A first generation BAC-based physical map of the Asian seabass (Lates calcarifer).
<h4>Background</h4>The Asian seabass (Lates calcarifer) is an important marine foodfish species in Southeast Asia and Australia. Genetic improvement of this species has been achieved to some extent through selective breeding programs since 1990s. Several genomic tools such as DNA markers...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2010-08-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20700486/?tool=EBI |
| _version_ | 1818425620314456064 |
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| author | Jun Hong Xia Felicia Feng Grace Lin Chun Ming Wang Gen Hua Yue |
| author_facet | Jun Hong Xia Felicia Feng Grace Lin Chun Ming Wang Gen Hua Yue |
| author_sort | Jun Hong Xia |
| collection | DOAJ |
| description | <h4>Background</h4>The Asian seabass (Lates calcarifer) is an important marine foodfish species in Southeast Asia and Australia. Genetic improvement of this species has been achieved to some extent through selective breeding programs since 1990s. Several genomic tools such as DNA markers, a linkage map, cDNA and BAC libraries have been developed to assist selective breeding. A physical map is still lacking, although it is essential for positional cloning of genes located in quantitative trait loci (QTL) and assembly of whole genome sequences.<h4>Methodology/principal findings</h4>A genome-wide physical map of the Asian seabass was constructed by restriction fingerprinting of 38,208 BAC clones with SNaPshot HICF FPC technique. A total of 30,454 were assembled into 2,865 contigs. The physical length of the assembled contigs summed up to 665 Mb. Analyses of some contigs using different methods demonstrated the reliability of the assembly.<h4>Conclusions/significance</h4>The present physical map is the first physical map for Asian seabass. This physical map will facilitate the fine mapping of QTL for economically important traits and the positional cloning of genes located in QTL. It will also be useful for the whole genome sequencing and assembly. Detailed information about BAC-contigs and BAC clones are available upon request. |
| first_indexed | 2024-12-14T14:16:50Z |
| format | Article |
| id | doaj.art-ed1b0aa5f8b8413f8a35ec65ad4b73d3 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T14:16:50Z |
| publishDate | 2010-08-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-ed1b0aa5f8b8413f8a35ec65ad4b73d32022-12-21T22:58:12ZengPublic Library of Science (PLoS)PLoS ONE1932-62032010-08-0158e1197410.1371/journal.pone.0011974A first generation BAC-based physical map of the Asian seabass (Lates calcarifer).Jun Hong XiaFelicia FengGrace LinChun Ming WangGen Hua Yue<h4>Background</h4>The Asian seabass (Lates calcarifer) is an important marine foodfish species in Southeast Asia and Australia. Genetic improvement of this species has been achieved to some extent through selective breeding programs since 1990s. Several genomic tools such as DNA markers, a linkage map, cDNA and BAC libraries have been developed to assist selective breeding. A physical map is still lacking, although it is essential for positional cloning of genes located in quantitative trait loci (QTL) and assembly of whole genome sequences.<h4>Methodology/principal findings</h4>A genome-wide physical map of the Asian seabass was constructed by restriction fingerprinting of 38,208 BAC clones with SNaPshot HICF FPC technique. A total of 30,454 were assembled into 2,865 contigs. The physical length of the assembled contigs summed up to 665 Mb. Analyses of some contigs using different methods demonstrated the reliability of the assembly.<h4>Conclusions/significance</h4>The present physical map is the first physical map for Asian seabass. This physical map will facilitate the fine mapping of QTL for economically important traits and the positional cloning of genes located in QTL. It will also be useful for the whole genome sequencing and assembly. Detailed information about BAC-contigs and BAC clones are available upon request.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20700486/?tool=EBI |
| spellingShingle | Jun Hong Xia Felicia Feng Grace Lin Chun Ming Wang Gen Hua Yue A first generation BAC-based physical map of the Asian seabass (Lates calcarifer). PLoS ONE |
| title | A first generation BAC-based physical map of the Asian seabass (Lates calcarifer). |
| title_full | A first generation BAC-based physical map of the Asian seabass (Lates calcarifer). |
| title_fullStr | A first generation BAC-based physical map of the Asian seabass (Lates calcarifer). |
| title_full_unstemmed | A first generation BAC-based physical map of the Asian seabass (Lates calcarifer). |
| title_short | A first generation BAC-based physical map of the Asian seabass (Lates calcarifer). |
| title_sort | first generation bac based physical map of the asian seabass lates calcarifer |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20700486/?tool=EBI |
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