Overcoming polyploidy pitfalls: a user guide for effective SNP conversion into KASP markers in wheat.

Overcoming polyploidy pitfalls: a user guide for effective SNP conversion into KASP markers in wheat. Theor Appl Genet. 2020 Jun 04;: Authors: Makhoul M, Rambla C, Voss-Fels KP, Hickey LT, Snowdon RJ, Obermeier C Abstract KEY MESSAGE: Conversion of SNP chip assays into locus-specific KASP markers requires adapted strategies in polyploid species with high genome homeology. Procedures are exemplified by QTL-associated SNPs in hexaploid wheat. Kompetitive allele-specific PCR (KASP) markers are commonly used in marker-assisted commercial plant breeding due to their cost-effectiveness and throughput for high sample volumes. However, conversion of trait-linked SNP markers from array-based SNP detection technologies into KASP markers is particularly challenging in polyploid crop species, due to the presence of highly similar homeologous and paralogous genome sequences. We evaluated strategies and identified key requirements for successful conversion of Illumina Infinium assays from the wheat 90 K SNP array into robust locus-specific KASP markers. Numerous examples showed that commonly used software for semiautomated KASP primer design frequently fails to achieve locus-specificity of KASP assays in wheat. Instead, alignment of SNP probes with multiple reference genomes and Sanger sequencing of relevant genotypes, followed by visual KASP primer placement, was critical for locus-specificity. To identify KASP assays resulting in false calling ...
Source: TAG. Theoretical and Applied Genetics - Category: Genetics & Stem Cells Authors: Tags: Theor Appl Genet Source Type: research
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