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Single Nucleotide Polymorphisms-SNPs01:05

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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,...
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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.
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The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
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Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations.

Josh Clevenger1, Carolina Chavarro2, Stephanie A Pearl2

  • 1Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793, USA.

Molecular Plant
|February 14, 2015
PubMed
Summary
This summary is machine-generated.

Predicting phenotypes from genotypes is key for crop improvement. This study explores single nucleotide polymorphism (SNP) calling in polyploid plants, offering best practices for accurate genotype-phenotype analysis.

Keywords:
genomicshomeolognext-generation sequencing (NGS)peanutpolyploidsingle nucleotide polymorphism (SNP)

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Area of Science:

  • Genomics
  • Plant Breeding
  • Bioinformatics

Background:

  • Understanding genotype-phenotype relationships is crucial for molecular breeding.
  • Whole-genome duplications in flowering plants, particularly neopolyploids, complicate genotype-phenotype analysis.
  • Single nucleotide polymorphisms (SNPs) are valuable for genetic mapping but challenging to discover and utilize in polyploids.

Purpose of the Study:

  • To summarize experimental approaches for SNP calling in polyploids.
  • To evaluate the impact of different software tools on SNP calling accuracy in polyploid genotypes.
  • To propose best practices for SNP calling in polyploid species.

Main Methods:

  • Comparison of SNP calling using BWA-mem and Bowtie 2 alignment programs.
  • Evaluation of variant callers SAMtools, GATK, and Freebayes.
  • Analysis of simulated Brassica napus polyploid genotypes to assess software performance (sensitivity and specificity).

Main Results:

  • Limited concordance (24.5%) was observed for SNPs called by SAMtools with either Bowtie 2 or BWA-mem alignments.
  • Very low concordance (1.4%) was found among SNPs called by SAMtools, GATK, and Freebayes.
  • SAMtools demonstrated the highest sensitivity and specificity on Bowtie 2 alignments for simulated Brassica napus polyploid genotypes.

Conclusions:

  • Software choice significantly impacts SNP calling results in polyploids.
  • SAMtools showed superior performance in sensitivity and specificity for SNP calling in the tested polyploid simulation.
  • The study proposes best practices for SNP calling in polyploid species to improve genotype-phenotype analysis.