Artificial InDel Marker Alleles for Plant Breeding
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Solution Overview
Problem
Current DNA marker technologies in plant breeding are laborious and time-consuming, especially for crops with large genomes, due to the challenges of identifying low copy number DNA segments and repetitive sequences, leading to markers of low sensitivity and reliability.
Innovation Solution
The development of artificial InDel marker alleles that are introduced into genetically linked genomic loci, allowing for increased sensitivity and reliability in identifying nucleic acids of interest, enabling efficient detection and introgression of desired traits in plant breeding.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional DNA marker technology is used to identify nucleic acids in plant breeding, then the process can detect genetic variation, but the process becomes laborious and time-consuming with low sensitivity and reliability
Solution Approach 1:
The patent applies preliminary action by pre-introducing artificial InDel marker alleles into genomic loci that are genetically linked to target nucleic acids. These pre-established markers can be directly detected using PCR and gel electrophoresis, eliminating the need for time-consuming searches for suitable natural polymorphisms and enabling rapid identification of target sequences in breeding populations.
Solution Approach 2:
The patent changes the parameter of marker type from relying on natural polymorphisms (SNPs, indels) to using artificial InDel marker alleles with defined insertion/deletion sequences. This parameter change enables the use of standardized detection methods with higher sensitivity and reliability, while the artificial markers can be introduced at specific genomic locations to ensure tight linkage with target genes.
2Ease of manufacture
If natural polymorphisms are searched for in large plant genomes, then diagnostic markers can be developed, but the process is obstructed by repetitive sequences and low copy number DNA segments
Solution Approach 1:
The patent extracts the problematic step of searching through complex genomes for suitable polymorphisms by directly introducing artificial InDel marker alleles at predetermined genomic loci. This extraction removes the obstacle of repetitive sequences and low copy number DNA segments, as the artificial markers are designed to be detectable with standard PCR primers regardless of genome complexity.
Solution Approach 2:
The patent introduces artificial InDel marker alleles as intermediary elements between the target nucleic acid and the detection system. These intermediary markers serve as reliable proxies that can be detected with high ease using standard molecular biology techniques, bypassing the need to directly analyze complex genomic regions while maintaining tight genetic linkage to the target gene.
3Measurement precision
If only DNA polymorphisms with extremely tight linkage to the trait gene are used, then marker accuracy is improved, but the selection process becomes highly limited
Solution Approach 1:
The patent achieves universality by designing artificial InDel marker alleles that can be introduced at multiple different genomic loci, each with tight linkage to different target genes or traits. This multi-functionality allows the same marker technology platform to be applied across diverse breeding programs and species, greatly enhancing versatility while maintaining high measurement precision through tight genetic linkage.
Data Source
AI summary
This invention relates to a method for making an artificial marker allele for the identification of a nucleic acid of interest in an organism. The invention also relates to determining the presence of a nucleic acid of interest in a mixed population and a method for introgressing a nucleic acid of interest into a population. The invention also relates to organisms, particularly plants and seeds, comprising such a marker allele and to various uses for the artificial marker allele.