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| Map Set Name: |
Almond-NL-F1-2010 |
[ Show Only This Set ] |
| Abbreviated Name: |
Almond-NL-F1-2010 |
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| Accession ID: |
157 |
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| Species: |
Prunus amygdalus (Almond) |
[ View Species Info ] |
| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 September, 2009 |
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Description:
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Peach and almond have been considered as model species for the family Rosaceae and other woody plants. Consequently, mapping and characterisation of genes in these species has important implications. High-resolution melting (HRM) analysis is a recent development in the detection of SNPs and other markers, and proved to be an efficient and cost-effective approach. In this study, we aimed to map genes corresponding to known proteins in other species using the HRM approach. Prunus unigenes were searched and compared with known proteins in the public databases. We developed single-nucleotide polymorphism (SNP) markers, polymorphic in a mapping population produced from a cross between the cloned cultivars Nonpareil and Lauranne. A total of 12 SNP-anchored putative genes were genotyped in the population using HRM, and mapped to an existing linkage map. These genes were mapped on six linkage groups, and the predicted proteins were compared to putative orthologs in other species. Amongst those genes, four were abiotic stress-responsive genes, which can provide a starting point for construction of an abiotic resistance map. Two allergy and detoxification related genes, respectively, were also mapped and analysed. Most of the investigated genes had high similarities to sequences from closely related species such as apricot, apple and other eudicots, and these are putatively orthologous. In addition, it was shown that HRM can be an effective means of genotyping populations for the purpose of constructing a linkage map. Our work provides basic genomic information for the 12 genes, which can be used for further genetic and functional studies. |
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| Map Set Name: |
Almond-RD-F1 |
[ Show Only This Set ] |
| Abbreviated Name: |
Almond-RD-F1 |
[ Download Map Set Data ] |
| Accession ID: |
57 |
[ View Map Set In Matrix ] |
| Species: |
Prunus amygdalus (Almond) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 February, 2010 |
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Description of 2007 map:
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Six tree traits (self-compatibility, blooming date, blooming density,
productivity, leafing date and ripening time) and five pomological
traits (kernel taste, in-shell weight, shell hardness, kernel weight and
double kernel) were studied in an F1 almond progeny of 167 seedlings
from the cross between the French cultivar R1000 and the Spanish
cultivar Desmayo Largueta . In addition, a set of 135 codominant
microsatellites or simple-sequence repeat (SSR) markers developed
from peach, cherry and almond were used for the molecular characterization
of the progeny. A genetic linkage map was constructed with
56 of these SSRs. Cosegregation analysis allowed the identification of
the map positions of two major genes to be confirmed for kernel taste
(Sk) in linkage group five (G5) and for self-incompatibility (S) in G6.
QTLs mapped include two for leafing date (Lf-Q1 and Lf-Q2) in G1
and G4, one for shell hardness (D-Q) in G2, one each for double kernel
(Dk-Q) and productivity (P-Q) in G4, one for blooming date (Lb-Q) in
G4, two for kernel weight (Kw-Q1 and Kw-Q2) in G1 and G4, and two
for in-shell weight (Shw-Q1 and Shw-Q2) in G1 and G2. Four SSR loci
(BPPCT011, UDP96-013, UDP96-003 and PceGA025) were linked to
the important agronomic traits of leafing date, shell hardness,
blooming date and kernel taste. Finally, the development of efficient
marker-assisted selection strategies applied to almond and other
Prunus breeding programmes was also discussed.
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Description of 2010 map:
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Upon crushing, amygdalin present in bitter almonds is hydrolysed to benzaldehyde, which gives a bitter flavour, and to cyanide, which is toxic. Bitterness is attributable to the recessive allele of the Sweet kernel (Sk/sk) gene and is selected against in breeding programmes. Almond has a long intergeneration period due to its long juvenile phase, so breeders must wait 3 or 4 years to evaluate fruit traits in the field. For this reason, it is important to develop molecular markers to distinguish between sweet and bitter genotypes. The Sk gene is known to map to linkage group five (G5) of the almond genome, but its function is still undefined. Candidate genes involved in the amygdalin pathway have been mapped, but none of them were located to G5. We have saturated G5 with additional Simple Sequence Repeats (SSRs) using the progeny from the cross "R1000" x "Desmayo Largueta" and found six SSRs (UDA-045, EPDCU2584, CPDCT028, BPPCT037, PceGA025, and CPDCT016) closely linked to the Sk locus. The genotypes of four of these SSRs flanking the Sk locus, in a number of parents and a few seedlings of the CEBAS-CSIC almond breeding programme, allowed us to estimate the haplotypes of the parents, identifying the marker alleles adequate for an early and highly efficient selection against bitter genotypes. This analysis has established the usefulness of SSRs for screening populations of fruit trees such as almond by an easy, polymerase chain reaction-based method. |
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| Map Set Name: |
Almond-RD-Parental |
[ Show Only This Set ] |
| Abbreviated Name: |
Almond-RD-Parental |
[ Download Map Set Data ] |
| Accession ID: |
58 |
[ View Map Set In Matrix ] |
| Species: |
Prunus amygdalus (Almond) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 February, 2010 |
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Description of 2007 map:
|
Six tree traits (self-compatibility, blooming date, blooming density,
productivity, leafing date and ripening time) and five pomological
traits (kernel taste, in-shell weight, shell hardness, kernel weight and
double kernel) were studied in an F1 almond progeny of 167 seedlings
from the cross between the French cultivar R1000 and the Spanish
cultivar Desmayo Largueta . In addition, a set of 135 codominant
microsatellites or simple-sequence repeat (SSR) markers developed
from peach, cherry and almond were used for the molecular characterization
of the progeny. A genetic linkage map was constructed with
56 of these SSRs. Cosegregation analysis allowed the identification of
the map positions of two major genes to be confirmed for kernel taste
(Sk) in linkage group five (G5) and for self-incompatibility (S) in G6.
QTLs mapped include two for leafing date (Lf-Q1 and Lf-Q2) in G1
and G4, one for shell hardness (D-Q) in G2, one each for double kernel
(Dk-Q) and productivity (P-Q) in G4, one for blooming date (Lb-Q) in
G4, two for kernel weight (Kw-Q1 and Kw-Q2) in G1 and G4, and two
for in-shell weight (Shw-Q1 and Shw-Q2) in G1 and G2. Four SSR loci
(BPPCT011, UDP96-013, UDP96-003 and PceGA025) were linked to
the important agronomic traits of leafing date, shell hardness,
blooming date and kernel taste. Finally, the development of efficient
marker-assisted selection strategies applied to almond and other
Prunus breeding programmes was also discussed.
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Description of 2010 map:
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Upon crushing, amygdalin present in bitter almonds is hydrolysed to benzaldehyde, which gives a bitter flavour, and to cyanide, which is toxic. Bitterness is attributable to the recessive allele of the Sweet kernel (Sk/sk) gene and is selected against in breeding programmes. Almond has a long intergeneration period due to its long juvenile phase, so breeders must wait 3 or 4 years to evaluate fruit traits in the field. For this reason, it is important to develop molecular markers to distinguish between sweet and bitter genotypes. The Sk gene is known to map to linkage group five (G5) of the almond genome, but its function is still undefined. Candidate genes involved in the amygdalin pathway have been mapped, but none of them were located to G5. We have saturated G5 with additional Simple Sequence Repeats (SSRs) using the progeny from the cross "R1000" x "Desmayo Largueta" and found six SSRs (UDA-045, EPDCU2584, CPDCT028, BPPCT037, PceGA025, and CPDCT016) closely linked to the Sk locus. The genotypes of four of these SSRs flanking the Sk locus, in a number of parents and a few seedlings of the CEBAS-CSIC almond breeding programme, allowed us to estimate the haplotypes of the parents, identifying the marker alleles adequate for an early and highly efficient selection against bitter genotypes. This analysis has established the usefulness of SSRs for screening populations of fruit trees such as almond by an easy, polymerase chain reaction-based method. |
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| Map Set Name: |
Almond-FT-F1 |
[ Show Only This Set ] |
| Abbreviated Name: |
Almond-FT-F1 |
[ Download Map Set Data ] |
| Accession ID: |
101 |
[ View Map Set In Matrix ] |
| Species: |
Prunus amygdalus (Almond) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
17 March, 2010 |
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FxT linkage map:
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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 'Ferragnes' 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 'Ferragnes' 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 'Ferragnes' (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. |
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Location of the self-incompatibility gene:
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A progeny obtained from the almond cross 'Ferragnhs' W 'Tuono' (Prunus amygdalus Batsch) was used to study the self-incompatibility trait in three different ways: fruit set, pollen tube growth and stylar ribonuclease activity. As expected from the genotypes of the parents, all progeny appeared phenotypically as self-compatible. However, the progeny could be scored for the segregation of stylar ribonuclease isozymes and thus allowed the incompatibility locus to be placed on the almond linkage map. |
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| Map Set Name: |
Almond-FB-F1 |
[ Show Only This Set ] |
| Abbreviated Name: |
Almond-FB-F1 |
[ Download Map Set Data ] |
| Accession ID: |
121 |
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| Species: |
Prunus amygdalus (Almond) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 March, 1998 |
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Description:
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This is an almond genetic map constructed from an F1 of a cross between 'Felisia' x 'Bertina' (FxB). 'Felisia' was initially called D-3-5.
Linkage group were constructed using RFLP, RAPD and Isozyme markers. |
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Reference 1:
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J. Ballester. 1998. Localitzacio I analisi de caracters d'interes agronomic de
l'ametller. Ph.D. Thesis. Universitat Autonoma de Barcelona. |
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| Cross-references: |
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| Map Set Name: |
Apple-FD-F1 |
[ Show Only This Set ] |
| Abbreviated Name: |
Apple-FD-F1 |
[ Download Map Set Data ] |
| Accession ID: |
37 |
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| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 August, 2006 |
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Description:
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new set of 148 apple microsatellite markers has been developed and mapped on the apple reference linkage map Fiesta x Discovery. One-hundred and seventeen markers were developed from genomic libraries enriched with the repeats GA, GT, AAG, AAC and ATC; 31 were developed from EST sequences. Markers derived from sequences containing dinucleotide repeats were generally more polymorphic than sequences containing trinucleotide repeats. Additional eight SSRs from published apple, pear, and Sorbus torminalis SSRs, whose position on the apple genome was unknown, have also been mapped. The transferability of SSRs across Maloideae species resulted in being efficient with 41% of the markers successfully transferred. For all 156 SSRs, the primer sequences, repeat type, map position, and quality of the amplification products are reported. Also presented are allele sizes, ranges, and number of SSRs found in a set of nine cultivars. All this information and those of the previous CH-SSR series can be searched at the apple SSR database (http://www.hidras.unimi.it) to which updates and comments can be added. A large number of apple ESTs containing SSR repeats are available and should be used for the development of new apple SSRs. The apple SSR database is also meant to become an international platform for coordinating this effort. The increased coverage of the apple genome with SSRs allowed the selection of a set of 86 reliable, highly polymorphic, and overall the apple genome well-scattered SSRs. These SSRs cover about 85% of the genome with an average distance of one marker per 15 cM. |
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| Map Set Name: |
Apple-A194-F1 |
[ Show Only This Set ] |
| Abbreviated Name: |
Apple-A194-F1 |
[ Download Map Set Data ] |
| Accession ID: |
64 |
[ View Map Set In Matrix ] |
| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
03 July, 2007 |
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Description:
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Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple
Background: Integrating plant genomics and classical breeding is a challenge for both plant
breeders and molecular biologists. Marker-assisted selection (MAS) is a tool that can be used to
accelerate the development of novel apple varieties such as cultivars that have fruit with
anthocyanin through to the core. In addition, determining the inheritance of novel alleles, such as
the one responsible for red flesh, adds to our understanding of allelic variation. Our goal was to
map candidate anthocyanin biosynthetic and regulatory genes in a population segregating for the
red flesh phenotypes.
Results: We have identified the Rni locus, a major genetic determinant of the red foliage and red
colour in the core of apple fruit. In a population segregating for the red flesh and foliage phenotype
we have determined the inheritance of the Rni locus and DNA polymorphisms of candidate
anthocyanin biosynthetic and regulatory genes. Simple Sequence Repeats (SSRs) and Single
Nucleotide Polymorphisms (SNPs) in the candidate genes were also located on an apple genetic
map. We have shown that the MdMYB10 gene co-segregates with the Rni locus and is on Linkage
Group (LG) 09 of the apple genome.
Conclusion: We have performed candidate gene mapping in a fruit tree crop and have provided
genetic evidence that red colouration in the fruit core as well as red foliage are both controlled by
a single locus named Rni. We have shown that the transcription factor MdMYB10 may be the gene
underlying Rni as there were no recombinants between the marker for this gene and the red
phenotype in a population of 516 individuals. Associating markers derived from candidate genes
with a desirable phenotypic trait has demonstrated the application of genomic tools in a breeding
programme of a horticultural crop species. |
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| Map Set Name: |
Red flesh apple 2007 |
[ Show Only This Set ] |
| Abbreviated Name: |
Red flesh apple 2007 |
[ Download Map Set Data ] |
| Accession ID: |
56 |
[ View Map Set In Matrix ] |
| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
03 July, 2007 |
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Description:
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Background
Integrating plant genomics and classical breeding is a challenge for both plant breeders and molecular biologists. Marker-assisted selection (MAS) is a tool that can be used to accelerate the development of novel apple varieties such as cultivars that have fruit with anthocyanin through to the core. In addition, determining the inheritance of novel alleles, such as the one responsible for red flesh, adds to our understanding of allelic variation. Our goal was to map candidate anthocyanin biosynthetic and regulatory genes in a population segregating for the red flesh phenotypes.
Results
We have identified the Rni locus, a major genetic determinant of the red foliage and red colour in the core of apple fruit. In a population segregating for the red flesh and foliage phenotype we have determined the inheritance of the Rni locus and DNA polymorphisms of candidate anthocyanin biosynthetic and regulatory genes. Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) in the candidate genes were also located on an apple genetic map. We have shown that the MdMYB10 gene co-segregates with the Rni locus and is on Linkage Group (LG) 09 of the apple genome.
Conclusion
We have performed candidate gene mapping in a fruit tree crop and have provided genetic evidence that red colouration in the fruit core as well as red foliage are both controlled by a single locus named Rni. We have shown that the transcription factor MdMYB10 may be the gene underlying Rni as there were no recombinants between the marker for this gene and the red phenotype in a population of 516 individuals. Associating markers derived from candidate genes with a desirable phenotypic trait has demonstrated the application of genomic tools in a breeding programme of a horticultural crop species. |
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| Map Set Name: |
Apple-M9R5-F1 |
[ Show Only This Set ] |
| Abbreviated Name: |
Apple-M9R5-F1 |
[ Download Map Set Data ] |
| Accession ID: |
55 |
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| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 January, 2009 |
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Description:
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Marker-assisted selection (MAS) offers quick and reliable prediction of the phenotypes of seedlings in large populations and thus opens new approaches for selection to breeders of apple (Malus x domestica Borkh.). The development of framework maps enables the discovery of genetic markers linked to desired traits. Although genetic maps have been reported for apple scion cultivars, none has previously been constructed for apple rootstocks. We report the construction of framework genetic maps in a cross between 'M.9' ('Malling 9') and 'R.5' ('Robusta 5') apple rootstocks. The maps comprise 224 simple sequence repeat (SSR) markers, 18 sequence-characterised amplified regions, 14 single nucleotide polymorphisms and 42 random amplified polymorphic DNAs. A new set of 47 polymorphic SSRs was developed from apple EST sequences and used for construction of this rootstock map. All 17 linkage groups have been identified and aligned to existing apple genetic maps. The maps span 1,175.7 cM ('M.9') and 1,086.7 cM ('R.5'). To improve the efficiency of mapping markers to this framework map, we developed a bin mapping set. Applications of these new genetic maps include the elucidation of the genetic basis of the dwarfing effect of the apple rootstock 'M.9' and the analysis of disease and insect resistance traits such as fire blight (Erwinia amylovora), apple scab (Venturia inaequalis) and woolly apple aphid (Eriosoma lanigerum). Markers for traits mapped in this population will be of direct use to apple breeders for MAS and for identification of causative genes by map-based cloning. |
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| Map Set Name: |
Apple Integrated Map |
[ Show Only This Set ] |
| Abbreviated Name: |
apple integrated map |
[ Download Map Set Data ] |
| Accession ID: |
16 |
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| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 July, 2009 |
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Description (from the supplementary notes):
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The genetic maps that were used to develop the integrated map for metacontig anchoring were
derived from six F1 populations totaling 720 individuals: 270 plants from the cross between 'Golden Delicious' and 'Scarlet', grown at FEM-IASMA (San Michele, TN, Italy), 88 plants from 'Golden Delicious' x 'Braeburn', IASMA; 91 plants from 'Golden Delicious' x 'McIntosh-Wijick', IASMA; 89 plants from 'Discovery' x apple hybrid TN 10-8, INRA (Angers France); 91 plants from 'Gala' x 'Dulmener Rosenapfel', INRA (Angers, France); 91 plants from 'Royal Gala' x 'Braeburn', Plant & Food Research, (Hawke's Bay, New Zealand).
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| Map Set Name: |
MRomeBeauty |
[ Show Only This Set ] |
| Abbreviated Name: |
MRomeBeauty |
[ Download Map Set Data ] |
| Accession ID: |
19 |
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| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 January, 1994 |
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Data Source:
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RoseDB (defunct)
Abstract: http://www.intl-pag.org/pag/7/abstracts/pag7770.html
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Description:
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Author: Norm Weeden
The markers were divided into three groups: (1) those segregating as a result of heterozygosity in White Angel;(2) those segregating as a result of heterozygosity in Rome Beauty; and (3)those segregating as a result of heterozygosity in both parents. For analysis of amplified DNA fragments, we considered a parent heterozygous for a particular segregating fragment if DNA from that parent generated the fragment when used as template DNA. The expected segregation ratio for a locus heterozygous in only one parent was 1:1, whereas loci heterozygous in both parents were expected to display either a 3:1 ratio for dominant characters such as RAPDs or a 1:2:1 ratio for codominant allozymes and RFLPs. Goodness-of-fit between observed and expected segregation ratios was tested using chi-square analysis as performed by LINKAGE-1. This data set are those loci heterozygous only in Rome Beauty. MAPMAKER 2.0 was used to confirm locus order for each linkage group and to determine multipoint recombination frequencies among loci. A log-likelihood score of 3.0 and a recombination distance of no more than 20 cM were the minimal criteria for establishing linkage between markers. The 'ripple' function on MAPMAKER was employed to assess the robustness of the order of markers on a linkage group. data type f2 backcross (AxH, S=A, F=H U=Missing) symbols 1=A 2=H 0=U |
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| Cross-references: |
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| Map Set Name: |
MRomeBeauty_2 |
[ Show Only This Set ] |
| Abbreviated Name: |
MRomeBeauty_2 |
[ Download Map Set Data ] |
| Accession ID: |
20 |
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| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 January, 1994 |
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Data Source:
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RoseDB (defunct)
Abstract: http://www.intl-pag.org/pag/7/abstracts/pag7770.html
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Description:
|
Author: Norm Weeden
The markers were divided into three groups: (1) those segregating as a result of heterozygosity in White Angel;(2) those segregating as a result of heterozygosity in Rome Beauty; and (3)those segregating as a result of heterozygosity in both parents. For analysis of amplified DNA fragments, we considered a parent heterozygous for a particular segregating fragment if DNA from that parent generated the fragment when used as template DNA. The expected segregation ratio for a locus heterozygous in only one parent was 1:1, whereas loci heterozygous in both parents were expected to display either a 3:1 ratio for dominant characters such as RAPDs or a 1:2:1 ratio for codominant allozymes and RFLPs. Goodness-of-fit between observed and expected segregation ratios was tested using chi-square analysis as performed by LINKAGE-1. This data set are those loci heterozygous only in Rome Beauty. MAPMAKER 2.0 was used to confirm locus order for each linkage group and to determine multipoint recombination frequencies among loci. A log-likelihood score of 3.0 and a recombination distance of no more than 20 cM were the minimal criteria for establishing linkage between markers. The 'ripple' function on MAPMAKER was employed to assess the robustness of the order of markers on a linkage group. data type f2 backcross (AxH, S=A, F=H U=Missing) symbols 1=A 2=H 0=U
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| Maps: |
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| Cross-references: |
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| Map Set Name: |
MWhiteAngel |
[ Show Only This Set ] |
| Abbreviated Name: |
MWhiteAngel |
[ Download Map Set Data ] |
| Accession ID: |
21 |
[ View Map Set In Matrix ] |
| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 January, 1994 |
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Data Source:
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RoseDB (defunct)
Abstract: http://www.intl-pag.org/pag/7/abstracts/pag7770.html |
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Description:
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Author: Norm Weeden
The markers were divided into three groups: (1) those segregating as a result of heterozygosity in White Angel;(2) those segregating as a result of heterozygosity in Rome Beauty; and (3)those segregating as a result of heterozygosity in both parents. For analysis of amplified DNA fragments, we considered a parent heterozygous for a particular segregating fragment if DNA from that parent generated the fragment when used as template DNA. The expected segregation ratio for a locus heterozygous in only one parent was 1:1, whereas loci heterozygous in both parents were expected to display either a 3:1 ratio for dominant characters such as RAPDs or a 1:2:1 ratio for codominant allozymes and RFLPs. Goodness-of-fit between observed and expected segregation ratios was tested using chi-square analysis as performed by LINKAGE-1. This data set are those loci heterozygous only in Rome Beauty. MAPMAKER 2.0 was used to confirm locus order for each linkage group and to determine multipoint recombination frequencies among loci. A log-likelihood score of 3.0 and a recombination distance of no more than 20 cM were the minimal criteria for establishing linkage between markers. The 'ripple' function on MAPMAKER was employed to assess the robustness of the order of markers on a linkage group. data type f2 backcross (AxH, S=A, F=H U=Missing) symbols 1=A 2=H 0=U
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| Maps: |
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| Cross-references: |
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| Map Set Name: |
MWhiteAngel_2 |
[ Show Only This Set ] |
| Abbreviated Name: |
MWhiteAngel_2 |
[ Download Map Set Data ] |
| Accession ID: |
22 |
[ View Map Set In Matrix ] |
| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 January, 1994 |
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Data Source:
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RoseDB (defunct)
Abstract: http://www.intl-pag.org/pag/7/abstracts/pag7770.html
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Description:
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Author: Norm Weeden
The markers were divided into three groups: (1) those segregating as a result of heterozygosity in White Angel;(2) those segregating as a result of heterozygosity in Rome Beauty; and (3)those segregating as a result of heterozygosity in both parents. For analysis of amplified DNA fragments, we considered a parent heterozygous for a particular segregating fragment if DNA from that parent generated the fragment when used as template DNA. The expected segregation ratio for a locus heterozygous in only one parent was 1:1, whereas loci heterozygous in both parents were expected to display either a 3:1 ratio for dominant characters such as RAPDs or a 1:2:1 ratio for codominant allozymes and RFLPs. Goodness-of-fit between observed and expected segregation ratios was tested using chi-square analysis as performed by LINKAGE-1. This data set are those loci heterozygous only in Rome Beauty. MAPMAKER 2.0 was used to confirm locus order for each linkage group and to determine multipoint recombination frequencies among loci. A log-likelihood score of 3.0 and a recombination distance of no more than 20 cM were the minimal criteria for establishing linkage between markers. The 'ripple' function on MAPMAKER was employed to assess the robustness of the order of markers on a linkage group. data type f2 backcross (AxH, S=A, F=H U=Missing) symbols 1=A 2=H 0=U
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| Map Set Name: |
MNY75441-58 |
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| Abbreviated Name: |
MNY75441-58 |
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| Accession ID: |
17 |
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| Species: |
Malus domestica (Apple) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 May, 1997 |
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Data Source:
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RoseDB (defunct)
Abstract: http://www.intl-pag.org/pag/7/abstracts/pag7770.html |
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Description:
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Genetic linkage maps were created for three apple (Malus x domestica Borkh.) cultivars using data from two progenies ('Wijcik McIntosh' x NY 75441-67 and 'Wijcik McIntosh' x NY 75441-58). The maps consist primarily of randomly amplified polymorphic DNA (RAPD) markers, but also contain six isozyme loci and four morphological markers (Rf, fruit skin color; Vf, scab resistance; Co, columnar growth habit; Ma, malic acid). Maps were constructed using a double pseudotestcross mapping format and JoinMap mapping software. An integrated 'Wijcik McIntosh' map was produced by combining marker data from both progenies into a single linkage map. Homologous linkage groups from paternal maps were paired with their counterparts in the 'Wijcik McIntosh' map using locus bridges composed of markers heterozygous in both parents of a progeny. The 'Wijcik McIntosh' map consists of 238 markers arranged in 19 linkage groups spanning 1206 cM. The NY 75441-67 map contains 110 markers in 16 linkage groups and the NY 75441-58 map consists of 183 markers in 18 linkage groups. The average distance between markers in the maps was ~5.0 cM |
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| Map Set Name: |
MNY75441-67 |
[ Show Only This Set ] |
| Abbreviated Name: |
MNY75441-67 |
[ Download Map Set Data ] |
| Accession ID: |
18 |
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| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 May, 1997 |
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Data Source:
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RoseDB (defunct)
Abstract: http://www.intl-pag.org/pag/7/abstracts/pag7770.html |
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Description:
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Genetic linkage maps were created for three apple (Malus x domestica Borkh.) cultivars using data from two progenies ('Wijcik McIntosh' x NY 75441-67 and 'Wijcik McIntosh' x NY 75441-58). The maps consist primarily of randomly amplified polymorphic DNA (RAPD) markers, but also contain six isozyme loci and four morphological markers (Rf, fruit skin color; Vf, scab resistance; Co, columnar growth habit; Ma, malic acid). Maps were constructed using a double pseudotestcross mapping format and JoinMap mapping software. An integrated 'Wijcik McIntosh' map was produced by combining marker data from both progenies into a single linkage map. Homologous linkage groups from paternal maps were paired with their counterparts in the 'Wijcik McIntosh' map using locus bridges composed of markers heterozygous in both parents of a progeny. The 'Wijcik McIntosh' map consists of 238 markers arranged in 19 linkage groups spanning 1206 cM. The NY 75441-67 map contains 110 markers in 16 linkage groups and the NY 75441-58 map consists of 183 markers in 18 linkage groups. The average distance between markers in the maps was ~5.0 cM |
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| Map Set Name: |
MWijcik_McIntosh |
[ Show Only This Set ] |
| Abbreviated Name: |
MWijcik_McIntosh |
[ Download Map Set Data ] |
| Accession ID: |
23 |
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| Species: |
Malus domestica (Apple) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 May, 1997 |
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Data Source:
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RoseDB (defunct)
Abstract: http://www.intl-pag.org/pag/7/abstracts/pag7770.html |
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Description:
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Genetic linkage maps were created for three apple (Malus x domestica Borkh.) cultivars using data from two progenies ('Wijcik McIntosh' x NY 75441-67 and 'Wijcik McIntosh' x NY 75441-58). The maps consist primarily of randomly amplified polymorphic DNA (RAPD) markers, but also contain six isozyme loci and four morphological markers (Rf, fruit skin color; Vf, scab resistance; Co, columnar growth habit; Ma, malic acid). Maps were constructed using a double pseudotestcross mapping format and JoinMap mapping software. An integrated 'Wijcik McIntosh' map was produced by combining marker data from both progenies into a single linkage map. Homologous linkage groups from paternal maps were paired with their counterparts in the 'Wijcik McIntosh' map using locus bridges composed of markers heterozygous in both parents of a progeny. The 'Wijcik McIntosh' map consists of 238 markers arranged in 19 linkage groups spanning 1206 cM. The NY 75441-67 map contains 110 markers in 16 linkage groups and the NY 75441-58 map consists of 183 markers in 18 linkage groups. The average distance between markers in the maps was ~5.0 cM |
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| Map Set Name: |
Apricot-GV-F1 |
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| Abbreviated Name: |
Apricot-GV-F1 |
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| Accession ID: |
33 |
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| Species: |
Prunus armeniaca (Apricot) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
14 June, 2002 |
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Description:
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Genetic linkage maps for two apricot cultivars
have been constructed using AFLP, RAPD, RFLP and
SSR markers in 81 F1 individuals from the cross 'Goldrich'
W 'Valenciano'. This family segregated for resistance
to 'plum pox virus' (PPV), the most-important virus
affecting Prunus species. Of the 160 RAPD arbitrary
primers screened a total of 44 were selected. Sixty one
polymorphic RAPD markers were scored on the mapping
population: 30 heterozygous in 'Goldrich', 19 heterozygous
in 'Valenciano', segregating 1:1, and 12 markers
heterozygous in both parents, segregating 3:1. A total of
33 and 19 RAPD markers were mapped on the 'Goldrich'
and 'Valenciano' maps respectively. Forteen primer combinations
were used for AFLPs and all of them detected
polymorphism. Ninety five markers segregating 1:1 were
identified, of which 62 were heterozygous in the female
parent 'Goldrich' and 33 in the male parent 'Valenciano'.
Forty five markers were present in both parents and segregated
3:1. A total of 82 and 48 AFLP markers were
mapped on the 'Goldrich' and 'Valenciano' maps. Twelve
RFLPs probes were screened in the population, resulting
in five loci segregating in the family, one locus heterozygous
for 'Valenciano' and four heterozygous for both,
segregating 1:2:1. Of the 45 SSRs screened 17 segregated
in the mapping family, resulting in seven loci heterozygous
for the maternal parent and ten heterozygous for
both, segregating 1:2:1 or 1:1:1:1. A total of 16 and 13
co-dominant markers were mapped in the female and
male parent maps respectively. A total of 132 markers
were placed into eight linkage groups on the 'Goldrich'. |
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| Map Set Name: |
Apricot-LL-F2 |
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| Abbreviated Name: |
Apricot-LL-F2 |
[ Download Map Set Data ] |
| Accession ID: |
34 |
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| Species: |
Prunus armeniaca (Apricot) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
14 March, 2003 |
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Description:
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A genetic linkage map of apricot (Prunus
armeniaca L.) was constructed using AFLP and SSR
markers. The map is based on an F2 population (76
individuals) derived from self-pollination of an F1 individual
('Lito') originated from a cross between 'Stark
Early Orange' and 'Tyrinthos'. This family, designated as
'Lito' x 'Lito', segregated for two important agronomical
traits: plum pox virus resistance (PPV) and self-incompatibility.
A total of 211 markers (180 AFLPs, 29 SSRs
and two agronomic traits) were assigned to 11 linkage
groups covering 602 cM of the apricot genome. The
average distance (cM/marker) between adjacent markers
is 3.84 cM. The PPV resistance trait was mapped on
linkage group G1 and the self-incompatibility trait was
mapped on linkage group G6. Twenty two loci held in
common with other Prunus maps allowed us to compare
and establish homologies among the respective linkage
groups. |
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| Map Set Name: |
Apricot-LB-F1 |
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| Abbreviated Name: |
Apricot-LB-F1 |
[ Download Map Set Data ] |
| Accession ID: |
50 |
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| Species: |
Prunus armeniaca (Apricot) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 July, 2007 |
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Description:
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Linkage maps of the apricot accessions 'Lito' and 'BO 81604311' were constructed using a total of 185 simple sequence repeat (SSR) markers sampled from those isolated in peach, almond, apricot and cherry; 74 were derived from a new apricot genomic library enriched for AG/CT microsatellite repeats (UDAp series), and in total, 98 had never been mapped in Prunus before. Eight linkage groups putatively corresponding to the eight haploid apricot chromosomes were identified for each parent. The two maps were 504 and 620 cM long, respectively, with 96 anchor markers showing a complete co-linearity between the two genomes. As few as three gaps larger than 15 cM were present in 'Lito' and six in the male parent; the maps align well with all the available SSR-based Prunus maps through the many common anchor loci. Only occasionally inverted positions between adjacent markers were found, and this can be explained by the small size of cross populations analysed in these Prunus maps and in those reported in literature. The newly developed apricot SSRs will help saturating the existing Prunus maps and will extend the choice of markers in the development of genetic maps for new breeding populations. |
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| Map Set Name: |
Apricot-PS-F1 |
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| Abbreviated Name: |
Apricot-PS-F1 |
[ Download Map Set Data ] |
| Accession ID: |
54 |
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| Species: |
Prunus armeniaca (Apricot) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 January, 2008 |
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Description:
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Several genetic linkage maps have been published
in recent years on different Prunus species
suggesting a high level of resemblance among the
genomes of these species. One of these maps (Joobeur et al., Theor Appl Genet 97:1034?1041 [(1998); Aranzana et al., Theor Appl Genet 106:819?825 (2002b)] constructed from interspecific almond Texas x peach Earlygold
F2 progeny (TxE) was considered to be saturated.
We selected 142 F1 apricot hybrids obtained from a cross between P. armeniaca cvs. Polonais and Stark Early Orange for mapping. Eighty-eight RFLP probes and 20 peach SSR primer pairs used for the 'reference map' were selected to cover the eight linkage groups. One P.davidiana and an additional 14 apricot simple sequence repeats (SSRs) were mapped for the F1 progeny. Eighty three amplified fragment length polymorphisms were added in order to increase the density of the maps. Separate maps were made for each parent according to the ?double pseudo-testcross? model of analysis. A total of
141 markers were placed on the map of Stark Early
Orange, defining a total length of 699 cM, and 110 markers were placed on the map of Polonais, defining a total length of 538 cM. Twenty-one SSRs and 18 restriction placed in the TxE map were heterozygous in both parents (anchor loci), thereby enabling the alignment of the eight homologous linkage groups of each map. Except for 15 markers, most markers present in each
linkage group in apricot were aligned with those in TxE map, indicating a high degree of colinearity between the apricot genome and the peach and almond genomes. These results suggest a strong homology of the genomes between these species and probably between Prunophora and Amygdalus sub-genera. |
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| Map Set Name: |
Peach-JF-F2 |
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| Abbreviated Name: |
Peach-JF-F2 |
[ Download Map Set Data ] |
| Accession ID: |
81 |
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| Species: |
Prunus persica (Peach) |
[ View Species Info ] |
| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 December, 2004 |
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Description:
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A genetic linkage map of peach [Prunus persica (L.) Batch] was constructed in order to identify
molecular markers linked to economically important agronomic traits that would be particularly useful for long-lived perennial species. An intraspecific F2 population was generated from self-pollinating a single F1 plant from a cross between a flat non-acid peach, 'Ferjalou Jalousia' and an acid round nectarin 'Fantasia'. Mendelian segregations were observed for 270 markers including four agronomic characters (peach/nectarine, flat/round fruit, acid/non-acid fruit, and pollen sterility) and 1 isoenzyme, 50 RFLP, 92
RAPD, 8 inter-microsatellite amplification (IMA), and 115 amplified fragment length polymorphism (AFLP) markers. Two hundred and forty-nine markers were mapped to 11 linkage groups covering 712 centiMorgans (cM). The average density between pairs of markers is 4.5 cM. For the four agronomic characters studied, molecular markers were identified. This map will be used for the detection of QTL controlling fruit quality in peach and, particularly, the acid and sugar content. |
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| Map Set Name: |
Peach PMP2 2005 |
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| Abbreviated Name: |
PMP2 |
[ Download Map Set Data ] |
| Accession ID: |
26 |
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| Species: |
Prunus persica (Peach) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 January, 2005 |
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Description:
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An F2 population from a single F1 plant from the cross of peach [Prunus persica (L.) Batsch] rootstock cultivars Harrow Blood (HB) x Okinawa (Oki) was used to locate the Mi locus, which conditions resistance to Meloidogyne incognita (race 1) (Kofoid and White) Chitwood. These data and comparison of common markers among published genetic linkage maps placed the Mi locus on Prunus L. linkage group 2. Two restriction fragment length polymorphisms (RFLPs) [linked at 4.8 and 6.8 centimorgan (cM), repulsion phase] and one random amplified polymorphic DNA (RAPD) marker (linked at 9.5 cM, coupling phase) were linked to Mi. The RAPD marker was cloned, sequenced, and converted to a polymerase chain reaction (PCR)-based cleaved amplified polymorphic sequence (CAPs) marker. Clones of resistance gene analogs (RGA) developed from Oki were highly polymorphic when used as RFLP probes. The RGA's mapped to four linkage groups but clustered on two of the four linkage groups, providing limited coverage of the genome. Even so, they may be useful as markers for disease resistance genes that occur in other populations. The linkage maps of the HB x Oki F2 population and a peach x almond (Prunus amygdalus Batsch) F2 population were colinear in certain regions, however, a significant number of markers mapped to different linkage groups among the two populations. The locus for the blood-flesh trait (red-violet mesocarp) mapped to the top of linkage group 4. |
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Reference:
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Gillen and Bliss 2005 J. Amer. Soc. Hort. Sci. 130(1):24-33 (ASHS) |
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| Map Set Name: |
Peach-AJ-F2-2005 |
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| Abbreviated Name: |
Peach-AJ-F2-2005 |
[ Download Map Set Data ] |
| Accession ID: |
35 |
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| Species: |
Prunus persica (Peach) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 January, 2005 |
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Description:
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An integrated genetic linkage map, based on an intraspecific peach F2 population, was constructed to include 94 simple sequence repeat (SSR) loci, 14 sequence tagged sites (STSs), 34 AFLPs, 24 RAPDs, 3 ISSRs, and 9 phenotypic traits. This map contains 178 markers placed in 8 linkage groups that correspond to the basic chromosome number of the species (n=8) with a map distance of 571 cM with an average distance of 3.2 cM between each pair of loci. Our peach genetic linkage map was completely aligned with the European Prunus reference map by using 42 common DNA markers as anchor loci and linkages; the order of all loci were conserved between the 2 maps. It also appears that this peach map covers almost the whole genome in comparison with the Prunus reference map. Nine phenotypic traits were identified in 4 linkage groups. Two kinds of root-knot nematode resistance loci Mia and Mja located on the top of linkage group were very close. Two loci corresponding to flower color (Fc) and flesh color around the stone (Cs), were mapped on the linkage group 3. Flesh adhesion (F), one of the more important characteristics of stone fruits, was mapped at the bottom of linkage group 4. The positions these phenotypic traits were compared with those from other Prunus maps and their relationships were examined in the paper. |
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| Map Set Name: |
Peach-HBOki-F2 |
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| Abbreviated Name: |
Peach-HBOki-F2 |
[ Download Map Set Data ] |
| Accession ID: |
65 |
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| Species: |
Prunus persica (Peach) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 January, 2005 |
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Description:
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Identification and mapping of markers linked to the Mi gene for root-knot nematode resistance in peach.
An F2 population from a single F1 plant from the cross of peach [Prunus persica (L.) Batsch] rootstock cultivars Harrow Blood ('HB') x Okinawa ('Oki') was used to locate the Mi locus, which conditions resistance to Meloidogyne incognita (race 1) (Kofoid and White) Chitwood. These data and comparison of common markers among published genetic linkage maps placed the Mi locus on Prunus linkage group 2. Two restriction fragment length polymorphisms ('RFLPs') [linked at 4.8 and 6.8 centimorgan ('cM'), repulsion phase] and one random amplified polymorphic DNA ('RAPD') marker (linked at 9.5 cM, coupling phase) were linked to Mi. The RAPD marker was cloned, sequenced and converted to a polymerase chain reaction ('PCR')-based cleaved amplified polymorphic sequence ('CAPs') marker. Clones of resistance gene analogs ('RGA') developed from Oki were highly polymorphic when used as RFLP probes. The RGA's mapped to four linkage groups but clustered on two of the four linkage groups, providing limited coverage of the genome. Even so, they may be useful as markers for disease resistance genes that occur in other populations. The linkage maps of the HB x Oki F2 population and a peach x almond (Prunus amygdalus Batsch) F2 population were colinear in certain regions, however a significant number of markers mapped to different linkage groups among the two populations. The locus for the blood-flesh trait (red-violet mesocarp) mapped to the top of linkage group 4. |
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