ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2008
SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 121 citations in OpenAlex.
- In Vitro Regeneration from Leaf Explants ofPlants (Basel, Switzerland) · 2024Article
- Molecular characterization and validation of sunflower (Helianthus annuus L.) hybrids through SSR markers.PloS one · 2022Article
- Genome-wideGene reports · 2021Article
- Discovery of miRNAs and Development of Heat-Responsive miRNA-SSR Markers for Characterization of Wheat Germplasm for Terminal Heat Tolerance Breeding.Frontiers in genetics · 2021Article
- Mining and comparative survey of EST-SSR markers among members of Euphorbiaceae family.Molecular biology reports · 2018Article
- Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits.BMC research notes · 2017Article
- Sunflower Hybrid Breeding: From Markers to Genomic Selection.Frontiers in plant science · 2017Review
- In silico search, characterization and validation of new EST-SSR markers in the genus Prunus.BMC research notes · 2016Article
- Article
- Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.).International journal of genomics · 2015Article
- Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using insertion-deletion (InDel) and simple sequence repeat (SSR) markers.BMC genetics · 2014Article
- A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12.PloS one · 2014Article
- De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach.BMC genomics · 2013Article
- High-density genetic maps for loci involved in nuclear male sterility (NMS1) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L., Asteraceae).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Genetic mapping of rust resistance genes in confection sunflower line HA-R6 and oilseed line RHA 397.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Molecular tagging of a novel rust resistance gene R(12) in sunflower (Helianthus annuus L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Toward a molecular cytogenetic map for cultivated sunflower (Helianthus annuus L.) by landed BAC/BIBAC clones.G3 (Bethesda, Md.) · 2013Article
- The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq.Biology · 2012Article
- Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses.G3 (Bethesda, Md.) · 2012Article
- Molecular mapping of the Pl(16) downy mildew resistance gene from HA-R4 to facilitate marker-assisted selection in sunflower.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
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Authors and funding
12 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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