Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 21, 2009
Publication Date: May 29, 2009
Citation: Bernardo, A.N., Bradbury, P., Ma, H., Hu, S., Bowden, R.L., Buckler Iv, E.S., Bai, G. 2009. Discovery and mapping of single feature polymorphisms in wheat using affymetrix arrays. Biomed Central (BMC) Genomics. 10:251. Interpretive Summary: Wheat is one of the most important agricultural crops in the U.S. However, the use of genetic markers to accelerate wheat variety improvement has been hampered by a lack of good markers. The development of markers for wheat has been difficult. We used a new tool called Affymetrix GeneChips to identify a specific genetic marker. Analysis of 71 inbred lines developed from a cross between Ning 7840 and Clark was able to identify place 870 new markers. Research also showed that about half the markers identified were the result of single nucleotide change in sequence (SFP). The Affymetrix array was shown to be a cost-effective platform for SFP discovery and mapping. The new map will be a useful tool for genetic studies in wheat.
Technical Abstract: Single feature polymorphisms (SFPs) can be a rich source of markers for gene mapping and function studies. To explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome, six wheat varieties of diverse origins were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified. A subset of 164 was sequenced and 54% showed polymorphism of probe sequences. Microarray analysis of 71 recombinant inbred lines from the cross Ning 7840/Clark identified 955 SFPs and placed 877 SFPs and 269 simple sequence repeats on a genetic map. Map positions of a selected set of SFPs were validated by mapping single nucleotide polymorphism using SNaPshot and comparing with EST mapping data. The Affymetrix array is a cost-effective platform for SFP discovery and mapping in wheat. The new map will be a useful tool for genetic studies in wheat.