Sugarcane Variety Identification via SSR DNA Markers
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Solution Overview
Problem
Current methods for identifying sugarcane varieties/lines are inefficient due to low precision and limited applicability, particularly in genomic complexity and cultivar-specific marker availability, making it difficult to breed desirable traits such as sugar content, disease resistance, and cold resistance.
Innovation Solution
Development of a method using novel DNA markers, specifically simple sequence repeat polymorphisms in characteristic DNA sequences from the Saccharum genome, for high-precision identification of sugarcane varieties/lines through PCR amplification and capillary electrophoresis-based genotyping.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If characteristics comparison or comparison of cultivation is used for identification, then the method is simple to operate, but the precision is reduced due to differences in cultivation conditions and lengthy field research
Solution Approach 1:
The patent replaces traditional mechanical/biological identification methods (characteristics comparison, field research) with molecular biology techniques (DNA extraction, PCR amplification, fragment length analysis). This substitution eliminates the time-consuming field research and cultivation comparison while achieving high-precision identification through DNA marker analysis.
Solution Approach 2:
The patent introduces DNA markers as an intermediary substance to enable identification. Instead of directly comparing plant characteristics or cultivation conditions, the method uses DNA fragments containing SSR sequences as mediators to reflect genetic differences, thereby achieving precise variety identification without lengthy field research.
2Measurement precision
If USDA SSR markers are used for genotyping, then the method is available for American/Australian varieties, but the precision is low due to small numbers of markers and polymorphisms
Solution Approach 1:
The patent segments the sugarcane genome into multiple specific loci, each containing SSR markers. By developing 12 distinct DNA marker sets targeting different genomic regions, the method increases the number of polymorphic markers available for genotyping, thereby improving precision while maintaining broad applicability across different sugarcane varieties.
Solution Approach 2:
The patent changes the parameters of the marker system by developing new SSR markers with higher polymorphism rates and selecting primer sets that amplify fragments of varying lengths. This increases the discriminatory power of the markers, improving genotyping precision while ensuring the markers are applicable to diverse sugarcane varieties including those cultivated in Japan, Taiwan, and India.
3Measurement precision
If field research based identification is used, then the method can identify plant characteristics, but it is difficult to conduct due to the large size of sugarcane plants
Solution Approach 1:
The patent replaces mechanical field research and visual inspection with molecular laboratory techniques. Instead of physically examining large sugarcane plants in the field, the method extracts DNA from small tissue samples and performs PCR amplification and fragment analysis in the laboratory, dramatically easing operational difficulty while maintaining or improving identification precision.
Solution Approach 2:
The patent creates molecular copies (PCR amplification products) of specific DNA regions containing SSR markers. These amplified fragments serve as readable copies of the genetic information, allowing precise identification without needing to handle or measure the actual large sugarcane plants, thus simplifying the operation.
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
Enables high-precision identification of a wide range of sugarcane varieties/lines with improved reproducibility, overcoming the limitations of existing methods by providing a kit for accurate variety identification and facilitating breeding for desirable traits.
Implementation Method 1
The identification method comprises using a simple sequence repeat polymorphism in at least one DNA sequence
Implementation Method 2
The determination of the molecular weights of the amplified DNA fragments in step (b) is performed by capillary electrophoresis
Data Source
AI summary
It is an object of the present invention to provide a method for identifying the variety/line of a plant of the genus Saccharum with the use of novel DNA markers that allow high-precision identification of a wide range of varieties/lines of plants of the genus Saccharum. A method for identifying the variety/line of a plant of the genus Saccharum, comprising using a simple sequence repeat polymorphism in at least one DNA sequence selected from SEQ ID NOS: 1 to 12 is provided.