Paternity testing single nucleotide polymorphism (SNP) label combinations and detection method for Holstein cattle group

A paternity test, Holstein cattle technology, applied in the field of Holstein cattle paternity test detection system, can solve the problems of long time and heavy workload, etc.

Active Publication Date: 2011-03-09
CHINA AGRI UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

If the detection sample is large, the traditional method takes a long time and has a large workload, so it is more suitable to choose high-throughput methods such as mass spectrometry of flight (MALDI-TOF) or chip

Method used

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  • Paternity testing single nucleotide polymorphism (SNP) label combinations and detection method for Holstein cattle group
  • Paternity testing single nucleotide polymorphism (SNP) label combinations and detection method for Holstein cattle group
  • Paternity testing single nucleotide polymorphism (SNP) label combinations and detection method for Holstein cattle group

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0045] Example 1: Selection of SNP marker combinations

[0046] The present invention has gone through three processes altogether to the selection of the SNP mark that is used for paternity identification system, specifically as follows:

[0047] (1) Preliminary screening of references and bovine microarray data

[0048] The main sources of the SNP markers initially selected in the present invention include two parts, one part comes from the partial SNP markers applied to cattle reported in the literature (Heaton et al., 2002; Werner et al., 2004), and the other part comes from the whole genome selection of cows in China Agricultural University. Research group ("948" project 2010C10) SNP marker chip (BovineSNP50 Genotyping BeadChip) data, a total of 149 SNP markers were obtained.

[0049] (2) Pool DNA sequencing

[0050] Primers were designed for the above 149 SNP markers, and 30 unrelated Holstein cattle mixed DNA pools were used as templates, and ABI 3730XL was used for di...

Embodiment 2

[0063] Example 2: Carrying out SNP polymorphism analysis and parentage inference on cattle herds by means of flight mass spectrometry:

[0064] 1. Genome Extraction

[0065] 1. Anticoagulant DNA extraction method

[0066] The blood sample in this test is bovine whole blood added with anticoagulant (sodium citrate). The blood was taken from the tail vein and stored in a freezer.

[0067] In this test, the spin column method was used to extract anticoagulant DNA, and the DP318 kit produced by Tiangen Company was used. The specific steps are as follows:

[0068] Shake the sample upside down, and take 600ul whole blood from the middle of the sample tube into a 2mL centrifuge tube.

[0069] Add 20ul proteinase K and 200ul buffer GB, use a vortexer for 15 seconds, and shake well.

[0070] Put the sample into a molecular hybridization oven at 56°C, pay attention to tightly cover the lid or use a parafilm to prevent leakage, digest for 5-10 hours, slowly invert and mix well while d...

Embodiment 3

[0126] Embodiment 3: Application in real groups

[0127] In order to verify the feasibility and accuracy of inferring the whole set of SNP markers in the actual population, ten family combinations (trios) were randomly selected from the experimental population to do the actual parent-child inference verification, and the data results obtained in Example 2 were used to carry out the mother-child test. The results of inference, father-son inference and parent inference are shown in Table 12 and Table 13 respectively.

[0128] Application of Table 1228 SNP marker combinations in actual populations

[0129]

[0130] Note: * Represents extremely significant parent-child relationship (confidence level exceeds 95%), + represents parent-child relationship is more significant (confidence level exceeds 85%) - represents parent-child relationship fails to meet the significant requirements (confidence level is less than 85%), all three situations indicate The parent-child relationshi...

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Abstract

The invention discloses paternity testing single nucleotide polymorphism (SNP) label combinations for a Holstein cattle group, and one of the combinations contains 28 SNP labels, and the other of the combinations contains 50SNP labels. In the combination, the nucleotide sequences of the forward primers of the 28 SNP labels are shown as SEQ ID NO.23-50 in turn, the nucleotide sequences of the reverse primers of the 28 SNP labels are shown as SEQ ID NO.73-100 in turn, and the nucleotide sequences of the single base extension primers of the 28 SNP labels are shown as SEQ ID NO.123-150 in turn; the nucleotide sequences of the forward primers of the 50 SNP labels are shown as SEQ ID NO.1-50 in turn, the nucleotide sequences of the reverse primers of the 50 SNP labels are shown as SEQ ID NO.51-100, and the nucleotide sequences of the single base extension primers of the 50 SNP labels are shown as SEQ ID NO.101-150. The SNP label combinations used for the Holstein cattle group have accurate results, optimally utilizes a flight mass spectrometry method, can quickly and conveniently detect SNP label polymorphisms with high-flux so as to conclude the parenthood of the cattle group.

Description

technical field [0001] The invention relates to a detection system for Holstein cattle paternity identification using SNP markers, in particular to 28 or 50 marker combinations, primer sequences and a detection method. Background technique [0002] According to literature reports, the average pedigree error rate of cattle herds around the world can reach 11% (Banos et al., 2001). Due to different feeding methods and production management conditions in different countries, the pedigree error rate also has certain differences. cannot be completely avoided. [0003] If the world average 11% pedigree error rate occurs in actual production, the genetic progress of milk production traits in the American dairy herd will be reduced by 12% to 15% (Banos et al., 2001), which will lead to inbreeding coefficient, sire variance Estimates of cross-country genetic correlations etc. are low. The simulation study of Israel and Weller et al. (2000) showed that if the pedigree error rate rea...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68G01N27/62G01N27/626
Inventor 王雅春李东俞英张毅孙东晓张沅
Owner CHINA AGRI UNIV
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