Egg-Type Chicken Whole-Genome SNP Chip for Local Breed Genotyping
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Solution Overview
Problem
Current whole-genome SNP chips for chickens, such as the Affymetrix 600K SNP chip, have limited applicability in Chinese local breeds due to poor polymorphism and high cost, hindering their practical application in large-scale populations in China.
Innovation Solution
A whole-genome SNP chip for egg-type chickens is developed, comprising 43,681 SNP loci, which include well-polymorphic SNPs from Chinese domestic lines, disease-resistant traits, economically significant traits, and supplementary SNPs from the SNP database, ensuring comprehensive genetic variation coverage.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If the Affymetrix 600K SNP chip is used, then the chip density and marker density are improved, but the cost increases and polymorphism in Chinese local breeds deteriorates
Solution Approach 1:
The patent applies local quality by customizing the SNP chip for specific Chinese local egg-type chicken breeds rather than using a universal commercial chip. The SNP loci are selectively derived from Chinese domestic lines (Houdan, Dongxiang blue-egg shell chicken, etc.) to ensure high polymorphism and reliability for these specific breeds, while maintaining appropriate chip density.
2Quantity of substance
If the Affymetrix 600K SNP chip is used, then the marker density is improved, but the cost increases and applicability in large-scale populations deteriorates
Solution Approach 1:
The patent employs the principle of using a cost-effective customized chip instead of expensive commercial chips. By deriving SNP loci from Chinese domestic lines and making the chip specifically for Chinese egg-type chicken breeds, the patent reduces cost while maintaining high applicability for large-scale population testing in China, making genomic selection economically feasible.
3Productivity
If commercial SNP chips are used, then the detection throughput is improved, but the genetic variation information specific to Chinese local breeds is lost
Solution Approach 1:
The patent applies segmentation by dividing the SNP chip into specific modules: SNP loci are segmented into different sources including Chinese domestic lines (Houdan, Dongxiang blue-egg shell chicken, etc.), commercial lines, and inbred lines. This segmentation allows the chip to maintain high detection throughput while preserving and emphasizing the genetic variation information specific to Chinese local breeds through dedicated SNP loci from these lines.
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 chip provides accurate genetic evaluation, improved genomic selection accuracy, and enhanced applicability in Chinese local breeds, meeting both scientific research and breeding needs while being cost-effective for large population sample testing.
Implementation Method 1
It works by means of hybridizing and binding the probe DNA strand with the test target genomic DNA
Implementation Method 2
fixing a large number of fluorescently labeled DNA probes on a glass substrate
Data Source
AI summary
Provided are an egg-type chicken whole-genome SNP chip and the use thereof. The SNP loci of the chip are respectively derived from 14,624 SNP loci shared by each line of the major egg-type chickens in China; 3,677 SNP loci associated with disease-resistant traits in egg-type chickens; 16,000 SNP loci associated with economic traits in egg-type chickens; and 9,358 SNP loci making up genomic regions not covered by the foregoing probes. The 43,681 SNPs on the egg-type chicken whole-genome SNP chip have DNA sequences as represented by SEQ ID NO. 1-43,681. The chip can specifically identify the genetic relationship between commercial egg-type chickens and egg-type chickens of local breeds, and can also perform applications such as whole-genome association analysis, genome selective breeding, and QTL location analysis of target traits and population genetic analysis.