InDel Marker for Ganoderma lucidum Strain Identification
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Solution Overview
Problem
Current methods for identifying high-quality Ganoderma lucidum strain HMGIM-M624 are inefficient, inaccurate, and complex, lacking specificity and stability, which hinders large-scale commercial cultivation and industrial production.
Innovation Solution
Development of an InDel molecular marker based on insertion/deletion sites in the genomic sequence, using specific primers for PCR amplification and agarose gel electrophoresis, providing a high-throughput, cost-effective, and stable identification method.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional molecular markers (RFLP, RAPD, SSR) are used for strain identification, then the identification process can be performed, but the operation becomes complicated, less reproducible, or produces unclear bands with technical defects
Solution Approach 1:
The patent extracts and focuses on a specific, unique molecular marker (InDel marker with specific primer pair) from the complex landscape of multiple molecular markers. By selecting a single well-defined marker located at a specific position in the genome with a clear insertion/deletion pattern, the patent simplifies the identification process while maintaining high reliability, avoiding the complexity of using multiple markers or complex analysis methods.
Solution Approach 2:
The patent changes the parameter of marker type from conventional markers (RFLP, RAPD, SSR) to an InDel marker with specific insertion/deletion characteristics. This parameter change enables simpler operation and better reproducibility, as the InDel marker provides clear banding patterns without the technical defects of other markers, while maintaining high identification reliability.
2Ease of operation
If SSR markers are used for identification, then the process is convenient and cost-effective, but some amplified bands are not clear and technical defects cause errors in genotyping
Solution Approach 1:
The patent adopts a simple, single-use InDel marker system that provides clear, unambiguous results without the need for complex analysis. The marker design ensures that each strain produces a distinct, clear banding pattern, eliminating the ambiguity and technical defects associated with SSR markers, while maintaining the convenience and cost-effectiveness of PCR-based identification.
Solution Approach 2:
The patent changes the marker parameter from SSR (simple sequence repeats) to InDel (insertion/deletion), which fundamentally alters the amplification characteristics. This parameter change results in clearer bands and eliminates genotyping errors, while preserving the ease of operation and cost-effectiveness through straightforward PCR amplification and gel electrophoresis.
3Measurement precision
If RFLP is used for strain identification, then specific DNA fragments can be detected, but the operation becomes more complicated due to radioisotope requirements
Solution Approach 1:
The patent replaces the complex RFLP system (which requires radioisotopes and complex probe hybridization) with a simpler PCR-based InDel marker system. This substitution maintains high detection specificity through the unique insertion/deletion pattern at a specific genomic position, while dramatically simplifying the operation through standard PCR amplification and gel electrophoresis, eliminating the need for radioisotope handling and complex probe preparation.
4Adaptability or versatility
If RAPD is used for strain identification, then arbitrary primers can bind to DNA sites, but the low annealing temperatures result in poor reproducibility
Solution Approach 1:
The patent applies local quality by designing primers that target a specific, well-defined region of the genome containing the InDel marker, rather than using arbitrary primers that bind to multiple sites. This localized approach ensures consistent and reliable amplification of the specific marker region, achieving high reproducibility while maintaining the flexibility to identify the target strain through the unique banding pattern.
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
The InDel molecular marker enables rapid, accurate, and specific identification of the high-quality Ganoderma lucidum strain HMGIM-M624, distinguishing it from other strains, ensuring quality control and protection for industrial applications.
Implementation Method 1
using specific primers for PCR amplification
Implementation Method 2
agarose gel electrophoresis
Data Source
AI summary
The present invention relates to a molecular marker, a specific primer pair, and an identification method of the high-quality Ganoderma lucidum strain HMGIM-M624. The high-quality Ganoderma lucidum strain HMGIM-M624 was preserved in Guangdong Microbial Culture Collection Center (address: 5th Floor, No. 59 Building of No. 100 Yard, Mid. Xianlie Road, Guangzhou City) with the preservation number of GDMCC No: 60889 on Nov. 7, 2019. The molecular marker is an InDel molecular marker. The high-quality Ganoderma lucidum strain HMGIM-M624 has a base deletion of CATGCTGTA at the 246451th-246460th site of the chromosome sca34. The present invention provides reagents for detecting the molecular marker of the high-quality Ganoderma lucidum strain HMGIM-M624. The reagents can distinguish the high-quality Ganoderma lucidum strain HMGIM-M624 from the other 11 G. lucidum strains for commercial cultivation, thus specifically identifying the high-quality Ganoderma lucidum strain HMGIM-M624.