Site-Specific Genomic Recombination for Faster Plant Trait Breeding

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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 and recombinases 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

VSEngineering Contradiction Analysis

1Reliability

If standard plant breeding techniques are used to integrate desirable traits, then genetic diversity is produced through natural mechanisms, but the process is slow and costly involving multiple rounds of back crossing and selection

Engineering Contradiction:

Improveproduction of plants with desirable traitsVSAvoidbreeding process duration

Core Design Contradiction:

ReliabilityVSLoss of time

Solution Approach 1:

The patent introduces site-specific genome modifications at predetermined genomic loci before recombination events occur. By pre-positioning modification sites using engineered nucleases or recombinases, the breeding process bypasses the need for multiple rounds of random mutation screening and back-crossing, dramatically accelerating trait integration while maintaining reliability

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent employs intermediary molecules including guide RNAs for CRISPR systems, DNA binding domains for zinc finger nucleases, and recombinase enzymes to mediate precise genome modifications at target loci. These intermediaries enable controlled recombination events between homologous and non-homologous chromosomes, replacing slow natural breeding mechanisms with directed molecular processes

Inventive Principle:

Principle #24Intermediary (Mediator)

2Reliability

If standard plant breeding techniques are used, then natural recombination events occur, but genetic linkages associated with unfavorable traits cannot be overcome

Engineering Contradiction:

Improveproduction of plants with desirable traitsVSAvoidovercoming genetic linkages

Core Design Contradiction:

ReliabilityVSAdaptability or versatility

Solution Approach 1:

The patent extends recombination beyond traditional homologous chromosome pairing by enabling exchanges between non-homologous chromosomes and multiple chromosome pairs simultaneously. This dimensional expansion of recombination possibilities allows breaking of tight genetic linkages that constrain standard breeding, enabling independent selection of desirable traits previously linked to unfavorable alleles

Inventive Principle:

Principle #17Another dimension (Dimensionality change)

Solution Approach 2:

Engineered recombinase enzymes and nuclease systems act as intermediaries to facilitate recombination at user-defined genomic loci regardless of chromosomal homology. These molecular mediators enable precise breaking of genetic linkages by directing recombination events to specific sites, decoupling desirable traits from unfavorable linked traits that cannot be separated through conventional breeding

Inventive Principle:

Principle #24Intermediary (Mediator)

3Reliability

If multiple rounds of back crossing and selection are performed, then desirable traits are integrated into elite germplasm, but the process becomes costly and time-consuming

Engineering Contradiction:

Improveintegration of desirable traits into elite germplasmVSAvoidbreeding program output

Core Design Contradiction:

ReliabilityVSProductivity

Solution Approach 1:

The patent performs preliminary genome modifications at target loci before crossing events, pre-loading desirable genetic variations into the elite germplasm background in a single step. This eliminates the need for sequential back-crossing and selection cycles, maintaining trait integration reliability while multiplying breeding program output by reducing generational requirements

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent replaces the mechanical, multi-generational process of back-crossing and phenotypic selection with a molecular-level system using engineered nucleases and recombinases. This substitution enables direct genetic editing and recombination control, achieving the same trait integration reliability with dramatically improved productivity by eliminating repetitive breeding cycles

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

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 cis-chromosome and multiple chromosome exchange events, enhancing resistance to various diseases.

Implementation Method 1

the genome modification is a double strand break (DSB)

Methodology Applied

Scientific EffectDouble strand break:

Implementation Method 2

the genome modification is a single strand break

Methodology Applied

Scientific EffectSingle strand break:

Implementation Method 3

the genome modification is a recombinase-mediated DNA exchange reaction

Methodology Applied

Scientific EffectRecombinase-mediated DNA exchange:

Data Source

PatentUS12460217B2Enhanced recombination of genomic loci

Publication Date: 2025.11.04 MONSANTO TECHNOLOGY LLC

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.