Salmonid QTL DNA Polymorphism for Piscirickettsia Resistance Prediction
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Solution Overview
Problem
Current methods for predicting resistance to Piscirickettsia salmonis infection in salmonids are inefficient, particularly as they require sacrificing fish for challenge tests or rely on unproven genetic markers, limiting the ability to use tested fish as broodstock and lacking predictive power.
Innovation Solution
Identification of a new quantitative trait locus (QTL) associated with resistance to Piscirickettsia salmonis infection, allowing for the prediction of resistance based on DNA polymorphisms within specific regions of the salmonid genome, enabling the use of resistant fish as broodstock and extending to various salmonid species through conserved genomic regions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If challenge tests are performed to identify resistant fish, then resistance prediction accuracy is improved, but all tested fish must be sacrificed which loses broodstock candidates
Solution Approach 1:
The patent replaces the mechanical/biological challenge test system (which requires sacrificing fish) with a molecular genetics system using DNA polymorphism analysis. This substitution allows resistance prediction without physical challenge, preserving broodstock candidates while maintaining prediction accuracy through identification of resistant alleles at specific loci.
Solution Approach 2:
The patent introduces DNA polymorphism markers as an intermediary between the fish and the resistance assessment. Instead of directly challenging fish with bacteria, the method uses genetic markers as mediators to predict resistance, eliminating the need to sacrifice fish while providing accurate resistance predictions through allele analysis.
2Loss of substance
If family selection is used to establish broodstock from siblings, then broodstock can be retained, but predictive power is limited due to reliance on between-family genetic variation
Solution Approach 1:
The patent changes the parameter basis from family-level phenotypic selection to individual-level genotypic selection. By analyzing DNA polymorphisms at specific loci associated with resistance, the method transforms the selection parameter from crude family performance to precise individual genetic markers, thereby improving prediction accuracy while retaining individual resistant fish as broodstock.
Solution Approach 2:
The patent segments the genome into specific loci with DNA polymorphisms that are associated with resistance. Instead of evaluating entire families or individuals holistically, the method focuses on specific genetic segments (loci with resistant alleles), allowing precise identification of resistant individuals within families and improving prediction power beyond what whole-family selection can achieve.
3Loss of substance
If existing genetic markers are used for marker assisted selection, then broodstock can be retained, but predictive power remains moderate with only SNP showing p=10-5 to 10-6 association
Solution Approach 1:
The patent changes from using existing genetic markers with moderate association (p=10-5 to 10-6) to identifying and using DNA polymorphisms at loci with much stronger statistical association (p<10-8). This parameter change in marker quality and statistical significance dramatically improves predictive power while maintaining the ability to retain broodstock.
Solution Approach 2:
The patent identifies and copies the resistant allele pattern from naturally resistant fish to create a predictive model. By analyzing DNA polymorphisms in resistant individuals and identifying consistent allele patterns at specific loci, the method creates a genetic signature that can be copied and applied to predict resistance in other fish, achieving high prediction accuracy without sacrificing animals.
Data Source
AI summary
The invention relates to methods of predicting resistance to Piscirickettsia salmonis infection in a salmonid, the method comprising determining in the salmonid the alleles present at one or more DNA polymorphism within a QTL, and predicting the ability of the salmonid to be resistant to Piscirickettsia salmonis infection based on the determination of the alleles, wherein the QTL is: —(a) located in linkage group 21 (GenBank ID NC 034194.1) within the coho salmon genome, or in the chromosome of coho salmon that corresponds to that linkage group, when the salmonid is a coho salmon, or; (b) a QTL that is located in a linkage group that corresponds to linkage group 21 within the coho salmon genome, or in the chromosome of a salmonid that corresponds to that linkage group, when the salmonid is not a coho salmon. The invention further relates to probes and arrays useful in such method and related methods.