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CN-121992109-A - 20K liquid phase chip for simultaneous accurate identification of various goose varieties and application

CN121992109ACN 121992109 ACN121992109 ACN 121992109ACN-121992109-A

Abstract

The invention provides a 20K liquid phase chip for simultaneously and accurately identifying various goose varieties and application thereof, wherein the 20K liquid phase chip covers 22005 SNP molecular markers, the SNP molecular markers specifically comprise 4991 goose variety genetic differentiation specific sites with a genetic differentiation index FST >0.5 between control varieties, 12 important character association sites and 17002 whole genome background sites, and the specific positions of the 22005 SNP molecular marker sites are shown in an instruction table 1. The invention can realize accurate discrimination of 16 goose varieties, has high identification efficiency, can finish the detection process within 24 hours, can detect 48-96 samples once, has the technical repetition rate of more than 99 percent, has the cost far lower than that of a high-density chip, is suitable for carrying out multi-variety and large-scale germplasm monitoring and identification work in a seed holding field, a scientific research unit and the like, and has strong practicability.

Inventors

  • HUANG ZENGWEN
  • WANG SILU
  • WANG JING
  • YANG CHAOYUN
  • LI DONGDONG
  • YAN GUANGWEN
  • LI JUN
  • HU ZHIQIANG
  • CHEN YIQUN
  • ZHAO JINGANG

Assignees

  • 西昌学院

Dates

Publication Date
20260508
Application Date
20260209

Claims (10)

  1. 1. The 20K SNP molecular marker combination for simultaneously and accurately identifying various goose varieties is characterized by comprising 22005 SNP molecular markers, specifically comprising 4991 goose variety genetic differentiation specific sites with a genetic differentiation index FST of more than 0.5 between control varieties, 12 important character association sites and 17002 whole genome background sites, wherein the specific positions of the 22005 SNP molecular marker sites are shown in table 1 of the specification.
  2. 2. The 20K SNP molecular marker combination according to claim 1, wherein the various goose varieties comprise local geese and introduced geese, and specifically comprise steel geese, fengcheng gray geese, yunnan geese, yili geese, sichuan white geese, taihu geese, guangfeng white feather geese, lande geese, zheDong white geese, lion head geese, seed geese, roman geese, lotus white geese, hu county white geese, hodoba geese and Ma Gang geese.
  3. 3. Use of a 20K SNP molecular marker combination as set forth in claim 1 or 2 and/or a probe for detecting a 20K SNP molecular marker combination as set forth in claim 1 or 2 for preparing a 20K SNP liquid chip.
  4. 4. The use according to claim 3, wherein the probe is a nucleotide sequence designed and synthesized by the molecular marker combination according to claim 1 or 2, is a single-stranded DNA oligonucleotide, has a probe length of 110bp, has a GC content of 40% -60%, and has a number of homology regions of 5 or less and biotin modification groups at the 5' ends.
  5. 5. A 20K SNP liquid chip for simultaneous and precise identification of a plurality of goose varieties, comprising the 20K SNP molecular marker combination according to claim 1 or 2 and/or a probe for detecting the 20K SNP molecular marker combination according to claim 1 or 2.
  6. 6. A kit comprising the 20K SNP liquid-phase chip of claim 5.
  7. 7. The method for preparing the 20K SNP liquid-phase chip according to claim 5, comprising the following steps: Step 1, screening and integrating genetic differentiation specific sites, whole genome background sites and important character associated sites among varieties according to whole genome sequencing data of various goose variety samples to obtain a 20K SNP molecular marker combination; and 2, designing a probe according to the obtained 20K SNP molecular marker combination.
  8. 8. Use of the 20K SNP liquid chip of claim 5 or the kit of claim 6 in goose germplasm resource identification and/or efficient breeding.
  9. 9. Use of the 20K SNP liquid chip of claim 5 or the kit of claim 6 in goose genetic diversity assessment and/or genetic map construction.
  10. 10. Use of the 20K SNP liquid chip of claim 5 or the kit of claim 6 in goose group structural analysis and/or genetic relationship identification.

Description

20K liquid phase chip for simultaneous accurate identification of various goose varieties and application Technical Field The invention relates to the technical field of gene chips, in particular to a 20K liquid phase chip for simultaneously and accurately identifying various goose varieties and application thereof, which are suitable for the accurate identification of germplasm resources, genetic diversity assessment, group structure analysis, genetic relationship identification, efficient breeding and the like of the various goose varieties, and provide a core technical tool for the protection and scientific utilization of the goose genetic resources. Background The Chinese geese have rich genetic resources and various local varieties including Sichuan white geese, steel geese, taihu geese, lion head geese, ma Gange and the like, and the varieties have unique excellent characters of delicious meat quality, cold resistance, disease resistance, strong adaptability and the like, thus being an important support for the vibration of the rural industry. However, the genetic resources of local geese in China are seriously damaged, especially part of rare varieties, due to the influence of factors such as impact introduced by foreign commercial mating lines (such as Landes geese, romans and Hodobby geese) and unscheduled hybridization. Taking Sichuan local varieties as an example, the third national general investigation of livestock and poultry genetic resources shows that the stock quantity of the existing steel geese is only 2442, and is reduced by 95% compared with 4.9 ten thousand of the steel geese in 2005, and the population is in an extremely endangered state. Meanwhile, unordered hybridization between local varieties and introduced varieties causes genetic background hybridization, and precise identification and protection are urgent. The accurate identification of varieties is a core precondition for genetic resource protection and reasonable utilization, but the prior art is difficult to meet the requirement of simultaneous and specific identification of various goose varieties: 1. The traditional identification method (morphology, cytology and biochemical markers) depends on phenotype characteristics or low-density markers, is easily influenced by subjective experience and environmental factors, has high misjudgment rate, and cannot accurately distinguish genetic differences of local varieties, introduced varieties and filial generations thereof; 2. The general molecular marker technology (SSR, conventional SNP) has insufficient marker density and sparse distribution, lacks specific sites for genetic differentiation between local varieties and introduced varieties in China, and is difficult to realize precise identification and germplasm characteristic identification of multiple varieties; 3. the existing high-density chip (Illumina 60K, beijing core No. one 55K) is high in cost, is mainly designed based on foreign commercial varieties, is not optimized for local varieties of goose genome characteristics in China, and is not suitable for large-scale resource identification and protection of multiple varieties; 4. the lack of special identification tools capable of distinguishing local varieties and introduced varieties simultaneously cannot systematically excavate special gene resources of different varieties, and is difficult to support genetic diversity assessment, variety purity detection, group structure analysis and directional breeding. Under the background, developing a low-density, high-precision and low-cost liquid phase chip capable of accurately identifying various goose varieties (covering local varieties and introduced varieties) simultaneously becomes a key technical requirement for solving the problem of germplasm resource identification and realizing the rescuing protection and efficient breeding of rare genetic resources. Disclosure of Invention The invention provides a 20K liquid phase chip for simultaneously and accurately identifying various goose varieties and application thereof, and aims to solve the technical pain point that the prior art is difficult to realize simultaneous and accurate identification of various goose varieties covering places and introduction and lack of efficient tools for genetic resource protection. In order to achieve the above purpose, the core technical scheme of the invention is as follows: in a first aspect, the invention provides a 20K SNP molecular marker combination for simultaneously and accurately identifying a plurality of goose varieties, wherein the SNP molecular marker combination consists of 22005 SNP molecular markers, and particularly consists of 4991 goose variety-to-goose variety genetic differentiation specific sites with a genetic differentiation index FST of more than 0.5 between control varieties, 12 important character association sites and 17002 genome-wide background sites, and the specific positions of the 22005 SNP molecular mar