Abstract
Fine mapping can accurately identify positional candidate genes for quantitative trait loci (QTLs) but can be time consuming, costly, and, for small-effect QTLs with low heritability, difficult in practice. We propose an alternative approach, which uses meta-analysis of original mapping data to produce a relatively small confidence interval for target QTLs, lists the underlying positional candidates, and then eliminates them using whole-genome transcriptomics. Finally, sequencing is conducted on the remaining candidate genes allowing identification of allelic variation in either expression or protein sequence. We demonstrate the approach using root-growth QTLs on chromosomes 2, 5, and 9 of the Bala x Azucena rice mapping population. Confidence intervals of 10.5, 9.6, and 5.4 cM containing 189, 322, and 81 genes, respectively, were produced. Transcriptomics eliminated 40% of candidate genes and identified nine expression polymorphisms. Sequencing of 30 genes revealed that 57% of the predicted proteins were polymorphic. The limitations of this approach are discussed. (C) 2008 Elsevier Inc. All rights reserved.
Original language | English |
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Pages (from-to) | 344-352 |
Number of pages | 9 |
Journal | Genomics |
Volume | 92 |
Issue number | 5 |
Early online date | 18 Sept 2008 |
DOIs | |
Publication status | Published - Nov 2008 |
Keywords
- affymetrix
- candidate genes
- microarray analysis
- quantitative trait loci
- rice
- root morphology
- wax layer
- oryza-sativa l.
- penetration
- map
- expression
- morphology
- cloning