High Density SNP Mapping to Identify Candidate Genes Underlying QTL for Pre-Harvest Sprouting in Wheat

Previous work by our group identified significant QTL for pre-harvest sprouting (PHS) traits on chromosomes 4A and 7D in the spring wheat population RL4452/AC Domain (Rasul et al., 2009) utilizing a simple sequence repeat based genetic map. Recently, a large number of SNP markers has become available in wheat and through community efforts many SNPs are now available via public databases (http://www.cerealsdb.uk.net/, http://129.130.90.211/snp/). In addition, a 90,000 gene-associated SNP genotyping assay is available based on the Illumina Infinium platform. Genotyping the 193 line RL4452/AC Domain population with this assay identified 12,351 polymorphic markers that were added to 419 existing SSR, DArT and EST markers. QTL analysis using phenotypic data from Rasul et al. (2009) revealed two QTL for sprouting index not identified in the previous study on chromosomes 3B and 7B and narrowed down the flanking region for the 4A and 7D QTL. The 7D QTL was for falling number and coincided with QTL for maturity and heading date. The genomic region on 4A was associated with QTL for germination index, falling number and sprouting index.

Utilizing synteny with Brachypodium distachyon the gene encoding gibberellin 20-oxidase was identified as a candidate for the dormancy QTL on chromosome 4A in the population RL4452/AC Domain. Analysis of the 5’-upstream region of the gene revealed an insertion in the non-dormant parent RL4452. The insertion marker was mapped into the region corresponding to the quantitative trait locus (QTL) for germination index. For 7D a candidate gene (Flowering time locus T (FT)) was identified through synteny and sequencing of parental lines identified a polymorphism previously known to be associated with maturity (Bonin et al. 2008). Further examination of these candidate genes is in progress.

References

Rasul G, Humphreys, DG, Brule-Babel A, McCartney CA, Knox RE, DePauw RM, Somers DJ. Euphytica168:363-378.

Bonin I, Rousset, M, Madur, D, Sourdille, P,Dupuits, C, Brunel, D, Goldringer, I. Theor. Appl. Genet. (2008) 116:383-394.