PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 251.
Published online May 29, 2009. doi:  10.1186/1471-2164-10-251
PMCID: PMC2698007
Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays
Amy N Bernardo,#1 Peter J Bradbury,#2 Hongxiang Ma,3,4 Shengwa Hu,4 Robert L Bowden,5 Edward S Buckler,2 and Guihua Baicorresponding author5
1Dept. of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
2ARS-USDA, Maize Genetic Diversity Laboratory, Ithaca, NY 14853, USA
3Institute of Plant Genetics and Biotechnology, JAAS, Nanjing, PR China
4Dept. of Agronomy, Kansas State University, Manhattan, KS 66506, USA
5ARS-USDA Plant Science and Entomology Unit, Manhattan, KS 66506, USA
corresponding authorCorresponding author.
#Contributed equally.
Amy N Bernardo: amy8/at/ksu.edu; Peter J Bradbury: Peter.Bradbury/at/ars.usda.gov; Hongxiang Ma: mahx/at/jaas.ac.cn; Shengwa Hu: hushengwu/at/hotmail.com; Robert L Bowden: Robert.bowden/at/ars.usda.gov; Edward S Buckler: esb33/at/cornell.edu; Guihua Bai: guihua.bai/at/ars.usda.gov
Received November 26, 2008; Accepted May 29, 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.
Articles from BMC Genomics are provided here courtesy of
BioMed Central