Sequence-Directed Plant Breeding via High-Throughput Nucleic Acid Sequencing
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Solution Overview
Problem
Traditional plant breeding methods rely on visual observations and phenotypic data, which are inefficient and prone to false marker-trait associations, limiting the accuracy and speed of genetic gain in molecular breeding.
Innovation Solution
The use of high-throughput sequencing for direct sequencing information in molecular plant breeding, allowing for Sequence Directed Selection, Breeding, and Fingerprinting, enabling precise selection of plants based on nucleic acid sequences rather than markers, and facilitating germplasm improvement.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional marker-based molecular breeding is used, then breeding efficiency is improved compared to visual selection, but false marker-trait associations reduce selection accuracy
Solution Approach 1:
The patent replaces indirect marker-based detection with direct nucleic acid sequencing. Instead of using molecular markers that correlate with traits, the invention sequences the actual nucleic acid regions associated with phenotypic traits, eliminating false associations and providing direct genetic information for selection decisions.
Solution Approach 2:
The patent introduces high-throughput sequencing technology as an intermediary between genotype and phenotype assessment. This sequencing intermediary directly reads the nucleic acid sequences responsible for traits, serving as a more accurate mediator than traditional markers and enabling precise parent and progeny selection.
2Ease of operation
If visual observations and phenotypic data are used for selection, then selection decisions can be made, but the process is inefficient and slow
Solution Approach 1:
The patent replaces phenotypic observation-based selection with genotypic selection through direct nucleic acid sequencing. By sequencing the actual genetic sequences associated with traits, the invention enables selection decisions to be made at the DNA level, dramatically accelerating the breeding process while maintaining selection capability.
3Measurement precision
If direct nucleic acid sequencing is implemented, then selection accuracy is improved by eliminating false marker associations, but sequencing cost and complexity increase
Solution Approach 1:
The patent segments the genome into specific nucleic acid regions associated with phenotypic traits for sequencing. Instead of sequencing the entire genome, the invention targets and sequences only the relevant genomic segments, reducing complexity and cost while maintaining high selection accuracy through direct sequencing of trait-associated regions.
Solution Approach 2:
The patent applies local quality by focusing sequencing efforts on specific nucleic acid regions that have local associations with phenotypic traits. This targeted approach sequences only the locally relevant genomic regions rather than the entire genome, reducing overall complexity while improving selection accuracy for specific traits.
4Loss of information
If traditional phenotyping methods are used, then trait assessment can be performed, but costly and time-consuming field trials are required
Solution Approach 1:
The patent performs preliminary nucleic acid sequencing to assess trait-associated sequences before conducting field trials. By sequencing the actual nucleic acid regions responsible for traits in advance, the invention provides trait information upfront, reducing or eliminating the need for lengthy and costly field trials while maintaining comprehensive trait assessment.
Data Source
AI summary
The present invention provides breeding methods and compositions to enhance the germplasm of a plant by the use of direct nucleic acid sequence information. The methods describe the identification and accumulation of preferred nucleic acid sequences in the germplasm of a breeding population of plants.