SNP (Single Nucleotide Polymorphism) molecular marker on pig chromosome 7 influencing pig nipple number

Abstract

The invention provides an SNP (Single Nucleotide Polymorphism) molecular marker on a pig chromosome 7 influencing the number of pig nipples. The SNP molecular marker is located at the 245th site from the 5'end on SEQ ID No.1, corresponds to the 91308348th site from the 5 'end on the No.7 chromosome of the international pig genome of the version 11.1, and is T or G.

Description

Technical Field

[0001] The present invention relates to the field of molecular markers, and particularly to SNP molecular markers on porcine chromosome 7 that affect the number of teats in pigs. Background Art

[0002] The number of teats in pigs, as one of the important phenotypic traits in porcine reproductive performance, directly affects the breeding efficiency and production performance of pigs. The number of teats in sows has an important impact on the litter-raising and lactation abilities of sows. In the actual breeding process, sows with fewer teats will have problems in fully nursing all their piglets, resulting in a decrease in the survival rate of piglets and thus affecting the overall production efficiency. Currently, the number of teats in sows has become one of the important indicators for evaluating the production performance of sows. How to increase the number of teats in sows during the breeding process has always been a research hotspot in porcine genetic improvement.

[0003] Traditionally, the selective breeding of the number of teats in pigs mostly relied on phenotypic data and the improvement of production performance, usually by selecting sows with more teats for breeding. However, the phenotypic selection method is greatly affected by environmental factors and measurement errors, and has a long breeding cycle and low efficiency, and cannot efficiently and accurately perform genetic improvement of the number of teats. In addition, the phenotypic selection method often ignores the role of complex genetic mechanisms, making the improvement process relatively slow.

[0004] Therefore, exploring the marker loci that affect the number of teats in pigs can be used to achieve precise and efficient improvement of pig breeds, thereby improving the litter-raising and lactation abilities of sows, increasing the survival rate of piglets, and increasing production benefits. Summary of the Invention

[0005] One aspect of the present invention provides a SNP molecular marker for pigs. The nucleic acid sequence of the SNP molecular marker is as shown in SEQ ID No.1. The SNP molecular marker is located at the 245th position from the 5'-end of SEQ ID No.1, corresponding to the 91308348th position from the 5'-end of chromosome 7 of the 11.1 version of the international porcine genome, and is either T or G.

[0006] The second aspect of the present invention provides an application of an SNP molecular marker in assisting in the identification of the number of right nipples and / or left nipples in pigs. The SNP molecular marker is located at the 245th position from the 5' end on SEQ ID No. 1, corresponding to the 91308348th position from the 5' end on chromosome 7 of the international pig genome version 11.1, and is T or G. That is, pigs with more right nipples and / or left nipples of the T / G genotype or T / T genotype can be screened out through high-throughput SNP molecular markers first, and then the number of right nipples and / or left nipples of the T / G genotype or T / T genotype can be quantitatively determined based on conventional methods as needed, or the quantitative determination step can be omitted, and a selection can be made only based on the genotype of the SNP marker. For example, only individuals with the T / T genotype are selected, or individuals with the T / G genotype and T / T genotype are selected.

[0007] In a specific embodiment, based on the number of right nipples and / or left nipples, the preferred order of the genotypes at the 245th position from the 5' end on SEQ ID No. 1 is: T / T genotype, T / G genotype, and G / G genotype in sequence.

[0008] In a specific embodiment, the pig is at least one of Duroc, Large White, and Landrace pigs or a hybrid chimeric pig of at least two of them.

[0009] The third aspect of the present invention provides a method for assisting pig genetic improvement. The method includes: determining an SNP molecular marker of a breeding pig in the core breeding pig population; the SNP molecular marker is located at the 245th position from the 5' end on SEQ ID No. 1, corresponding to the 91308348th position from the 5' end on chromosome 7 of the international pig genome version 11.1, and is T or G; making a corresponding selection according to the SNP molecular marker: selecting breeding pig individuals with the T / T genotype and / or T / G genotype at the 245th position from the 5' end on SEQ ID No. 1 in the core breeding pig population, and eliminating breeding pig individuals with the G / G genotype to gradually increase the frequency of allele T from generation to generation.

[0010] In a specific embodiment, breeding pig individuals with the T / T genotype at the 245th position from the 5' end on SEQ ID No. 1 are selected in the core breeding pig population, and breeding pig individuals with the T / G genotype and G / G genotype at the 245th position from the 5' end are eliminated to gradually increase the frequency of allele T from generation to generation.

[0011] In a specific embodiment, the SNP molecular marker of the breeding pig as described in the first aspect of the present invention is determined by analyzing the nucleic acid sequence of the breeding pig, wherein the nucleic acid sequence is as shown in SEQ ID No. 1.

[0012] In a specific embodiment, the source of the pigs is at least one of Duroc, Large White, and Landrace pigs or a hybrid chimeric pig of at least two of them.

[0013] In a specific embodiment, the traits of the genetic improvement of the pigs are the number of right nipples and / or the number of left nipples.

[0014] Advantages of the present invention:

[0015] The 7_91308348 SNP marker of the present invention is significantly correlated with the number of right nipples and the number of left nipples of pigs. Therefore, the genotype of this locus in the pig population can be determined by the SNP marker of the present invention, and the number of right nipples and the number of left nipples of pigs can be assisted in identification or the genetic improvement of the number of right nipples and the number of left nipples of the pig population can be carried out through this SNP marker.

[0016] By improving the 7_91308348 SNP molecular marker locus, increasing the frequency of allele T and decreasing the frequency of allele G, the number of nipples of sows can be increased. By increasing the number of nipples of sows, the litter-rearing and lactation abilities of sows can be improved, the survival rate of piglets can be increased, and the production income can be increased. Description of the Drawings

[0017] Figure 1 Shows the Manhattan plot of the number of right nipples of Duroc, Landrace, and Large White pigs in GWAS analysis. Among them, the X-axis is the chromosome number, and the Y-axis is -log 10 (P value), and the red dots are the leading SNPs (lead SNP).

[0018] Figure 2 Shows the Manhattan plot of the number of left nipples of Duroc, Landrace, and Large White pigs in GWAS analysis. Among them, the X-axis is the chromosome number, and the Y-axis is -log 10 (P value), and the red dots are the leading SNPs (lead SNP).

[0019] Figure 3 Shows the analysis diagram of the number of right nipples of pigs with different genotypes.

[0020] Figure 4 Shows the analysis diagram of the number of left nipples of pigs with different genotypes. Specific Embodiments

[0021] The present invention will be further described below in conjunction with embodiments, but the embodiments of the present invention are only exemplary descriptions, and this embodiment does not constitute a limitation to the present invention in any case.

[0022] The pig populations used in this invention are Duroc, Landrace and Yorkshire pigs from Jiangxi Jiada Group Co., Ltd., among which there are 719 Duroc pigs, 1294 Landrace pigs and 2573 Yorkshire pigs; 1559 boars and 3027 sows.

[0023] The pigs in the herd eat and drink, and the entire feeding method, feeding conditions, etc. are always kept consistent, all of which are conventional feeding methods.

[0024] Example 1

[0025] 1. Obtaining, quality control and genotyping of whole-genome resequencing data of pigs

[0026] Ear tissues of each individual were collected from the pig population, and genomic DNA of each individual was extracted by the standard phenol-chloroform method. The extracted genomic DNA was dissolved in TE buffer. The quality of the extracted genomic DNA was detected by a Nanodrop-ND1000 spectrophotometer, and the quality standard was reached when the A260 / 280 ratio was between 1.8 - 2.0 and the A260 / 230 ratio was around 1.7 - 1.9.

[0027] The concentration of the DNA samples meeting the standards was diluted to 50 ng / μl, and each DNA sample was genotyped using the "Zhongxin No. 1" 50K chip to obtain genotype information at 57,466 loci. Plink1.9 was used to perform quality control on the obtained genotype data, removing SNPs with a minor allele frequency (MAF) lower than 0.01, a genotype missing rate higher than 0.01, lacking chromosome position information, and located on the sex chromosome, obtaining 44,766 high-quality SNPs. Then Shapite v5.1.1 was used for haplotype construction, and subsequently Beagle v5.4 was used for genotype imputation. Quality control was performed on the obtained genotype data through Plink, removing SNPs with a correlation with the actual alleles lower than 0.85, a minor allele frequency lower than 0.01, and a missing rate higher than 0.01. Finally, 8,206,050 molecular markers were retained.

[0028] 2. Determination of the phenotypic number of nipples in pigs

[0029] When the pigs were at the age of 136 to 217 days, the number of right nipples and left nipples of the pigs was counted.

[0030] The descriptive statistical results of the number of nipples were calculated by R language software, and the results are shown in Table 1.

[0031] Table 1. Descriptive statistical results of the number of nipples in all individuals

[0032] Trait Number of individuals Maximum value Minimum value Mean value Standard deviation Coefficient of variation Number of right nipples 4560 10 5 7.17 0.54 7.47％ Number of left nipples 4571 9 4 7.10 0.50 7.03％

[0033] As can be seen from Table 1, the coefficient of variation of the number of right nipples and the number of left nipples is greater than 5%, indicating that there is still a large room for breeding for this trait.

[0034] 3. Genome-wide association (GWAS) analysis

[0035] Using the mixed linear model in the GEMMA (Genome-wide Efficient Mixed Model Association algorithm, version number 0.98.1) software, the molecular marker information of the obtained pig population and the number of nipples of the corresponding individuals were respectively subjected to GWAS analysis. The expression is as follows: y = Xa + Qb + u + e; u ∼ MVNn(0, βt -1 K), e ∼ MVNn(0, t -1 E). Where y represents the phenotypic value vector of all individuals, X represents the covariate matrix, a represents the corresponding coefficient vector including 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 ratio of the two variances, t -1 represents the variance of the residuals, K represents the kinship matrix, E represents the identity matrix, and MVNn represents the multivariate normal distribution.

[0036] The GWAS analysis results of the number of right nipples and the number of left nipples in the pig population are shown in Figure 1 and Figure 2 . From Figure 1 and Figure 2 , it can be seen that the locus most significantly affecting the number of pig nipples is located on chromosome 7.

[0037] The present invention only focuses on the situation of the physical position 91308348 corresponding to the right nipple number P = 1.345735E-14 and the left nipple number P = 1.670793E-15 on chromosome 7. This molecular marker locus is located at the 245th site starting from the 5' end of SEQ ID No. 1. The basic genetic parameter information of the number of nipples in the pig population at this molecular marker locus is shown in Table 2.

[0038] Table 2. Basic genetic parameter information of the molecular marker locus of the number of nipples in the pig population

[0039] Trait Number of right nipples Number of left nipples Molecular marker name 7_91308348 7_91308348 Chromosome 7 7 Physical location 91308348 91308348 Mutation information T / G T / G Minor allele frequency 0.48 0.48 Effect value 0.089 0.085 P value 1.345735E-14 1.670793E-15

[0040] From the results in Table 2, it can be seen that the 7_91308348 molecular marker has a significant effect on both the number of left and right nipples.

[0041] The genotypes of each individual in the pig population at the molecular marker locus 7_91308348 were extracted from the sequencing files using the PLINK software. After counting the number of individuals with each genotype, the genotypes of these individuals were corresponded to their respective right or left teat numbers. Then, the stat_compare_means function in the ggpubr package of R language was used to statistically analyze the differences in phenotypic distributions under different genotypes. The results are shown in Figure 3 and Figure 4 and Table 3. Among them, the P value is obtained from the variance test.

[0042] Table 3. Effect of molecular marker locus 7_91308348 on teat number

[0043] Trait T / T T / G G / G P value Number of right nipples 7.06±1.76 7.05±1.47 7.02±1.00 2.2E-16 Number of left nipples 7.06±1.37 7.01±1.30 6.97±0.75 2.2E-16

[0044] From Figure 3 、 Figure 4 and Table 3, it can be seen that the molecular marker 7_91308348 can significantly affect the right and left teat numbers. When the number of right or left teats increases, the litter-raising and lactation abilities of sows can be improved, the survival rate of piglets can be increased, and the production income can be increased. Therefore, the preferred ranking of alleles at this locus for teat number is all T / T > T / G > G / G.

[0045] 4. Size of phenotypic variation explained by molecular marker locus

[0046] Heritability is one of the most important basic genetic parameters in quantitative genetics and can be divided into broad-sense heritability, narrow-sense heritability, and realized heritability. Heritability in the breeding process generally refers to narrow-sense heritability (h 2 ), which refers to the proportion of the variance of breeding values of quantitative traits in the phenotypic variance and is the additive effect part after excluding the dominant effect and epistatic effect, and can be stably inherited during generation transmission.

[0047] Since the present invention uses an additive effect model to perform GWAS analysis on the right and left teat numbers, the size of the phenotypic variance explained (PVE) by the molecular marker locus is the size of h 2 explained by this marker. The PVE value explained by the molecular marker locus for the right teat number is 1.41%, and the PVE value explained by the molecular marker locus for the left teat number is 1.38%. This result indicates that the phenotype that this locus can explain has an impact on teat number.

[0048] Although the present invention has been described with reference to specific embodiments, those skilled in the art should understand that various changes can be made without departing from the true spirit and scope of the present invention. In addition, various changes can be made to the subject matter, spirit and scope of the present invention to adapt to specific situations, materials, material compositions and methods. All such changes are included within the scope of the claims of the present invention.

Claims

1. A SNP molecular marker of a pig, the nucleic acid sequence of the SNP molecular marker is as shown in SEQ ID No.1, the SNP molecular marker is located at the 245th position starting from the 5'-end on SEQ ID No.1, corresponding to the 91308348th position starting from the 5'-end on chromosome 7 of the international pig genome version 11.1, and is T or G.

2. An application of a SNP molecular marker in assisting in identifying the number of right nipples and / or left nipples of a pig, the SNP molecular marker is located at the 245th position starting from the 5'-end on SEQ ID No.1, corresponding to the 91308348th position starting from the 5'-end on chromosome 7 of the international pig genome version 11.1, and is T or G.

3. The application according to claim 2, characterized in that, Based on the number of right nipples and / or left nipples, the preferred order of the genotypes at the 245th position starting from the 5'-end on SEQ ID No.1 is: T / T genotype, T / G genotype, and G / G genotype.

4. The application according to claim 2, characterized in that, The pig is at least one of Duroc, Large White, and Landrace pigs or a hybrid chimeric pig of at least two of them.

5. A method for assisting pig genetic improvement, the method comprising: A SNP molecular marker for determining breeding pigs in a breeding pig core group; The SNP molecular marker is located at the 245th position starting from the 5'-end on SEQ ID No.1, corresponding to the 91308348th position starting from the 5'-end on chromosome 7 of the international pig genome version 11.1, and is T or G; make corresponding selections according to the SNP molecular marker: select breeding pig individuals with T / T genotype and / or T / G genotype at the 245th position starting from the 5'-end on SEQ ID No.1 in the breeding pig core group, and eliminate breeding pig individuals with G / G genotype to gradually increase the frequency of allele T.

6. The method according to claim 5, characterized in that Select breeding pig individuals with T / T genotype at the 245th position starting from the 5'-end on SEQ ID No.1 in the breeding pig core group, and eliminate breeding pig individuals with T / G genotype and G / G genotype at the 245th position starting from the 5'-end to gradually increase the frequency of allele T.

7. The method according to claim 5 or 6, characterized in that Determine the SNP molecular marker of the breeding pig as described in claim 1 by analyzing the nucleic acid sequence of the breeding pig, wherein the nucleic acid sequence is as shown in SEQ ID No.

1.

8. The method according to claim 5 or 6, characterized in that The source of the pig is at least one of Duroc, Large White, and Landrace pigs or a hybrid chimeric pig of at least two of them.

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