Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon

• Published in: BMC Genomics
• Main Authors: Palm Daniel, Gross Riho, Vasemägi Anti, Paaver Tiit, Primmer Craig R
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2010
• Subjects: Biotechnology; TP248.13-248.65; Genetics; QH426-470; Indel’; Atlantic salmon; Salmo salar
• Online Access: https://doi.org/10.1186/1471-2164-11-156; https://doaj.org/article/ca5a9b7973dd4b2a896193c9b10e0195

Abstract Background For decades, linkage mapping has been one of the most powerful and widely used approaches for elucidating the genetic architecture of phenotypic traits of medical, agricultural and evolutionary importance. However, successful mapping of Mendelian and quantitative phenotypic traits depends critically on the availability of fast and preferably high-throughput genotyping platforms. Several array-based single nucleotide polymorphism (SNP) genotyping platforms have been developed for genetic model organisms during recent years but most of these methods become prohibitively expensive for screening large numbers of individuals. Therefore, inexpensive, simple and flexible genotyping solutions that enable rapid screening of intermediate numbers of loci (~75-300) in hundreds to thousands of individuals are still needed for QTL mapping applications in a broad range of organisms. Results Here we describe the discovery of and application of insertion-deletion (INDEL) polymorphisms for cost-efficient medium throughput genotyping that enables analysis of >75 loci in a single automated sequencer electrophoresis column with standard laboratory equipment. Genotyping of INDELs requires low start-up costs, includes few standard sample handling steps and is applicable to a broad range of species for which expressed sequence tag (EST) collections are available. As a proof of principle, we generated a partial INDEL linkage map in Atlantic salmon ( Salmo salar ) and rapidly identified a number of quantitative trait loci (QTLs) affecting early life-history traits that are expected to have important fitness consequences in the natural environment. Conclusions The INDEL genotyping enabled fast coarse-mapping of chromosomal regions containing QTL, thus providing an efficient means for characterization of genetic architecture in multiple crosses and large pedigrees. This enables not only the discovery of larger number of QTLs with relatively smaller phenotypic effect but also provides a cost-effective means for ...