A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping: an example using rice root-growth QTLs

A - Papers appearing in refereed journals

Norton, G. J., Aitkenhead, M. J., Khowaja, F. S., Whalley, W. R. and Price, A. H. 2008. A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping: an example using rice root-growth QTLs. Genomics. 92 (5), pp. 344-352.

AuthorsNorton, G. J., Aitkenhead, M. J., Khowaja, F. S., Whalley, W. R. and Price, A. H.
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 × 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.

KeywordsAffymetrix; Candidate genes; Microarray analysis; Quantitative trait loci; Rice; Root morphology; Wax layer
Year of Publication2008
JournalGenomics
Journal citation92 (5), pp. 344-352
Digital Object Identifier (DOI)doi:10.1016/j.ygeno.2008.07.002
Open accessPublished as bronze (free) open access
Funder project or codeSEF
Project: 4723
Bio-physics of the soil-root interface
Publisher's version
Copyright license
Publisher copyright
Output statusPublished
Publication dates
Online18 Sep 2008
Publication process dates
Accepted11 Jul 2008
ISSN0888-7543
PublisherAcademic Press Inc Elsevier Science

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