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| Map Set Name: |
Fragaria-815x903-BC1 |
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| Abbreviated Name: |
Fragaria-815x903-BC1 |
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| Accession ID: |
36 |
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| Species: |
Fragaria (Strawberry) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 May, 2006 |
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Description:
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We have produced a reduced linkage map of a diploid Fragaria backcross progeny (F. vesca W [F. vesca W F. viridis]) denoted 815 x 903BC from 31 microsatellite (SSR) and two gene-specific markers selected from the diploid Fragaria reference map FV W FN. The 33 sequence tagged-site (STS) markers selected, segregated in seven linkage groups, and marker order was conserved between FV W FN and 815 x 903BC. Significant segregation distortion, observed on three of the seven linkage groups, was accompanied by a reduction in observed recombination frequency and, therefore, genetic distance between markers mapped in these linkage groups. However, this distortion did not affect marker order compared to FV W FN and may indicate non-random chromosomal divergence during speciation in Fragaria. Our findings indicate that no major genome reorganisation has occurred during speciation in the genus, and suggest that STS linkage maps of other Fragaria populations, including those of the cultivated strawberry F. W ananassa, could be constructed using the diploid Fragaria reference map FV W FN as a standard reference point. |
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Updates:
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Sargent et al. The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera. Accepted for TAG
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Abstract of the updates:
We have developed 46 primer pairs from exon sequences flanking polymorphic introns of 23 Fragaria gene sequences and one Malus sequence deposited in the EMBL database. Sequencing of a set of the PCR products amplified with the novel primer pairs in diploid Fragaria showed the products to be homologous to the sequences from which the primers were originally designed. By scoring the segregation of the 24 genes in two diploid Fragaria progenies FVWFN (F. vesca W F. nubicola F2) and 815W903BC (F. vesca W F. viridis BC1) 29 genetic loci at discrete positions on the seven linkage groups previously characterised could be mapped, bringing to 35 the total number of known function genes mapped in Fragaria. Twenty primer pairs, representing 14 genes, amplified a product of the expected size in both Malus and Prunus. To demonstrate the applicability of these gene-specific loci to comparative mapping in Rosaceae, five markers that displayed clear polymorphism between the parents of a Malus and a Prunus mapping population were selected. The markers were then scored and mapped in at least one of the two additional progenies. |
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| Map Set Name: |
Fragaria-FVxFN-F2-2010 |
[ Show Only This Set ] |
| Abbreviated Name: |
Fragaria-FVxFN-F2-2010 |
[ Download Map Set Data ] |
| Accession ID: |
8 |
[ View Map Set In Matrix ] |
| Species: |
Fragaria (Strawberry) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
27 March, 2010 |
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Description (2008 Map):
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The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map.
We have identified a set of plants (the bin set) to permit "selective" or "bin" mapping using the diploid strawberry mapping population FV x FN, derived from the F2 cross F. vesca 815 x F. nubicola 601, which has been used to develop the Fragaria reference map. The bin set consists of 8 plants: the F. vesca 815 parent, the F1 hybrid individual, and 6 seedlings of the F2 population. This bin set divides the 578 cM of the diploid Fragaria genome into 46 bins, the largest mapping bin being 26 cM in length and the average bin size being 12.6 cM. To validate the FV x FN bin set, we used it to locate 103 loci into bins on the FV x FN map. These loci comprised 61 previously described SSRs, 38 new SSRs developed in this investigation from Fragaria x ananassa genomic DNA, EST and gene sequences, and 4 ripening-related genes developed for Prunus. The 103 markers were located to bins on all 7 linkage groups of the Fragaria map and a new mapping bin was identified with the novel markers, demonstrating that the map covers the majority of the diploid Fragaria genome and that the 6 bin-set seedlings selected were appropriate for bin mapping using this progeny. |
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Update (2010):
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SNP discovery and genetic mapping of T-DNA insertional mutants in Fragaria vesca L.
As part of a program to develop forward and reverse genetics platforms in the diploid strawberry [Fragaria vesca L.; (2n = 2x = 14)] we have generated insertional mutant lines by T-DNA mutagenesis using pCAMBIA vectors. To characterize the T-DNA insertion sites of a population of 108 unique single copy mutants, we utilized thermal asymmetric interlaced PCR (hiTAIL-PCR) to amplify the flanking region surrounding either the left or right border of the T-DNA. Bioinformatics analysis of flanking sequences revealed little preference for insertion site with regard to G/C content; left borders tended to retain more of the plasmid backbone than right borders. Primers were developed from F. vesca flanking sequences to attempt to amplify products from both parents of the reference F. vesca 815 x F. bucharica 601 mapping population. Polymorphism occurred as: presence/absence of an amplification product for 16 primer pairs and different size products for 12 primer pairs, For 46 mutants, where polymorphism was not found by PCR, the amplification products were sequenced to reveal SNP polymorphism. A cleaved amplified polymorphic sequence/derived cleaved amplified polymorphism sequence (CAPS/dCAPS) strategy was then applied to find restriction endonuclease recognition sites in one of the parental lines to map the SNP position of 74 of the T-DNA insertion lines. BLAST search of flanking regions against GenBank revealed that 46 of 108 flanking sequences were close to presumed strawberry genes related to annotated genes from other plants. |
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Update (2011):
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The genome sequence of the woodland strawberry (Fragaria vesca L.) is an important resource providing a reference for comparative genomics studies and future sequenced rosaceous species and has great utility as a model for the development of markers for mapping in the cultivated strawberry Fragaria x ananassa Duchesne ex Rozier. A set of 152 microsatellite simple sequence repeat (SSR) primer pairs was developed and mapped, along with 42 previously published but unmapped SSRs, permitting the precise assignment of 28.2 Mbp of previously unanchored genome sequence scaffolds (13% of the F. vesca genome sequence). The original ordering of F. vesca sequence scaffolds was performed without a physical map, using predominantly SSR markers to order scaffolds via anchoring to a comprehensive linkage map. This report complements and expands resolution of the Fragaria spp. reference map and refines the scaffold ordering of the F. vesca genome sequence using newly devised tools. The results of this study provide two significant resources: (i) the concurrent validation of a substantial set of SSRs associated with these previously unmapped regions of the Fragaria spp. genome and (ii) the precise placement of previously orphaned genomic sequence. Together, these resources improve the resolution and completeness of the strawberry genome sequence, making it a better resource for downstream studies in Fragaria spp. and the family Rosaceae. |
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