CN104982387B - A kind of molecular marker-assisted selection method of MUC13 and FUT1 genes - Google Patents

Abstract

The invention discloses a molecular marker-assisted selection method of MUC13 and FUT1 genes, comprising the following steps: analyzing the gene frequencies of MUC13 genes and FUT1 genes in existing populations; Frequency distribution; analysis of the correlation of combined genotypes of two genes in existing populations with traditional breeding traits; development of adapted molecular marker-assisted methods. The method of the present invention carries out molecular breeding for the two genes of MUC13 gene and FUT1 gene at the same time, and the selection and breeding of piglet diarrhea disease resistance is relatively comprehensive; the present invention carries out two anti-diarrhea genes according to the scale of the core group of breeding pigs, combined with seed selection and matching links Molecular marker-assisted selection breeding combines the analysis results with the actual situation of the existing populations to establish a highly operable and comprehensive molecular breeding method for anti-piglet diarrhea that meets the needs of the enterprise, so as to quickly improve the breeding efficiency and take into account the benefits of the enterprise.

Description

A molecular marker-assisted selection method for MUC13 and FUT1 genes

technical field

The invention belongs to the field of pig molecular breeding, more specifically, the invention relates to a molecular marker-assisted selection method of MUC13 and FUT1 genes.

Background technique

Most of the existing molecular marker-assisted selection breeding for mucin 13 (mucin 13, MUC13) and a1-fucosyltransferase gene (FUT1) anti-diarrhea genes are separate genes, or are just scientific research, and there is no The effective combination with the traditional breeding methods on the spot cannot take into account the benefits of the enterprise, so that it is impossible to carry out molecular marker-assisted selection breeding of anti-diarrhea genes in the core group of breeding pigs for a long time. Most of the research focuses on the genetic variation analysis of the two genes in different pig herds, or the correlation analysis with diarrhea phenotype, meat quality, carcass traits and litter size, and there is no specific application plan for molecular breeding in enterprises research and dissertation. Some studies on simple molecular breeding only focus on one gene in MUC13 and FUT1, without considering the actual operation of the enterprise, especially the impact of selection and elimination of a large number of breeding pigs on the profit of the enterprise, the operability is not strong, and there is no more practical molecular breeding The method of program creation.

The most prominent problem of the existing technology is that it is not combined with the field practice breeding, not combined with the existing breeding pig breeding goals, does not consider the enterprise benefit, and cannot achieve both enterprise benefit and breeding efficiency, so that molecular breeding cannot be carried out for a long time.

Contents of the invention

In view of this, in order to overcome the above-mentioned problems in the prior art, the present invention provides a molecular marker-assisted selection method of how to establish two different anti-diarrhea genes MUC13 and FUT1 genes in the core population of breeding pigs. This method can be effectively combined with on-site traditional breeding. Through the analysis of each link, different anti-diarrhea gene molecular marker-assisted selection breeding programs are used for different groups, which is more suitable for enterprise breeding applications, taking into account enterprise benefits and breeding efficiency.

In order to realize the above-mentioned purpose of the invention, the present invention adopts the following technical solutions:

A molecular marker-assisted selection method for MUC13 and FUT1 genes, comprising the following steps:

1) Analyze the gene frequency of MUC13 gene and FUT1 gene in the existing population;

2) Analyze the number and frequency distribution of the two gene combination genotype individuals in the existing population;

3) Analyze the correlation between the combined genotype of the two genes in the existing population and the main selection traits of traditional breeding;

4) Develop adapted molecular marker-assisted methods.

In some of these embodiments, step 1) is: use plink software to analyze the gene frequency of the MUC13 gene and the FUT1 gene in the existing population, if the minimum allele frequency MAF<0.05, it means that this locus is basically homozygous, not Molecular marker-assisted selection is required; if MAF>0.05, it indicates that there is variation in the population, and molecular marker-assisted selection is performed.

In some of these embodiments, step 2) is: analyze the number and frequency distribution of the two gene combination genotype individuals of the existing population, if the frequency of the dominant allele combination genotype is relatively high in the existing core group , then select individuals with dominant combination genotypes in the selection and retention of boars and sows at the same time; Individuals with dominant combination genotypes are selected; if the frequency of dominant allele combination genotypes is low in the existing core group, it is only required to select individuals with the same phenotype when the phenotype is determined at the time of selection, and individuals with dominant combination genotypes are preferentially selected.

In some of these embodiments, the higher frequency means the frequency is greater than 0.7, the neither high nor low frequency means the frequency is 0.3-0.7, and the lower frequency means the frequency is less than 0.3.

In some of these embodiments, step 3) is: analyzing the correlation between the combined genotype of the two genes in the existing population and the main selection traits of traditional breeding, the main selection shapes of traditional breeding are daily gain, feed-to-meat ratio, Backfat thickness, lean meat percentage, paternal index, maternal index, and body shape and appearance; if the combined genotype of the two genes is positively correlated with daily gain, lean meat percentage, paternal index, maternal index, and body shape and appearance, Negative or no correlation with feed-to-meat ratio and backfat thickness, it means that the molecular breeding selection of the two genes is consistent with the on-site breeding goal, and the dominant allele type is taken as a necessary condition for selection when selecting and retaining; if it is consistent with the above situation Different, contradictory with some breeding traits, the breeding of on-site measured traits is taken as the first reference, and the anti-diarrhea genotype is used as the second reference. Breeding pigs with the same performance at the time of retention are selected, and the dominant combination genotype is preferentially selected. Individuals, do not make necessary conditions for selection and retention, insist on selection for a long time, and gradually complete the optimization of anti-diarrhea genes.

In some of these embodiments, the size of the existing population described in steps 1)-3) is larger than the core group of 500 heads, the larger the population size, the larger the selection space, and the accuracy of molecular markers and field phenotyping traits combined selection higher.

Through different research and analysis methods, the present invention has invented the MUC13 and FUT1 gene molecular marker-assisted selection application method that can be combined with traditional breeding, the analysis process established according to the MUC13 and FUT1 gene molecular marker-assisted selection method, and how to analyze different results. Conduct judgment and evaluation of molecular breeding research. Compared with the prior art, the present invention has the following beneficial effects:

1) The method of the present invention simultaneously carries out molecular breeding on two genes, the MUC13 gene affecting pre-weaning piglet diarrhea and the FUT1 gene affecting post-weaning piglet diarrhea, so that the selection and breeding of piglet diarrhea disease resistance is relatively comprehensive;

2) In addition to separately analyzing the variation of the two genes in the existing population, the method of the present invention increases the frequency of the combined genotype of the two genes in the existing population, and evaluates the variation of the population and the combined genotype in the existing population. The distribution of piglets can be judged according to the degree of difficulty of breeding, and different breeding schemes for different situations can be given to optimize the anti-diarrhea ability of piglets in a more comprehensive way;

3) The correlation between the gene and the diarrhea phenotype has not been analyzed repeatedly, and the correlation with the meat quality and carcass traits has not been carried out. (daily gain, feed-to-meat ratio, backfat thickness, lean meat percentage, paternal index, maternal index, body shape appearance and other phenotypic traits) to evaluate whether the molecular selection of the two genes is consistent with the existing breeding goals Consistent, taking into account the on-site selection and selection and retention operations, through the above analysis, we can better formulate the application plan of MUC13 and FUT1 gene molecular marker-assisted selection breeding suitable for different breeding pig groups of the enterprise;

4) The method of the present invention carries out two anti-diarrhea gene molecular marker assisted selection breeding according to the size of the core group of breeding pigs, combined with the selection and matching links, and combines the analysis results with the actual situation of the existing population to establish an operable pig that meets the needs of the enterprise. Strong and comprehensive molecular breeding method for anti-piglet diarrhea, which can quickly improve breeding efficiency and take into account enterprise benefits.

Description of drawings

Fig. 1 is the flowchart of establishing the molecular marker-assisted selection method of MUC13 and FUT1 genes in Example 1 of the present invention;

Fig. 2 is two genotype combination distribution figures of Duroc population in the embodiment of the present invention 2;

Fig. 3 is a graph showing the combined distribution of two genotypes of the Pietrain population in Example 2 of the present invention.

detailed description

In order to make the object, technical solution and advantages of the present invention clearer, the present invention will be further described in detail below in conjunction with the accompanying drawings and embodiments. It should be understood that the specific embodiments described here are only used to explain the present invention, not to limit the present invention.

Example 1 A molecular marker-assisted selection method for MUC13 and FUT1 genes

Please refer to Fig. 1, which is a flow chart of establishing a molecular marker-assisted selection method for MUC13 and FUT1 genes in this embodiment, including the following steps:

1) Gene frequency analysis of mucin 13 (mucin 13, MUC13) gene and a1-fucosyltransferase gene (FUT1) in the existing population

This step is to use the plink software to analyze the degree of gene variation. The main measure and judgment index is MAF—the minimum allele frequency. In theory, if MAF<0.05, it means that this locus is basically homozygous, and molecular marker-assisted selection is not required. ; If MAF>0.05, it means that there is variation in the population, and molecular marker-assisted selection can be performed.

2) Analyze the distribution of the two gene combinations in the existing population, including the number and frequency of individual genotypes in each combination

Use the statistical graphing function of excel to analyze the distribution of the two gene combinations. Through this step, the degree of difficulty of carrying out molecular breeding of the two genes in the existing population can be judged. The dominant allele combination genotype GG/AA occupies different proportions in the existing core population, and different breeding programs can be adopted:

a. If the frequency is relatively high (greater than 0.7), individuals with dominant combination genotypes can be selected in the selection and retention of boars and sows at the same time;

b. If the frequency is not high or low (0.3-0.7), it is only required to select individuals with dominant combination genotypes when selecting and retaining boars;

c. If the frequency is low (less than 0.3), it is only required to select individuals with the same dominant genotype when the phenotype is determined at the time of selection.

In the above three cases, under the same conditions, priority will be given to individuals with superior combination genotypes when matching.

3) Analyze the combined genotype of the two genes in the existing population and the main selection traits of traditional breeding (daily gain, feed to meat ratio, backfat thickness, lean meat percentage, paternal index, maternal index, body shape and appearance and other phenotypic traits) relevance of

The correlation between the combined genotypes of the two genes in the existing population and the main selection traits of traditional breeding was analyzed by R software, and the model was: y=1μ+Zα+e. Among them, y is the measured phenotype value, μ is the overall average value, Z is the indicator matrix of genotype, α is the SNP random additive genetic effect vector, and α—N(0, Gσα2) (G is the molecular consanguinity Correlation matrix, σα2 is the additive genetic variance), Zα is the genotype effect, and e is the residual. Correlation of combined genotypes of two genes in existing populations with traditional breeding primary selection traits. Through the positive and negative correlation analysis of this step, it can be judged whether the genotype of the dominant allele combination is consistent with the performance of the traits selected in the field practice:

a. If it is positively correlated or not correlated with traits such as daily gain, lean meat rate, paternal index, maternal index, body shape appearance score, etc., and negatively correlated or not correlated with feed-to-meat ratio, backfat thickness, it means that the two genes Molecular breeding selection is consistent with on-site breeding goals, and the dominant allele type can be used as a necessary condition for selection when selecting and retaining;

b. If it is different from the above situation and contradicts with some breeding traits, it is necessary to balance the breeding, comprehensively consider the breeding management situation of the breeding farm, the market development needs, etc., and take the breeding of the traits measured on the spot as the first reference, anti-diarrhea The genotype is the second reference, and the selection of breeding pigs with the same performance at the time of retention is given priority to the selection of individuals with the dominant genotype combination, and no necessary conditions are selected for retention. Through this method, long-term selection can gradually complete the optimization of anti-diarrhea genes .

The above two methods in different situations have realized the organic combination of pig molecular breeding and on-site traditional breeding, which is suitable for the application of pig breeding enterprises, can quickly improve the breeding efficiency and take into account the benefits of the enterprise. On the other hand, through the analysis of this link, it can be judged which combination The genotypes were consistent with the field selection goals.

4) Develop adapted molecular marker-assisted methods

Through the analysis of steps 1)-3), combined with the existing core group size (the larger the group size, the larger the selection space, the higher the accuracy of the combination of molecular markers and on-site phenotyping traits) and on-site selection and selection link, to formulate adaptive molecular marker-assisted methods. For example, if the size of the core group is small and there is not much room for selection, you can choose to focus on the selection of boars first, and give priority to the selection of dominant allelic genotypes for sows under the same conditions of on-site breeding phenotypes.

Example 2 Molecular marker-assisted selection method of MUC13 and FUT1 genes of Duroc population and Pietrain population

The establishment process of a molecular marker-assisted selection method for MUC13 and FUT1 genes in this embodiment includes the following steps:

1) Gene frequency analysis of mucin 13 (mucin 13, MUC13) gene and a1-fucosyltransferase gene (FUT1) in the existing population

Use plink software to detect the genotypes of the two anti-diarrhea genes of 604 Duroc populations and 315 Pietrain populations, and analyze the degree of gene variation:

MUC13 Gene Variation Analysis:

Analysis of FUT1 gene variation:

The MAFs of the two genes in the above two populations were both greater than 0.05, indicating that there were variations in the two genes in the two populations, and molecular marker-assisted selection breeding could be carried out.

2) Analyze the distribution of the two gene combinations in the existing population, including the number and frequency of individual genotypes in each combination

The distributions of the two genotype combinations of the two populations are shown in Figure 2 and Figure 3, respectively. The results show that there are 5 combination types in the Duroc population, among which the MUC13 and FUT1 genes are the number of individuals of the dominant genotype combination GG/AA There are 222 heads, accounting for 36.75% (222/604) of the total population, and it is only required to select individuals with dominant combination genotypes when selecting and retaining boars; there are 8 combination types in the Pietrain population, only 11 of which are dominant combination genotypes Individuals, accounting for 3.49% (11/315) of the total population, are only required to select and retain when the phenotype is equal to the same performance, and preferentially select individuals with dominant combination genotypes.

3) Analyze the correlation between the combined genotypes of the two genes in the existing population and the main traits of traditional breeding by R software, and the analysis results are shown in Table 1 and Table 2 below:

By analyzing the genotype distribution of the two anti-diarrhea gene combinations, it was found that:

In the Duroc population, the GG/AA type combination (222 heads) accounted for 36.75% of the population. The correlation analysis between various combination genotypes and each production trait showed that the comprehensive production performance of GG/GA combination individuals was the best, followed by GG/AA type individuals. It was judged that the combination types GG/GA and GG/AA were dominant combination types, and the proportion of the two genotypes in the population was 78.8%. In view of this, in the Duroc population, the two dominant allele types can be used as a necessary condition for selection when selecting and retaining. Due to the large population size (604 core populations), it can be carried out simultaneously in boars and sows. optimization.

In the Pietrain population, the combination type of the dominant allele was significantly negatively correlated with body height, head shape score, limb and hoof score and other body shape appearance traits, but was relatively positively correlated with 100kg lean meat percentage and backfat thickness production traits. And the frequency of favorable combined genotypes was low in the population, only 3.49%. In the Pietrain breeding program formulated according to the current market demand analysis, body shape and appearance are the key breeding directions. Therefore, considering factors such as the low genotype frequency of the dominant allele combination in the population, the negative correlation with body shape and appearance, and the small population size (315 core populations), the Pietrain population is not suitable for molecular marker-assisted selection of anti-diarrhea genes.

The above-mentioned embodiments only express the implementation manner of the present invention, and the description thereof is relatively specific and detailed, but should not be construed as limiting the patent scope of the present invention. It should be pointed out that those skilled in the art can make several modifications and improvements without departing from the concept of the present invention, and these all belong to the protection scope of the present invention. Therefore, the protection scope of the patent for the present invention should be based on the appended claims.

Claims (4)

1. a kind of molecular marker-assisted selection method of MUC13 and FUT1 genes, it is characterised in that comprise the following steps：

1) gene frequency of MUC13 genes and FUT1 genes in existing colony is analyzed；

2) two assortment of genes genotype individuals quantity and frequency distribution situation of existing colony are analyzed：To two of existing colony Assortment of genes genotype individuals quantity and frequency distribution situation are analyzed, if advantage allelic combination genotype is in existing core When frequency is more than 0.7 in heart group, then the selective advantage combination gene type individual in the selecting and remain of boar and sow simultaneously；If advantage etc. Position assortment of genes genotype is then only required in selective advantage group when boar is selected and remain when frequency is 0.3-0.7 in existing core group Close genotype individuals；If advantage allelic combination genotype in existing core group frequency be less than 0.3 when, require nothing more than and select and remain When determine phenotype on an equal basis performance under, preferentially select and remain advantageous combination genotype individuals；

3) correlation of the combination gene type and traditional breeding method major traitses of two genes in existing colony is analyzed；

4) the molecular labeling householder method adapted to is formulated.

2. the molecular marker-assisted selection method of MUC13 and FUT1 genes according to claim 1, it is characterised in that step It is rapid 1) to be：The gene frequency of MUC13 genes and FUT1 genes in existing colony is carried out using plink softwares to analyze, if minimum Gene frequency MAF<0.05, illustrate that this site is substantially homozygous, be not required to carry out molecular marker assisted selection；If MAF>0.05, Illustrate that colony has variation, then carry out molecular marker assisted selection.

3. the molecular marker-assisted selection method of MUC13 and FUT1 genes according to claim 1, it is characterised in that step It is rapid 3) to be：Analyze the correlation of the combination gene type and traditional breeding method major traitses of two genes in existing colony, the tradition The main choosing of breeding is shaped as daily gain, feedstuff-meat ratio, the thickness of backfat, lean meat percentage, paternal index, maternal index and appearance traits；If two The combination gene type of gene and daily gain, lean meat percentage, paternal index, maternal index, appearance traits positive correlation or non-correlation, with Feedstuff-meat ratio, thickness of backfat negative correlation or non-correlation, then illustrate that two gene molecule breeding selections are consistent with live breeding goal, Necessary condition when selecting and remain by advantage allelotype alternatively；

If different from the above situation, contradict, then taken first using the seed selection of on-site measurement character as the with some Breeding Traits One reference, anti diar rhea genotype are the second reference, the boar that equal performance shows when selecting and remain, preferentially select and remain advantageous combination genotype Individual, necessary condition is not done and is selected and remain, adheres to selecting for a long time, is gradually completing the optimization of anti diar rhea gene.

4. the molecular marker-assisted selection method of the MUC13 and FUT1 genes according to any one of claims 1 to 3, it is special Sign is, step 1) -3) described in the scale of existing colony be more than 500.