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| Map Set Name: |
Prunus Bin Map |
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| Abbreviated Name: |
Prunus Bin Map |
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| Accession ID: |
30 |
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| Species: |
Prunus (Prunus) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
22 August, 2005 |
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Description:
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The concept of selective (or bin) mapping is used here for the first time taking as an example the Prunus reference map constructed with an almond x peach F2 population. Based on this map, a set of six plants was selected that jointly defined 65 possible different genotypes for the codominant markers mapped on it. Sixty-three of these joint
genotypes corresponded to a single chromosomal region (a bin) of the Prunus genome, and the two remaining to two bins each. The 67 bins defined by these six plants had 7.8 cM average length and maximum individual length of 24.7 cM. Using a unit of analysis composed of these six plants, their F1 hybrid parent and one of the parents of the hybrid, we mapped 264 microsatellite (or simple-sequence repeat: SSR) markers from 401
different microsatellite primer pairs. Bin mapping proved to be a fast and economic strategy that could be used for further map saturation, the addition of valuable markers, such as those based on microsatellites or ESTs, and to give a wider scope to, and more efficient use of, reference mapping populations. |
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bin and bin-mapped markers:
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The bins in this map can be defined as an interval between one recombination breakpoint or telomere and the next one (within the set of the selected individuals). As a result, the real limit between the bins is a recombination breakpoint and not a marker unless the recombination breakpoint has generated a marker. Thus the first and the last marker of the bins are the ones that are closest to the recombination breakpoint (or telomere) but not the limit itself. For this reason it can be that a marker within a certain bin can actually be located above or below the first or the last marker of this bin depending where the recombination breakpoint is located. For simpler display, all the bin-mapped markers are displayed as aliases of the bin name in CMap. |
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Contact:
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P. Arus (pere.arus@irta.es)
W. Howad (Werner.Howad@irta.es) |
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RosCOS mapping:
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BACKGROUND: Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. RESULTS: We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae. CONCLUSION: Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL analyses. |
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