CN-122012736-A - SNP haplotype molecular marker related to rib logarithmic character of quincuncial pig and application thereof

Abstract

The invention discloses an SNP haplotype molecular marker related to a rib logarithmic character of a quincuncial star pig and application thereof, wherein the molecular marker is mainly used for screening/identifying excellent varieties, and comprises (1) SNP polymorphism of chr7_91137916 locus is G/T, (2) SNP polymorphism of chr7_91167100 locus is A/G, and (3) SNP polymorphism of chr7_91517487 locus is T/A. The invention has the advantages that the invention is beneficial to improving the breeding efficiency and the selection accuracy, and can improve the gene frequency of the excellent economic character of multi-rib logarithm in the population, and pertinently improve the rib logarithm character of the population, thereby improving the carcass performance and the meat production economic benefit of the whole population.

Inventors

• CHEN HONGBO
• SHI LIANGYU
• LIU SHA
• ZHOU HUANHUAN
• YANG CAICHUN
• CHEN QIONG
• LIU XIONG

Assignees

• 武汉轻工大学
• 黄梅县强立畜牧有限公司

Dates

Publication Date

20260512

Application Date

20260303

Claims (10)

1. 1. The SNP haplotype molecular marker related to the rib logarithmic character of the quincuncial pig is characterized by comprising the following sites: The chr7_91137916 locus, the polymorphism of which is G/T, the chr7_91167100 locus, the polymorphism of which is A/G, the chr7_91517487 locus, the polymorphism of which is T/A, and the three loci form GAT haplotypes, TAT haplotypes, GGA haplotypes and GAA haplotypes, wherein the logarithm of GAT haplotypes is greater than the logarithm of TAT haplotypes and the logarithm of GGA haplotypes is greater than the logarithm of GAA haplotypes; The SNP molecular marker is obtained by comparing pig genome Sus scrofa 11.1.
2. 2. The molecular marker of claim 1, wherein the chr7_91137916, chr7_91167100, chr7_91517487 molecular markers correspond to rib log-rich genotypes or haplotypes as dominant genotypes, accounting for 22.11% of rib log phenotype variances.
3. 3. The amplification primer for detecting the rib logarithmic character of the quincuncial pig is characterized in that the amplification primers for detecting the upstream and downstream of the SNP polymorphism of the chr7_91137916 locus are shown as SEQ ID NO.1-SEQ ID NO.2, the upstream and downstream primers for detecting the SNP polymorphism of the chr7_91167100 locus are shown as SEQ ID NO.3-SEQ ID NO.4, and the upstream and downstream primers for detecting the SNP polymorphism of the chr7_91517487 locus are shown as SEQ ID NO.5-SEQ ID NO. 6.
4. 4. The probe for detecting the rib logarithmic character of the quincuncial pig is characterized by being used for detecting SNP polymorphism of chr7_91137916, chr7_91167100 and chr7_ 91517487.
5. 5. A gene chip for detecting the rib logarithmic character of a quincuncial pig, which is characterized by comprising the probe according to claim 2.
6. 6. The KASP marker for detecting the rib logarithmic character of the quincuncial pig is characterized by being used for detecting SNP polymorphism of chr7_91137916, chr7_91167100 and chr7_ 91517487.
7. 7. A kit for detecting rib log traits in a quincuncial pig, comprising the amplification primer of claim 3 or the probe of claim 4 or the gene chip of claim 5 or the KASP marker of claim 6.
8. 8. The method for detecting the pig rib logarithmic character of the quincuncial star is characterized in that the amplification primer of claim 3 or the probe of claim 4 or the gene chip of claim 5 or the KASP mark of claim 6 is adopted to detect a sample to be detected, and the pig rib logarithmic character of the sample is judged according to the detection result.
9. 9. The amplification primer of claim 3 or the probe of claim 4 or the gene chip of claim 5 or the KASP marker of claim 6 is used for: (1) Detecting the size of the pig body with the quincuncial star; (2) Screening and/or identifying rib character varieties of the quincuncial pigs; (3) Adjusting the output of the quincuncial pig group; (4) Screening and/or identifying the excellent breeds of the breeding plum blossom star pigs; (5) Screening and/or identifying genetic resources of excellent plum blossom star pig breeds.
10. 10. The breeding prediction method for the rib traits of the quincuncial pigs is characterized by calculating the detection result of a sample to be detected by using a haplotype rib number prediction model, and judging the breeding value of the rib traits of the pig of the sample to be detected according to the calculation result; The haplotype rib number prediction model adopts an ordered logistic regression model, takes GGA haplotypes as references, and constructs a rib number prediction formula based on 3 main haplotypes: Wherein the method comprises the steps of 、 、 The expected doses (value range 0-2) of GAA, GAT, TAT haplotypes respectively, and Z is a linear prediction value; preferably, based on the linear prediction value Z, the rib number prediction rule is as follows: Predicted rib number = 。

Description

SNP haplotype molecular marker related to rib logarithmic character of quincuncial pig and application thereof Technical Field The invention belongs to the technical field of animal genetic breeding, and particularly relates to a SNP haplotype molecular marker related to the rib logarithmic character of a quincuncial star pig and the technical field of application of the SNP haplotype molecular marker. Background The pig raising industry in China has long history and rich pig species resources, and Chinese local pigs are taken as important components of a pig germplasm resource library in China, and a relatively unique genetic background and production performance are formed through long-term natural selection and manual selection. The quincuncial pig belongs to Yangxin pig subgroups, is one of local pig breeds with excellent Hubei in China, 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. The rib logarithmic character affects the body shape and carcass performance of pigs, and researches show that every increase of the number of the ribs of pigs leads to an increase of 80 mm in carcass length and a concomitant increase in carcass weight. 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 are primarily designed to combine data collection, pretreatment and result interpretation of a system by correlating genomic-wide genetic variations (e.g., single nucleotide polymorphisms, SNPs) with a trait of interest in order to find genomic regions or loci that are significantly associated with the trait of interest. Existing studies have identified genetic loci associated with rib numbers on multiple chromosomes of different swine breeds. For example, patent CN104232630a discloses a major marker located on chromosome 7 of swine to increase the number of ribs in swine and its use in genetic improvement of breeding swine, which locates the major site affecting the number of ribs within a 947kb range on chromosome 7 by GWAS analysis. In addition, it has also been studied that the 6:107016475A > G site variable cleavage mutation located on chromosome 6 MIB1 gene in Beijing black pig population is significantly related to rib number. However, traditional GWAS analysis may be affected by linkage disequilibrium (Linkage Disequilibrium, LD) when dealing with complex traits, resulting in a significant signal detected that is not an independent causal variation, but a false positive signal that is highly linked to a true causal site. In order to more accurately identify independent genetic signals, a Conditional & Joint analysis (COJO) method was introduced into the GWAS follow-up analysis. GCTA-COJO is a commonly used tool to incorporate the most significant SNP as covariates into a model by stepwise regression to identify independent association signals, effectively distinguishing independent signals from false positive signals due to LD. Furthermore, studies of GWAS on the logarithmic characteristics of pig ribs still suffer from the following (1) population-specific limitations. The genetic markers currently identified often exhibit population specificity, i.e., markers that are significant in a population of a particular pig breed, may perform poorly or lack statistical significance in other pig breeds or strains, which greatly restricts their versatility in broader breeding practices (2) independent verification is inadequate. Some studies failed to adequately replicate the validation in independent validation populations after significant association sites were found. The lack of such verification may lead to false positive results, thereby compromising the reliability of the markers found and their value in practical applications (3) the potential for high-precision data utilization is undermined. With the rapid development of high-throughput sequencing technology, the chip data is filled and then subjected to GWAS analysis, so that high-density and high-pr