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Open Access Research article

Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays

Amy N Bernardo1, Peter J Bradbury2, Hongxiang Ma34, Shengwa Hu4, Robert L Bowden5, Edward S Buckler2 and Guihua Bai5*

Author Affiliations

1 Dept. of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA

2 ARS-USDA, Maize Genetic Diversity Laboratory, Ithaca, NY 14853, USA

3 Institute of Plant Genetics and Biotechnology, JAAS, Nanjing, PR China

4 Dept. of Agronomy, Kansas State University, Manhattan, KS 66506, USA

5 ARS-USDA Plant Science and Entomology Unit, Manhattan, KS 66506, USA

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BMC Genomics 2009, 10:251  doi:10.1186/1471-2164-10-251

Published: 29 May 2009

Abstract

Background

Wheat (Triticum aestivum L.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (~17,000 Mb) and high levels of repetitive sequences; the whole genome sequence may not be expected in the near future. Available linkage maps have low marker density due to limitation in available markers; therefore new technologies that detect genome-wide polymorphisms are still needed to discover a large number of new markers for construction of high-resolution maps. A high-resolution map is a critical tool for gene isolation, molecular breeding and genomic research. Single feature polymorphism (SFP) is a new microarray-based type of marker that is detected by hybridization of DNA or cRNA to oligonucleotide probes. This study was conducted to explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome.

Results

Six wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified. A subset of 164 unigenes was sequenced and 54% showed polymorphism within probes. Microarray analysis of 71 recombinant inbred lines from the cross Ning 7840/Clark identified 955 SFPs and 877 of them were mapped together with 269 simple sequence repeat markers. The SFPs were randomly distributed within a chromosome but were unevenly distributed among different genomes. The B genome had the most SFPs, and the D genome had the least. Map positions of a selected set of SFPs were validated by mapping single nucleotide polymorphism using SNaPshot and comparing with expressed sequence tags mapping data.

Conclusion

The Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat. The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat.