Pig 10K mSNP Liquid-Phase Chip for Low-Cost Genomic Selection
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
The high cost of genomic selection in pig breeding using existing 50K SNP chips, particularly due to the limited availability and high price of solid-phase chips, and the inefficiency of using low-density chips like 10K chips, which lack sufficient marker density and accuracy for early piglet selection, hinder widespread implementation in the pig industry.
Innovation Solution
Development of a 10K liquid-phase chip based on multiple single nucleotide polymorphism (mSNP) technology, optimizing probe design and marker selection to enhance marker density and accuracy, allowing for cost-effective genomic selection by incorporating mSNPs upstream and downstream of target sites, compatible with 50K chips through genotype imputation.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If 50K SNP chips are used for genomic selection in pigs, then genotyping accuracy is improved, but testing cost increases significantly
Solution Approach 1:
The patent develops a 10K liquid-phase chip that uses disposable probe sets for genotyping. Instead of reusing expensive solid-phase chips, the liquid-phase system employs cost-effective probes that can be discarded after single use, significantly reducing per-sample testing costs while maintaining adequate genotyping accuracy for early piglet selection
Solution Approach 2:
The patent extracts and utilizes multiple single nucleotide polymorphisms (mSNPs) from upstream and downstream regions of target sites. By capturing these additional SNP markers alongside the primary target SNPs, the system increases the effective marker density and information content without proportionally increasing testing costs, thereby improving genotyping value at lower cost
2Quantity of substance
If 10K low-density chips are used to reduce costs, then testing cost decreases, but marker density and selection accuracy are insufficient
Solution Approach 1:
The patent merges multiple SNP detection functions into a unified liquid-phase chip system. By combining target site SNP detection with mSNP detection from upstream and downstream regions, the system achieves effective marker density comparable to higher-density chips while maintaining the cost structure of a 10K chip design
Solution Approach 2:
The patent changes the detection parameters by utilizing mSNPs with moderate linkage disequilibrium. By selecting and detecting these additional polymorphic sites, the system transforms the information content and marker effectiveness, achieving improved selection accuracy without increasing the nominal chip density
3Reliability
If solid-phase chip technology is used, then genotyping reliability is maintained, but flexibility and customization are limited
Solution Approach 1:
The patent transitions from static solid-phase chip designs to a dynamic liquid-phase system. The liquid-phase chip allows flexible adjustment of probe sequences and target SNPs based on specific breeding needs, enabling customization of marker panels while maintaining detection reliability through standardized liquid-phase hybridization protocols
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
The 10K liquid-phase chip reduces genomic selection costs by one-third compared to 50K solid-phase chips and half of 50K liquid-phase chips, maintaining accuracy and enabling large-scale genomic breeding with effective genotype imputation, achieving similar results to 50K chips.
Implementation Method 1
through multiple sequencing and hybridization of probes, select probes containing high-quality mSNPs
Data Source
Figure 1~2
Figure 3A~3B
Figure 4~5B
AI summary
This invention relates to the field of genetic molecular breeding, specifically to a pig 10K liquid-phase chip based on multiple single nucleotide-polymorphism and its application. The present invention, while adhering to the basic principles of liquid phase chip design, adds new markers to existing chips and optimizes probes using multiple single nucleotide-polymorphism technology. This results in the generation of more SNP markers with high genotyping quality and moderate linkage disequilibrium with target SNP loci within the probe region, thereby increasing the effective marker count of the chip. The mSNP liquid phase chip of the present invention increases the number of detectable SNPs to 1.5-2 times the number of target SNP markers, addressing the issue of existing chips that only contain target SNPs and cannot provide mSNP markers, without increasing the cost. By using genotype imputation technology, genotype data from the chip of the present invention is imputed into mainstream 50K chips for genomic selection, achieving molecular breeding accuracy comparable to or similar to that of the 50K chips, thereby reducing the cost of pig molecular breeding.