Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Poster: SSR
            

SIMPLE SEQUENCE REPEATS MINED FROM SUNFLOWER EXPRESSED SEQUENCE TAGS

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

² Department of Vegetable Crops, University of California, Davis, California, 95616

One of the goals of the Compositae Genome Project (CGP) has been to increase the density of the genetic linkage map of cultivated sunflower (Helianthus annuus) by developing and mapping PCR-based DNA markers for several hundred expressed sequence tags (ESTs). The CGP produced 44,061 H. annuus ESTs from pooled cDNA libraries constructed using two genotypes (RHA280 and RHA801), several tissues and developmental stages, and various chemical and abiotic stress treatments (12 cDNA libraries were constructed per genotype). The ESTs were assembled into 4,430 contigs and 7,645 singletons and searched for single nucleotide polymorphisms (SNPs), insertion-deletion (INDEL) polymorphisms, and simple sequence repeats (SSRs). One hundred and fifty SNPs and 52 INDEL polymorphisms were identified in contigs, while 862 SSRs (n > 4) were identified in contigs and singletons. SSR primers were designed for 735 SSRs and are presently being screened for utility and polymorphisms among eight domesticated and wild H. annuus germplasm sources (RHA280, RHA801, RHA373, RHA377, and HA383, Hopi, Havasupai, and ANN1811), five wild sunflower species (H. tuberosus, H. deserticola, H. argophyllus, H. anomalus, and H. paradoxus), safflower (Carthamus tinctorius), lettuce (Lactuca sativa), and wild lettuce (L. seriola). Thus far, 210 out of 316 SSR primers (67%) have yielded functional SSR markers. The DNA markers are being used to create a transcript-based genetic linkage map of the sunflower genome and should greatly increase the density of high-throughput DNA markers in gene-rich regions.