High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes.
To date, microarray-based genotyping of large, complex plant genomes has been complicated by the need to perform genome complexity reduction to obtain sufficiently strong hybridization signals. Genome complexity reduction techniques are, however, tedious and can introduce unwanted variables into gen...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2010-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2996289?pdf=render |
| _version_ | 1811268718211104768 |
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| author | Yan Fu Nathan M Springer Kai Ying Cheng-Ting Yeh A Leonardo Iniguez Todd Richmond Wei Wu Brad Barbazuk Dan Nettleton Jeff Jeddeloh Patrick S Schnable |
| author_facet | Yan Fu Nathan M Springer Kai Ying Cheng-Ting Yeh A Leonardo Iniguez Todd Richmond Wei Wu Brad Barbazuk Dan Nettleton Jeff Jeddeloh Patrick S Schnable |
| author_sort | Yan Fu |
| collection | DOAJ |
| description | To date, microarray-based genotyping of large, complex plant genomes has been complicated by the need to perform genome complexity reduction to obtain sufficiently strong hybridization signals. Genome complexity reduction techniques are, however, tedious and can introduce unwanted variables into genotyping assays. Here, we report a microarray-based genotyping technology for complex genomes (such as the 2.3 GB maize genome) that does not require genome complexity reduction prior to hybridization. Approximately 200,000 long oligonucleotide probes were identified as being polymorphic between the inbred parents of a mapping population and used to genotype two recombinant inbred lines. While multiple hybridization replicates provided ∼97% accuracy, even a single replicate provided ∼95% accuracy. Genotyping accuracy was further increased to >99% by utilizing information from adjacent probes. This microarray-based method provides a simple, high-density genotyping approach for large, complex genomes. |
| first_indexed | 2024-04-12T21:27:57Z |
| format | Article |
| id | doaj.art-63eda58c94374245bd25a73c4ed4b00c |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T21:27:57Z |
| publishDate | 2010-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-63eda58c94374245bd25a73c4ed4b00c2022-12-22T03:16:07ZengPublic Library of Science (PLoS)PLoS ONE1932-62032010-01-01512e1417810.1371/journal.pone.0014178High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes.Yan FuNathan M SpringerKai YingCheng-Ting YehA Leonardo IniguezTodd RichmondWei WuBrad BarbazukDan NettletonJeff JeddelohPatrick S SchnableTo date, microarray-based genotyping of large, complex plant genomes has been complicated by the need to perform genome complexity reduction to obtain sufficiently strong hybridization signals. Genome complexity reduction techniques are, however, tedious and can introduce unwanted variables into genotyping assays. Here, we report a microarray-based genotyping technology for complex genomes (such as the 2.3 GB maize genome) that does not require genome complexity reduction prior to hybridization. Approximately 200,000 long oligonucleotide probes were identified as being polymorphic between the inbred parents of a mapping population and used to genotype two recombinant inbred lines. While multiple hybridization replicates provided ∼97% accuracy, even a single replicate provided ∼95% accuracy. Genotyping accuracy was further increased to >99% by utilizing information from adjacent probes. This microarray-based method provides a simple, high-density genotyping approach for large, complex genomes.http://europepmc.org/articles/PMC2996289?pdf=render |
| spellingShingle | Yan Fu Nathan M Springer Kai Ying Cheng-Ting Yeh A Leonardo Iniguez Todd Richmond Wei Wu Brad Barbazuk Dan Nettleton Jeff Jeddeloh Patrick S Schnable High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. PLoS ONE |
| title | High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. |
| title_full | High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. |
| title_fullStr | High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. |
| title_full_unstemmed | High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. |
| title_short | High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. |
| title_sort | high resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes |
| url | http://europepmc.org/articles/PMC2996289?pdf=render |
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