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. https://doi.org/10.1016/j.ygeno.2008.07.002

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)https://doi.org/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

Permalink - https://repository.rothamsted.ac.uk/item/8q069/a-bioinformatic-and-transcriptomic-approach-to-identifying-positional-candidate-genes-without-fine-mapping-an-example-using-rice-root-growth-qtls

17 total views
4 total downloads
0 views this month
0 downloads this month
Download files as zip