Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Analysis Of Single Feature Polymorphism Markers With A Lettuce Affymetrix Genechip For Massively Parallel Marker Discovery, Genotyping And Mapping.

Hans van Leeuwen¹ , Kevin Stoffel² , Smitha Mathrakott¹ , Fallon Chen¹ , Xiaoping Tan¹ , Jiqiang Yao² , Gene Wong¹ , Xinping Cui³ , Alexander Kozik¹ , María José Truco¹ , Richard W Michelmore¹ , Allen Van Deynze²

¹  UC Davis Genome Center, University of California, Davis, CA, 95616, USA

²  Seed Biotechnology Center, University of California, Davis, CA, 95616, USA

³  Department of Statistics, University of California, Riverside, CA, 92521, USA

Currently, there is the need for high-resolution genetic and physical maps in many crops to characterize the genetic mechanisms controlling agriculturally important traits. Although the discovery of sequence-based markers has become relatively straightforward, their identification and analysis in mapping populations or germplasm screens currently remains laborious and expensive. Single Feature Polymorphisms (SFPs) based on microarray hybridization is emerging as a powerful marker technology because of its highly parallel nature. Current gene expression arrays rarely provide redundancy for any one SFP, leading to both false positive and negative scoring of SFPs and subsequently to incorrect mapping or associations. Furthermore, a limited proportion of each gene is represented on expression chips, limiting SFP detection in species with low polymorphism such as lettuce. We have developed a 6.6 million feature Affymetrix GeneChip for both robust SFP discovery, genotyping and gene expression analysis. Probes from ~29,000 cultivated lettuce (L. sativa) unigenes and an additional ~6,000 unique sequences from four other related lettuce species (L. serriola, L. saligna, L. virosa and L. perennis) were synthesized on the GeneChip, with an average of 173 probes tiled per unigene. We have successfully used the GeneChip for cDNA and gDNA hybridizations and refined our SFP detection algorithms to robustly detect SFPs in our L. sativa × L. serriola RIL population, and in a panel of more than 50 diverse lettuce breeding lines and wild species. The efficiency of the custom design and analysis algorithms to detect SFPs will be presented.