ArticleGenome research2013
MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 244 papers, 1 of them a synthesis that pooled it.
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Who cites it
244 citing papers in PubMed, 1 synthesis or guideline pooled it, 484 citations in OpenAlex.
- QTL analysis and candidate gene prediction for seed density per silique by QTL-seq and RNA-seq in spring Brassica napus L.PloS one · 2023Pooled it
- NAM-BSA: A Bulked Segregant Analysis Method Using a NAM Population.Plants (Basel, Switzerland) · 2026Article
- High‑density mapping of stripe rust resistance gene YrH8 in wheat line Hangmai 8.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- A terminal deletion in wheat chromosome arm 3BS contains gene YrJ262 conferring adult plant resistance to stripe rust.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- A Novel Mutation in Maize D1 (Dwarf 1) Confers a Severe Dwarf Phenotype.Current issues in molecular biology · 2026Article
- Integrated BSA-Seq and RNA-Seq reveals genes associated with salt tolerance at the germination stage in foxtail millet (Setaria italica (L.) P. Beauv.).BMC plant biology · 2026Article
- Bulked Segregant Analysis Revealed the Common Resistant QTLs Associated with Fusarium Ear Rot and Gibberella Ear Rot in Maize.Plants (Basel, Switzerland) · 2026Article
- Integrating BSA-Seq, QTL Mapping, and RNA-Seq to Identify Candidate Genes for Hollow Heart in Cucumber Fruits.Plants (Basel, Switzerland) · 2026Article
- QTL mapping, validation, and candidate gene predicting for maize plant architecture traits via bulked segregant analysis plus linkage analysis with F₂ population.BMC plant biology · 2026Article
- Telomere-to-telomere genome assembly and comprehensive mutation library facilitate bitter gourd breeding and functional genomics research.Plant communications · 2026Article
- Fine mapping of a powdery mildew resistance gene PmCWI16926 from cultivated emmer wheat.Communications biology · 2026Article
- Identification of candidate regions associated with resistance to early blight in tomato (Solanum lycopersicum L.) using BSA-seq.Journal of applied genetics · 2026Article
- Integrating BSA-Seq and RNA-Seq to Identify Major QTLs and Candidate Genes Conferring Resistance to Fusarium Ear Rot in Maize.Plants (Basel, Switzerland) · 2026Article
- Functional 5Bq allele is responsible for the compact spike phenotype in common wheat (Triticum aestivum L.).BMC plant biology · 2026Article
- Genetic Mapping and Identification of Candidate Genes for a New Multi-Branching MutantInternational journal of molecular sciences · 2026Article
- Identification of candidate genes associated with regreening stage in rapeseed (Brassica Rapa L.) by combined application of BSA-Seq and RNA-Seq.BMC plant biology · 2026Article
- A comprehensive analysis of two Chinese cucumber genomes and a mutant population as resources for precision breeding.Horticulture research · 2026Article
- Two bHLH Transcription Factor GenesPlants (Basel, Switzerland) · 2026Article
- Regulatory networks and molecular mechanisms underlying salt stress tolerance in rice.Frontiers in plant science · 2026Review
- Integrated multi-omics analysis reveals candidate genes for cuticular wax biosynthesis and molecular characteristics of a glossy mutant in rapeseed under natural drought stress.Frontiers in plant science · 2026Article
184 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Forward genetic screens in model organisms are vital for identifying novel genes essential for developmental or disease processes. One drawback of these screens is the labor-intensive and sometimes inconclusive process of mapping the causative mutation. To leverage high-throughput techniques to improve this mapping process, we have developed a Mutation Mapping Analysis Pipeline for Pooled RNA-seq (MMAPPR) that works without parental strain information or requiring a preexisting SNP map of the organism, and adapts to differential recombination frequencies across the genome. MMAPPR accommodates the considerable amount of noise in RNA-seq data sets, calculates allelic frequency by Euclidean distance followed by Loess regression analysis, identifies the region where the mutation lies, and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can exploit RNA-seq data sets from isolated tissues or whole organisms that are used for gene expression and transcriptome analysis in novel mutants. We tested MMAPPR on two known mutant lines in zebrafish, nkx2.5 and tbx1, and used it to map two novel ENU-induced cardiovascular mutants, with mutations found in the ctr9 and cds2 genes. MMAPPR can be directly applied to other model organisms, such as Drosophila and Caenorhabditis elegans, that are amenable to both forward genetic screens and pooled RNA-seq experiments. Thus, MMAPPR is a rapid, cost-efficient, and highly automated pipeline, available to perform mutant mapping in any organism with a well-assembled genome.
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Registered trials
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.