Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Workshop: Compositae
            

SNP DISCOVERY, DIVERSITY, AND GENOTYPING IN SUNFLOWER.

¹ Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331 USA

² Advanta Seeds UK Ltd., Station Road, Docking, King's Lynn, Norfolk, PE31 8LS, UK

³ Advanta Semillas, Balcarce Research Station, Ruta 226, KM 60.3 (7620), Balcarce PCIA DE BS.AS., Argentina

⁴ Advanta Biotechnology Department, SES-Europe NV/SA, Industriepark, Soldatenplein Z2 nr. 15, B3300 Tienen, Belgium

⁵ Department of Biochemistry, University of Nevada, Reno, NV 89557 USA

Single nucleotide polymorphisms (SNPs) are the most abundant class of DNA polymorphisms in plant and animal genomes and are often functionally important. SNPs can be genotyped using high-throughput and massively parallel methods and hold great promise as tools for molecular breeding and genomics research. The first large scale analysis of SNPs in sunflower (Helianthus annuus L.) is described herein. Our aims were to (i) estimate SNP genotype and haplotype frequencies for 81 genes dispersed throughout the genome, (ii) develop and test SNP markers for each of the 81 loci, (iii) assess the validity of SNP markers on 12 sequenced (reference) genotypes, and (iv) assess the utility and polymorphisms of SNP markers among several unsequenced (test) genotypes. The cDNA probes for the 81 RFLP markers were sequenced. DNA fragments were amplified from 12 genotypes and 68 loci using long-distance PCR. The amplicons were cloned and single-pass sequenced from each end to produce ~1,000 bp of DNA sequence per locus per genotype. SNPs were found in every gene. The mean SNP frequency was 1/68 bp, the mean insertion-deletion (INDEL) frequency was 1/200 bp, and the mean haplotype frequency was 12/kb. We are presently testing SNP genotyping assays for several loci and plan to describe the utility and polymorphisms of SNP markers among wild and domesticated sunflowers. The SNP and INDEL markers described herein create the basis for producing second generation genetic maps and greatly increase the utility of the public RFLP map of sunflower.