Integration of linkage maps for the Amphidiploid <it>Brassica napus </it>and comparative mapping with <it>Arabidopsis </it>and <it>Brassica rapa</it>
<p>Abstract</p> <p>Background</p> <p>The large number of genetic linkage maps representing <it>Brassica </it>chromosomes constitute a potential platform for studying crop traits and genome evolution within <it>Brassicaceae</it>. However, the alig...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2011-02-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/12/101 |
| _version_ | 1818142142788272128 |
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| author | Delourme Régine Falentin Cyril Parkin Isobel AP Lydiate Derek J Wang Jun Carion Pierre WC King Graham J |
| author_facet | Delourme Régine Falentin Cyril Parkin Isobel AP Lydiate Derek J Wang Jun Carion Pierre WC King Graham J |
| author_sort | Delourme Régine |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The large number of genetic linkage maps representing <it>Brassica </it>chromosomes constitute a potential platform for studying crop traits and genome evolution within <it>Brassicaceae</it>. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available.</p> <p>Results</p> <p>We report the first genome-wide integration of <it>Brassica </it>maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid <it>Brassica napus </it>(2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the <it>B. napus </it>integrated map we identified 103 conserved collinearity blocks relative to <it>Arabidopsis</it>, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of <it>Brassica rapa</it>.</p> <p>Conclusions</p> <p>Our results provide a comprehensive genetic integration of the <it>B. napus </it>genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.</p> |
| first_indexed | 2024-12-11T11:11:05Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-11T11:11:05Z |
| publishDate | 2011-02-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-074a8ff65c03478482776aefe60d97752022-12-22T01:09:32ZengBMCBMC Genomics1471-21642011-02-0112110110.1186/1471-2164-12-101Integration of linkage maps for the Amphidiploid <it>Brassica napus </it>and comparative mapping with <it>Arabidopsis </it>and <it>Brassica rapa</it>Delourme RégineFalentin CyrilParkin Isobel APLydiate Derek JWang JunCarion Pierre WCKing Graham J<p>Abstract</p> <p>Background</p> <p>The large number of genetic linkage maps representing <it>Brassica </it>chromosomes constitute a potential platform for studying crop traits and genome evolution within <it>Brassicaceae</it>. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available.</p> <p>Results</p> <p>We report the first genome-wide integration of <it>Brassica </it>maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid <it>Brassica napus </it>(2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the <it>B. napus </it>integrated map we identified 103 conserved collinearity blocks relative to <it>Arabidopsis</it>, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of <it>Brassica rapa</it>.</p> <p>Conclusions</p> <p>Our results provide a comprehensive genetic integration of the <it>B. napus </it>genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.</p>http://www.biomedcentral.com/1471-2164/12/101 |
| spellingShingle | Delourme Régine Falentin Cyril Parkin Isobel AP Lydiate Derek J Wang Jun Carion Pierre WC King Graham J Integration of linkage maps for the Amphidiploid <it>Brassica napus </it>and comparative mapping with <it>Arabidopsis </it>and <it>Brassica rapa</it> BMC Genomics |
| title | Integration of linkage maps for the Amphidiploid <it>Brassica napus </it>and comparative mapping with <it>Arabidopsis </it>and <it>Brassica rapa</it> |
| title_full | Integration of linkage maps for the Amphidiploid <it>Brassica napus </it>and comparative mapping with <it>Arabidopsis </it>and <it>Brassica rapa</it> |
| title_fullStr | Integration of linkage maps for the Amphidiploid <it>Brassica napus </it>and comparative mapping with <it>Arabidopsis </it>and <it>Brassica rapa</it> |
| title_full_unstemmed | Integration of linkage maps for the Amphidiploid <it>Brassica napus </it>and comparative mapping with <it>Arabidopsis </it>and <it>Brassica rapa</it> |
| title_short | Integration of linkage maps for the Amphidiploid <it>Brassica napus </it>and comparative mapping with <it>Arabidopsis </it>and <it>Brassica rapa</it> |
| title_sort | integration of linkage maps for the amphidiploid it brassica napus it and comparative mapping with it arabidopsis it and it brassica rapa it |
| url | http://www.biomedcentral.com/1471-2164/12/101 |
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