ArticlePloS one2012
Fast homozygosity mapping and identification of a zebrafish ENU-induced mutation by whole-genome sequencing.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed, 44 citations in OpenAlex.
- Exploring hematopoiesis in zebrafish using forward genetic screening.Experimental & molecular medicine · 2024Review
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- Identification of the hub genes related to adipose tissue metabolism of bovine.Frontiers in veterinary science · 2022Article
- Functional and evolutionary analysis of the Arabidopsis 4R-MYB protein SNAPc4 as part of the SNAP complex.Plant physiology · 2021Article
- Article
- Selection of growth-related genes and dominant genotypes in transgenic Yellow River carp Cyprinus carpio L.Functional & integrative genomics · 2018Article
- Whole Genome Sequencing-Based Mapping and Candidate Identification of Mutations from Fixed Zebrafish Tissue.G3 (Bethesda, Md.) · 2017Article
- Article
- Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method.Horticulture research · 2017Article
- SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish.Development (Cambridge, England) · 2015Article
- A genome-wide screen identifies PAPP-AA-mediated IGFR signaling as a novel regulator of habituation learning.Neuron · 2015Article
- Review
- Kinesin family member 6 (kif6) is necessary for spine development in zebrafish.Developmental dynamics : an official publication of the American Association of Anatomists · 2014Article
- Characterization of the mutagenic spectrum of 4-nitroquinoline 1-oxide (4-NQO) in Aspergillus nidulans by whole genome sequencing.G3 (Bethesda, Md.) · 2014Article
- Using next-generation sequencing to isolate mutant genes from forward genetic screens.Nature reviews. Genetics · 2014Review
- Using zebrafish to study podocyte genesis during kidney development and regeneration.Genesis (New York, N.Y. : 2000) · 2014Review
- Production of haploid zebrafish embryos by in vitro fertilization.Journal of visualized experiments : JoVE · 2014Article
- Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii.BMC genomics · 2014Article
- Mutagenesis and phenotyping resources in zebrafish for studying development and human disease.Briefings in functional genomics · 2014Review
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Forward genetics using zebrafish is a powerful tool for studying vertebrate development through large-scale mutagenesis. Nonetheless, the identification of the molecular lesion is still laborious and involves time-consuming genetic mapping. Here, we show that high-throughput sequencing of the whole zebrafish genome can directly locate the interval carrying the causative mutation and at the same time pinpoint the molecular lesion. The feasibility of this approach was validated by sequencing the m1045 mutant line that displays a severe hypoplasia of the exocrine pancreas. We generated 13 Gb of sequence, equivalent to an eightfold genomic coverage, from a pool of 50 mutant embryos obtained from a map-cross between the AB mutant carrier and the WIK polymorphic strain. The chromosomal region carrying the causal mutation was localized based on its unique property to display high levels of homozygosity among sequence reads as it derives exclusively from the initial AB mutated allele. We developed an algorithm identifying such a region by calculating a homozygosity score along all chromosomes. This highlighted an 8-Mb window on chromosome 5 with a score close to 1 in the m1045 mutants. The sequence analysis of all genes within this interval revealed a nonsense mutation in the snapc4 gene. Knockdown experiments confirmed the assertion that snapc4 is the gene whose mutation leads to exocrine pancreas hypoplasia. In conclusion, this study constitutes a proof-of-concept that whole-genome sequencing is a fast and effective alternative to the classical positional cloning strategies in zebrafish.
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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.