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Related Concept Videos

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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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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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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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.
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Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
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Frequency and Distribution of Crossovers in Caenorhabditis elegans Meiosis by SNP Genotyping using Real-time PCR
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Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs.

Jamie A Ivy1, Andrea S Putnam1, Asako Y Navarro1

  • 1From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr).

The Journal of Heredity
|May 22, 2016
PubMed
Summary

Generating single nucleotide polymorphism (SNP) data using genotyping methods like Illumina BovineHD BeadChip and ddRAD sequencing can accurately resolve unknown relationships in captive wildlife breeding programs, even in bottlenecked populations.

Keywords:
SNP chipddRADkinshippedigree analysisrelatedness

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Area of Science:

  • Conservation genetics
  • Wildlife management
  • Population genetics

Background:

  • Captive breeding programs for wildlife conservation rely on accurate pedigrees for genetic management.
  • Poorly known pedigrees can hinder effective genetic management and long-term genetic variation retention.
  • Resolving unknown relationships is crucial for optimizing breeding strategies in zoo populations.

Purpose of the Study:

  • To evaluate two methods for generating single nucleotide polymorphism (SNP) data to resolve unknown relationships in captive breeding programs.
  • To compare the effectiveness of Illumina BovineHD BeadChip and double digest restriction site-associated DNA (ddRAD) sequencing for relationship estimation.
  • To assess the utility of molecular data in complementing or validating existing pedigree information.

Main Methods:

  • SNP data generation for an addax (Addax nasomasculatus) population using Illumina BovineHD BeadChip and ddRAD sequencing.
  • Estimation of allele sharing (AS) between individuals using generated SNP data.
  • Statistical analysis of AS variances across different numbers of loci.
  • Correlation analysis between SNP-derived AS estimates and traditional pedigree-based kinship calculations.

Main Results:

  • Both SNP genotyping methods produced low variances in allele sharing estimates, indicating accurate relationship resolution.
  • Sufficient loci (≥250 for SNP chip, ≥500 for ddRAD) were identified for reliable relationship estimation.
  • High correlation (0.88) was observed between AS datasets from both methods when subsampling 500 loci.
  • Pedigree-based kinship estimates were significantly correlated with molecularly derived AS estimates (P << 0.001).

Conclusions:

  • Both Illumina BovineHD BeadChip and ddRAD sequencing are effective for generating SNP data to accurately estimate relationships in captive wildlife.
  • Molecular data can successfully resolve unknown relationships and validate existing pedigrees in genetically managed populations.
  • This study provides a model for applying molecular techniques to enhance genetic management in captive breeding programs.