InDel Marker Genotype Database for Apple Germplasm Identification
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Solution Overview
Problem
Current methods for identifying and distinguishing apple varieties are labor-intensive and environmentally influenced, lacking precision due to the repeated use of limited genetic backbone parents, which complicates the accurate identification of apple germplasm resources.
Innovation Solution
Development of an InDel marker genotype database for Malus, utilizing multiplex PCR and specific primer pairs to generate molecular identity information stored in a two-dimensional code, allowing for precise identification and paternity testing of apple germplasm resources.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional field test method is used for variety identification, then the identification can be performed without specialized equipment, but the method is time-consuming and laborious with low efficiency
Solution Approach 1:
The patent replaces traditional mechanical field testing methods with molecular marker-based DNA analysis. Specifically, it uses InDel markers detected through PCR amplification and electrophoresis to substitute for phenotypic field observations, enabling rapid genetic fingerprinting without time-consuming growth period requirements.
Solution Approach 2:
The patent creates a molecular copy of the variety's genetic identity through DNA marker profiling. By analyzing specific InDel marker genotypes (presence/absence patterns), the system generates a genetic fingerprint that replicates the variety's unique identity, allowing identification without physical plant examination.
2Reliability
If traditional field test method is used for variety identification, then no molecular equipment is needed, but the results are greatly affected by environmental factors
Solution Approach 1:
The patent substitutes environmental-dependent phenotypic observations with environment-independent genotypic analysis. DNA marker detection occurs in controlled laboratory conditions, eliminating confounding environmental variables that affect field test reliability such as climate, soil conditions, and pest pressure.
Solution Approach 2:
The patent extracts the genetic identity information from the complex phenotypic expression that is influenced by environment. By isolating and analyzing specific DNA sequences (InDel markers), the method separates the stable genetic blueprint from the variable environmental expression, ensuring consistent identification regardless of growing conditions.
3Productivity
If backbone parents are repeatedly used in cross breeding, then new varieties can be cultivated efficiently, but the genetic differences between varieties become smaller making identification more difficult
Solution Approach 1:
The patent applies local quality analysis by focusing on specific genomic regions containing InDel markers rather than requiring genome-wide differentiation. This targeted approach detects subtle local genetic variations even among varieties with high overall similarity, enabling precise identification of minor genetic differences resulting from repeated use of common parents.
Solution Approach 2:
The patent changes the measurement parameter from macroscopic phenotypic traits to microscopic molecular markers. By detecting presence/absence patterns of specific InDel alleles, the system transforms the detection scale to a level where even minor genetic divergences from repeated backcrossing can be reliably identified.
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 marker genotype database enables efficient, stable, and accurate identification of apple germplasm resources, overcoming environmental influences and providing a robust tool for protecting new apple varieties and managing genetic resources.
Implementation Method 1
genotyping InDel markers of genomic DNA samples of Malus germplasm resources by using primer pairs and multiplex PCR
Implementation Method 2
InDel marker, called the most promising molecular marker, is a special type of biallelic genetic marker. The advantages of InDel marker are suitable for constructing multiple electrophoresis
Data Source
AI summary
The disclosure provides an InDel marker genotype database of whole genome of Malus and use in specific identification of germplasm resources thereof, belonging to the technical field of molecular biology. The constructing method of the genotype database comprises: genotyping InDel markers of genomic DNA samples of Malus germplasm resources by using primer pairs and multiplex PCR; recording one line data for each Malus germplasm resource according to the genotype of InDel marker; collecting all germplasm resources records to obtain an InDel marker genotype database of the whole genome of Malus. The whole genome InDel marker genotype database of Malus provided by the disclosure can identify the specificity of apple germplasm simply, efficiently and stably, thus overcoming the limitation that DUS test is easily influenced by environment, and providing a powerful tool for the protection of new apple varieties and the management of germplasm resources.