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.
|Authors||Norton, G. J., Aitkenhead, M. J., Khowaja, F. S., Whalley, W. R. and Price, A. H.|
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.
|Keywords||Affymetrix; Candidate genes; Microarray analysis; Quantitative trait loci; Rice; Root morphology; Wax layer|
|Year of Publication||2008|
|Journal citation||92 (5), pp. 344-352|
|Digital Object Identifier (DOI)||doi:10.1016/j.ygeno.2008.07.002|
|Open access||Published as bronze (free) open access|
|Funder project or code||SEF|
|Bio-physics of the soil-root interface|
|Online||18 Sep 2008|
|Publication process dates|
|Accepted||11 Jul 2008|
|Publisher||Academic 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