Next Article in Journal
STAT5-Interacting Proteins: A Synopsis of Proteins that Regulate STAT5 Activity
Previous Article in Journal
Ornithine Aminotransferase, an Important Glutamate-Metabolizing Enzyme at the Crossroads of Multiple Metabolic Pathways
Article Menu

Export Article

Open AccessReview
Biology 2017, 6(1), 21; doi:10.3390/biology6010021

SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete?

1
School of Agriculture and Food Sciences, University of Queensland, St. Lucia 4072, QLD, Australia
2
School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth 6009, WA, Australia
*
Author to whom correspondence should be addressed.
Academic Editor: Chris O’Callaghan
Received: 13 February 2017 / Revised: 7 March 2017 / Accepted: 8 March 2017 / Published: 11 March 2017
View Full-Text   |   Download PDF [749 KB, uploaded 11 March 2017]   |  

Abstract

Increasing evidence suggests that a single individual is insufficient to capture the genetic diversity within a species due to gene presence absence variation. In order to understand the extent to which genomic variation occurs in a species, the construction of its pangenome is necessary. The pangenome represents the complete set of genes of a species; it is composed of core genes, which are present in all individuals, and variable genes, which are present only in some individuals. Aside from variations at the gene level, single nucleotide polymorphisms (SNPs) are also an important form of genetic variation. The advent of next-generation sequencing (NGS) coupled with the heritability of SNPs make them ideal markers for genetic analysis of human, animal, and microbial data. SNPs have also been extensively used in crop genetics for association mapping, quantitative trait loci (QTL) analysis, analysis of genetic diversity, and phylogenetic analysis. This review focuses on the use of pangenomes for SNP discovery. It highlights the advantages of using a pangenome rather than a single reference for this purpose. This review also demonstrates how extra information not captured in a single reference alone can be used to provide additional support for linking genotypic data to phenotypic data. View Full-Text
Keywords: pangenome; single nucleotide polymorphism; SNP discovery; copy number variation; presence absence variation; gene; assembly; genetic diversity; core genome; variable genome pangenome; single nucleotide polymorphism; SNP discovery; copy number variation; presence absence variation; gene; assembly; genetic diversity; core genome; variable genome
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Hurgobin, B.; Edwards, D. SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete? Biology 2017, 6, 21.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Biology EISSN 2079-7737 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top