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

BMC Genomics

Methodology Article

Riho Gross¹  Tiit Paaver¹  Craig R Primmer²  Anti Vasemägi³  Daniel Palm⁴ 

[1] Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014, Tartu, Estonia;Department of Biology, 20014, University of Turku, Finland;Department of Biology, 20014, University of Turku, Finland;Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014, Tartu, Estonia;Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden;

关键词: Quantitative Trait Locus;    Linkage Group;    Atlantic Salmon;    Quantitative Trait Locus Analysis;    Quantitative Trait Locus Mapping;   

DOI  :  10.1186/1471-2164-11-156

 received in 2009-04-06, accepted in 2010-03-08,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundFor 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.ResultsHere 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.ConclusionsThe 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 evaluation of the frequency of segregating QTLs in outbred populations which is important for further understanding how genetic variation underlying phenotypic traits is maintained in the wild.

【 授权许可】

CC BY   
© Vasemägi et al; licensee BioMed Central Ltd. 2010