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Updated: May 17, 2026
09:40
Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
Novel SNP Discovery in African Buffalo, Syncerus caffer, using high-throughput Sequencing
Nikki le Roex1, Harry Noyes, Andrew Brass
1DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa.
Plos One
|November 13, 2012
Summary
Researchers discovered numerous single nucleotide polymorphisms (SNPs) in African buffalo (Syncerus caffer) DNA, aiding studies on host genetics and disease resistance. This genetic information is crucial for conservation and broader genomics research in this vital savannah species.
Area of Science:
- Genomics
- Conservation Biology
- Wildlife Health
Background:
- African buffalo (Syncerus caffer) are ecologically vital savannah megafauna.
- They serve as prey and hosts for various pathogens, making disease susceptibility research important.
- Large-scale genetic data is needed for host-pathogen interaction studies and conservation efforts.
Purpose of the Study:
- To discover a large number of single nucleotide polymorphisms (SNPs) in the African buffalo.
- To provide valuable genomic resources for future research on disease resistance and conservation.
Main Methods:
- DNA from 9 African buffalo was sequenced using an ABI SOLiD4 sequencer.
- Short reads were mapped to the Bos taurus genome (UMD3.1) using BWA and Bowtie.
- Identified SNPs were validated through fluorescent genotyping in 87 individuals.
Main Results:
- A mean sequencing coverage of 2.7× was achieved.
- BWA and Bowtie identified up to 2,222,665 and 276,847 SNPs, respectively.
- Validation confirmed 43-58% of identified SNPs were polymorphic, with BWA showing higher confirmation rates.
Conclusions:
- The study successfully identified a substantial number of polymorphic SNPs in African buffalo.
- These SNPs represent a valuable resource for advancing research in African buffalo genetics, disease susceptibility, and conservation genomics.
Related Concept Videos
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,...
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%...
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
01:11Genome-wide Association Studies-GWAS
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.