SMAP design

SMAP design generates multiplex PCR amplicon primers and CRISPR guide RNAs to enable high-throughput genotyping and mutation screening across diverse genomes.

Key Features:

• Multiplex primer and gRNA generation: Simultaneous design of primers and CRISPR guide RNAs for multiple loci to support multiplex PCR and CRISPR screens.
• High-throughput capability: Facilitates large-scale generation of amplicon and gRNA designs for many targets in parallel.
• Design flexibility: Supports design across various genomes and gene families, enabling broad target selection.
• Design success rate: Achieves successful designs for over 80–90% of target genes as reported.
• Specificity optimization: Produces designs that emphasize high specificity and reliability when handling complex genomic data.
• Cross-species validation: Tested on diverse genomes including Arabidopsis, soybean, maize, and non-plant species.

Scientific Applications:

• Eco‑tilling screens: Design of PCR amplicons for detecting natural or induced variation in eco‑tilling studies.
• CRISPR-based genotyping screens: gRNA and amplicon design to enable targeted mutation screening in CRISPR experiments.
• Illumina multiplex amplicon sequencing: Generation of amplicons suitable for Illumina multiplexed sequencing workflows.
• Sanger sequencing validation: Amplicon designs applicable for Sanger sequencing confirmation of variants.
• Cichorium intybus haploid induction study: Used to design eco‑tilling PCR amplicons for nine candidate genes, identifying thirteen knockout haplotypes among 60 accessions.

Methodology:

Computational generation of primers and guide RNAs using advanced algorithms that optimize specificity for multiplex PCR amplicon and CRISPR gRNA design and handle complex genomic data from multiple species.