TY - JOUR
T1 - SSRs and INDELs mined from the sunflower EST database
T2 - Abundance, polymorphisms, and cross-taxa utility
AU - Heesacker, Adam
AU - Kishore, Venkata K.
AU - Gao, Wenxiang
AU - Tang, Shunxue
AU - Kolkman, Judith M.
AU - Gingle, Alan
AU - Matvienko, Marta
AU - Kozik, Alexander
AU - Michelmore, Richard M.
AU - Lai, Zhao
AU - Rieseberg, Loren H.
AU - Knapp, Steven J.
N1 - Funding Information:
This research was supported by grants from the National Science Foundation Plant Genome Program (No. 0421630) and United States Department of Agriculture Plant Genome Program (No. 2000-04292) to S.J.K, R.W.M, and L.H.R, and Advanta Seeds, Pioneer Hi-Bred International, Syngenta, and the Paul C. Berger Endowment to S.J.K.
PY - 2008/11
Y1 - 2008/11
N2 - 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 ≥ 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.
AB - 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 ≥ 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.
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U2 - 10.1007/s00122-008-0841-0
DO - 10.1007/s00122-008-0841-0
M3 - Article
C2 - 18633591
AN - SCOPUS:53849112948
SN - 0040-5752
VL - 117
SP - 1021
EP - 1029
JO - Theoretical and Applied Genetics
JF - Theoretical and Applied Genetics
IS - 7
ER -