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

Area of Science:

• Plant Genomics
• Molecular Genetics
• Bioinformatics

Background:

• Wheat (Triticum aestivum L.) is a vital global food crop with a large, complex genome hindering complete sequencing.
• Existing linkage maps lack marker density, necessitating novel technologies for genome-wide polymorphism discovery.
• High-resolution maps are crucial for gene isolation, molecular breeding, and advanced genomic studies.

Purpose of the Study:

• To assess the feasibility of using Affymetrix GeneChip arrays for discovering and mapping single feature polymorphisms (SFPs) in the hexaploid wheat genome.
• To develop a high-density genetic map for wheat utilizing SFPs.
• To explore the utility of SFPs as markers in wheat genetics.

Main Methods:

• Microarray analysis using Affymetrix GeneChips on diverse wheat varieties and recombinant inbred lines.
• Identification of probe sets exhibiting significant probe-by-variety interactions indicative of SFPs.
• Sequencing of a subset of unigenes to confirm polymorphism and validation of SFP map positions using SNP and EST mapping data.

Main Results:

• Identified 396 probe sets with SFPs across six wheat varieties.
• Discovered 955 SFPs in recombinant inbred lines, with 877 mapped alongside 269 SSR markers.
• SFPs showed random distribution within chromosomes but uneven distribution across genomes (B>A>D).
• Map positions were validated using SNP and EST mapping.

Conclusions:

• Affymetrix arrays provide a cost-effective platform for SFP discovery and mapping in wheat.
• The developed high-density map serves as a valuable resource for wheat genetic and genomic research.
• SFPs represent a promising marker type for advancing wheat genomics.