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High-throughput SNP discovery in the rabbit (Oryctolagus cuniculus) genome by next-generation semiconductor-based
F Bertolini1, G Schiavo, E Scotti
1Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy.
Animal Genetics
|January 22, 2014
Summary
Researchers identified 62,491 single nucleotide polymorphisms (SNPs) in the European rabbit genome using reduced representation libraries (RRLs). This discovery advances rabbit genetic research and supports cost-effective SNP genotyping for various applications.
Area of Science:
- Genomics
- Animal Genetics
- Molecular Biology
Background:
- The European rabbit (Oryctolagus cuniculus) is a significant domesticated species with broad economic and scientific applications.
- Existing rabbit genome information (oryCun2.0) is available, but comprehensive studies on genetic variability and polymorphism discovery are limited.
Purpose of the Study:
- To identify single nucleotide polymorphisms (SNPs) in the European rabbit genome.
- To expand the knowledge of rabbit genetic variability.
- To provide a foundation for cost-effective high-throughput SNP genotyping.
Main Methods:
- Sequencing of two reduced representation libraries (RRLs) created from pooled DNA of 10 diverse rabbit breeds.
- Utilizing Ion Torrent Personal Genome Machine for sequencing.
- Mapping reads to the oryCun2.0 rabbit genome assembly and calling SNPs using ad hoc filtering procedures.
Main Results:
- Generated over 2.9 and 4 million reads per RRL, with substantial portions mapping to the rabbit genome (90% and 91%).
- Successfully identified and reliably called 62,491 SNPs across the sequenced regions.
- Validated a subset of SNPs via Sanger sequencing and mapped them using the Variant Effect Predictor tool.
Conclusions:
- The study presents a significant discovery of SNPs in the European rabbit genome.
- These findings will benefit applied and basic research programs involving rabbits.
- The identified SNPs offer potential for developing efficient and affordable high-throughput genotyping solutions.
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