Snps on pig chromosome 4 affecting pig body size traits

Abstract

The application provides a SNP marker on a pig chromosome 4 affecting pig body size traits. The sequence of the nucleic acid of the SNP marker is shown as SEQ ID No. 1, and the site of the SNP marker is located at the 301th position from the 5' end on the nucleic acid shown as SEQ ID No. 1, corresponding to the 75643517th position from the 5' end on the chromosome 4 of the international pig genome version 11.1, being T or C.

Description

TECHNICAL FIELD

[0001] The present application relates to the field of molecular markers, in particular to a SNP marker on pig chromosome 4 affecting pig body size traits. BACKGROUND

[0002] Pig breeding, as one of the key fields of animal husbandry, provides important support for meeting human food demand. Pig body size traits are key economic traits of commercial pig farming and have a significant impact on pig production.

[0003] Body size is usually measured by height or length, which is not only an important indicator of human growth and health, but also closely related to pig growth rate, carcass yield and carcass composition, and thus is an important indicator of pig body size, which has a crucial impact on pig production. Head weight is one of the important indicators of pig growth, which can reflect the growth performance and health status of pigs, and pig head meat is rich in collagen and has a delicious taste, which has a high edible value. Carcass length and head weight of different breeds of pigs differ greatly, and body size traits have become one of the main goals of pig breeding programs. Genetic and non-genetic effects, including pig breeds, feeding behavior and nutritional levels, will affect pig body size traits. In the past few decades, pig body size performance has been improved through traditional feeding methods. However, body size traits are complex quantitative traits controlled by a few major genes and a large number of minor genes, and their genetic structure is very complex. Therefore, the effect of improving body size traits by improving feeding methods or conventional breeding is limited.

[0004] In order to better eliminate pigs with poor body size growth in pig populations, it is of great significance to explore molecular markers affecting the quality of body size traits and to improve breeding populations for the production and economic benefits of pig breeding industry. SUMMARY

[0005] One of the present application provides a pig SNP marker, the nucleic acid sequence of the SNP marker is shown as SEQ ID No. 1, the site of the SNP marker is located at the 301st position from the 5' end on the nucleic acid shown as SEQ ID No. 1, corresponding to the 75643517th position from the 5' end on chromosome 4 of the 11.1 version international pig genome, which is T or C.

[0006] The application two provides the application of the SNP marker in the application one in assisting in identifying the pig body shape trait. That is, the T / T genotype and / or T / C genotype of the higher head weight, carcass straight length or carcass oblique length can be screened out through the SNP marker high-throughput screening, and then the related traits of the T / T genotype and / or T / C genotype pig are quantitatively determined based on the conventional method, or the quantitative determination step is omitted, and only the genotype of the SNP marker is selected, for example, only the individual of the T / T genotype is selected, or the individual of the T / T genotype and the T / C genotype is selected.

[0007] In one specific embodiment, the body shape trait comprises at least one of the head weight, the carcass straight length and the carcass oblique length.

[0008] In one specific embodiment, based on the pig body shape trait, the preferred order of the genotype of the 301st site from the 5' end on SEQ ID No. 1 is T / T genotype, T / C genotype and C / C genotype in turn.

[0009] In one specific embodiment, based on the head weight, the preferred order of the genotype of the 301st site from the 5' end on SEQ ID No. 1 is T / T genotype, T / C genotype and C / C genotype in turn.

[0010] In one specific embodiment, based on the carcass straight length, the preferred order of the genotype of the 301st site from the 5' end on SEQ ID No. 1 is T / T genotype, T / C genotype and C / C genotype in turn.

[0011] In one specific embodiment, based on the carcass oblique length, the preferred order of the genotype of the 301st site from the 5' end on SEQ ID No. 1 is T / T genotype, T / C genotype and C / C genotype in turn.

[0012] In one specific embodiment, the pig is a hybrid chimeric breed of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang and Tibetan pig.

[0013] In one specific embodiment, the pig is the F6 generation, the F7 generation or the offspring of the F7 generation of the hybrid chimeric breed of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang and Tibetan pig.

[0014] The third aspect of the present application provides a method for assisting genetic improvement of pigs, comprising: determining the SNP marker of a breeding pig in a breeding pig core group according to any one of the present application, and making a corresponding selection according to the SNP marker: selecting a breeding pig individual with T / T genotype at the 301st site from the 5' end on SEQ ID No. 1 in the breeding pig core group, and eliminating a breeding pig individual with C / C genotype at the site, so as to increase the frequency of allele T at the site generation by generation.

[0015] In a specific embodiment, a breeding pig individual with T / T genotype at the 301st site from the 5' end on SEQ ID No. 1 in the breeding pig core group is selected, and a breeding pig individual with T / C and C / C genotype at the site is eliminated, so as to increase the frequency of allele T at the site generation by generation.

[0016] In a specific embodiment, the SNP marker of a breeding pig is determined by analyzing the sequence of the nucleic acid of the breeding pig, wherein the sequence of the nucleic acid is shown in SEQ ID No. 1.

[0017] In a specific embodiment, the pig is a hybrid chimeric breed of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang and Tibetan pig.

[0018] In a specific embodiment, the pig is a hybrid chimeric breed of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang and Tibetan pig.

[0019] Advantages of the present application:

[0020] The SNP marker 4_75643517 of the present application is significantly related to the body shape traits of pigs, especially significantly related to head weight, carcass straight length and carcass oblique length, so that the SNP marker of the present application can be used to determine the site of the pig population, and the related body shape traits of pigs can be assisted to be identified or the genetic improvement of the related body shape traits of the pig population can be carried out through the SNP marker.

[0021] By improving the 4_75643517 SNP site, increasing the frequency of allele T at the site and reducing the frequency of allele C, the body shape traits of related pigs can be improved, so as to improve the yield. BRIEF DESCRIPTION OF DRAWINGS

[0022] Figure 1 Manhattan plots (Manhattan Plot) of head weight (HeadWt) in GWAS analysis of chimeric F6 population and F7 population are shown. Among them, the X axis is the position of the molecular marker site on the chromosome, and the Y axis is the corresponding -log 10(P value).

[0023] Figure 2 Figure 6 shows Manhattan Plot of carcass StrLen in GWAS analysis of the intercross F6 population and F7 population. Wherein, X axis is the position of molecular marker site on chromosome, Y axis is the corresponding -log10 of P value of molecular marker site. 10 (P value).

[0024] Figure 3 Figure 7 shows Manhattan Plot of carcass DialLen in GWAS analysis of the intercross F6 population and F7 population. Wherein, X axis is the position of molecular marker site on chromosome, Y axis is the corresponding -log10 of P value of molecular marker site. 10 (P value).

[0025] Figure 4 Figure 8 shows Box Plot of head weight of different genotypes of the most significant site 4_75643517 in F6 population. Wherein, X axis represents the genotype of the molecular marker site, Y axis represents the phenotypic value of head weight of individual, and the number above the Box Plot represents the number of individuals with each genotype in the pig population.

[0026] Figure 5 Figure 9 shows Box Plot of carcass StrLen of different genotypes of the most significant site 4_75643517 in F6 population. Wherein, X axis represents the genotype of the molecular marker site, Y axis represents the phenotypic value of carcass StrLen of individual, and the number above the Box Plot represents the number of individuals with each genotype in the pig population.

[0027] Figure 6 Figure 10 shows Box Plot of carcass DialLen of different genotypes of the most significant site 4_75643517 in F6 population. Wherein, X axis represents the genotype of the molecular marker site, Y axis represents the phenotypic value of carcass DialLen of individual, and the number above the Box Plot represents the number of individuals with each genotype in the pig population.

[0028] Figure 7 Figure 11 shows Box Plot of head weight of different genotypes of the most significant site 4_75643517 in F7 population. Wherein, X axis represents the genotype of the molecular marker site, Y axis represents the phenotypic value of head weight of individual, and the number above the Box Plot represents the number of individuals with each genotype in the pig population.

[0029] Figure 8The Box Plot of the different genotypes of the most significant locus 4_75643517 in the F7 population for carcass straight length is shown. In which, the X axis represents the genotypes of the molecular marker locus, the Y axis represents the phenotypic values of the individual's carcass straight length, and the numbers above the Box Plot represent the number of individuals in the pig population of each genotype.

[0030] Figure 9 The Box Plot of the different genotypes of the most significant locus 4_75643517 in the F7 population for carcass straight length is shown. In which, the X axis represents the genotypes of the molecular marker locus, the Y axis represents the phenotypic values of the individual's carcass straight length, and the numbers above the Box Plot represent the number of individuals in the pig population of each genotype. DETAILED DESCRIPTION

[0031] The application will be further described in conjunction with the examples, but the examples of the application are only exemplary description, and the implementation manner does not constitute a limitation to the application in any case.

[0032] The F6 pig population and the F7 pig population used in the application are all offspring produced by multiple generations of crossbreeding of 4 western commercial breeds (Duroc, Landrace, Large White, Pietrain) and 4 Chinese local breeds (Erhuamian, Laiwu, Bama Xiang, Tibetan pig).

[0033] Example 1

[0034] 1. Obtaining, quality control and genotyping of whole genome resequencing data of pigs

[0035] A small piece of muscle tissue sample was collected from each individual in the F6 population (n=836) and the F7 population (n=668) at random, and the genomic DNA of each individual was extracted by the standard phenol chloroform method, and the extracted genomic DNA was dissolved in TE buffer. The quality of the extracted genomic DNA was detected by Nanodrop-ND1000 spectrophotometer, and the quality standard was reached when the A260 / 280 ratio was about 1.8-2.0 and the A260 / 230 ratio was about 1.7-1.9.

[0036] The concentration of the qualified DNA samples was diluted to 50 ng / μl, and each DNA sample was subjected to low-depth resequencing (average sequencing depth of about 7.8x) using the HiSeqXTen sequencing instrument platform of Illumina. The obtained all double-end reads were aligned to the international pig genome version 11.1 using BWA software, and then the genotype data of each individual was obtained using software such as SAMTools, Platypus and Beagle in turn. The obtained genotype data was subjected to quality control using Plink1.9, and individuals with a minor allele frequency (MAF) of less than 0.03 and a Mendelian error rate higher than 0.1 were removed. Finally, it was determined that there were 29441528 and 29198737 molecular marker sites in the F6 population and the F7 population, respectively.

[0037] 2. Phenotype measurement

[0038] The pigs in the F6 population and the F7 population were slaughtered at about 240 days of age, and the head weight, carcass straight length (carcassStrLen) and carcass diagonal length (carcassDiaLen) were measured. Among them, after the pigs were slaughtered, the left carcass was hung upside down, and the length from the front edge of the pubic symphysis to the concave part of the first cervical vertebra was measured using a tape measure, which was the carcass straight length; the length from the front edge of the pubic symphysis to the inner edge of the first rib and the sternum junction was the carcass diagonal length. Pig head weight (HeadWt) determination: the same slaughter master separated the pig head from the carcass from the junction of the first cervical vertebra and the skull according to the same standard, and placed the pig head on an electronic scale for weighing. The descriptive statistical results of the head weight, carcass straight length and carcass diagonal length were calculated by the stat.desc() function of the pastecs function package in R language, and the statistical results are shown in Table 1.

[0039] Table 1

[0040]

[0041] As can be seen from Table 1, the coefficients of variation of the three trait phenotypes are all greater than 6%, indicating that these traits have a large breeding space.

[0042] 3. Genome-wide association (GWAS) analysis

[0043] The molecular marker information of F6 population and F7 population obtained by the second-generation resequencing technology and the corresponding head weight, carcass straight length and carcass slant length of F6 population and F7 population individuals are subjected to GWAS analysis by using a mixed linear model in GEMMA (Genome-wide Efficient Mixed Model Association algorithm, version number 0.98.1) software, and the expression is as follows: y=Xa+Qb+u+e; u~MVNn(0,βK) -1 K), e~MVNn(0,t -1 E). Wherein y represents the phenotype value vector of all individuals, X represents the covariate matrix, a represents the corresponding coefficient vector containing the intercept, Q represents the genotype vector of the molecular marker, b represents the influence effect of the molecular marker, u represents the random effect vector, e represents the error vector, β represents the proportion of two kinds of variances, t -1 represents the variance of the residual, K represents the kinship matrix, E represents the unit matrix, and MVNn represents the multivariate normal distribution. Wherein, the GWAS analysis corrects the covariates including gender, slaughter age and slaughter batch.

[0044] The GWAS analysis results of the head weight, carcass straight length and carcass slant length in F6 population and F7 population are shown in Figures 1 to 3 . Figures 1 to 3 It is shown that the most significant sites affecting the head weight, carcass straight length and carcass slant length of pigs all fall on two chromosomes, and one site falls on chromosome 4.

[0045] The present application only focuses on the case that the highest-log P value of chromosome 4 corresponds to the physical position 75643517, and the molecular marker site is located at the 301st site from the 5' end on SEQ ID No. 1. The basic genetic parameter information of F6 population and F7 population body shape traits at the molecular marker site is shown in Table 2.

[0046] Table 2. Basic genetic parameter information of F6 population and F7 population molecular marker sites

[0047]

[0048] From the results in Table 2, it can be known that the molecular marker 4_75643517 has a significant influence on the head weight, carcass straight length and carcass slant length.

[0049] The genotype of each individual in F6 population and F7 population at the molecular marker site 4_75643517 is extracted from the sequencing file by using the PLINK software, the number of individuals of each genotype is counted, the genotype of these individuals is corresponded to the corresponding body shape traits, then the difference of the phenotype distribution under different genotypes is counted by using the multGomp package in R language, and the results are shown inFigures 4 to 9 and Table 3. Wherein, P value is obtained by variance test.

[0050] Table 3. Effect of molecular marker site 4_75643517 on body type

[0051]

[0052] From Table 3, it can be seen that the 4_75643517 T or C genotype has a significant effect on head weight, carcass straight length and carcass oblique length. Figures 4 to 9 From Table 3, it can be seen that the 4_75643517 T or C genotype has a significant effect on head weight, carcass straight length and carcass oblique length.

[0053] 4. Size of phenotypic variance explained by molecular marker site

[0054] Heritability is the most important basic genetic parameter in quantitative genetics, which can be divided into broad-sense heritability, narrow-sense heritability and realized heritability. The heritability in the breeding process generally refers to the narrow-sense heritability (h 2 ), which refers to the proportion of quantitative trait breeding value variance to phenotype variance, is the additive effect part after removing the dominant effect and epistatic effect, and can be stably inherited in the process of generation transmission.

[0055] Since the additive effect model is used in the GWAS analysis of body type traits in the present application, the size of the phenotypic variance explained by the molecular marker site (PVE) is the size of the h 2 explained by the molecular marker site. The detailed information of the PVE explained by the molecular marker site for the body type traits of the F6 population and the F7 population is shown in Table 4.

[0056] Table 4. Size of phenotypic variance explained by significant molecular marker site 4_75643517 for body type traits

[0057] Population Head-heavy PVE Body straight PVE Body oblique PVE F6 12.43％ 9.95％ 11.00％ F7 10.07％ 8.27％ 8.59％

[0058] From Table 4, it can be seen that the most significant phenotype explained by the site is head weight, and the site can also significantly affect carcass straight length and carcass oblique length.

[0059] Although the present application has been described with reference to specific embodiments, it is understood by those skilled in the art that various changes can be made without departing from the true spirit and scope of the present application. In addition, various changes can be made to the subject matter, spirit and scope of the present application to adapt to specific situations, materials, material compositions and methods. All these changes are included in the scope of the claims of the present application.

Claims

1. The application of a reagent for detecting SNP markers in pigs in assisting in the identification of pig body size traits, wherein the sequence of the SNP-marked nucleic acid is shown in SEQ ID No. 1, and the SNP marker site is located at position 301 from the 5' end on the nucleic acid shown in SEQ ID No. 1, corresponding to position 75643517 from the 5' end on chromosome 4 of the 11.1 version of the International Pig Genome, and is T or C; The body type trait is at least one of head weight, straight body length, and oblique body length; Based on the pig body type trait, the preferred order of genotypes at the 301st locus from the 5' end on SEQ ID No. 1 is: T / T genotype, T / C genotype, and C / C genotype. The pigs mentioned are a hybrid chimeric breed of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang, and Tibetan pigs.

2. The application according to claim 1, characterized in that, Based on the head weight, the preferred order of genotypes at the 301st locus starting from the 5' end on SEQ ID No. 1 is: T / T genotype, T / C genotype, and C / C genotype; and / or Based on the carcass length, the preferred order of genotypes at the 301st locus starting from the 5' end on SEQ ID No. 1 is: T / T genotype, T / C genotype, and C / C genotype; and / or Based on the carcass oblique length, the preferred order of genotypes at the 301st locus starting from the 5' end on SEQ ID No. 1 is: T / T genotype, T / C genotype, and C / C genotype.

3. A method for assisting in the genetic improvement of pigs, the method comprising: Identify the SNP markers of breeding pigs in the core breeding pig herd, and make corresponding selections based on the SNP markers: The sequence of the SNP-tagged nucleic acid is shown in SEQ ID No.

1. The SNP-tagged site is located at position 301 from the 5' end on the nucleic acid shown in SEQ ID No. 1, corresponding to position 75643517 from the 5' end on chromosome 4 of the 11.1 version of the International Pig Genome, and is T or C. In the core breeding pig population, breeding pig individuals with the T / C or T / T genotype at the 301st locus from the 5' end of SEQ ID No. 1 are selected, and breeding pig individuals with the C / C genotype at that locus are culled to increase the frequency of the T allele at that locus generation by generation. The genetically modified trait is a body type trait, which is at least one of head weight, straight body length, and oblique body length. The pigs mentioned are a hybrid chimeric breed of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang, and Tibetan pigs.

4. The method according to claim 3, characterized in that, In the core breeding population, breeding pig individuals with the T / T genotype at the 301st locus (starting from the 5' end) on SEQ ID No. 1 are selected, and breeding pig individuals with the T / C and C / C genotypes at that locus are culled to increase the frequency of the T allele at that locus generation by generation.

5. The method according to claim 3 or 4, characterized in that, The SNP marker of the breeding pig as described in claim 1 is determined by analyzing the sequence of the nucleic acid of the breeding pig, wherein the sequence of the nucleic acid is shown in SEQ ID No. 1.

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