Detection of genomic deletions in rice using oligonucleotide microarrays
The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations...
| Autores principales: | , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2009
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/166196 |
| _version_ | 1855524097120796672 |
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| author | Bruce, Myron Hess, Ann Bai, Jianfa Mauleon, Ramil Diaz, M Genaleen Sugiyama, Nobuko Bordeos, Alicia Wang, Guo-Liang Leung, Hei Leach, Jan E. |
| author_browse | Bai, Jianfa Bordeos, Alicia Bruce, Myron Diaz, M Genaleen Hess, Ann Leach, Jan E. Leung, Hei Mauleon, Ramil Sugiyama, Nobuko Wang, Guo-Liang |
| author_facet | Bruce, Myron Hess, Ann Bai, Jianfa Mauleon, Ramil Diaz, M Genaleen Sugiyama, Nobuko Bordeos, Alicia Wang, Guo-Liang Leung, Hei Leach, Jan E. |
| author_sort | Bruce, Myron |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL). However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions.We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations http://irfgc.irri.org/cgi-bin/gbrowse/IR64_deletion_mutants/.We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a database saturated with deletions across the rice genome. This community resource can continue to grow with further hybridizations, allowing researchers to quickly identify mutants that harbor deletions in candidate genomic regions, for example, regions containing QTL of interest. |
| format | Journal Article |
| id | CGSpace166196 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2009 |
| publishDateRange | 2009 |
| publishDateSort | 2009 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1661962025-05-14T10:24:04Z Detection of genomic deletions in rice using oligonucleotide microarrays Bruce, Myron Hess, Ann Bai, Jianfa Mauleon, Ramil Diaz, M Genaleen Sugiyama, Nobuko Bordeos, Alicia Wang, Guo-Liang Leung, Hei Leach, Jan E. chromosomes databases dna hybridization dna libraries genes genomics mutants oligonucleotides phenotypes quantitative trait loci The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL). However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions.We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations http://irfgc.irri.org/cgi-bin/gbrowse/IR64_deletion_mutants/.We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a database saturated with deletions across the rice genome. This community resource can continue to grow with further hybridizations, allowing researchers to quickly identify mutants that harbor deletions in candidate genomic regions, for example, regions containing QTL of interest. 2009-12 2024-12-19T12:55:59Z 2024-12-19T12:55:59Z Journal Article https://hdl.handle.net/10568/166196 en Springer Bruce, Myron; Hess, Ann; Bai, Jianfa; Mauleon, Ramil; Diaz, M Genaleen; Sugiyama, Nobuko; Bordeos, Alicia; Wang, Guo-Liang; Leung, Hei and Leach, Jan E. 2009. Detection of genomic deletions in rice using oligonucleotide microarrays. BMC Genomics, Volume 10, no. 1 |
| spellingShingle | chromosomes databases dna hybridization dna libraries genes genomics mutants oligonucleotides phenotypes quantitative trait loci Bruce, Myron Hess, Ann Bai, Jianfa Mauleon, Ramil Diaz, M Genaleen Sugiyama, Nobuko Bordeos, Alicia Wang, Guo-Liang Leung, Hei Leach, Jan E. Detection of genomic deletions in rice using oligonucleotide microarrays |
| title | Detection of genomic deletions in rice using oligonucleotide microarrays |
| title_full | Detection of genomic deletions in rice using oligonucleotide microarrays |
| title_fullStr | Detection of genomic deletions in rice using oligonucleotide microarrays |
| title_full_unstemmed | Detection of genomic deletions in rice using oligonucleotide microarrays |
| title_short | Detection of genomic deletions in rice using oligonucleotide microarrays |
| title_sort | detection of genomic deletions in rice using oligonucleotide microarrays |
| topic | chromosomes databases dna hybridization dna libraries genes genomics mutants oligonucleotides phenotypes quantitative trait loci |
| url | https://hdl.handle.net/10568/166196 |
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