Plant & Animal Genomes XVI Conference

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

A Whole Genome Microarray Designed For Marker Discovery, Genotyping And Mapping In Pepper

Jiqiang Yao¹ , Jim Prince³ , Alexander Kozik² , Allen Van Deynze¹

¹  Dept of Plant Sciences, University of California, 1 Shields Ave., Davis, CA, USA, 95616

²  Genome and Biomedical Sciences Facility, University of California, 1 Shields Ave., Davis, CA, USA, 95616

³  Biology Department, Science 314B, California State University, Fresno, CA, USA 93740

Traits or genes controlling them can be tracked using DNA markers in breeding programs. However, for DNA markers to be useful, they must be informative in breeding germplasm and inexpensive to assay. Although pepper has a moderately populated genetic map based on crosses between wild and cultivated germplasm, the low polymorphism in breeding germplasm and the type of many of the current markers (AFLP, RFLP, SSR) make these resources useful for tracking individual traits but less informative or cost-effective in breeding germplasm. This project builds on the current genomic resources for pepper to develop a highly informative DNA array specifically designed to efficiently discover and validate SFPs in breeding and research germplasm. SFPs are differences in hybridization of cDNA or DNA from different genotypes to probes (oligos) on an array. The precise molecular basis for each SFP is unknown and may be due to one or more single nucleotide polymorphisms (SNPs) or insertion/deletions (indels). We have designed a whole genome tiling array that will simultaneously assay over 30,000 unigenes in pepper. The array is being used to concurrently measure SFP diversity in relevant breeding lines and mapping parents and map unigenes in a phenotypically characterized mapping population relative to quantitative trait loci (QTL). This information will translate the genomic pepper information such that it can be directly used for breeding.