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. 1. Introduction The advent of high-throughput sequencing technologies is revolutionizing our ability to discover and exploit single-nucleotide polymorphisms (SNPs). Polyploidy occurs in many animals and plants but is particularly widespread in flowering plants, including many major crops. However, most methods used to discover and validate predicted SNPs are optimized for diploid species, so specific challenges related to polyploidy remain to be addressed. Many polyploid plants including coffee (Coffea arabica), wheat (Triticum durum Desf.), cotton (Gossypium hirsutum L.), and peanut (Arachis hypogaea L.) are allopolyploids and contain two or more distinct genomes (homoeologous chromosomes) after interspecific hybridization between related diploid species and chromosome doubling. As a consequence, allopolyploid genomes hold different copies of the most of their genes and genomic merger and doubling leads to an extensive array of genomic effects, including alterations in the expression of these duplicate genes (“homoeologs”). In an allopolyploid, the chromosomes derived from different parental species do not pair at meiosis and the gene copies, “homoeoalleles” or “homoeologs,” derived from different parental species have no allelic relationships and can consequently be distinguished from true alleles. In other words, sequence variation between subgenomes coexists with allelic variation within subgenomes. Accurate identification of homoeoSNPs (i.e., polymorphisms that occurred in only one of the subgenomes) in tetraploid sequence data is a challenge due to the coassembly of homoeologs. In a co-assembly, single nucleotide differences between the two subgenomes could be confused with SNP at a single locus. The sequencing of transcripts using high-throughput sequencing methods (RNA-Seq) can provide fresh insights into polyploid biology [1]. Typically, the
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