Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Development Of A Lettuce (Lactuca sativa) 6.6 Million Feature Affymetrix Genechip For Massively Parallel Genotyping And Gene Expression Analysis

David G Caldwell¹ , Alex Kozik¹ , Fallon Chen¹ , María José Truco¹ , Richard W Michelmore¹ , Allen Van Deynze²

¹  University of California, UC Davis Genome Center, 4302 GBSF, 451 E. Health Sciences Drive, Davis, CA, 95616, USA

²  University of California, Seed Biotechnology Center, Plant Reproductive Biology, Rm 1103, Extension Center Drive, Davis, CA, 95616, USA

Currently, there is the need for high-resolution genetic and physical maps in many crop species to identify the genetic mechanisms controlling agriculturally important traits. The ability to identify sequence based markers (SNPs or InDels) has become relatively straightforward, but the implementation of these markers into 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. To date, however, most SFPs are scored using arrays designed for gene expression analysis, which rarely provide redundancy for any one SFP. This can lead 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. We are developing a 6.6 million feature Affymetrix Genechip for both robust SFP genotyping and gene expression analysis in lettuce. Approximately 240 probes per unigene will be tiled across highly polymorphic coding and non-coding regions in 2bp increments for at least ~25,000 unigenes. The design and the analysis tools we are developing should provide greater than a 95% chance of scoring any SFP correctly. In addition, a set of probes for each unigene will be designed using the standard Affymetrix parameters for expression analysis which will allow for existing microarray expression analysis packages to be used. These expression probes will be designed to conserved regions of each gene and therefore may be useful in analysis of heterologous species in the Compositae.