CNVmap: a method and software to detect copy number variants from linkage mapping data

Abstract

Single nucleotide polymorphisms (SNPs) are widely used for detecting quantitative trait loci or for searching for causal variants of diseases. Nevertheless, structural variations such as copy-number variants (CNVs) represent a large part of natural genetic diversity and contribute significantly to trait variation. Over the past decade, numerous methods and softwares have been developed to detect CNVs. Such approaches are based on exploiting sequencing data or SNP arrays, but they bypass a wealth of information such as genotyping data from segregating populations, produced e.g. for QTL mapping. Here we propose an original method to both detect and genetically map CNVs using mapping panels. Specifically, we exploit the apparent heterozygous state of duplicated loci: peaks in appropriately defined genome-wide allelic profiles provide highly specific signatures that identify the nature and position of the CNVs. Our original method and software can detect and map automatically up to 33 different predefined types of CNVs based on segregation data only. We validate this approach on simulated and experimental bi-parental mapping panels in two maize and one wheat populations. Most of the events found correspond to having just one extra copy in one of the parental lines but the corresponding allelic value can be that of either parent. We also find cases with two or more additional copies, especially in wheat where these copies locate to homeologues. More generally, our computational tool can be used to give additional value, at no cost, to many datasets produced over the past decade from genetic mapping panels.