SNP molecular markers associated with the length of farrowing in Duroc pigs and their application

Abstract

The present application discloses a SNP molecular marker related to the length of Duroc pig farrowing and its application, aiming to solve the current technical problem of the lack of research on genetic traits related to sow farrowing. The SNP molecular marker is: based on the international pig genome version 11.1 reference sequence, there is a G / T mutation at the 71873698th base of chromosome 11. The genotype of the 71873698th site of chromosome 11 of the sows in the Duroc pig population is detected and determined; the sow individuals with the GT or GG genotype at the 71873698th site are selected, and the sow individuals with the TT genotype at the site are eliminated, so as to increase the frequency of the allele G at the site from generation to generation, thereby shortening the farrowing time of the offspring pigs.

Description

Technical Field

[0001] The present invention relates to the technical field of marker-assisted selection (MAS) in pigs, and in particular to a SNP molecular marker associated with the farrowing length of Duroc pigs and an application thereof. Background Art

[0002] The farrowing duration (FAR) of a sow refers to the time it takes to give birth to a litter of piglets, usually from the birth of the first piglet to the birth of the last piglet. With the improvement of pig genetic breeding, the reproductive performance of sows has been greatly improved, especially the litter size has been greatly improved. Studies have found that the farrowing duration of sows is significantly prolonged with the increase in litter size. However, a longer farrowing duration is also an important factor causing high perinatal mortality in piglets. Therefore, it is necessary to explore whether there are genomic regions that affect the farrowing duration of Duroc pigs, so as to evaluate the possibility of selective breeding for sow farrowing traits.

[0003] The reproductive traits of sows are one of the key factors that directly affect the benefits of farmers. They account for a large weight in pig breeding and are one of the main economic traits. The litter size is an important reproductive trait of sows, and the longer labor process has a significant impact on the number of stillborn piglets. The labor process is one of the important factors affecting the survival rate of piglets and the health of sows, and is closely related to the incidence of stillbirth of piglets. Nearly 75% of stillbirths during sow delivery occur during the delivery process. A longer labor process will affect the reproductive performance of sows and the health level of piglets, reduce the service life of sows, and affect the survival rate of piglets, thereby affecting the economic benefits of pig farms. Although there are relevant studies on the sow's labor process, there is currently no genomic research on the sow's labor process at home and abroad. Therefore, it is necessary to conduct systematic research on the sow's labor process in order to better carry out pig breeding.

[0004] The information disclosed in this background technology section is only used to deepen the understanding of the background technology of the present disclosure, and should not be regarded as acknowledging or suggesting in any form that the information constitutes the prior art known to those skilled in the art. Summary of the invention

[0005] The purpose of the present invention is to provide a SNP molecular marker related to the length of Duroc pig farrowing and its application, and to apply it in genotype identification, genetic breeding, etc., aiming to solve the current technical problem of lack of research on genetic traits related to sow farrowing.

[0006] Using the whole genome sequence of pigs and high-density SNP (single nucleotide polymorphism) chips, molecular markers related to the length of Duroc pig farrowing were identified based on the pig genome-wide association study (GWAS). If SNPs are applied to molecular marker-assisted selection and genomic selection, the genetic improvement process of pigs can be promoted to improve the economic benefits of breeding. The specific technical solutions are as follows:

[0007] According to one aspect of the present disclosure, a SNP molecular marker associated with the length of Duroc pig farrowing is provided, based on the presence of a G / T mutation at base 71873698 on chromosome 11 of the international porcine genome version 11.1 reference sequence, recorded as mutation site rs80892265.

[0008] According to another aspect of the present disclosure, the SNP molecular marker is applied in screening pig strains associated with the length of the farrowing process.

[0009] According to another aspect of the present disclosure, primers or kits for detecting the SNP molecular markers are used in breeding pig strains related to the length of the farrowing process.

[0010] According to another aspect of the present disclosure, a method for detecting the length of Duroc pig labor is provided, comprising the following steps:

[0011] (1) Extraction of whole genome DNA from Duroc pig tissue samples;

[0012] (2) scanning the whole genome DNA using a gene chip;

[0013] (3) Obtain chip data and, based on the international porcine genome version 11.1 reference sequence, check the base site 71873698 (rs80892265) on chromosome 11 and interpret the G / T polymorphism of this site.

[0014] According to another aspect of the present disclosure, a method for screening a short-parturition sow strain is provided, comprising the following steps:

[0015] (1) Based on the international porcine genome version 11.1 reference sequence, the genotype of chromosome 11, locus 71873698, of sows in the Duroc pig population was determined;

[0016] (2) Select individual sows with the GT or GG genotype at the 71873698th locus and eliminate those with the TT genotype at the locus, so as to increase the frequency of the G allele at the locus generation by generation, thereby shortening the delivery time of the offspring pigs.

[0017] One or more technical solutions provided in the embodiments of the present application have at least the following technical effects or advantages:

[0018] The SNP marker provided by the present invention is significantly correlated with the length of Duroc's labor process, and can effectively shorten the Duroc pig's labor process without affecting the litter size, thereby reducing the perinatal piglet mortality rate of sows and increasing the rate of re-estrus in sows after parturition.

[0019] By identifying the SNP markers described in the present invention to screen sows with better delivery processes, the efficiency of breeding sows can be improved, thereby obtaining a pig herd with significantly improved comprehensive economic benefits. BRIEF DESCRIPTION OF THE DRAWINGS

[0020] Figure 1 It is a Manhattan plot of genome-wide association analysis (GWAS) of Duroc pigs on chromosome 11 for labor length in one embodiment of the present application; wherein the horizontal axis represents the pig chromosome number, and the vertical axis represents the -logP value. DETAILED DESCRIPTION

[0021] In order to better understand the technical solution of the present application, the above technical solution will be described in detail below in conjunction with the accompanying drawings and specific implementation methods.

[0022] Unless otherwise specified, the instruments and equipment involved in the following examples are all conventional instruments and equipment; the reagents and raw materials involved are all commercially available conventional products unless otherwise specified; the test methods involved are all conventional methods unless otherwise specified.

[0023] Example: Determination of SNP loci associated with Duroc pig farrowing length and development of molecular markers

[0024] 1. Source of experimental animals

[0025] The experimental group used in this case is a group of 249 purebred Duroc pigs from a pig farm in Henan Province. The pigs were allowed to eat and drink freely, and the entire feeding method and feeding conditions were always the same, which was a conventional method.

[0026] 2. Sample collection and phenotypic recording

[0027] The ear tissues of the above pigs were collected, placed in 75% alcohol, and stored in a -20°C refrigerator, and the delivery process of each sow was recorded.

[0028] 3. Pig whole genome 50K SNP typing

[0029] The whole genome was extracted from the ear tissue of the Duroc pig population using an animal tissue DNA extraction kit (Shanghai Jierui Bioengineering Co., Ltd.). The concentration and OD value of each sample were measured using a UV spectrophotometer, 100 ng DNA was extracted and mixed with 1 μ Loading Buffer, loaded into a 1% agarose gel, and electrophoresed at 120 V for 30 min. The gel imaging device was used to observe and take pictures to detect the integrity of the DNA.

[0030] The DNA was diluted to about 20 ng / μL and sent to Beijing Compson Biotechnology Co., Ltd. for genotyping of the whole pig genome 50K SNP chip. Plink 1.9 software was used to control the 50K chip data quality, and individuals and sites with a detection rate lower than 95%, sites with a minimum allele frequency lower than 1%, and sites that did not correspond to the pig 11.1 reference genome were deleted. Finally, 249 valid individuals and 36,977 SNP valid genotype data were obtained.

[0031] 4. Genome-wide association analysis

[0032] Principal component analysis was performed using Plink 1.9 software, and GWAS analysis was performed using GEMMA v0.98.5 software.

[0033] A univariate mixed linear model was used to analyze the association between the chip data after quality control and the Duroc pig farrowing phenotype. The model is as follows:

[0034] ;

[0035] Among them, y is the phenotypic value of the corresponding reproductive trait; W is the fixed effect matrix, which consists of fixed effects and column vector 1; α is the vector of corresponding coefficients including the intercept; x is the genotype vector of Marker; β is the effect size of Marker; u is the n-vector of random effects; ε is the n-vector of errors.

[0036] GWAS analysis results Figure 1 As shown. Figure 1 It can be seen that in the Duroc pig population, there is a locus on chromosome 11 that significantly affects the birth process of Duroc pigs.

[0037] 5. Analysis of the association between different genotypes and sow farrowing phenotypes

[0038] From the above analysis results, it can be seen that the SNP site of the molecular marker corresponds to the 71873698th mutation of chromosome 11 of the international pig genome version 11.1 reference sequence and is extremely significantly correlated with the farrowing traits of Duroc pigs (P<0.01), indicating that the molecular marker significantly affects the farrowing traits of Duroc pigs; further statistical analysis shows that the farrowing process of Duroc pigs with a base of G at this site is significantly shorter than that of pigs with a base of T. Therefore, eliminating pigs with the TT genotype can bring more economic benefits. In the process of breeding, it is necessary to eliminate TT-type breeding pigs and retain GT-type and GG-type breeding pigs to increase the frequency of the allele G at this site from generation to generation. This shortens the time of farrowing and speeds up the breeding process.

[0039] Although some preferred embodiments of the present application have been described, those skilled in the art may make additional changes and modifications to these embodiments once they have learned the basic creative concept. Therefore, the appended claims are intended to be interpreted as including the preferred embodiments and all changes and modifications falling within the scope of protection of the present application.

[0040] Obviously, those skilled in the art can make various changes and modifications to the present application without departing from the spirit and scope of the present invention. Thus, if these modifications and variations to the present application fall within the scope of the claims of the present application and their equivalents, the present application is also intended to include these modifications and variations.

Claims

1. Application of SNP molecular markers associated with Duroc pig farrowing length in the selection of Duroc pig strains associated with farrowing length, wherein the SNP molecular marker is a G / T mutation at base 71873698 of chromosome 11 based on the reference sequence of the international porcine genome version 11.

1.

2. The use of primers or kits for detecting SNP molecular markers associated with the length of the Duroc pig's farrowing process in the selection of Duroc pig strains associated with the length of the farrowing process, wherein the SNP molecular marker is a G / T mutation at base 71873698 of chromosome 11 based on the reference sequence of the international porcine genome version 11.

1.

3. A method for detecting the length of Duroc pig labor, characterized in that: The steps include: (1) Extraction of whole genome DNA from Duroc pig tissue samples; (2) scanning the whole genome DNA using a pig whole genome SNP chip; (3) Obtain chip data, check the genotype of locus 71873698 on chromosome 11 based on the international porcine genome version 11.1 reference sequence, interpret the G / T polymorphism of this locus, and determine the length of labor according to the following criteria: When the genotype at locus 71873698 is GG or GT, the length of labor is shorter; When the genotype of locus 71873698 is TT, the labor process is longer.

4. A method for screening short-term sow strains, characterized in that: The steps include: (1) Based on the international porcine genome version 11.1 reference sequence, the genotype of chromosome 11, locus 71873698 of sows in the Duroc pig population was determined; (2) Select individual sows with the GT or GG genotype at the 71873698th locus and eliminate those with the TT genotype at the same locus, so as to increase the frequency of the G allele at this locus generation by generation, thereby shortening the delivery time of the offspring pigs.

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