ArticleBMC plant biology2012
Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat.
Article in BMC plant biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 155 papers, 1 of them a synthesis that pooled it.
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Who cites it
155 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses.Frontiers in genetics · 2022Pooled it
- CRISPR/Cas9-Mediated Knockout of LbSP1 and LbSP5G1 Reveals Efficient Customization of Shoot Architecture in Black Goji Berry.Plant biotechnology journal · 2026Article
- Identification of candidate gene for the wheat powdery mildew resistance gene Pm40 by bulked segregant analysis coupled with whole-genome sequencing (BSA-seq).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Mapping and Functional Characterization of Homologous Genes AhSUCA06 and AhSUCA16 Underlying Sucrose, Oil and Protein Contents in Peanut (Arachis hypogaea L.).Plant biotechnology journal · 2026Article
- Article
- Development of KASP molecular markers and fingerprinting based on reduced representation genome sequencing of garlic.Frontiers in plant science · 2026Article
- Unveiling leaf rust resistance introgressed from non-progenitor wild species Aegilops kotschyi into hexaploid wheat.Scientific reports · 2025Article
- Uncovering a stable QTLMolecular breeding : new strategies in plant improvement · 2025Article
- A head-to-head NLR gene pair from wild emmer confers stripe rust resistance in wheat.Nature genetics · 2025Article
- Fine Mapping and Screening of Candidate Gene for Yellow-to-Green Mutation in Snap Bean (International journal of molecular sciences · 2025Article
- A TOPLESS-related gene regulates both male and female sterility in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Identification and validation of a novel tiller inhibition locus (Molecular breeding : new strategies in plant improvement · 2025Article
- Natural variation in MdNAC5 contributes to fruit firmness and ripening divergence in apple.Horticulture research · 2025Article
- Mapping and characterization of a novel powdery mildew resistance locus (PM2) inFrontiers in plant science · 2025Article
- Partial unidirectional translocation from 5AL to 7BS leads to dense spike in an EMS-induced wheat mutant.BMC genomics · 2024Article
- Identification of Clubroot (Genes · 2024Article
- Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis.BMC genomics · 2024Article
- Genetic diversity and population structure analysis of 418 tomato cultivars based on single nucleotide polymorphism markers.Frontiers in plant science · 2024Article
- Transcript profiling of hairy vetch (Vicia villosa Roth) identified interesting genes for seed dormancy.The plant genome · 2023Article
- Fine mapping and causal gene identification of a novel QTL for early flowering by QTL-seq, Target-seq and RNA-seq in spring oilseed rape.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
95 more citing papers are in PubMed but not listed here.
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6 authors.
Funding
Abstract
backgroundNext generation sequencing (NGS) technologies are providing new ways to accelerate fine-mapping and gene isolation in many species. To date, the majority of these efforts have focused on diploid organisms with readily available whole genome sequence information. In this study, as a proof of concept, we tested the use of NGS for SNP discovery in tetraploid wheat lines differing for the previously cloned grain protein content (GPC) gene GPC-B1. Bulked segregant analysis (BSA) was used to define a subset of putative SNPs within the candidate gene region, which were then used to fine-map GPC-B1.
resultsWe used Illumina paired end technology to sequence mRNA (RNAseq) from near isogenic lines differing across a ~30-cM interval including the GPC-B1 locus. After discriminating for SNPs between the two homoeologous wheat genomes and additional quality filtering, we identified inter-varietal SNPs in wheat unigenes between the parental lines. The relative frequency of these SNPs was examined by RNAseq in two bulked samples made up of homozygous recombinant lines differing for their GPC phenotype. SNPs that were enriched at least 3-fold in the corresponding pool (6.5% of all SNPs) were further evaluated. Marker assays were designed for a subset of the enriched SNPs and mapped using DNA from individuals of each bulk. Thirty nine new SNP markers, corresponding to 67% of the validated SNPs, mapped across a 12.2-cM interval including GPC-B1. This translated to 1 SNP marker per 0.31 cM defining the GPC-B1 gene to within 13-18 genes in syntenic cereal genomes and to a 0.4 cM interval in wheat.
conclusionsThis study exemplifies the use of RNAseq for SNP discovery in polyploid species and supports the use of BSA as an effective way to target SNPs to specific genetic intervals to fine-map genes in unsequenced genomes.
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