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CN-122012752-A - Application of duck molecular marker combination, duck 40K liquid phase chip, method and application

CN122012752ACN 122012752 ACN122012752 ACN 122012752ACN-122012752-A

Abstract

The invention relates to the technical field of molecular detection, and particularly discloses application of a duck molecular marker combination, a duck 40K liquid phase chip, a method and application, wherein the application comprises duck genotyping, duck variety identification, duck genetic relationship judgment or duck economic character prediction, the molecular marker comprises 43229 SNP loci, physical positions of 43229 SNP loci are determined based on whole genome sequence comparison of a duck reference genome ZJU1.0, and 43229 SNP loci are shown in table 1. The invention not only can be used for genotyping ducks, identifying duck varieties, judging the genetic relationship of ducks, predicting economic traits of ducks and selectively breeding duck genomes, but also can solve the problems of insufficient total quantity of loci of the low-density SNP chip of the existing laying ducks and cross-variety polymorphism attenuation.

Inventors

  • ZENG TAO
  • LI RONGYANG
  • LI QINGYI
  • YU HUI
  • SU JIAYI
  • QU YUANQI
  • LU LIZHI
  • GU TIANTIAN
  • TIAN YONG
  • CAI CHAOXIA
  • CHEN LI
  • XU WENWU
  • REN JINDONG
  • ZHOU WEI

Assignees

  • 浙江省农业科学院

Dates

Publication Date
20260512
Application Date
20260414

Claims (10)

  1. 1. The application of the duck molecular marker combination is characterized by comprising the steps of duck genotyping, duck variety identification, duck genetic relationship judgment, duck economic character prediction or duck genome selective breeding, wherein the molecular marker comprises 43229 SNP loci, the physical positions of 43229 SNP loci are determined based on whole genome sequence comparison of a duck reference genome ZJU1.0, and 43229 SNP loci are shown in table 1; TABLE 1
  2. 2. The use of a combination of duck molecular markers as claimed in claim 1 in a genetic breeding chip, wherein the genetic breeding chip comprises a liquid phase chip.
  3. 3. A duck 40K liquid phase chip, wherein genotyping of said duck 40K liquid phase chip comprises 43229 SNP sites as set forth in claim 1.
  4. 4. The duck 40K liquid phase chip of claim 3, wherein the duck 40K liquid phase chip comprises a probe combination designed to cover the gene sequences of 43229 SNP sites.
  5. 5. The duck 40K liquid phase chip according to claim 4, wherein the GC content ratio of the probe combination is 30-70%, the probe length is 110bp, the number of homologous regions is less than or equal to 5, and SSR and GAP regions are avoided.
  6. 6. The method for designing a duck 40K liquid chip as claimed in any one of claims 3 to 5, comprising the steps of: S1, sample collection, namely obtaining DNA samples of 17 varieties of ducks, wherein the 17 varieties of ducks comprise Shaoxing ducks, cherry valley ducks, pedal lake ducks, brown Lai ducks, jinding ducks, jinyun sheldrake, green head wild ducks, beijing ducks, gao-mail ducks, jian red-feather ducks, lian cheng white ducks, longsheng green ducks, mawang ducks, pu-field black ducks, sansui ducks, mountain sheldrake and Shan county sheldrake; S2, obtaining candidate SNP loci, namely carrying out whole genome re-sequencing on a duck DNA sample to obtain original SNP loci, sequentially carrying out preliminary filtration on the original SNP loci, and carrying out duck reference genome comparison screening to obtain candidate SNP loci; S3, obtaining functional sites, namely obtaining the functional sites based on whole genome association analysis from candidate SNP sites and consulting literature; S4, obtaining background sites, namely selecting uniformly distributed background sites from candidate SNP sites which are compared with the duck genome in the step S2 through quality control filtering; S5, core sites are obtained, namely core sites are selected from candidate SNP sites which are compared with duck exam genome in the step S2, wherein the selection principle is that the probe design is successful and MAF is more than or equal to 0.35; And S6, designing the probes, namely, designing the probes based on all the sites obtained in the steps S3-S5, removing sites which cannot be successfully synthesized into the probes, sites with poor capture stability and corresponding probes, and remaining 43229 SNP sites and corresponding probes.
  7. 7. Use of a duck 40K liquid phase chip as claimed in any one of claims 3-5 in duck genotyping.
  8. 8. Use of the duck 40K liquid phase chip of any one of claims 3-5 in duck species identification, duck genetic relationship determination, duck economic trait prediction, or duck genome selective breeding.
  9. 9. A kit comprising a duck 40K liquid chip as claimed in any one of claims 3-5, or a probe combination for detecting 43229 SNP sites.
  10. 10. The use of a kit according to claim 9, wherein the use comprises duck genotyping, duck breed identification, duck genetic relationship determination, duck economic trait prediction or duck genome selective breeding.

Description

Application of duck molecular marker combination, duck 40K liquid phase chip, method and application Technical Field The invention relates to the technical field of molecular detection, in particular to application of a duck molecular marker combination, a duck 40K liquid phase chip, a method and application. Background Ducks are important waterfowl in China, the annual slaughtering amount is more than 40 hundred million, and meat and egg products of the ducks occupy important positions in dietary structures. Molecular marker technology (Molecular Marker Technology) is an important tool in molecular breeding. First generation Restriction Fragment Length Polymorphism (RFLP) and second generation Simple Sequence Repeat (SSR) play an important role in early genetic research, but due to sparse genome distribution, complicated experimental procedures and low flux, the requirements of current large-scale commercial breeding on high-density, low-cost and automatic detection are difficult to meet. Single Nucleotide Polymorphisms (SNPs) are widely used in livestock and poultry genome breeding as third generation molecular markers due to high density and accurate typing. Third generation molecular markers have become the dominant tools for animal population identification, genetic structure analysis, functional gene mapping, whole genome association analysis (GWAS), and Genome Selection (GS). With the popularization of high throughput sequencing technology, SNP typing methods based on whole genome re-sequencing or simplified genome sequencing are becoming a research hotspot. However, for breeding enterprises or seed farms lacking high deep resequencing costs, a need exists for a medium-low density dedicated chip that combines marker density, typing cost, data accuracy and operational flexibility. At present, duck SNP detection mainly depends on a solid-phase chip (such as an Illumina 60K duck chip), and has the following defects: ① The high site density results in high parting cost, ② is based on foreign commercial variety design, polymorphism in Chinese local duck variety is insufficient, ③ solid phase process can not flexibly increase and decrease sites as required, ④ lacks special medium-low density chip for slaughter, propagation, appearance and other economic characters. In addition, the patent with publication number CN118086527B discloses a '20K low-density SNP chip of laying ducks based on targeted capture sequencing', the total number of sites is 20000, the average distance is about 200kb, and no meat trait markers such as slaughter or feed conversion are involved. The chip is designed only for 5 local varieties of laying ducks, the polymorphism in meat ducks including green head wild ducks, beijing ducks, gaoyou ducks and the like and local special duck species groups is obviously reduced, and the cross-variety universality is limited. Disclosure of Invention The invention aims to provide application of a duck molecular marker combination, a duck 40K liquid phase chip, a method and application, which not only can be used for duck genotyping, duck variety identification, duck genetic relationship judgment, duck economic character prediction and duck genome selective breeding, but also can solve the problems of insufficient total quantity of loci and cross-variety polymorphism attenuation of the existing 20K low-density SNP chip of a laying duck. The invention is realized by the following technical scheme: The application of the duck molecular marker combination comprises the steps of duck genotyping, duck variety identification, duck genetic relationship judgment or duck economic character prediction, wherein the molecular marker comprises 43229 SNP loci, the physical positions of 43229 SNP loci are determined based on whole genome sequence alignment of a duck reference genome ZJU1.0, and 43229 SNP loci are shown in table 1; TABLE 1 The 43229 SNP loci are obtained based on 17 local duck varieties through resequencing, the sample sources are wider and more comprehensive than the sources of the existing 20K low-density SNP chips of the ducks, and the problems of insufficient total loci and cross-variety polymorphism attenuation of the existing 20K low-density SNP chips of the ducks can be solved. The detection rate of the liquid phase chip prepared based on 43229 SNP loci to 43229 SNP loci is more than 99.7%, the number of SNP loci is relatively large, the application of duck genotyping, duck variety identification, duck genetic relationship judgment or duck economic character prediction can be well realized, in the application of duck variety identification, the identified varieties are more than 20K low-density SNP chips, the accuracy of duck economic character prediction is good, and the selective breeding of duck genome can be realized based on duck economic character prediction. The application of the duck molecular marker combination in a genetic breeding chip comprises a liquid phase chip. A duck 40K li