population

Bean rust, caused by Uromyces appendiculatus, is an important disease of common bean (Phaseolus vulgaris L.). The objective was to identify RAPD markers linked to the gene (Ur-6) for specific resistance to rust race 51 using bulked segregant analysis in an F2 segregating population from the common bean cross pinto `Olathe' (resistant to rust) × great northern Nebraska #1 selection 27 (susceptible to rust). A single dominant gene controlling specific resistance to race 51 was hypothesized based on F2 segregation, and then was confirmed in the F3 generation. A good fit to a 3:1 ratio for band presence to band absence for each of three markers was observed in 100 F2 plants. Three RAPD markers were detected in a coupling phase linkage with the Ur-6 gene. Coupling-phase RAPD marker OAB14.600 was the most closely linked to the Ur-6 gene at a distance of 3.5 cM among these markers. No RAPD markers were identified in a repulsion phase linkage with the Ur-6 gene. The RAPD markers linked to the gene for specific rust resistance of Middle American origin detected here, along with other independent rust resistance genes from other germplasm, could be utilized to pyramid multiple genes into a bean cultivar for more durable rust resistance.

scholarly journals A DNA Marker for Columnar Growth Habit in Apple Contains a Simple Sequence Repeat

1997 ◽  
Vol 122 (3) ◽  
pp. 347-349 ◽  
Author(s):  
Minou Hemmat ◽  
Norman F. Weeden ◽  
Patrick J. Conner ◽  
Susan K. Brown
Keyword(s):  
Simple Sequence Repeat ◽  
Rapd Markers ◽  
Null Allele ◽  
Growth Habit ◽  
Bulked Segregant Analysis ◽  
Rapd Marker ◽  
Close Linkage ◽  
Sequence Repeat ◽  
Dna Fragment ◽  
Simple Sequence

The columnar mutation `Wijcik McIntosh' has attracted much attention because of its compact growth habit, which is compatible with high-density plantings. Using bulked segregant analysis, we identified several randomly amplified polymorphic DNA (RAPD) markers that displayed a close linkage with the columnar locus (Co). The RAPD marker that displayed the closest linkage was end sequenced to develop a sequence tagged site for rapidly screening segregating populations. A simple sequence repeat (SSR) of (GA)17 was identified within the DNA fragment. Four allelic forms, including an apparent null allele, could be distinguished among the cultivars tested. The null allele displayed close linkage with Co in two progenies, and we used this marker to identify the location of the gene on the apple linkage map.

Development of molecular markers linked to a gene controlling fruit acidity in citrus

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 841-849 ◽  
Author(s):  
D. Q. Fang ◽  
C. T. Federici ◽  
M. L. Roose
Keyword(s):  
Citric Acid ◽  
Acid Content ◽  
Fruit Juice ◽  
Scar Marker ◽  
Bulked Segregant Analysis ◽  
Rapd Marker ◽  
Recessive Gene ◽  
Marker Allele ◽  
Fruit Acidity ◽  
Citric Acid Content

Fruit juice pH, titratable acidity, or citric acid content was measured in 6 populations derived from an acidless pummelo (pummelo 2240) (Citrus maxima (Burm.) Merrill). The acidless trait in pummelo 2240 is controlled by a single recessive gene called acitric. Using bulked segregant analysis, three RAPD markers were identified as linked to acitric. RAPD marker OpZ20410, which mapped 1.2 cM from acitric, was cloned and sequenced, and a sequence characterized amplified region (SCAR) marker (SCZ20) was developed. The SCZ20-410 marker allele that is linked to the acitric allele occurs only in pummelo 2240 and other pummelos, and therefore, this SCAR marker should be useful as a dominant or codominant marker for introgressing acitric into mandarins and other citrus species. Using the cloned OpZ20410 band as a hybridization probe revealed a codominant RFLP marker called RFZ20 that mapped 1.2 cM from acitric. Progeny homozygous (acac) for the acitric allele had citric acid content below 10 μM, the minimum level detectable by high pressure liquid chromatography. The citric acid content of fruit juice from progeny predicted to be heterozygous (Acac) for acitric by the above markers was about 30% lower than that of juice from individuals predicted to be homozygous (AcAc) for the normal acid allele. Markers OpZ20410, SCZ20, and RFZ20 were highly polymorphic among 59 citrus accessions, and using one or more of these markers would allow citrus breeders to select seedling progeny heterozygous for acitric in nearly all crosses between pummelo 2240 or its offspring and other citrus genotypes.Key words: Citrus, fruit acidity, citric acid, RAPD, SCAR, RFLP.

Detection and Mapping of RAPD Markers Associated with QTL Affecting Seed Size and Shape in Common Bean

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 547b-547
Author(s):  
Soon O. Park ◽  
Dermot P. Coyne ◽  
Geunhwa Jung ◽  
E. Arnaud-Santana ◽  
H. Ariyarathne
Keyword(s):  
Linkage Group ◽  
Common Bean ◽  
Seed Size ◽  
Phenotypic Variation ◽  
Seed Weight ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Seed Shape ◽  
Seed Length ◽  
Ri Lines

Seed size is an important trait in common bean. The objective was to identify RAPD markers associated with QTL for seed weight, seed length, and seed height in a molecular marker-based linkage map in a recombinant inbred (RI) population from the common bean cross of the larger seeded (100 seed/39 to 47 g) PC-50 (ovate seed shape) × smaller seeded (100 seed/26 to 35 g) XAN-159 (flat rhomboidal seed shape). The parents and RI lines were grown in two separate greenhouse and two field (Wisconsin, Dominican Republic) experiments using a RCBD. Continuous distributions for seed weight, seed length, and seed height were observed for RI lines indicating quantitative inheritance. One to three QTLs affecting seed weight explained 17% to 41% of the phenotypic variation. Two to three QTLs for seed length explained 23% to 45% of the phenotypic variation. One to four QTL associated with seed height explained 17% to 39% of the phenotypic variation. A RAPD marker M5.850 in linkage group 3 was consistently associated with seed weight, seed length, and seed height in all experiments and explained 7% to 13% of the phenotypic variation for these traits. A seedcoat pattern morphological marker (C) in linkage group 1 was associated with seed weight and seed height in two greenhouse experiments.

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.

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