title: SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility.
abstract: Simple sequence repeats (SSRs) are abundant and frequently highly polymorphic in transcribed sequences and widely targeted for marker development in eukaryotes. Sunflower (Helianthus annuus) transcript assemblies were built and mined to identify SSRs and insertions-deletions (INDELs) for marker development, comparative mapping, and other genomics applications in sunflower. We describe the spectrum and frequency of SSRs identified in the sunflower EST database, a catalog of 16,643 EST-SSRs, a collection of 484 EST-SSR and 43 EST-INDEL markers developed from common sunflower ESTs, polymorphisms of the markers among the parents of several intraspecific and interspecific mapping populations, and the transferability of the markers to closely and distantly related species in the Compositae. Of 17,904 unigenes in the transcript assembly, 1,956 (10.9%) harbored one or more SSRs with repeat counts of n > or = 5. EST-SSR markers were 1.6-fold more polymorphic among exotic than elite genotypes and 0.7-fold less polymorphic than non-genic SSR markers. Of 466 EST-SSR or INDEL markers screened for cross-species amplification and polymorphisms, 413 (88.6%) amplified alleles from one or more wild species (H. argophyllus, H. tuberosus, H. anomalus, H. paradoxus, and H. deserticola), whereas 69 (14.8%) amplified alleles from safflower (Carthamus tinctorius) and 67 (14.4%) amplified alleles from lettuce (Lactuca sativa); hence, only a fraction were transferable to distantly related genera in the Compositae, whereas most were transferable to wild relatives of H. annuus. Several thousand additional SSRs were identified in the EST database and supply a wealth of templates for EST-SSR marker development in sunflower.
authors.affiliation: Center for Applied Genetic Technologies, The University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Heesacker
authors.forename: Venkata K
authors.initials: VK
authors.lastname: Kishore
authors.forename: Wenxiang
authors.initials: W
authors.lastname: Gao
authors.forename: Shunxue
authors.initials: S
authors.lastname: Tang
authors.forename: Judith M
authors.initials: JM
authors.lastname: Kolkman
authors.forename: Alan
authors.initials: A
authors.lastname: Gingle
authors.forename: Marta
authors.initials: M
authors.lastname: Matvienko
authors.forename: Alexander
authors.initials: A
authors.lastname: Kozik
authors.forename: Richard M
authors.initials: RM
authors.lastname: Michelmore
authors.forename: Zhao
authors.initials: Z
authors.lastname: Lai
authors.forename: Loren H
authors.initials: LH
authors.lastname: Rieseberg
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Knapp
mesh_terms: D019659:Asteraceae / Q000145:classification; D019295:Computational Biology; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D006368:Helianthus / Q000235:genetics*; D054643:INDEL Mutation; D018598:Minisatellite Repeats; D011110:Polymorphism, Genetic; D013045:Species Specificity
chemical_list: D005819:Genetic Markers