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Copy number variations identified in the chicken using a 60K SNP BeadChip
1Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Animal Genetics
|November 24, 2012
Summary
This study identifies copy number variations (CNVs) in chickens using a 60K SNP array, a novel approach for chicken genetics. The findings provide a foundation for linking CNVs to economically important chicken traits.
Area of Science:
- Genomics
- Animal Genetics
- Molecular Biology
Background:
- Copy number variation (CNV) is a significant source of genetic diversity influencing economically important traits in chickens.
- Traditional methods for CNV detection, like comparative genomic hybridization arrays, have limitations.
- High-density single nucleotide polymorphism (SNP) arrays offer a more accessible alternative for identifying CNVs in chicken populations.
Purpose of the Study:
- To identify copy number variations (CNVs) in two distinct chicken genetic lines (White Leghorn and dwarf) utilizing a high-density SNP array.
- To validate the identified CNVs using quantitative PCR (qPCR).
- To establish the feasibility of using SNP arrays for CNV detection in chickens and its potential for future genetic studies.
Main Methods:
- Employed a chicken 60K SNP BeadChip for high-throughput genotyping.
- Utilized the PENNCNV program for CNV detection and analysis.
- Validated selected CNVs through quantitative PCR (qPCR) on a subset of individuals.
Main Results:
- Identified a total of 209 copy number variation (CNV) regions across autosomes 1-28.
- CNV regions collectively spanned 13.55 Mb, representing 1.42% of the chicken autosomal genome.
- Quantitative PCR (qPCR) confirmed three out of seven selected CNVs, validating the SNP array approach in 73.2% of individuals.
- Reported 190 novel CNVs, highlighting the effectiveness of the 60K SNP BeadChip.
Conclusions:
- This study represents the first report of CNV identification in chickens using a SNP array.
- The chicken 60K SNP BeadChip is a feasible tool for detecting CNVs, providing a valuable resource for future research.
- These findings lay the groundwork for investigating the association between CNVs and economically important phenotypes in chickens.
Related Concept Videos
02:26Comparing Copy Number Variations and SNPs
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...