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.

Morphological variation of mutant sunflowers (Helianthus annuus) induced by space flight and their genetic background detection by SSR primers

“…Until now, only Tang et al (2002) reported the sequence information amplified by primers ORS759, ORS838, ORS840, ORS1112, and only one fragment was achieved by each of the primers. By comparing the alignment of our results with previous report (Tang et al, 2002), it was found that the homologies of all variation sequences are greater than 92%, or even as high as 99%, indicating the high conservation of genomic sequence of sunflower (Heesacker et al, 2008). Based on the high conservation of the sequences, the analysis of sequence variation showed that deletion, insertion and replacement occurred at some sites in the genomic DNA of sunflower, which was probably the main reason for the major change in morphological characters induced by space flight.…”

Salt and drought stresses in safflower: a review

“…In addition, Heesacker et al (2008) developed 16,643 EST-SSR markers from common sunflower EST libraries and inquired their transferability to closely and distantly related species of the Compositae family. Even though a low presence of these markers were common to safflower, still, their contribution to dense linkage mapping and drought-tolerant QTLs identification may be beneficial.…”

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

“…Initial EST library content and methods of library construction, sequencing, and assembly are described in Heesacker et al (2008). Subsequent library construction and sequencing have produced new EST collections for H. ciliaris, H. exilis, and H. tuberosus.…”