CN110176274A - A method of boar blood lineage is divided based on full-length genome SNP information - Google Patents
A method of boar blood lineage is divided based on full-length genome SNP information Download PDFInfo
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Abstract
The invention discloses a kind of methods for carrying out blood lineage's division to boar based on full-length genome SNP information.First to object acquisition bodily tissue is divided, DNA is extracted, parting is carried out by genome SNP of certain genotyping technique to every individual, by Quality Control, filters out qualified SNP site.The additive inheritance correlation between individual is calculated by genome SNP genotype, then 1 is used to subtract the value as " distance " between individual two-by-two, next clustering is carried out by R language " hclust " function to combination of two, takes 0.9844 threshold value as division blood lineage.The relatively traditional blood lineage's division methods of the present invention, obtained result is clearly succinct, and has fully absorbed the allelic information from parent both sides' transmitting, has higher reliability to the division of blood lineage.
Description
Technical field
The present invention relates to animal breeding field more particularly to a kind of boar blood lineage is divided based on full-length genome SNP information
Method.
Background technique
Have been generally acknowledged that (i.e. offspring's coefficient of inbreeding is greater than mating parents within 6 generations apart from common ancestor's number in thremmatology
It 0.78%) is then inbred, abbreviation inbreeding.Since inbreeding can increase the probability that recessive deleterious homozygotes occur, thus have
It may cause inbreeding depression.Therefore, core kind pig farm carries out the purpose of close-inbreeding to be usually being to avoid the generation of inbreeding, and field
Inside having enough blood lineages then is the necessary condition for preventing inbreeding depression.For guarantee have enough blood lineages, then need in field to
Pig of choosing seeds carries out accurate blood lineage's division, and the boar quantity of each blood lineage is fully ensured that in seed selection.Therefore, accurate to divide kind
Pig blood system is to guarantee seed selection and the apolegamy prerequisite that everything goes well with your work carries out.
In seed selection, breeder except using performance as seed selection foundation in addition to, often also take into account blood lineage, however the division of blood lineage
But there is dispute in method.By taking boar as an example, it is generally recognized that both ends herd boar does not have any genetic connection that can then divide within 6 generations
Into two blood lineages, but in practical applications, since individual amount is numerous and pedigree record is sufficiently complex, for convenient for sight
It examines, breeder often only considers the pedigree information in terms of the father.If both ends boar has on paternal origin within 6 generations
Common ancestor then belongs to same blood lineage, is otherwise different blood lineages.This method is although easy to operate, but has ignored depositing for mother
Because sow is multiparous animal, it can mate in different parity from different boars, it is thus possible to will appear a large amount of " with female different
The case where father ", and above-mentioned blood lineage's division methods can not consider such case.In addition, there may be mistakes for the record of pedigree, even if
Record accurate, allele repeatedly transmits in the generation, between offspring gene similarity degree how many also not known to.Therefore,
Urgent need finds a kind of more accurate boar blood lineage division methods.
Summary of the invention
It is an object of the invention to establish a kind of boar blood lineage's division methods based on full-length genome SNP information, solve existing
There are division methods in technology unreliable, only considers the problems of the pedigree information in terms of the father.
Specific technical solution of the present invention is as follows:
With the development of high throughput sequencing technologies, the SNP letter of genes of individuals group can be obtained on animals and plants at present
Breath is just proposed the concept of gene group selection early in Meuwissen in 2001 et al., is predicted using the SNP of genome high-density
The breeding value of individual is simultaneously chosen seeds.The basic reason that Accurate Prediction individual breeding value is capable of in gene group selection is this method standard
The affiliation between individual is really predicted, and more accurate with relationship between pedigree prediction individual than conventional breeding.Pass through gene
Group SNP data can calculate the correlation of the additive inheritance between two individuals, and additive inheritance correlation is equal to the 2 of two individual coefficient of coparentage
Times, coefficient of coparentage is the coefficient of inbreeding of offspring produced by two stud matings, therefore can predict two by genome SNP data
A possibility that inbreeding, occurs for stud mating.It is therefore believed that can be divided with a kind of blood lineage based on full-length genome SNP marker
Method substitutes traditional blood lineage's division methods, and the new method developed should have higher on dividing boar blood lineage than conventional method
Reliability.
One aspect of the present invention discloses a kind of method for carrying out boar blood lineage division based on full-length genome SNP information, passes through
The SNP genotype for excavating pig genes of individuals group calculates the additive inheritance correlation between individual two-by-two by genomic data, then really
All boars, are divided into different blood lineages by the threshold value for determining blood lineage's division by clustering.
Wherein, genome SNP parting means are not limited solely to certain experimental technique and analysis of biological information method, own
The genome SNP that mature experimental technique and analysis of biological information method obtains is used equally for carrying out boar blood lineage division.
Preferably, specifically includes the following steps:
S1: DNA is extracted from the pig individual divided to blood lineage, obtains the genotype information of genome SNP；
The control of S2, SNP mass: genome SNP site obtained in S1 is screened, and chooses SNP site, the SNP
Site meets claimed below:
1) only there are two types of the SNP sites of allele for selection；2) group's minimum gene frequency MAF >=0.01；3) it breathes out
Generation-Weinberg equilibrium examines P-value >=1 × 10-5；4) single locus miss rate in group is lower than 20%；
S3: the additive inheritance correlation between individual two-by-two is calculated by genome SNP data, then by clustering to institute
There is individual to be clustered, delimit threshold value and carry out blood lineage's division.
It should be understood that the present invention is not limited to above-mentioned steps, the step of can also including other, such as before step S1,
It include also other additional steps between step S1 and S2, between step S2 and S3, after step S3, and without departing from the present invention
Protection scope.
In S2, for the SNP site of missing, carries out or all may be used without genotype filling.
Preferably, in S2, it is assumed that allele in certain SNP site reference sequences is A, mutation allele a, right
It is 0,1 and 2 that all SNP sites, which are that AA, Aa and aa recode respectively according to genotype, if having certain individual in the site deletion,
It is encoded to 5.
Preferably, in S3, the additive inheritance being calculate by the following formula between individual is related:
Wherein AijFor the additive inheritance correlation of i-th of body and j-th of body, a shared m effectively SNP site (missing SNP
Site is not involved in calculating), BikFor the genotype of i-th k-th of body effective SNP site, BjkFor j-th k-th of body effective SNP
The genotype in site, pkFor frequency of the allele a in group of k-th of effective SNP site.
It should be appreciated that those skilled in the art can choose any appropriate meter the present invention is not limited to above-mentioned calculation formula
Formula is calculated to complete technical solution of the present invention, and within protection scope of the present invention.
Preferably, it is diploid species that the additive inheritance calculation formula, which adapts to species,.Monoploid or polyploid species are not
It is calculated using the formula.
Preferably, the additive inheritance correlation calculated between individual is passed through into formula Aij'=1-AijIt is converted, then to institute
A after having conversionij' using the class method of average progress clustering in R language " hclust " function.
Preferably, according to the definition of close relative, two stud matings of the additive inheritance correlation equal to 0.0078 × 2=0.0156 will
It is considered as inbreeding, therefore, using Aij'=0.9844 as the threshold value for dividing blood lineage, between class distance will be considered less than 0.9844
It is same blood lineage.
The relevant calculation of above-mentioned additive inheritance has fully absorbed the specifying information that allele transmits between generations, and
The information in terms of the father is not only utilized, also takes full advantage of the information in terms of mother.
Above-mentioned additive inheritance relevant calculation is only related with the genotype of individual, not related with specific character.
Preferably, in S1, DNA is extracted by clip ear tissue, the pig structure of blood lineage's division is treated using GBS technology
Build genomic library.
It is enterprising in IlluminaHiSeq X Ten high-flux sequence platform in a particular preferred embodiment of the invention
The initial data of row sequencing, acquisition carries out Quality Control by Fastqc software, and processed segment passes through BWA 0.7.15 software ratio
To on reference genome, after carrying out base mass calibration, passes through GATK 4.0.6.0 software and carry out SNP parting.
Application of the above-mentioned method in animal breeding field of the present invention second disclosure of the invention.
On the basis of common knowledge of the art, above-mentioned each optimum condition, can any combination, and without departing from structure of the invention
Think of and protection scope.
The invention has the benefit that having fully absorbed and having come from based on the method that genome SNP information divides boar blood lineage
In parent both sides allele generation transmit between specifying information, compared to only consider paternal origin conventional blood lineage divide
Method, the present invention are more accurate between the prediction of the affiliation individual, so as to more accurately be divided to blood lineage；This
Outside, new division methods interface is clearly succinct, convenient for providing reference in practical applications for breeder.
Detailed description of the invention
Fig. 1 is the flow chart for carrying out blood lineage's division in the embodiment of the present invention based on genome SNP data.
Fig. 2 is blood lineage's dendrogram based on genome SNP data in the embodiment of the present invention
(bloodlineclusterdendrogram), wherein all individuals in respective red frame belong to the same blood lineage.
Fig. 3 is the family tree based on all pedigree informations of parent in the embodiment of the present invention, wherein what 60 herd boars were numbered
Initial indicates that remaining boar indicates that sow is indicated with D with S with V.
Fig. 4 is the family tree that father's pedigree information is based only in the embodiment of the present invention.
Specific embodiment
Technical solution of the present invention is described in detail with reference to the accompanying drawings and examples, but therefore will be not of the invention
It is limited among the embodiment described range.
In the following examples, the experimental methods for specific conditions are not specified, according to conventional methods and conditions, or says according to commodity
Bright book selection.The reagents and materials used in the present invention are commercially available.
Embodiment 1 is divided based on the blood lineage of genome SNP data
Experimental material: experimental material is in the two area original seed pig farm of Qingyuan City of Wen Shi food Group Plc subordinate
60 herd boars (initial is indicated with V).All 60 herd boars have passed through GBS (genotyping-by-sequencing)
Technology carries out genome SNP genotype and excavates.
The present embodiment flow chart is shown in Fig. 1, the specific steps are as follows:
All boars extract DNA by clip ear tissue, using the simplification base based on two kinds of restriction enzymes of EcoRI and MspI
Because group (GBS) technology constructs genomic library to all boars, and on IlluminaHiSeq X Ten high-flux sequence platform
It is sequenced.The initial data of acquisition carries out Quality Control by Fastqc software, and processed segment passes through BWA 0.7.15 software
It compares on reference genome, after carrying out base mass calibration, SNP parting is carried out by GATK 4.0.6.0 software.To obtaining
The SNP obtained carries out Quality Control, the standard selected and remain are as follows: only selection includes the SNP site of two allele, minimum gene frequency
MAF >=0.01, Hardy-Weinberg equilibrium examine P-value >=1 × 10-5It is lower than 20% SNP site with site deletion rate, most
197 483 effective SNP sites are obtained eventually.For the SNP site of missing, select to fill without genotype here.
SNP genotype is converted into 012 format by Vcftools 0.1.13 software, deletion Genotype is indicated with 5.Meter
The additive inheritance correlation of all boars between any two is calculated, and subtracts the value with 1, next uses R language " hclust " function
In the class method of average carry out clustering, the individual by between class distance less than 0.9844 is divided into a blood lineage.What blood lineage divided
As a result see Fig. 2,60 boars are divided into 11 blood lineages altogether.
The new blood lineage's division methods of embodiment 2 are compared with traditional division methods
Experimental material: all ancestors' information that parent to the great-grandfather's generation of above-mentioned 60 herd boars are recalled from pedigree (remove 60
Remaining outer boar initial of head boar indicates that sow is indicated with D with S), all ancestors excavate without genome SNP, as biography
The material that the blood lineage that unites divides, for being compared with blood lineage's division result of the invention.
It recalls all 60 boars in field and pedigree structure is carried out by Pedigraph software, as general to the pedigree in great-grandfather's generation
After all parents of 60 boars all take into account pedigree, result as shown in Figure 3 is generated, it can be seen that pedigree structure pole
It is complicated, is difficult for individual to be divided into some blood lineage.Therefore consider that only absorbing the information from father carries out pedigree structure, knot
Fruit is as shown in Figure 4.Pass through comparison diagram 2 and Fig. 4's as a result, result that the two divides blood lineage is all identical on most of individual
, but also have exception.In addition to the possible mistake of individual pedigree records, the identical individual of mother can not be divided into a blood by Fig. 4
In system.By taking boar V12 and V40 as an example, this is unique a pair of father difference but the identical combination of mother (D40) in 60 boars
(Fig. 3), therefore be uterine half sibs brother, but since conventional method only considers the information of father, by both ends pig
It is divided into two blood lineages (Fig. 4).And in blood lineage's division methods based on genome SNP information, this both ends pig is then divided into
Same blood lineage (Fig. 2), therefore new method is more rationally more reliable than conventional method.And the interface that new method obtains is clearly simple
It is clean, other pig information are not adulterated, convenient for providing reference in practical applications for breeder.
The above embodiment is a preferred embodiment of the present invention, but embodiments of the present invention are not by above-described embodiment
Limitation, other any changes, modifications, substitutions, combinations, simplifications made without departing from the spirit and principles of the present invention,
It should be equivalent substitute mode, be included within the scope of the present invention.
Claims (10)
1. a kind of method for carrying out boar blood lineage division based on full-length genome SNP information, which is characterized in that by excavating pig individual
The SNP genotype of genome calculates the additive inheritance correlation between individual two-by-two by genomic data, then determines that blood lineage divides
Threshold value, all boars are divided into different blood lineages by clustering.
2. the method according to claim 1, wherein the following steps are included:
S1: DNA is extracted from the pig individual divided to blood lineage, obtains the genotype information of genome SNP；
The control of S2, SNP mass: genome SNP site obtained in S1 is screened, and chooses SNP site, the SNP site
Meet claimed below:
1) only there are two types of the SNP sites of allele for selection；2) group's minimum gene frequency MAF >=0.01；3) Hardy-temperature
Burger balance check P-value >=1 × 10-5；4) single locus miss rate in group is lower than 20%；
S3: the additive inheritance correlation between individual two-by-two is calculated by genome SNP data, then by clustering to all
Body is clustered, and delimited threshold value and is carried out blood lineage's division.
3. according to the method described in claim 2, it is characterized in that, in S2, it is assumed that the equipotential in certain SNP site reference sequences
Gene is A, mutation allele a, be that AA, Aa and aa recode respectively according to genotype is 0,1 He to all SNP sites
2, if there is certain individual in the site deletion, it is encoded to 5.
4. according to the method described in claim 2, it is characterized in that, in S3, the additive inheritance that is calculate by the following formula between individual
It is related:
Wherein AijFor the additive inheritance correlation of i-th of body and j-th of body, a shared m effectively SNP sites (lack SNP site
It is not involved in calculating), BikFor the genotype of i-th k-th of body effective SNP site, BjkFor j-th k-th of body effective SNP site
Genotype, pkFor frequency of the allele a in group of k-th of effective SNP site.
5. according to the method described in claim 4, it is characterized in that, it is diploid that the additive inheritance calculation formula, which adapts to species,
Species.
6. according to the method described in claim 4, it is characterized in that, the additive inheritance correlation calculated between individual is passed through formula
Aij'=1-AijIt is converted, then to the A after all conversionsij' carried out using the class method of average in R language " hclust " function
Clustering.
7. according to the method described in claim 6, it is characterized in that, by Aij'=0.9844 is as the threshold value for dividing blood lineage, between class
Distance will be considered as same blood lineage less than 0.9844.
8. according to the method described in claim 2, it is characterized in that, extracting DNA in S1 by clip ear tissue, adopting
Genomic library is constructed with the pig that GBS technology treats blood lineage's division.
9. according to the method described in claim 2, it is characterized in that, in IlluminaHiSeq X Ten high-flux sequence platform
On be sequenced, the initial data of acquisition carries out Quality Control by Fastqc software, and processed segment is soft by BWA 0.7.15
Part is compared onto reference genome, after carrying out base mass calibration, carries out SNP parting by GATK 4.0.6.0 software.
10. application of the method in animal breeding field described in -9 any one according to claim 1.
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| CN110973057A (en) * | 2019-12-11 | 2020-04-10 | 温氏食品集团股份有限公司 | Breeding method of breeding pigs |
| CN111370058A (en) * | 2020-03-19 | 2020-07-03 | 广西大学 | Method for tracing buffalo blood line source and carrying out genome matching based on whole genome SNP information |
| CN112466395A (en) * | 2020-10-30 | 2021-03-09 | 苏州赛美科基因科技有限公司 | SNP (Single nucleotide polymorphism) polymorphic site based sample identification label screening method and sample identification detection method |
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