Surface Plasmon Resonance Genotyping for Rapid Plant SNP Detection
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Solution Overview
Problem
Traditional plant breeding methods are time-consuming and costly, and existing technologies have not effectively utilized Surface Plasmon Resonance (SPR) for genotyping and sequencing of polynucleotides to facilitate activities such as line development and trait identification in plants.
Innovation Solution
The use of SPR assays for genotyping plant polynucleotides by providing oligonucleotide probes, hybridizing them with plant polynucleotides, and quantitating their affinity to determine the presence or absence of Single Nucleotide Polymorphisms (SNPs) on an SPR biosensor chip, which can be applied for high-throughput sequencing and genotyping.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional plant breeding methods are used, then plant breeding activities can be conducted, but the process is time-consuming and costly
Solution Approach 1:
The patent replaces traditional mechanical and chemical breeding methods with optical detection technology (Surface Plasmon Resonance). The SPR system uses light interaction with metal surfaces to detect biomolecular interactions, enabling rapid genotyping and sequencing without time-consuming PCR amplification or gel electrophoresis steps.
Solution Approach 2:
The patent changes the detection parameters from indirect methods (requiring amplification and visualization) to direct real-time optical detection. By monitoring refractive index changes at the sensor surface, the system achieves rapid detection of DNA hybridization events, reducing breeding evaluation time from days to minutes.
2Productivity
If SPR technology is applied for genotyping and sequencing, then speed and accuracy are improved, but the technology has not been readily applied to plant breeding
Solution Approach 1:
The patent designs the SPR system to perform multiple functions: genotyping, sequencing, and polymorphism detection. The same platform can analyze different plant species and different genetic markers, making it universally applicable to various plant breeding programs without requiring separate systems for each application.
Solution Approach 2:
The patent uses oligonucleotide probes as intermediaries between the target DNA and the SPR detection system. These probes hybridize to specific genomic regions and enable the SPR sensor to detect genetic variations through label-free optical measurement, bridging the gap between complex genetic analysis and simple optical detection.
3Measurement precision
If SPR assays are used for high-throughput sequencing and genotyping, then accuracy and throughput are enhanced, but the complexity of the system increases
Solution Approach 1:
The patent extracts only the essential detection function from complex molecular biology workflows. By removing the need for PCR amplification, fluorescent labeling, and electrophoresis, the system retains high accuracy for SNP detection while significantly simplifying the overall process to a single-step hybridization assay monitored by SPR.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This method enables rapid and accurate identification of SNPs in plants, facilitating plant breeding activities like genetic mapping, trait discovery, and marker-assisted selection, thereby enhancing the efficiency and accuracy of plant breeding processes.
Implementation Method 1
Surface Plasmon Resonance (SPR) is an optical biosensing technology that has be applied to quantitative and qualitative analysis in analytical chemistry, biochemistry, physics and engineering. The application of SPR utilizes polarized light that is directed through a prism towards a metal film and the resulting reflected light is collected and analyzed.
Data Source
AI summary
The present disclosure relates to compositions and methods for the use Surface Plasmon Resonance to genotype and sequence polynucleotides. Applications of these methods and compositions utilize Surface Plasmon Resonance for sequencing of a plant genome. Other applications include utilizing the sequence data for plant breeding.