To validate the conversion of selected SNPs from the Illumina 90 k array to the Kompetitive Allele-Specific PCR (KASP) genotyping platform (LGC Genomics, UK), DNAs were extracted from the eight MAGIC founder varieties. Marker co-dominance was investigated using a 50:50 mix of DNAs from two varieties known from the 90 k SNP dataset to contrast for allele call. Additionally, DNA was extracted from a panel of 48 UK varieties that post-date the AM panel, released to the AHDB Recommended List between 2009 and 2017 (Supplementary Table 2). All DNAs were extracted from two week old leaves using a modified Tanksley protocol (Fulton et al. 1995 ), and concentration was determined using a Nanodrop 200 spectrophotometer (Thermo Scientific). DNA sequences flanking each targeted SNP were used to design KASP primers using the software PolyMarker (Ramirez-Gonzalez et al. 2015 (link)). Primers were synthesised by Sigma-Aldrich (Cambridge, UK) and KASP genotyping undertaken as described by Cockram et al. (2015 ). The results were visualised using SNP Viewer v.1.99 (https://lgcgenomics.com/ ). The subset of plants that post-dated the AM panel were grown and phenotyped for ToxB sensitivity and genotyped with the KASP marker, following the methods described above.
Kasp genotyping platform
Manufactured by LGC
Sourced in United Kingdom
The KASP genotyping platform is a flexible and robust genotyping solution developed by LGC. It utilizes a fluorescent-based detection method to accurately determine the genetic makeup of samples. The platform's core function is to provide reliable and cost-effective genotyping capabilities to researchers and laboratories.
Automatically generated - may contain errors
Lab products found in correlation
Nano drop model nd 2000, by Thermo Fisher Scientific (2 mentions)
Dneasy plant mini kit, by Qiagen (2 mentions)
Nanodrop 200, by Thermo Fisher Scientific (1 mentions)
Abi 7700 sequence detection system, by Thermo Fisher Scientific (1 mentions)
Axiom lat1 array, by Thermo Fisher Scientific (1 mentions)
Infinium coreexome 24 beadchip, by Illumina (1 mentions)
Kasp genotyping assay, by LGC (1 mentions)
6 protocols using kasp genotyping platform
1
Validating SNP Conversion from Array to KASP Genotyping
2
Genotyping and Mutation Analysis of CRISPR-Cas9 Transgenic Plants
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Leaflets were collected from each T0 plant, and genomic DNA was extracted using a standard cetyl‐trimethyl‐ammonium bromide protocol (Porebski et al., 1997 ). Each plant was genotyped with respect to the presence of transgene using PCR primers designed to amplify a fragment of Cas9. To evaluate the types of mutations generated, T0 transgenic plants were analysed by PCR with primers that flanked the sgRNA target. All PCR products were purified and cloned into the pMD18‐T vector, and the resulting Escherichia coli colonies were sequenced using the M13F and M13R primers. A KASP marker was developed to identify the CR‐slstr1‐3‐6 mutation using the KASP genotyping platform (LGC Genomics, UK, https://www.lgcgroup.com; Semagn et al., 2014 ).
3
Genotyping Methods Across Asthma Studies
4
SNP Genotyping of Tomato Cultivars
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Genomic DNA of young leaf tissues of each line and parent were extracted using DNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA, Spain). A Nano Drop (Model ND-2000, Thermo Scientific Inc., Wilmington, DE, USA) was used to quantify each DNA sample. Approximately 50 ng/µL of DNA was prepared from each sample for SNP genotyping. We used an optimized subset of 384 SNPs markers that were derived from the 7,725 SNP array developed by the Solanaceae Coordinated Agricultural Project (SolCAP) [36 (link),37 (link)]. The subset of markers was selected based on polymorphism rates among six fresh market tomato accessions including Fla.7776, Fla.8383, NC33EB-1, 091120-7, Fla. 7775, and NC 1CELBR. In addition, genetic position in the genome based on recombination [36 (link)] and physical position were considered as important selection criteria to insure genome coverage. These 384 SNPs were analyzed using the KASP genotyping platform (LGC Genomics, Beverly, MA, USA).
5
APOE Genotyping by Competitive Allele-Specific PCR
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APOE genotyping was performed by competitive allele-specific PCR, using KASP™ genotyping assays (LGC Genomics, Hoddesdon, UK) for both rs7412 and rs429358. Subsequent genotype data was converted into APOE allele status [70 (link)]. Full methods for the KASP™ genotyping platform are available from LGC Genomics (http://www.lgcgenomics.com/genotyping/kasp-genotyping-reagents/ ).
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APOE genotyping was performed by competitive allele-specific PCR, using KASP™ genotyping assays (LGC Genomics, Hoddesdon, UK) for both rs7412 and rs429358. Subsequent genotype data was converted into APOE allele status [70 (link)]. Full methods for the KASP™ genotyping platform are available from LGC Genomics (
6
Tomato SNP Genotyping Protocol
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Genomic DNA of young leaf tissues of each parent and individual plant from F2 generation was extracted using the DNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA). A NanoDrop (Model ND-2000, Thermo Scientific Inc., Wilmington, DE) was used to quantify each DNA sample. Approximately, 50 ng/µl of DNA was prepared from each sample for SNP genotyping. We used an optimized subset of 384 SNPs markers that were derived from the 7,725 SNP array developed by the Solanaceae Coordinated Agricultural Project (SolCAP) (Sim et al., 2012a (link); Sim et al., 2012b (link)). The subset of markers was selected based on polymorphism rates among six fresh market tomato accessions, including Fla.7776, Fla. 8383, NC33EB-1, 091120-7, Fla. 7775, and NC 1CELBR. Also, the genetic position in the genome based on recombination (Sim et al., 2012a (link)) and the physical position was considered important selection criteria to ensure genome coverage. These 384 SNPs were analyzed using the Kompetitive Allele Specific PCR (KASP) genotyping platform (LGC Genomics, Beverly, MA).
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