ArticlePloS one2015
Mutation Scanning in Wheat by Exon Capture and Next-Generation Sequencing.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 71 citations in OpenAlex.
- Advances in mutant characterization for detecting causal mutations in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Advances in gene cloning and functional genomics approaches for wheat (Triticum aestivum L.) improvement.The plant genome · 2026Review
- Population Genomics Reveals Distinct Lineage of the Asian Soybean Rust Fungus Phakopsora pachyrhizi in the United States of America Unrelated to Brazilian Populations.Molecular plant pathology · 2025Article
- Wheat improvement through advances in single nucleotide polymorphism (SNP) detection and genotyping with a special emphasis on rust resistance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Review
- Stacked mutations in wheat homologues of rice SEMI-DWARF1 confer a novel semi-dwarf phenotype.BMC plant biology · 2024Article
- Evaluation of altered starch mutants and identification of candidate genes responsible for starch variation in wheat.BMC plant biology · 2023Article
- Boosting wheat functional genomics via an indexed EMS mutant library of KN9204.Plant communications · 2023Article
- Screening of Induced Mutants Led to the Identification of Starch Biosynthetic Genes Associated with Improved Resistant Starch in Wheat.International journal of molecular sciences · 2022Article
- Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops.Heredity · 2022Article
- Whole-exome sequencing of selected bread wheat recombinant inbred lines as a useful resource for allele mining and bulked segregant analysis.Frontiers in genetics · 2022Article
- Whole Exome Sequencing-Based Identification of a Novel Gene Involved in Root Hair Development in Barley (International journal of molecular sciences · 2021Article
- Exploring the diversity of promoter and 5'UTR sequences in ancestral, historic and modern wheat.Plant biotechnology journal · 2021Article
- Identification of a major and stable QTL on chromosome 5A confers spike length in wheat (Molecular breeding : new strategies in plant improvement · 2021Article
- Ph2 encodes the mismatch repair protein MSH7-3D that inhibits wheat homoeologous recombination.Nature communications · 2021Article
- Identification of Rice Blast Loss-of-Function Mutant Alleles in the Wheat Genome as a New Strategy for Wheat Blast Resistance Breeding.Frontiers in genetics · 2021Article
- Highly Efficient and Comprehensive Identification of Ethyl Methanesulfonate-Induced Mutations inFrontiers in plant science · 2021Article
- Accurate staging of reproduction development in Cadenza wheat by non-destructive spike analysis.Journal of experimental botany · 2020Article
- Development of model web-server for crop variety identification using throughput SNP genotyping data.Scientific reports · 2019Article
- Contribution of recent technological advances to future resistance breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
- Novel Informatic Tools to Support Functional Annotation of the Durum Wheat Genome.Frontiers in plant science · 2019Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
Targeted Induced Local Lesions in Genomes (TILLING) is a reverse genetics approach to identify novel sequence variation in genomes, with the aims of investigating gene function and/or developing useful alleles for breeding. Despite recent advances in wheat genomics, most current TILLING methods are low to medium in throughput, being based on PCR amplification of the target genes. We performed a pilot-scale evaluation of TILLING in wheat by next-generation sequencing through exon capture. An oligonucleotide-based enrichment array covering ~2 Mbp of wheat coding sequence was used to carry out exon capture and sequencing on three mutagenised lines of wheat containing previously-identified mutations in the TaGA20ox1 homoeologous genes. After testing different mapping algorithms and settings, candidate SNPs were identified by mapping to the IWGSC wheat Chromosome Survey Sequences. Where sequence data for all three homoeologues were found in the reference, mutant calls were unambiguous; however, where the reference lacked one or two of the homoeologues, captured reads from these genes were mis-mapped to other homoeologues, resulting either in dilution of the variant allele frequency or assignment of mutations to the wrong homoeologue. Competitive PCR assays were used to validate the putative SNPs and estimate cut-off levels for SNP filtering. At least 464 high-confidence SNPs were detected across the three mutagenized lines, including the three known alleles in TaGA20ox1, indicating a mutation rate of ~35 SNPs per Mb, similar to that estimated by PCR-based TILLING. This demonstrates the feasibility of using exon capture for genome re-sequencing as a method of mutation detection in polyploid wheat, but accurate mutation calling will require an improved genomic reference with more comprehensive coverage of homoeologues.
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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.