Chicken Whole-Genome SNP Chip for Indigenous Breed Genomic Selection
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Solution Overview
Problem
Current chicken whole-genome SNP chips lack genome variation information for Chinese indigenous chicken breeds, limiting their application in Chinese indigenous chicken breeding and related research, and there is a need for a cost-effective SNP chip suitable for large population sample testing.
Innovation Solution
Development of a chicken whole-genome SNP chip with 50,000 SNP/INDEL molecular markers, including 19,600 SNPs with a minor allele frequency greater than 0.05 uniformly distributed across the genome, 14,000 SNPs associated with economic traits, and 16,400 SNPs to cover genomic regions not covered by the first two types, using ThermoFisher's Axiom platform technology for in-situ photolithography synthesis, enabling detection of genetic variations in both indigenous and abroad chicken breeds.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If a commercial SNP chip is used, then detection accuracy is improved, but it lacks genome variation information for Chinese indigenous chicken breeds
Solution Approach 1:
The patent applies local quality by designing a customized SNP chip specifically tailored for Chinese indigenous chicken breeds. The chip includes 50,000 SNP markers selected from the genome of Chinese indigenous chickens, ensuring that the detection system has optimal local adaptation to the specific genetic characteristics of these breeds while maintaining high detection accuracy through standardized chip technology.
2Quantity of substance
If a high-density SNP chip is used, then genome coverage is improved, but cost increases making it unsuitable for large population testing
Solution Approach 1:
The patent applies partial action by selecting 50,000 SNP markers that provide sufficient genome coverage for breeding applications without using the full capacity of high-density chips. This moderate flux design covers key genomic regions and economically important traits while reducing per-chip cost, making it economically viable for large population genomic selection in chicken breeding programs.
3Ease of manufacture
If a moderate flux SNP chip is developed, then cost is reduced, but marker density may be insufficient for accurate genomic selection
Solution Approach 1:
The patent applies parameter changes by optimizing the number of SNP markers to 50,000, which balances cost and precision. This parameter was selected to provide sufficient marker density for accurate genomic prediction while maintaining cost-effectiveness for large-scale application. The chip also incorporates SNPs with different minor allele frequencies to ensure accurate detection across diverse Chinese indigenous chicken breeds.
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 universal applicability for indigenous and abroad chicken breeds, with high accuracy in estimating breeding values and genetic research, offering moderate throughput and low cost, while ensuring standardized and automated detection, enhancing the analysis of genetic diversity and breeding efficiency.
Implementation Method 1
in-situ photolithographic technology is used to in-situ synthesize gene probe sequences on a substrate by photolithography
Implementation Method 2
It works by means of base-pairing reaction of the DNA marker sequences immobilized on the chip with the target genome so as to accurately identify the genetic information
Data Source
AI summary
Provided in the present invention is a chicken whole-genome SNP chip and application thereof. There are a total of 50,000 SNP loci on the chip: including 19,600 SNP loci for white-feather broilers, yellow-feather and partridge chickens having a MAF value greater than 0.05 and uniformly distributed across the genome which were derived from the data of the whole-genome resequencing of main indigenous chicken breeds in China and introduced chicken breeds; 14,000 SNP loci associated with economic traits, and 16,400 SNP loci for making up for the genomic regions that are not covered by the first two types of probes. The 50,000 SNP loci on the chicken whole-genome SNP chip of the present invention have DNA sequences represented by SEQ ID NOs. 1 to 50,000. The SNP loci on the chip are uniformly distributed across the whole genome, and associated with traits such as feed efficiency, meat production rate, lipid metabolism, meat quality, general resistance to diseases, reproduction and the like, and the chip has moderate through-put and low cost, and could be used universally for chicken breeds at indigenous and abroad.