ArticleBMC genomics2013
De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 85 citations in OpenAlex.
- Invasive patterns of Biomphalaria straminea revealed by genetic mapping in the Greater Bay Area, China.Infectious diseases of poverty · 2026Article
- Genetic diversity study and molecular marker development for economic traits in Korean pine based on RAD-Seq.Frontiers in plant science · 2026Article
- Transcriptome analysis identifies genes regulating self-compatibility, flowering time, and oil biosynthesis in Noug (Guizotia abyssinica).Scientific reports · 2025Article
- Applications of Molecular Markers for Developing Abiotic-Stress-Resilient Oilseed Crops.Life (Basel, Switzerland) · 2022Review
- Characterization and mapping of a downy mildew resistance gene,Molecular breeding : new strategies in plant improvement · 2022Article
- Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq.BMC genomics · 2020Article
- Diversification of the downy mildew resistance gene pool by introgression of a new gene, PlTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- QTL fine-mapping of soybean (Glycine max L.) leaf type associated traits in two RILs populations.BMC genomics · 2019Article
- Resolving population structure and genetic differentiation associated with RAD-SNP loci under selection in tossa jute (Corchorus olitorius L.).Molecular genetics and genomics : MGG · 2019Article
- Linkage Mapping and Genome-Wide Association Studies of theFrontiers in genetics · 2019Article
- A Multi-Level Strategy Based on Metabolic and Molecular Genetic Approaches for the Characterization of DifferentMolecules (Basel, Switzerland) · 2018Article
- Article
- A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting.Ecology and evolution · 2018Article
- Monitoring Response of a Few bZip Transcription Factors in Response to Osmotic Stress in Sunflower.Iranian journal of biotechnology · 2018Article
- Article
- MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation.Scientific reports · 2017Article
- Development and dissection of diagnostic SNP markers for the downy mildew resistance genes PlMolecular genetics and genomics : MGG · 2017Article
- A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage.Scientific reports · 2017Article
- Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation.Molecular ecology resources · 2017Article
- Characterization of Leaf Transcriptome in Banksia hookeriana.Genomics, proteomics & bioinformatics · 2017Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundApplication of Single Nucleotide Polymorphism (SNP) marker technology as a tool in sunflower breeding programs offers enormous potential to improve sunflower genetics, and facilitate faster release of sunflower hybrids to the market place. Through a National Sunflower Association (NSA) funded initiative, we report on the process of SNP discovery through reductive genome sequencing and local assembly of six diverse sunflower inbred lines that represent oil as well as confection types.
resultsA combination of Restriction site Associated DNA Sequencing (RAD-Seq) protocols and Illumina paired-end sequencing chemistry generated high quality 89.4 M paired end reads from the six lines which represent 5.3 GB of the sequencing data. Raw reads from the sunflower line, RHA 464 were assembled de novo to serve as a framework reference genome. About 15.2 Mb of sunflower genome distributed over 42,267 contigs were obtained upon assembly of RHA 464 sequencing data, the contig lengths ranged from 200 to 950 bp with an N50 length of 393 bp. SNP calling was performed by aligning sequencing data from the six sunflower lines to the assembled reference RHA 464. On average, 1 SNP was located every 143 bp of the sunflower genome sequence. Based on several filtering criteria, a final set of 16,467 putative sequence variants with characteristics favorable for Illumina Infinium Genotyping Technology (IGT) were mined from the sequence data generated across six diverse sunflower lines.
conclusionHere we report the molecular and computational methodology involved in SNP development for a complex genome like sunflower lacking reference assembly, offering an attractive tool for molecular breeding purposes in sunflower.
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