دورية أكاديمية
أعرض في EDS

Rapid genome wide mapping of phosphine resistance loci by a simple regional averaging analysis in the red flour beetle, Tribolium castaneum.

التفاصيل البيبلوغرافية
العنوان: Rapid genome wide mapping of phosphine resistance loci by a simple regional averaging analysis in the red flour beetle, Tribolium castaneum.
المؤلفون: Jagadeesan R; School of Biological Sciences, University of Queensland, St, Lucia, QLD, 4072, Australia. david.schlipalius@daff.qld.gov.au., Fotheringham A, Ebert PR, Schlipalius DI
المصدر: BMC genomics [BMC Genomics] 2013 Sep 24; Vol. 14, pp. 650. Date of Electronic Publication: 2013 Sep 24.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2000-
مواضيع طبية MeSH: Chromosome Mapping/*methods , Genetic Loci/*genetics , Genome, Insect/*genetics , Insecticide Resistance/*genetics , Phosphines/*toxicity , Tribolium/*genetics, Animals ; Chromosomes, Insect/genetics ; Crosses, Genetic ; Epistasis, Genetic ; Female ; Genetic Association Studies ; Genetic Fitness ; Male ; Physical Chromosome Mapping ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Tribolium/drug effects
مستخلص: Background: Next-generation sequencing technology is an important tool for the rapid, genome-wide identification of genetic variations. However, it is difficult to resolve the 'signal' of variations of interest and the 'noise' of stochastic sequencing and bioinformatic errors in the large datasets that are generated. We report a simple approach to identify regional linkage to a trait that requires only two pools of DNA to be sequenced from progeny of a defined genetic cross (i.e. bulk segregant analysis) at low coverage (<10×) and without parentage assignment of individual SNPs. The analysis relies on regional averaging of pooled SNP frequencies to rapidly scan polymorphisms across the genome for differential regional homozygosity, which is then displayed graphically.
Results: Progeny from defined genetic crosses of Tribolium castaneum (F₄ and F₁₉) segregating for the phosphine resistance trait were exposed to phosphine to select for the resistance trait while the remainders were left unexposed. Next generation sequencing was then carried out on the genomic DNA from each pool of selected and unselected insects from each generation. The reads were mapped against the annotated T. castaneum genome from NCBI (v3.0) and analysed for SNP variations. Since it is difficult to accurately call individual SNP frequencies when the depth of sequence coverage is low, variant frequencies were averaged across larger regions. Results from regional SNP frequency averaging identified two loci, tc_rph1 on chromosome 8 and tc_rph2 on chromosome 9, which together are responsible for high level resistance. Identification of the two loci was possible with only 5-7× average coverage of the genome per dataset. These loci were subsequently confirmed by direct SNP marker analysis and fine-scale mapping. Individually, homozygosity of tc_rph1 or tc_rph2 results in only weak resistance to phosphine (estimated at up to 1.5-2.5× and 3-5× respectively), whereas in combination they interact synergistically to provide a high-level resistance >200×. The tc_rph2 resistance allele resulted in a significant fitness cost relative to the wild type allele in unselected beetles over eighteen generations.
Conclusion: We have validated the technique of linkage mapping by low-coverage sequencing of progeny from a simple genetic cross. The approach relied on regional averaging of SNP frequencies and was used to successfully identify candidate gene loci for phosphine resistance in T. castaneum. This is a relatively simple and rapid approach to identifying genomic regions associated with traits in defined genetic crosses that does not require any specialised statistical analysis.
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المشرفين على المادة: 0 (Phosphines)
FW6947296I (phosphine)
تواريخ الأحداث: Date Created: 20130925 Date Completed: 20140630 Latest Revision: 20211021
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC3849015
DOI: 10.1186/1471-2164-14-650
PMID: 24059691
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2164
DOI:10.1186/1471-2164-14-650