Genome Editing for Causal Gene Mapping in Low-Recombination Regions
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Solution Overview
Problem
Existing genetic mapping methods struggle with genomic regions of low recombination frequency or non-colinear regions, making it difficult to isolate causal genes for desired traits in plants.
Innovation Solution
Introduce site-specific modifications, such as deletions or insertions, in endogenous genomic loci using CRISPR-Cas systems, and screen for phenotype changes to identify causal genes or regions responsible for desired traits.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If standard genetic mapping methods are used, then mapping can be performed in regions with high recombination frequency, but mapping fails or is extremely difficult in regions of low recombination or non-colinear regions
Solution Approach 1:
The patent replaces the mechanical/recombination-based genetic mapping system with a genome editing system. Instead of relying on natural recombination events to separate linked genes, the invention uses CRISPR-Cas9 to create precise targeted deletions and mutations in candidate genes. This substitution allows mapping to work in regions where natural recombination is suppressed, directly resolving the contradiction between adaptability to low recombination regions and mapping reliability.
Solution Approach 2:
The patent changes the fundamental parameter of how genetic mapping is achieved - from using recombination frequency as the mapping mechanism to using targeted genome editing. By altering the approach from passive observation of recombination to active creation of genetic variants, the system becomes applicable to all genomic regions regardless of their recombination characteristics, thereby improving both adaptability and reliability simultaneously.
2Measurement precision
If traditional fine mapping iterations are performed, then causal genes can be identified through multiple generations, but the process takes one or more iterations and significant time
Solution Approach 1:
The patent applies preliminary action by using genome editing to create and introduce genetic variants directly into the candidate genes before traditional phenotypic screening. Instead of waiting for natural recombination to occur over multiple generations, the invention pre-creates the genetic differences needed for mapping using CRISPR-Cas9. This preliminary genetic modification dramatically reduces the time required to identify causal genes while maintaining high precision, as the edited variants can be directly associated with phenotypic effects in the same generation.
Solution Approach 2:
The patent skips the traditional multi-generation fine mapping iterations by using genome editing to directly create and test candidate gene variants. Rather than progressively narrowing down intervals through sequential recombination events across F2, BC1, BC2 generations, the invention rushes through the process by creating targeted mutations that can be phenotypically assessed immediately, thereby reducing time loss while preserving measurement precision.
3Ease of manufacture
If recombination is used to isolate causal genes, then mapping can be performed in colinear regions, but recombination cannot occur in non-colinear or low homology regions
Solution Approach 1:
The patent replaces the recombination-based gene isolation mechanism with a genome editing mechanism that does not depend on homology or colinearity. CRISPR-Cas9 can target and edit specific sequences regardless of their genomic context, making the system equally effective in colinear and non-colinear regions. This substitution eliminates the barrier that previously limited ease of gene isolation to regions with suitable recombination characteristics.
Solution Approach 2:
The patent makes the gene isolation method universal by using CRISPR-Cas9, which can function across all genomic regions regardless of their structural characteristics. The editing system is not limited to colinear regions with high homology but can operate in any genomic context, thereby achieving both ease of manufacture and broad adaptability simultaneously across diverse genomic landscapes.
Data Source
AI summary
The field is molecular biology, and more specifically, methods for editing the genome of a plant cell to identify causal alleles of a desired trait or to fine map a desired trait to small region of the genome for gene identification.