CN-121975949-A - Molecular marker for analyzing rib logarithmic character of quincuncial pig and application of molecular marker

Abstract

The application relates to the field of animal breeding, in particular to a molecular marker for analyzing the rib logarithmic character of a quincuncial star pig and application thereof. And provides a primer pair for analyzing the specificity of the loci, thereby realizing early and accurate pig breeding. The technical scheme has the advantages of simple operation, low cost, accurate detection and the like, and has important application value in molecular precise breeding of pig rib logarithmic characters.

Inventors

• CHEN HONGBO
• SHI LIANGYU
• ZHOU HUANHUAN
• LIU SHA

Assignees

• 武汉轻工大学

Dates

Publication Date

20260505

Application Date

20260303

Claims (10)

1. 1. The molecular marker for analyzing the rib logarithmic character of the quincuncial pig is characterized in that the SV molecular marker comprises SV312 or/and SV245 or/and SV303 or/and SV296, The base sequence of SV312 is shown in SEQ ID NO.9, and the structural variation of the region is 312 bp segment between positions 118-429 of deletion or non-deletion in genome, wherein the logarithm of the-/-type rib > +/+ type rib logarithm; the base sequence of SV245 is shown in SEQ ID NO.10, and the structural variation of the region is a 245 bp fragment between the positions 278-522 which are deleted or not deleted in the genome, wherein the logarithm of the rib of the-/-type > +/-logarithm of the rib of the type > +/+ type; the base sequence of SV303 is shown in SEQ ID NO.11, and the structural variation of the region is a 303 bp fragment between positions 212-514, which are deleted or not deleted in the genome, wherein the logarithm of the rib of the-/-type > +/-logarithm of the rib of the type > +/+ type; The base sequence of SV296 is shown in SEQ ID NO.12, and the structural variation of the region is a 296bp fragment between the positions 482-778 deleted or not deleted in the genome, wherein the logarithm of the ribs of the +/+ type > +/the logarithm of the ribs of the +/type > -/-type; the position was determined by comparison with the reference genome Sus_scrofa.Srcrofa 11.1 of pigs.
2. 2. The primer sequence of the primer combination for detecting the rib logarithmic character of the quincuncial pig is shown as SEQ ID NO.1-SEQ ID NO. 8.
3. 3. The probe combination for detecting the rib logarithmic character of the quincuncial pig is used for detecting the structural variation of SV312, SV245, SV303 and SV296 in a sample to be detected.
4. 4. A gene chip for detecting the rib logarithmic character of a quincuncial pig, wherein the gene chip is loaded with the molecular probe combination of claim 3.
5. 5. Detection of the KASP markers of the rib log trait of the jackpot, characterized in that they are capable of detecting the typing results of the molecular markers described in claim 1.
6. 6. A kit for detecting rib log traits in a jackpot pig, comprising the primer set of claim 2 or the probe set of claim 3 or the gene chip of claim 4 or the KASP marker of claim 5.
7. 7. A gene prediction model for analyzing the rib logarithmic character of a quincuncial pig, which is characterized in that the model is constructed based on the molecular marker of claim 1 and specifically comprises the following steps: Wherein, the The probability is represented by a probability that, Representing the probability of an individual at different rib numbers, In order to be an intercept term, For the effect coefficient of the ith SV, k represents the rib number, 。
8. 8. The method for detecting the rib log character of the pig of the quincuncial star is characterized by comprising the steps of detecting the genotype of the molecular marker in the genome of a pig sample to be detected, and judging the rib log of the pig of the quincuncial star according to a genotype result; preferably, the detection of the genotype of the molecular marker according to claim 1 in the genome of the pig sample to be tested is performed by using a kit having the primer combination according to claim 2 or the probe combination according to claim 3 or the gene chip according to claim 4 or the KASP marker according to claim 5 or the kit according to claim 6.
9. 9. The method of claim 8, wherein the determining the rib log of the quincuncial pig according to the genotype results can calculate the probability of an individual in different rib numbers by the model of claim 7 to predict whether the individual can increase the rib number of the population.
10. 10. Use of the molecular marker of claim 1 or the primer combination of claim 2 or the molecular probe combination of claim 3 or the gene chip of claim 4 or the KASP marker of claim 5 or the kit of claim 6 or the gene prediction model of claim 7, characterized in that it is applied in: (1) Detecting the size of the pig body with the quincuncial star; (2) Screening the plum blossom star pig rib logarithmic character variety; (3) Identification of the rib logarithmic character of the quincuncial pig; (4) Application in breeding of quincuncial pigs; (5) The application in the protection of the germplasm resources of the quincuncial pigs; (6) The application in the improvement of the germplasm resources of the quincuncial pigs.

Description

Molecular marker for analyzing rib logarithmic character of quincuncial pig and application of molecular marker Technical Field The invention belongs to the field of animal breeding, in particular to the technical field of biological detection, and more particularly relates to an SV molecular marker combination for analyzing the rib logarithmic character of a pig with a quincuncial star and application thereof. Background The pig belongs to Yangxin pigs, and has the advantages of good reproductive performance, coarse feeding resistance, good stress resistance, tender and fragrant meat quality and the like. In slaughter test experiments of the quincuncial pig, obvious difference exists in rib logarithm, and compared with other pig species, the quincuncial pig has the characteristic of richer rib logarithm character genetic variation. The rib logarithm of the pig is one of important economic traits, and has obvious influence on the economic benefit of the pig farming industry. Studies show that every time the number of pig ribs increases, the carcass length of the pig ribs increases by 80 mm, and the carcass weight also increases. In addition, studies have shown that there is a certain correlation between the number of taps and the genetic mechanism of the number of ribs, and that some genes associated with rib development are also strong candidate genes affecting the number of taps. Therefore, in the modern pig raising production, the multi-ribbed breeding has a key effect on improving the production efficiency and economic benefit of pigs. The rib logarithmic character can affect the body shape and growth performance of pigs, and researches show that every one increase of the rib number of pigs can increase the carcass length by 80 mm and the carcass weight can also increase. In addition, studies have shown that there is a certain correlation between the number of taps and the genetic mechanism of the number of ribs, and that some genes associated with rib development are also strong candidate genes affecting the number of taps. Therefore, the genetic markers related to the number of the pig ribs are identified and applied to molecular breeding, and the method has important significance for improving the production efficiency and economic benefit of pigs. Currently, genome-wide association analysis (Genome-Wide Association Study, GWAS) has become an important means of resolving complex trait genetic structures. GWAS combine data collection, preprocessing and result interpretation of a system to find genomic regions or loci that are significantly associated with a trait of interest, primarily by performing association analysis of genetic variation across the genome with the trait of interest. Existing studies have identified genetic loci associated with rib numbers on multiple chromosomes of different swine breeds. Genomic genetic variation is an important genetic basis for causing differences in individual traits. Genomic variations can be classified by size into single nucleotide polymorphisms (single nucleotide polymorphism, SNPs), indels (insertion and deletion, indels) and structural variations (structural variation, SV). Genomic structural variation (Structural variations, SV) refers to a change in length or orientation of a DNA sequence greater than 50 bp in the genome, including types such as Insertion (INS), deletion (DEL), inversion (INV), duplication (Duplication, DUP), and translocation (Translocation, TRA). Studies have shown that SV has the characteristics of being base-based, wide in coverage, and easier to detect than SNP, and its effect on genome is far more than that caused by SNP. Therefore, the attempt is made to develop a new molecular marker based on the SV locus so as to improve the breeding efficiency and accuracy of the pig rib logarithmic character, thereby helping breeding and being an important technical means for promoting the technical development in the field. Disclosure of Invention Aiming at the problems of low efficiency and poor reliability of the existing breeding method, the invention provides a molecular marker combination based on Structural Variation (SV) and application thereof. The technical scheme discovers two obviously related SV sites through whole genome association analysis (GWAS), and provides specific PCR primer pairs for detecting the sites, so that early and accurate pig breeding is realized. In order to achieve the purpose, the technical scheme adopted by the invention is that SV molecular markers of the rib logarithmic characters of the quincuncial star pigs are detected, wherein the SV molecular markers comprise SV312 or/and SV245 or/and SV303 or/and SV296. The base sequence of SV312 is shown in SEQ ID NO.9, and the structural variation of the region is 312 bp segment between positions 118-429 of deletion or non-deletion in genome, wherein the logarithm of the-/-type rib > +/+ type rib logarithm; the base sequence of SV245 is shown in SEQ ID NO.10, and t