2010
DOI: 10.1186/1471-2164-11-156
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Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon

Abstract: 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 organis… Show more

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Cited by 50 publications
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“…InDels in coding regions probably have functional roles and are considered to be a significant source of evolutionary change in eucaryotic and bacterial evolution (Britten et al 2003). InDels in genes with functional diversity between alleles should be highly useful for marker-assisted selection (Raman et al 2006) or QTL mapping (Vasemägi et al 2010). Using the increasing amounts of sequence information acquired by new technologies (454-Roche, SOLiD system-Applied biosystems or Solexa-Illumina), the development of PCR-based InDel markers will become an important source of genetic markers that are easy and inexpensive to use in phylogenetic and genetic association studies in Citrus.…”
Section: Discussionmentioning
confidence: 99%
See 1 more Smart Citation
“…InDels in coding regions probably have functional roles and are considered to be a significant source of evolutionary change in eucaryotic and bacterial evolution (Britten et al 2003). InDels in genes with functional diversity between alleles should be highly useful for marker-assisted selection (Raman et al 2006) or QTL mapping (Vasemägi et al 2010). Using the increasing amounts of sequence information acquired by new technologies (454-Roche, SOLiD system-Applied biosystems or Solexa-Illumina), the development of PCR-based InDel markers will become an important source of genetic markers that are easy and inexpensive to use in phylogenetic and genetic association studies in Citrus.…”
Section: Discussionmentioning
confidence: 99%
“…In general, InDels arise from the insertion of retroposons or other mobile elements, slippage in simple sequence replication or unequal crossover events (Britten et al 2003). At the technical level, InDels can be genotyped with simple procedures based on size separation after targeted PCR (Vasemägi et al 2010). InDels have been used successfully for genetic studies in wheat (Raman et al 2006), rice (Hayashi et al 2006) and natural populations (Väli et al 2008).…”
Section: Introductionmentioning
confidence: 99%
“…The combination of PKD-realF and PKX4R amplifies a longer (756 bp) fragment of the same 18S rRNA gene. The salmonid-specific forward (5'-GCC CAA AAT GTA CAG GCA AT-3') and reverse (5'-GAT TCT CAT GTT AGC CGT CCA-3') primers were originally designed for Atlantic salmon (GenBank EST database accession number CA064223; Vasemägi et al 2010) but also served as a control for successful PCR reactions in brown trout (Fig. 1).…”
Section: Tetracapsuloides Bryosalmonae Infectingmentioning
confidence: 99%
“…Multiplex PCR was used to amplify a Salmo sp. specific fragment (GenBank accession number CA064223, Vasemägi et al 2010) and 3 T. bryosalmonae-specific fragments of the 18s rRNA gene (298, 166, and 756 bp) as in Dash & Vasemägi (2014). Co-amplification of a DNA fragment from a salmonid host served as an internal PCR control, which ensured that a failure of amplification of T. bryosalmonae-specific fragments was not misinterpreted as the absence of parasite in that sample (Fig.…”
mentioning
confidence: 99%