Highly selective detection of single nucleotide polymorphism (SNP) using a dumbbell DNA probe with a gap-filling approach

Feature Compression Applications of Genetic Algorithm

With the rapid development of molecular breeding technology and many new varieties breeding, a method is urgently needed to identify different varieties accurately and quickly. Using this method can not only help farmers feel convenient and efficient in the normal cultivation and breeding process but also protect the interests of breeders, producers and users. In this study, single nucleotide polymorphism (SNP) data of 533 Oryza sativa, 284 Solanum tuberosum and 247 Sus scrofa and 544 Manihot esculenta Crantz were used. The original SNPs were filtered and screened to remove the SNPs with deletion number more than 1% or the homozygous genotype 0/0 and 1/1 number less than 2. The correlation between SNPs were calculated, and the two adjacent SNPs with correlation R² > 0.95 were retained. The genetic algorithm program was developed to convert the genotype format and randomly combine SNPs to calculate a set of a small number of SNPs which could distinguish all varieties in different species as fingerprint data, using Matlab platform. The successful construction of three sets of fingerprints showed that the method developed in this study was effective in animals and plants. The population structure analysis showed that the genetic algorithm could effectively obtain the core SNPs for constructing fingerprints, and the fingerprint was practical and effective. At present, the two-dimensional code of Manihot esculenta Crantz fingerprint obtained by this method has been applied to field planting. This study provides a novel idea for the Oryza sativa, Solanum tuberosum, Sus scrofa and Manihot esculenta Crantz identification of various species, lays foundation for the cultivation and identification of new varieties, and provides theoretical significance for many other species fingerprints construction.

High-efficiency and high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases to assist LR-LAMP for the genotyping of single-nucleotide polymorphisms

A high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases was developed to assist LR-LAMP for genotyping of SNPs.

Single-nucleotide variant of PIK3CA H1047R gene assay by CRISPR/Cas12a combined with rolling circle amplification

PIK3CA ^H1047R gene plays an important role in the PI3K/Akt/mTOR signaling pathway, and its mutation is closely related to the occurrence and development of breast cancer and Lipoblastoma. Therefore, it is of great value to detect the PIK3CA ^H1047R mutant gene. Here, an analytical method coupled CRISPR/Cas12a with rolling circle amplification (RCA) technology was constructed for ultra-sensitive and specific detection of the single-nucleotide variant (SNV) of the PIK3CA ^H1047R gene. With efficient amplification of RCA and CRISPR/Cas12a, the detection limit of the mutant target and mixture of the mutant with wild-type target were as low as 10 aM and 0.036%, respectively. The detection limit of the RCA-CRISPR/Cas12a method was lower than that of allelic specific PCR (AS-PCR) for detecting SNV of the PIK3CA ^H1047R gene. Hence, this RCA-CRISPR/Cas12a method is sensitive and specific for the detection of SNV. What's more, this strategy provides a new idea for medical diagnosis and lays a technical foundation for the research of PI3K/Akt/mTOR signaling pathways.