Site-Specific Genomic Recombination for Breaking Trait Linkage
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Solution Overview
Problem
Current plant breeding methods rely on slow and costly processes to integrate desirable traits, such as resistance to new plant pathogen biotypes, and struggle with genetic linkages associated with unfavorable traits.
Innovation Solution
Introduce site-specific genome modifications using enzymes like endonucleases, recombinases, and transposases to induce recombination between arrays of tandemly duplicated genes, facilitating the generation of new arrays with enhanced genetic diversity and disease resistance.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If standard plant breeding methods are used to integrate desirable traits, then genetic diversity can be produced through natural mutation and recombination, but the process is slow and costly involving multiple rounds of back crossing and selection
Solution Approach 1:
The patent applies preliminary action by pre-engineering specific genomic loci with recognition sites for site-specific nucleases before breeding. This allows recombination events to be directed to predetermined locations in advance, eliminating the need for multiple rounds of backcrossing and selection. The recognition sites are installed beforehand so that when the nuclease is applied, recombination occurs immediately at the desired loci, dramatically accelerating the breeding process while maintaining trait reliability.
Solution Approach 2:
The patent uses site-specific nucleases as intermediary tools to mediate recombination between donor and recipient genomes. Instead of relying on natural, random recombination processes, the nuclease acts as a controlled intermediary that facilitates precise DNA cutting and rejoining at predetermined loci. This intermediary mechanism enables efficient integration of desirable traits without the lengthy backcrossing required by traditional breeding.
2Reliability
If standard breeding techniques are used, then natural recombination events can occur, but they cannot overcome certain genetic linkages associated with unfavorable traits
Solution Approach 1:
The patent applies the taking out principle by extracting the constraint of genetic linkage through site-specific recombination. By using predetermined recognition sites and site-specific nucleases, the method enables separation of desirable traits from unfavorable linked traits. The recombination occurs at specific engineered loci rather than through natural crossing-over, effectively 'taking out' the limitation imposed by genetic linkage and allowing independent integration of desired traits regardless of their chromosomal position.
Solution Approach 2:
The patent changes the fundamental parameter of recombination from random natural processes to controlled site-specific events. By engineering recognition sites at predetermined genomic loci and using specific nucleases, the location and timing of recombination are changed from unpredictable to precisely controllable. This parameter change enables overcoming genetic linkages by directing recombination to occur at specific locations independent of natural chromosomal associations.
3Productivity
If site-specific genome modifications are introduced to accelerate breeding, then chromosome exchange events can be stimulated, but the process requires sophisticated enzyme systems and genomic engineering
Solution Approach 1:
The patent applies universality by designing a modular system where site-specific nucleases can be applied across different crop species and trait combinations. The recognition sites are engineered into the genome once, and the same nuclease system can be used for different recombination events. This multi-functional approach reduces the need for developing separate complex enzyme systems for each breeding scenario, as the universal nuclease-recognition site pair can address multiple breeding objectives across different plants and traits.
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
Accelerates the development of plants with improved environmental adaptation and agronomic traits by stimulating chromosome exchanges, leading to increased resistance against various diseases.
Implementation Method 1
inducing recombination with a second array of tandemly duplicated genes
Implementation Method 2
contacting a plant cell with a first site-specific genome modification enzyme that introduces a genome modification
Data Source
AI summary
The present disclosure provides methods to accelerate recombination at selected genomic loci, allowing recombination to occur, and selecting events with molecular variation within the selected loci. The accelerated recombination generates novel variations in gene clusters that are present in the plant or mammalian genomes.