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CN-121975956-A - Sex-related SNP molecular marker of jewfish, detection reagent and application thereof

CN121975956ACN 121975956 ACN121975956 ACN 121975956ACN-121975956-A

Abstract

The invention relates to a sex-related SNP molecular marker of jewfish, and a detection reagent and application thereof, belonging to the technical field of fish molecular breeding. The invention provides a reagent for detecting SNP loci in a jewfish genome, which is used for detecting genotypes of SNP locus 1, SNP locus 2 and SNP locus 3, wherein the SNP locus 1 is positioned at 4806373 bp of a jewfish genome No. 4 chromosome, the SNP locus 2 is positioned at 16421908 bp of a jewfish genome No. 5 chromosome, and the SNP locus 3 is positioned at 7808123 bp of a jewfish genome No. 18 chromosome. The invention screens a group of SNP molecular markers related to the sex of the jewfish, is used for molecular marker-assisted sex identification and early breeding of the jewfish, and provides technical tools and reference basis for realizing rapid screening and cultivation of the parthenogenetic jewfish population with better growth characters.

Inventors

  • CHENG JIE
  • WANG FENGCHI
  • YANG QI
  • ZHANG QINGKE

Assignees

  • 中国海洋大学三亚海洋研究院

Dates

Publication Date
20260505
Application Date
20260409

Claims (10)

  1. 1. A reagent for detecting SNP sites in the genome of jewfish, characterized in that the SNP sites comprise SNP1, SNP2 and SNP3, the reagent being used to detect genotypes of SNP1, SNP2 and SNP 3; The SNP1 is positioned at 4806373 bp of the genome 4 of the jewfish, the SNP2 is positioned at 16421908 bp of the genome 5 of the jewfish, the SNP3 is positioned at 7808123 bp of the genome 18 of the jewfish, and the GenBank accession number of the genome of the jewfish is GCA_031216445.1.
  2. 2. The reagent of claim 1, wherein the reagent comprises a primer set; The nucleotide sequences of the primer group for detecting SNP1 are shown as SEQ ID NO.1 and SEQ ID NO. 2; the nucleotide sequences of the primer group for detecting SNP2 are shown as SEQ ID NO.3 and SEQ ID NO. 4; The nucleotide sequences of the primer group for detecting SNP3 are shown as SEQ ID NO.5 and SEQ ID NO. 6.
  3. 3. Use of the agent of claim 1 or 2 for identifying the sex of jewfish.
  4. 4. Use of the reagent according to claim 1 or 2 for the preparation of a kit for identifying the sex of jewfish.
  5. 5. Use of the agent of claim 1 or 2 in the breeding of jewfish.
  6. 6. A kit for identifying the sex of the jewfish, characterized in that the kit contains the reagent according to claim 1 or 2.
  7. 7. The kit of claim 6, further comprising a Master Mix and water.
  8. 8. A method for identifying the sex of the jewfish, which is characterized by detecting the genotype of SNP loci of the jewfish to be detected, wherein the SNP loci comprise SNP1, SNP2 and SNP3; The SNP1 is positioned at 4806373 bp of a Lateolabrax genome 4, the SNP2 is positioned at 16421908 bp of a Lateolabrax genome 5, the SNP3 is positioned at 7808123 bp of a Lateolabrax genome 18, and the GenBank accession number of the Lateolabrax genome is GCA_031216445.1; Selecting a jewfish to construct a training population, sequencing genotypes of the training population to obtain genotype data as a training set, digitally encoding the sex of the jewfish, marking the female as 0, marking the male as 1, marking the sex of the jewfish as a dependent variable, and constructing a random forest classification model by taking genotypes of the jewfish at the SNP1, the SNP2 and the SNP3 as independent variables; According to genotypes of the to-be-detected Lateolabrax at SNP1, SNP2 and SNP3, predicting the sex of the to-be-detected Lateolabrax by using a random forest classification model to obtain a classification result and a sex prediction value of the to-be-detected Lateolabrax, judging that the sex of the to-be-detected Lateolabrax is female when the sex prediction value is less than or equal to 0.4, and judging that the sex of the to-be-detected Lateolabrax is male when the sex prediction value is less than or equal to 0.6 and less than or equal to 1.
  9. 9. The method according to claim 8, wherein the genotypes of SNP1, SNP2 and SNP3 of the jewfish to be detected are detected with the reagent according to claim 1 or 2.
  10. 10. A method of breeding a jewfish, characterized in that female and/or male jewfish is obtained for breeding according to the method of claim 8.

Description

Sex-related SNP molecular marker of jewfish, detection reagent and application thereof Technical Field The invention relates to the technical field of fish molecular breeding, in particular to a sex-related SNP molecular marker of jewfish, and a detection reagent and application thereof. Background The Lateolabrax japonicus (Lateolabrax maculatus), commonly called Lateolabrax japonicus, lateolabrax japonicus or Lagerstroemia, belongs to the order of Lateolabrax, the family of Lateolabrax, and the genus Lateolabrax, and is mainly distributed in coastal waters and open-sea river waters, has advantages of delicious meat quality, high protein and low fat, rapid growth, and strong adaptability, and is an important economic fish for sea water and fresh water culture. However, in large-scale artificial breeding, the phenomenon that the sex ratio is seriously disregulated is common in the jewfish population, and the number of male individuals is significantly more than that of female individuals, which is in sharp contrast with the relatively balanced sex ratio in the natural population. The unbalance of the sex ratio directly affects the economic benefit and the breeding efficiency of the culture. However, for the important economic species of jewfish, genetic breeding, particularly sex-controlled breeding, still relies largely on traditional gonadal dissection or histological observation methods, without suitable molecular markers as references. In recent years, rapid development of molecular breeding technology has innovated the aquaculture industry. Wherein, single nucleotide polymorphism (Single Nucleotide Polymorphism, SNP) is used as a third generation molecular marker, and has become a core tool for constructing fish genetic map, positioning important character genes and molecular marker assisted breeding due to the characteristics of dense distribution, stable inheritance, co-dominance and the like in genome. With the rapid development and cost reduction of high-throughput sequencing technology, whole genome association analysis (GWAS) combined with high-throughput sequencing technology has been widely applied to genetic analysis of fish complex traits. Although the GWAS strategy based on genome re-sequencing has been successfully applied in a variety of fish sex-determining studies, systematic mining and validation of molecular markers related to the sex of jewfish remains blank. The prior art mainly has the following limitations that (1) the specific sex markers of the jewfish are not disclosed at present, SNP markers or combinations which can be used for early sex identification of the jewfish through large-scale verification are not supported by molecular tools, the traditional identification method has destructiveness and hysteresis, the sex judgment cannot be carried out before sexual maturity by a method relying on dissection or gonad observation, individuals are damaged, the sex judgment is difficult to use for early screening of offspring and living sports, and (3) the complex character analysis is insufficient, the sex judgment of the jewfish is possibly regulated by a polygenic micro-effect system rather than single major sex decision gene control, and the prior research fails to develop a corresponding multi-sex decision site judgment strategy from the complex genetic architecture. Disclosure of Invention The invention aims to overcome the defects of the prior art and provide a Lateolabrax gender-related SNP molecular marker based on GWAS and machine learning, and a detection reagent and application thereof. In order to achieve the above purpose, the technical scheme adopted by the invention is as follows: In a first aspect, the present invention provides a reagent for detecting SNP loci including SNP1, SNP2 and SNP3 in the genome of jewfish, the reagent being used for detecting genotypes of SNP1, SNP2 and SNP 3; The SNP1 is positioned at 4806373 bp of the genome 4 of the jewfish, the SNP2 is positioned at 16421908 bp of the genome 5 of the jewfish, the SNP3 is positioned at 7808123 bp of the genome 18 of the jewfish, and the GenBank accession number of the genome of the jewfish is GCA_031216445.1. The whole genome association analysis (GWAS) adopted by the invention combines a machine learning algorithm to screen the strategies of the sex-related SNP of the jewfish, and 3 molecular markers of the sex-related SNP of the jewfish are screened out, so that the method can be used for molecular marker-assisted sex identification and early breeding of the jewfish. Further, the reagent comprises a primer set; The nucleotide sequences of the primer group for detecting SNP1 are shown as SEQ ID NO.1 and SEQ ID NO. 2; the nucleotide sequences of the primer group for detecting SNP2 are shown as SEQ ID NO.3 and SEQ ID NO. 4; The nucleotide sequences of the primer group for detecting SNP3 are shown as SEQ ID NO.5 and SEQ ID NO. 6. In a second aspect, the invention provides the use of the agent in identifying