BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping.
Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical "contig" maps were generated independently prior to merging. Here, we develop a new and...
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| Language: | English |
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Public Library of Science (PLoS)
2010-02-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0009089&type=printable |
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| author | Giang T H Vu Paul H Dear Peter D S Caligari Mike J Wilkinson |
| author_facet | Giang T H Vu Paul H Dear Peter D S Caligari Mike J Wilkinson |
| author_sort | Giang T H Vu |
| collection | DOAJ |
| description | Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical "contig" maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS) markers spanning approximately 10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome) samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual "BAC-HAPPY-mapping" to convert BAC landing data into BAC linkage contigs is possible. |
| format | Article |
| id | doaj-art-c2b31d02618449ce8db9ec458c1cbb43 |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2010-02-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-c2b31d02618449ce8db9ec458c1cbb432025-08-20T03:07:40ZengPublic Library of Science (PLoS)PLoS ONE1932-62032010-02-0152e908910.1371/journal.pone.0009089BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping.Giang T H VuPaul H DearPeter D S CaligariMike J WilkinsonPhysical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical "contig" maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS) markers spanning approximately 10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome) samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual "BAC-HAPPY-mapping" to convert BAC landing data into BAC linkage contigs is possible.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0009089&type=printable |
| spellingShingle | Giang T H Vu Paul H Dear Peter D S Caligari Mike J Wilkinson BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping. PLoS ONE |
| title | BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping. |
| title_full | BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping. |
| title_fullStr | BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping. |
| title_full_unstemmed | BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping. |
| title_short | BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping. |
| title_sort | bac happy mapping bap mapping a new and efficient protocol for physical mapping |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0009089&type=printable |
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