ArticleBMC genomics2013
BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower.
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 26 papers.
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26 citing papers in PubMed, 73 citations in OpenAlex.
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- BSR and Full-Length Transcriptome Approaches Identified Candidate Genes for High Seed Ratio inCurrent issues in molecular biology · 2022Article
- Conjunctive Analyses of BSA-Seq and BSR-Seq Unveil theInternational journal of molecular sciences · 2022Article
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- Conjunctive Analyses of BSA-Seq and BSR-Seq to Reveal the Molecular Pathway of Leafy Head Formation in Chinese Cabbage.Plants (Basel, Switzerland) · 2019Article
- Diversification of the downy mildew resistance gene pool by introgression of a new gene, PlTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Mapping of the male sterile mutant gene ftms in Brassica rapa L. ssp. pekinensis via BSR-Seq combined with whole-genome resequencing.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Transcriptome Profiling and Characterization of Drought-Tolerant Potato Plant (Molecules and cells · 2018Article
- Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy.Rice (New York, N.Y.) · 2018Article
- Combining QTL-seq and linkage mapping to fine map a wild soybean allele characteristic of greater plant height.BMC genomics · 2018Article
- Screening of Genes Related to Early and Late Flowering in Tree Peony Based on Bulked Segregant RNA Sequencing and Verification by Quantitative Real-Time PCR.Molecules (Basel, Switzerland) · 2018Article
- Identification of a locus conferring dominant resistance to maize rough dwarf disease in maize.Scientific reports · 2018Article
- Development and dissection of diagnostic SNP markers for the downy mildew resistance genes PlMolecular genetics and genomics : MGG · 2017Article
- Rapid identification of QTLs underlying resistance to Cucumber mosaic virus in pepper (Capsicum frutescens).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- Sunflower Hybrid Breeding: From Markers to Genomic Selection.Frontiers in plant science · 2017Review
- Bulked sample analysis in genetics, genomics and crop improvement.Plant biotechnology journal · 2016Review
- Genetic mapping and molecular marker development for Pi65(t), a novel broad-spectrum resistance gene to rice blast using next-generation sequencing.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- Mining candidate genes associated with powdery mildew resistance in cucumber via super-BSA by specific length amplified fragment (SLAF) sequencing.BMC genomics · 2015Article
- Comparative quantitative trait loci for silique length and seed weight in Brassica napus.Scientific reports · 2015Article
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Authors and funding
10 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSunflower belongs to the largest plant family on earth, the genomically poorly explored Compositae. Downy mildew Plasmopara halstedii (Farlow) Berlese & de Toni is one of the major diseases of cultivated sunflower (Helianthus annuus L.). In the search for new sources of downy mildew resistance, the locus Pl(ARG)on linkage group 1 (LG1) originating from H. argophyllus is promising since it confers resistance against all known races of the pathogen. However, the mapping resolution in the Pl(ARG) region is hampered by significantly suppressed recombination and by limited availability of polymorphic markers. Here we examined a strategy developed for the enrichment of molecular markers linked to this specific genomic region. We combined bulked segregant analysis (BSA) with next-generation sequencing (NGS) and de novo assembly of the sunflower transcriptome for single nucleotide polymorphism (SNP) discovery in a sequence resource combining reads originating from two sunflower species, H. annuus and H. argophyllus.
resultsA computational pipeline developed for SNP calling and pattern detection identified 219 candidate genes. For a proof of concept, 42 resistance gene-like sequences were subjected to experimental SNP validation. Using a high-resolution mapping population, 12 SNP markers were mapped to LG1. We successfully verified candidate sequences either co-segregating with or closely flanking Pl(ARG).
conclusionsThis study is the first successful example to improve bulked segregant analysis with de novo transcriptome assembly using next generation sequencing. The BSTA pipeline we developed provides a useful guide for similar studies in other non-model organisms. Our results demonstrate this method is an efficient way to enrich molecular markers and to identify candidate genes in a specific mapping interval.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.