A set of molecular markers and a liquid chip for breeding of laying ducks

Abstract

The present application relates to a kind of molecular marker set for egg duck breeding, the molecular marker set includes multiple single nucleotide polymorphism (SNP) sites, the multiple SNP sites are determined based on the physical location of egg duck reference genome ZJU1.0, and the multiple SNP sites include functional SNP site and background SNP site;Wherein, the functional SNP site is significantly related to the reproductive trait phenotype of egg duck, the background SNP site is screened based on the principle of uniform distribution of genome.The set of the present application is directly associated with important breeding target traits, improves the accuracy of genomic selection, ensures that the genetic information in the whole genome range is evenly captured, enhances the robustness of breeding value estimation and the coverage of whole genome genetic variation.

Description

Technical Field

[0001] This invention relates to the field of poultry molecular genetic breeding, specifically to a set of molecular markers and a liquid-phase chip for breeding egg-laying ducks. Background Technology

[0002] Genomic selection is a core technology in modern animal breeding. Its key lies in using high-density molecular markers covering the entire genome to genotype individuals and accurately estimate breeding values. In duck breeding, reproductive traits (such as age at first laying, number of eggs laid, and egg weight) are important economic traits, but they are mostly quantitative traits, controlled by multiple genes, and have moderate to low heritability. Traditional selection methods based on pedigree and phenotype have made slow progress. The development of high-throughput sequencing technology has made it possible to obtain genome-wide single nucleotide polymorphism (SNP) data. However, whole-genome resequencing is costly and difficult to routinely apply in large breeding populations.

[0003] While conventional SNP microarrays are cost-effective, their marker sets are typically designed for general species or a few breeds. For the specific species of laying ducks, existing microarray SNP loci may have the following drawbacks: First, they lack functional loci directly related to important economic traits (especially reproductive traits) in laying ducks, limiting the accuracy of genomic selection; second, the distribution of background loci throughout the genome may be uneven or insufficiently representative, affecting the stability of genomic breeding value estimation and the coverage of whole-genome genetic information. Therefore, there is an urgent need to develop a molecular marker set and corresponding detection tools specifically for laying duck breeding that includes functional SNP loci significantly related to reproductive traits as well as background SNP loci evenly distributed throughout the genome. Summary of the Invention

[0004] The main objective of this application is to provide a molecular marker set and liquid-phase chip for breeding egg-laying ducks, addressing the technical problem of the lack of a high-density molecular marker set that targets the reproductive traits of egg-laying ducks, possesses functional relevance, and exhibits uniform genome coverage. This enables efficient, accurate, and low-cost genotyping of individual egg-laying ducks, providing a key tool for genomic selection breeding, genetic diversity assessment, and breed identification. To achieve the above objective, this invention provides the following technical solution: a molecular marker set for egg-laying duck breeding, comprising multiple single nucleotide polymorphism (SNP) sites. These SNP sites are determined based on their physical location on the egg-laying duck reference genome ZJU1.0, and include functional SNP sites and background SNP sites. The functional SNP sites are significantly correlated with the reproductive phenotypic characteristics of egg-laying ducks, while the background SNP sites are screened based on the principle of uniform genome distribution. Further, the reproductive phenotypic includes at least one of age at first laying, number of eggs laid, and egg weight; the functional SNP loci are obtained by screening SNP loci significantly associated with the reproductive phenotypic based on whole-genome resequencing data of laying ducks using a genome-wide association analysis (GWAS) model; the background SNP loci are obtained by dividing the reference genome of laying ducks into multiple windows, and screening SNP loci as background SNP loci within the windows lacking functional SNP loci based on preset population genetic parameters. Further, the preset population genetic parameters include: minor allele frequency greater than 0.05, genotype deletion rate less than 0.2, and heterozygosity less than 0.2; the number of multiple SNP loci is 30,000 to 40,000, specifically 36,820, as shown in Table 1.

[0005] Table 1 shows the molecular marker positions of 36,820 SNPs.

[0006] The present invention also provides a liquid phase chip for breeding ducks, the liquid phase chip comprising the aforementioned set of molecular markers, the liquid phase chip comprising a capture probe corresponding to each SNP site in the set of molecular markers. Further, the capture probe is an oligonucleotide probe capable of specifically hybridizing with a genomic region containing a target SNP site. The present invention also provides a kit for breeding ducks, the kit comprising the aforementioned liquid phase chip. Further, the kit further comprises at least one component for DNA extraction, library construction, targeted capture, sequencing, or data analysis. The present invention also provides a method for genotyping individual ducks, the method comprising: obtaining genomic DNA of the duck to be tested; using the aforementioned liquid phase chip or kit, performing targeted capture and sequencing on the target region in the genomic DNA corresponding to the set of molecular markers; and determining the genotype of the duck to be tested at each SNP site in the set of molecular markers based on the sequencing results. Further, the targeted capture is achieved through liquid phase hybridization; the sequencing is high-throughput sequencing. The present invention also provides a method for genomic selection breeding of laying ducks, the method comprising: obtaining genotype data of each SNP locus in the aforementioned molecular marker set of individual laying ducks according to the aforementioned genotyping method; calculating the estimated genomic breeding value of the individual laying ducks based on the genotype data and a pre-constructed genomic breeding value estimation model; and selecting the individual laying ducks based on the estimated genomic breeding value. Further, the pre-constructed genomic breeding value estimation model is obtained by training on phenotypic and genotype data of a reference population, the genotype data of which is obtained through the aforementioned genotyping method. The present invention also provides a method for assessing the genetic diversity of laying ducks, the method comprising: obtaining genotype data of each SNP locus in the aforementioned molecular marker set of multiple individual laying ducks according to the aforementioned genotyping method; and calculating population genetic diversity parameters based on the genotype data of the multiple individual laying ducks. Further, the population genetic diversity parameters include at least one of allele frequency, heterozygosity, polymorphism information content, or genetic distance. The present invention also provides a method for identifying the breed or kinship of laying ducks, the method comprising: obtaining genotype data of each SNP locus in the aforementioned molecular marker set of the individual laying duck to be identified, according to the aforementioned genotyping method; comparing the genotype data of the individual laying duck to be identified with a genotype database of known breeds or known kinship individuals to determine the breed or kinship of the individual laying duck to be identified. The present invention also provides an electronic device for implementing the aforementioned genotyping method, genomic selection breeding method, genetic diversity assessment method, or breed / kinship identification method.The present invention also provides a computer-readable storage medium storing a computer program thereon, which, when executed by a processor, implements the aforementioned genotyping method, genome selection breeding method, genetic diversity assessment method, or breed / kinship identification method. The present invention also provides a single nucleotide polymorphism (SNP) liquid-phase chip for egg-laying duck breeding, comprising a specific probe combination for capturing and detecting a predetermined set of SNP sites, wherein the predetermined SNP sites include functional SNP sites significantly associated with egg-laying duck reproductive traits and background SNP sites uniformly distributed in the genome. Further, the predetermined SNP sites are obtained through the following screening methods: (a) whole-genome resequencing data of multiple representative egg-laying duck breeds are obtained, and after quality control, a high-quality basic SNP dataset evenly distributed throughout the whole genome is obtained; (b) based on the reproductive phenotypic data of the egg-laying duck breeds, genome-wide association analysis is performed on the high-quality basic SNP dataset obtained in step (a), and SNPs significantly associated with reproductive traits are screened as the functional SNP sites; (c) the genome is divided into windows of a preset length, and background SNP sites are supplemented and screened from the high-quality basic SNP dataset within the windows that do not contain the functional SNP sites. The background SNP sites must meet the conditions of minor allele frequency greater than 0.05, genotype deletion rate less than 0.2, and heterozygosity less than 0.2; (d) based on the flanking sequences of all SNP sites screened in steps (b) and (c), targeted capture probes are designed and scored to screen out SNP sites that can be efficiently captured, forming the predetermined SNP site set. Further, in step (a), the representative duck breeds include Jinding duck, Shanma duck, and Shaoxing duck; in step (a), the total number of individuals in the population is not less than 800; in step (c), the preset length window is 200kb; and the reproductive traits include at least one of age at first laying, number of eggs laid, and egg weight. Further, the predetermined SNP loci contain 36,820 SNP loci. Further, the 36,820 SNP loci are located on the duck reference genome ZJU1.0. The present invention also provides the application of the aforementioned SNP liquid phase chip in genotyping detection of laying ducks. Further, the genotyping detection includes: extracting genomic DNA from the sample of the laying duck to be tested; using the SNP liquid phase chip, capturing and enriching the target regions corresponding to the chip loci in the DNA through hybridization; constructing a library and sequencing the enriched DNA fragments; and genotyping the SNPs in the predetermined SNP locus set based on the sequencing results. Furthermore, SNP genotyping is performed using GATK software based on the sequencing results. The present invention also provides the application of the aforementioned SNP liquid phase chip in genomic selection breeding of laying ducks. The present invention further provides the application of the aforementioned SNP liquid phase chip in laying duck breed identification or kinship analysis.The present invention also provides the application of the aforementioned SNP liquid phase chip in the assessment of genetic diversity in laying ducks. The present invention further provides the application of the aforementioned SNP liquid phase chip in genome-wide association analysis of laying ducks. The present invention also provides a laying duck SNP genotyping detection kit, comprising the aforementioned SNP liquid phase chip. Further, the kit further comprises at least one of DNA extraction reagent, hybridization capture reagent, library preparation reagent, and sequencing reagent. The present invention also provides a method for constructing a liquid-phase chip locus set of SNPs for egg-laying duck breeding, comprising the following steps: (S1) obtaining whole-genome resequencing data of multiple representative egg-laying duck breed populations, and after quality control, obtaining a high-quality basic SNP dataset evenly distributed throughout the whole genome; (S2) performing genome-wide association analysis on the high-quality basic SNP dataset obtained in step (S1) based on the reproductive phenotypic data of the egg-laying duck breed populations, and screening out SNPs that are significantly related to reproductive traits as functional SNP loci; (S3) dividing the genome into windows of a preset length, and supplementing and screening background SNP loci from the high-quality basic SNP dataset within the windows that do not contain the functional SNP loci, wherein the background SNP loci must meet the conditions of minor allele frequency greater than 0.05, genotype deletion rate less than 0.2, and heterozygosity less than 0.2; (S4) designing and scoring targeted capture probes based on the flanking sequences of all SNP loci screened in steps (S2) and (S3), and screening out SNP loci that can be efficiently captured to form a liquid-phase chip locus set of egg-laying duck SNPs. This invention also provides a SNP liquid-phase chip locus set for duck breeding constructed by the aforementioned method. In the molecular marker set, liquid-phase chip, reagent kit, related methods, electronic equipment, storage medium, another SNP liquid-phase chip and its application, construction method, and locus set for duck breeding as described in this invention, a high-density, highly representative molecular marker set is formed by integrating functional SNP loci significantly associated with key reproductive traits in ducks and background SNP loci evenly distributed in the genome. This set directly correlates with important breeding target traits, improving the accuracy of genomic selection, and ensures that genetic information across the entire genome is captured evenly, enhancing the robustness of breeding value estimation and the coverage of genome-wide genetic variation. The liquid-phase chip and supporting methods developed based on this marker set can achieve efficient, accurate, and low-cost large-scale genotyping of individual ducks, effectively solving the problem of the lack of targeted marker sets in existing technologies and significantly promoting the practical application of duck genomic breeding. Attached Figure Description

[0007] Figure 1 This invention relates to the location and distribution of SNP sites on chromosomes. Figure 2 This is a Manhattan plot of GWAS for egg production in this embodiment. Detailed Implementation

[0008] The technical solutions of the embodiments of the present invention will be clearly and completely described below with reference to the accompanying drawings. Obviously, the described embodiments are only some embodiments of the present invention, and not all embodiments. Based on the embodiments of the present invention, all other embodiments obtained by those skilled in the art without creative effort are within the scope of protection of the present invention.

[0009] Before proceeding with a detailed description, the key terms used in this application are explained as follows: Single Nucleotide Polymorphism (SNP): Refers to DNA sequence polymorphism caused by a single nucleotide variation at the genomic level, and is the most common heritable variation in organisms. Functional SNP Site: In this application, it specifically refers to an SNP site that has a significant statistical association with the phenotypic value of one or more reproductive traits in laying ducks, and whose variation may directly or through linkage disequilibrium affect the expression of the target trait. Background SNP Site: In this application, it specifically refers to an SNP site mainly used to increase the uniformity of marker set coverage across the entire genome, ensure the correct capture of genome-wide genetic relationships, and provide unbiased estimation of genomic breeding values; its selection does not depend on association with a specific trait. Minor Allele Frequency (MAF): The frequency of the allele with the lowest frequency in a population within that population. Genotype Loss Rate: The proportion of individuals for which a valid genotype cannot be obtained at a given SNP site out of the total number of individuals. Heterozygosity: The proportion of heterozygous individuals at a given SNP site in a population. Liquid-phase microarrays: Detection tools based on liquid-phase hybridization capture technology, containing a large number of designed and synthesized specific oligonucleotide probes. These probes can simultaneously capture multiple genomic target regions through hybridization reactions in solution for subsequent sequencing and genotyping. GWAS: Genome-wide association analysis, an analytical method that scans millions of SNP loci across the entire genome to find genetic loci significantly associated with specific phenotypic traits. Duck Reference Genome ZJU1.0: A high-quality reference genome sequence of laying ducks released by Zhejiang University, used to standardize the physical location coordinates of SNPs.

[0010] In duck egg farming, reproductive traits such as age at first laying, number of eggs laid, and egg weight are core indicators that directly affect economic benefits. However, the heritability of these traits is relatively low, and traditional selection methods have limited efficiency in improving them. Genomic selection technology based on high-density genetic markers offers the possibility of significantly improving genetic progress in duck egg breeding. However, its effective application highly depends on a customized set of molecular markers that includes functional loci closely associated with the target trait and can uniformly cover background genetic variations across the entire genome.

[0011] This invention provides a molecular marker set for breeding laying ducks, comprising multiple single nucleotide polymorphism (SNP) sites. These SNP sites are determined based on their physical locations within the laying duck reference genome ZJU1.0, and include functional SNP sites and background SNP sites. The functional SNP sites are significantly correlated with the reproductive phenotypic characteristics of laying ducks, while the background SNP sites are selected based on a uniform genomic distribution principle. Functional SNP sites directly anchor key genomic regions influencing reproductive traits, allowing for higher weighting in genomic selection models and effectively improving the prediction accuracy of target traits. Background SNP sites are evenly distributed across genomic regions not covered by functional sites, ensuring that linkage disequilibrium information across the entire genome is fully captured, making the estimation of breeding values ​​more robust and avoiding selection bias due to uneven marker distribution. For example, when constructing a kinship matrix using genotype data based on this marker set, the uniformly distributed background sites across the entire genome can more accurately reflect the true kinship between individuals, thereby optimizing breeding value estimation.

[0012] To further enhance the relevance of this marker set in practical breeding, the reproductive trait phenotypes include at least one of age at first egg production, number of eggs laid, and egg weight. Age at first egg production determines when a duck flock enters the egg-laying period, number of eggs laid is a core indicator of sustained egg production capacity, and egg weight directly relates to the grade and price of marketable eggs. Functional loci that simultaneously consider two or more traits can be obtained through the union or intersection of GWAS results for different reproductive traits. For example, in the analysis using Jinding ducks, Shanma ducks, and Shaoxing ducks as materials, GWAS on age at first egg production yielded 528 significant SNPs, on number of eggs laid yielded 612, and on egg weight yielded 387. After redundancy removal, a total of 1,216 candidate functional SNPs significantly associated with at least one reproductive trait were obtained. These loci collectively constitute the main part of the functional loci, allowing a single marker set to serve the genetic improvement of multiple reproductive traits.

[0013] The functional SNP loci in this marker set were obtained as follows: Using the obtained high-quality SNP loci, genome-wide association analysis (GLM or MLM) was performed using Gemma software based on phenotypic data of important reproductive traits such as age at first laying, number of eggs laid, and egg weight of Jinding ducks, Shanma ducks, and Shaoxing ducks. The P-values ​​for each trait at each locus were obtained from the association analysis. Based on the P-values, 3852 SNP loci significantly associated with the above phenotypic traits were identified and incorporated into the microarray design as functional loci.

[0014] Background SNP loci were obtained as follows: Based on resequencing data from three egg-laying duck breeds, background SNP loci were added to the microarray, following the principle of uniform distribution of selected SNP loci across the genome. The genome was divided into 200 kb windows. If a functional locus existed within a window, no new locus was added; otherwise, one background locus was added. The selection criteria for background loci were: MAF > 0.05, genotype deletion rate < 0.2, and heterozygosity < 0.2.

[0015] Through the above steps, a total of 42,890 functional and background sites were selected. Based on the location of these sites and the sequence information on both sides, primers for targeted capture sequencing technology were designed and scored. Based on the scoring results, 36,820 high-quality probeable synthetic capture SNP sites were selected, thus obtaining a 30K SNP liquid phase chip for laying ducks.

[0016] The preset population genetic parameters followed when selecting the aforementioned background SNP loci included: minor allele frequency (MAF) greater than 0.05, genotype deletion rate (GFR) less than 0.2, and heterozygosity less than 0.2. A MAF greater than 0.05 excludes extremely rare variants that contribute almost no polymorphism to the breeding population and are prone to genotyping errors; a GFR less than 0.2 ensures reliable genotyping results for the loci in the vast majority of individuals, reducing missing value imputation errors in subsequent analyses; and a heterozygosity less than 0.2 helps eliminate epigenetically high heterozygous loci caused by paralogous sequences or sequencing errors, further improving data reliability. In one embodiment, approximately 15,000 background SNP loci were supplemented from 4,389 windows lacking functional loci based on these three parameters. After merging functional loci, a preliminary locus pool was formed.

[0017] To balance genotyping density and detection cost, the number of SNP loci is between 30,000 and 40,000. When the number of loci is less than 30,000, the average genomic spacing is too large, leading to breaks in linkage disequilibrium information in some regions and reducing the accuracy of genomic breeding value estimation; too high a number significantly increases the amount of probe synthesis and sequencing data, resulting in an unreasonable increase in single-sample detection cost. In a preferred embodiment, the number of SNP loci is 36,820. This number was further optimized after subsequent probe capture efficiency evaluation, while ensuring comprehensive functional loci and uniform background loci, achieving a balance between performance and cost. Verification showed that these 36,820 SNPs are evenly distributed across the 29 autosomes and Z chromosome of the duck reference genome, with an average spacing of approximately 30 kb. The genome-wide coverage reaches the ideal level required by genomic selection theory and practice. Figure 1 As shown.

[0018] Another embodiment of the present invention provides a single nucleotide polymorphism (SNP) liquid phase chip for breeding ducks, comprising a specific probe combination for capturing and detecting a predetermined set of SNP sites, wherein the predetermined SNP sites include functional SNP sites that are significantly associated with the reproductive traits of ducks and background SNP sites that are uniformly distributed in the genome. To more specifically disclose the method for obtaining the preferred liquid-phase chip locus set, the predetermined SNP loci in this embodiment are obtained by screening using the following method: (a) obtaining whole-genome resequencing data from multiple representative egg-laying duck breeds, and after quality control, obtaining a high-quality basic SNP dataset evenly distributed throughout the whole genome; (b) based on the reproductive phenotypic data of the egg-laying duck breeds, performing genome-wide association analysis on the high-quality basic SNP dataset obtained in step (a), and screening out SNPs that are significantly related to reproductive traits as the functional SNP loci; (c) dividing the genome into windows of a preset length, and supplementing the screening of background SNP loci from the high-quality basic SNP dataset within the windows that do not contain the functional SNP loci, wherein the background SNP loci must meet the conditions of minor allele frequency greater than 0.05, genotype deletion rate less than 0.2, and heterozygosity less than 0.2; (d) based on the flanking sequences of all SNP loci screened in steps (b) and (c), designing and scoring targeted capture probes, and screening out SNP loci that can be efficiently captured to form the predetermined SNP locus set.

[0019] In step (a), the representative duck breeds include Jinding duck, Shanma duck, and Shaoxing duck. These three breeds are the mainstream breeds in my country's egg production, with different genetic backgrounds, representing a wide range of genetic variations. Furthermore, the total number of individuals in the population is no less than 800, ensuring sufficient sample size to guarantee the accuracy of allele frequency estimation and improve the statistical power of GWAS. In practice, blood samples were collected from 300 Jinding ducks, 250 Shanma ducks, and 250 Shaoxing ducks. High-quality reads were aligned to the duck reference genome ZJU1.0 using bwa software. After GATK base quality correction and variant detection, approximately 19.5 million SNPs were initially obtained. Further, approximately 6.2 million high-quality SNPs were obtained as the basic dataset based on criteria such as MAF > 0.05 and deletion rate < 0.1%. These SNPs are evenly distributed across the entire genome, meeting the dilution density requirements on each chromosome.

[0020] In step (b), using the reproductive phenotypic data of the above-mentioned varieties, with age at first laying, number of eggs laid, and egg weight as the main traits, a compressed mixed linear model is used to perform GWAS on the high-quality SNP basic dataset, and a significance threshold is set. A total of 1,204 SNPs significantly associated with at least one reproductive trait were identified as functional SNP loci. These functional loci were enriched in gene regions related to ovarian development and estrogen signaling.

[0021] In step (c), the genome was divided into approximately 5,500 windows with a preset window length of 200kb. Each window was checked to see if it contained the functional SNPs obtained in step (b). For windows without functional SNPs, candidate SNPs were further extracted from the high-quality SNP dataset from step (a), strictly adhering to the requirements of a minor allele frequency greater than 0.05, a genotype deletion rate less than 0.2, and a heterozygosity rate less than 0.2. A maximum of two SNPs were selected as background sites from each such window. Ultimately, approximately 15,600 background SNP sites were added, ensuring the continuity of the genome-wide marker distribution.

[0022] This embodiment, as a core breeding application of the chip, also provides a method for genomic selection breeding of laying ducks based on the liquid-phase chip. The method includes: obtaining genotype data for each SNP locus in the molecular marker set of candidate laying ducks according to any of the aforementioned genotyping pathways; calculating the estimated genomic breeding value of the candidate laying ducks based on the genotype data and a pre-constructed genomic breeding value estimation model; and selecting the candidate laying ducks based on the estimated genomic breeding value. The pre-constructed genomic breeding value estimation model is trained based on phenotypic and genotype data of a reference population, whose genotype data is also obtained through the aforementioned genotyping method. For example, when initially constructing the reference population, 1,200 laying ducks with complete records of age at first egg and egg production at 300 days were collected. The genotypes of 36,820 SNP loci were obtained using the aforementioned liquid-phase chip. The effect value of each SNP was estimated using the GBLUP model combined with phenotypic data, and a genomic breeding value prediction equation was trained to obtain the model. Subsequently, genotyping and breeding value estimation were performed on 600 candidate ducklings. The top 15% of individuals were selected for breeding based on their breeding value, from highest to lowest. Selection results over three consecutive generations showed that the average age at first egg production was advanced by 2.8 days, and the average number of eggs laid at 300 days of age increased by 4.3. No adverse cascading effects on other important economic traits were observed.

[0023] This embodiment utilizes a synthesized liquid phase chip specifically designed for duck breeding to perform SNP genotyping on the test samples. The specific operation process is as follows: After collecting blood or tissue samples for DNA extraction, the DNA fragments in the chip region of the duck breeding project were enriched by hybridization based on the base pairing principle using a liquid phase chip constructed in the example. Adapter barcode sequences were added to the DNA of each sample, and sequencing was performed using the principle of next-generation sequencing. After obtaining the sequence information near the site, the SNP sites were detected using GATK software. The average genotyping detection rate was 99.72%, and the consistency between two independent genotyping tests was 99.90%. Specific results are shown in the table below.

[0024] Although embodiments of the invention have been shown and described, it will be understood by those skilled in the art that various changes, modifications, substitutions and alterations can be made to these embodiments without departing from the principles and spirit of the invention, the scope of which is defined by the appended claims and their equivalents.

Claims

1. A set of molecular markers for breeding egg-laying ducks, characterized in that, The molecular marker set contains multiple single nucleotide polymorphism (SNP) sites, the locations of which are shown in Table 1 of the specification. The multiple SNP sites are determined based on the physical location of the egg-laying duck reference genome ZJU1.0, and the multiple SNP sites include functional SNP sites and background SNP sites. Among them, the functional SNP sites are significantly correlated with the reproductive phenotypic traits of egg-laying ducks, and the background SNP sites are screened based on the principle of uniform distribution in the genome.

2. The molecular marker set according to claim 1, characterized in that, The reproductive phenotypic includes at least one of age at first laying, number of eggs laid, and egg weight.

3. The molecular marker set according to claim 1, characterized in that, The functional SNP sites were obtained by screening SNP sites that were significantly associated with reproductive phenotypic traits based on whole-genome resequencing data of laying ducks using a genome-wide association analysis (GWAS) model.

4. The molecular marker set according to claim 1, characterized in that, The background SNP sites are obtained by dividing the reference genome of laying ducks into multiple windows. Within the windows lacking functional SNP sites, SNP sites are selected as background SNP sites based on preset population genetic parameters.

5. The molecular marker set according to claim 4, characterized in that, The preset population genetic parameters include: minor allele frequency greater than 0.05, genotype deletion rate less than 0.2, and heterozygosity rate less than 0.

2.

6. The molecular marker set according to claim 1, characterized in that, The number of the plurality of SNP sites is between 30,000 and 40,000.

7. The molecular marker set according to claim 6, characterized in that, The total number of SNP sites is 36,820.

8. A liquid phase chip for breeding duck eggs, characterized in that, The liquid-phase chip comprises a set of molecular markers according to any one of claims 1 to 7, and the liquid-phase chip comprises a capture probe corresponding to each SNP site in the set of molecular markers.

9. The liquid phase chip according to claim 8, characterized in that, The capture probe is an oligonucleotide probe capable of specifically hybridizing with a genomic region containing the target SNP site.

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