Table of Contents
International Journal of Plant Genomics
Volume 2013, Article ID 890123, 6 pages
http://dx.doi.org/10.1155/2013/890123
Methodology Report

SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species

UMR RPB, IRD (Institut de Recherche pour le Développement), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France

Received 15 May 2013; Revised 26 July 2013; Accepted 30 July 2013

Academic Editor: Manuel Talon

Copyright © 2013 Marine Peralta et al. 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.

Abstract

High-throughput sequencing is a common approach to discover SNP variants, especially in plant species. However, methods to analyze predicted SNPs are often optimized for diploid plant species whereas many crop species are allopolyploids and combine related but divergent subgenomes (homoeologous chromosome sets). We created a software tool, SNiPloid, that exploits and interprets putative SNPs in the context of allopolyploidy by comparing SNPs from an allopolyploid with those obtained in its modern-day diploid progenitors. SNiPloid can compare SNPs obtained from a sample to estimate the subgenome contribution to the transcriptome or SNPs obtained from two polyploid accessions to search for SNP divergence.