CN111518921A - Method for identifying Liancheng white duck by adopting SNP molecular marker technology - Google Patents
Method for identifying Liancheng white duck by adopting SNP molecular marker technology Download PDFInfo
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- CN111518921A CN111518921A CN202010604863.5A CN202010604863A CN111518921A CN 111518921 A CN111518921 A CN 111518921A CN 202010604863 A CN202010604863 A CN 202010604863A CN 111518921 A CN111518921 A CN 111518921A
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Abstract
A method for identifying Liancheng white ducks by adopting an SNP molecular marker technology belongs to the technical field of zootechnics and molecular biology. Sequencing 12 duck genetic resources by using a whole genome re-sequencing technology, mining re-sequencing data, screening specific 10 SNP (single nucleotide polymorphism) sites capable of identifying the Liancheng white duck, and combining the 10 SNP sites to identify the Liancheng white duck. The invention can use molecular marking technology to carry out scientific variety specificity identification on pure varieties and hybrid varieties, standardizes the production and management of duck genetic resources in China, can provide effective guarantee for duck genetic resource protection, and supports and guides the monitoring and evaluation of duck genetic resources.
Description
Technical Field
The invention relates to a method for identifying variety of Liancheng white duck, in particular to a method for identifying Liancheng white duck by adopting SNP molecular marker technology, belonging to the technical field of zootechnics and molecular biology.
Background
The phenomena of homonymy and heteronymy and homonymy foreign matter may exist in the duck market in China, even some companies may sell the hybridized variety as a pure breed in order to improve profits, the pure breed and the hybridized variety are difficult to distinguish only by means of appearance characteristics, however, the character separation may occur when the hybridized variety is used as germplasm resources to breed offspring, and the consistency of the group is influenced.
SNP (Single Nucleotide Polymorphism), called Single Nucleotide Polymorphism, is a third generation genetic marker, is universally present on chromosomes, has allele frequency not less than 1%, and is widely applied to paternity test and variety test at present because of the universal existence in DNA.
Disclosure of Invention
The invention aims to provide a molecular marker for identifying the specificity of the Liancheng white duck, in particular to a method for identifying the Liancheng white duck by adopting an SNP molecular marker technology, which utilizes the molecular marker technology to identify the specificity of the genetic resources of the duck.
The technical scheme of the invention is as follows:
a method for identifying Liancheng white ducks by adopting an SNP molecular marker technology is characterized in that 12 duck genetic resources are sequenced by utilizing a whole-genome re-sequencing technology, and SNP for variety identification is screened out by mining re-sequencing data.
The SNP sites are as follows:
| serial number | Chromosome | Site of the body | Reference genome | Mutations |
| 51 | CM018339.1 | 2804 | A | G |
| 120 | CM018359.1 | 172985 | C | T |
| 117 | CM018356.1 | 1235779 | C | T |
| 89 | CM018346.1 | 347406 | A | G |
| 37 | CM018335.1 | 1416702 | G | A |
| 50 | CM018339.1 | 1984 | T | G |
| 35 | CM018335.1 | 35146 | T | A |
| 28 | CM018333.1 | 2423437 | C | A |
| 13 | CM018329.1 | 1325873 | G | A |
| 87 | CM018346.1 | 23167 | C | A |
The 10 SNP sites can be used for distinguishing Liancheng white ducks from Jinyun sheldrake, Sansui duck, Zhongshan sheldrake, Shanma duck, Jinding duck, Taiwan brown sheldrake, Longsheng green duck, Pu Tian black duck, Pu Tian white duck, you county sheldrake and Ji' an red hair duck.
The invention can use molecular marking technology to carry out scientific variety specificity identification on pure varieties and hybrid varieties, standardizes the production and management of duck genetic resources in China, can provide effective guarantee for duck genetic resource protection, and supports and guides the monitoring and evaluation of duck genetic resources.
Drawings
FIG. 1 is a flowchart illustrating alignment with a reference genome in an embodiment of the present invention.
Detailed Description
1. Materials and methods
1.1 Experimental materials
Selecting 10 Jinyun sheldrake, Zhongshan sheldrake, Shanma sheldrake, Jinding duck, Taiwan brown sheldrake, Liancheng white duck, Longsheng green duck, Putian black duck, Putian white duck, you county sheldrake, Sansui duck and 300-day-old male and female ducks of Jian red hair duck respectively, taking blood from a wing vein by about 3mL, placing the obtained blood into a blood collection tube containing EDTA anticoagulant, and extracting genome DNA.
1.2 Whole genome Re-sequencing
Qualified DNA samples were randomly fragmented into fragments of 350bp in length by Covaris ultrasonication. The DNA fragment is subjected to end repair, ployA tail addition, sequencing joint addition, purification, PCR amplification and other steps to complete the preparation of the whole library. The constructed library was sequenced by an illumina sequencer. After the library is constructed, firstly using Qubit2.0 to carry out preliminary quantification, diluting the library to 1 ng/. mu.l, then using Agilent 2100 to detect the insert size of the library, and after the insert size meets the expectation, using Q-PCR to accurately quantify the effective concentration of the library (the effective concentration of the library is more than 2nM) so as to ensure the quality of the library.
1.3 alignment with a reference genome as shown in FIG. 1.
Adopting FastQC software to carry out quality control on high-throughput sequencing original data, adopting BWA software to compare the qualified data of quality control with green-head wild duck genome (CAU-Wild1.0), and adopting GATK software to carry out SNP detection and typing.
2. Results
Through whole genome re-sequencing data mining, 10 SNP combinations can distinguish Liancheng white ducks from other 11 duck genetic resources. Therefore, the 10 SNP sites can be used as a specific molecular marker for identifying the Liancheng white duck. The molecular marker is applied to identifying duck varieties, the operation is relatively simple, the specificity and the repeatability are high, and a new scientific basis is added for the correct storage and the reasonable utilization of poultry variety resources.
The combination of 10 SNPs can distinguish the liancheng white duck from 12 genetic resources, the combination of 51 SNPs can distinguish the liancheng white duck from the jin yun sheldrake, the combination of 51 SNPs can distinguish the liancheng white duck from the san sui duck, the combination of 120 SNPs can distinguish the liancheng white duck from the zhong sheldrake, the combination of 117 SNPs can distinguish the liang white duck from the jin shui duck, the combination of 89 SNPs can distinguish the liang white duck from the jin shui duck, the combination of 37 SNPs can distinguish the liang white duck from the taiwan brown sheldrake duck, the combination of 50 SNPs can distinguish the liang white duck from the long sheng cui duck, the combination of 35 SNPs can distinguish the liang white duck from the pun field black duck, the combination of 28 SNPs can distinguish the lian white duck from the jin tian white duck, the combination of 13 SNPs can distinguish the lian white duck from the county sheldrake duck, and the 87 SNPs can.
The 10 SNPs were as follows:
| serial number | Chromosome | Site of the body | Reference genome | Mutations |
| 51 | CM018339.1 | 2804 | A | G |
| 120 | CM018359.1 | 172985 | C | T |
| 117 | CM018356.1 | 1235779 | C | T |
| 89 | CM018346.1 | 347406 | A | G |
| 37 | CM018335.1 | 1416702 | G | A |
| 50 | CM018339.1 | 1984 | T | G |
| 35 | CM018335.1 | 35146 | T | A |
| 28 | CM018333.1 | 2423437 | C | A |
| 13 | CM018329.1 | 1325873 | G | A |
| 87 | CM018346.1 | 23167 | C | A |
Claims (3)
1. A method for identifying the Liancheng white duck by adopting an SNP molecular marker technology is characterized in that 12 duck genetic resources are sequenced by utilizing a whole-genome re-sequencing technology, 10 specific SNP sites capable of identifying the Liancheng white duck are screened out by mining re-sequencing data, and the 10 SNP sites are combined to identify the Liancheng white duck.
2. The method of claim 1, wherein the 12 duck genetic resources are respectively from the Liancheng white ducks, Jinyun sheldrake, Sansui ducks, Zhongshan sheldrake, Shanma ducks, Jindingducks, Taiwan brown duck, Longsheng green ducks, Pu Tian black ducks, Pu Tian white ducks, you county sheldrakes and Jian red hair ducks.
3. The method as claimed in claim 2, wherein 10 SNP sites for the Liancheng white ducks are selected to be 51, 120, 117, 89, 37, 50, 35, 28, 13 and 87 respectively, and the 10 SNP sites can be used to distinguish the Liancheng white ducks from the Jinyun sheldrake, Sansui ducks, Zhongshan sheldrake, Shanma ducks, Jindingya, Taiwan brown sheldrake, Longshengsu ducks, Pu Tian black ducks, Pu Tian white ducks, you county sheldrake and Jian Hongyou ducks.
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Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN113308558A (en) * | 2021-07-21 | 2021-08-27 | 江苏省家禽科学研究所 | Application of SNP locus combination in identifying Liancheng white duck variety |
| CN113308559A (en) * | 2021-07-21 | 2021-08-27 | 江苏省家禽科学研究所 | SNP locus combination for identifying variety of Mongolian snakegourd and identification method thereof |
| CN113322334A (en) * | 2021-07-21 | 2021-08-31 | 江苏省家禽科学研究所 | SNP primer combination for identifying variety of golden duck and identification method |
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| CN113308558A (en) * | 2021-07-21 | 2021-08-27 | 江苏省家禽科学研究所 | Application of SNP locus combination in identifying Liancheng white duck variety |
| CN113308559A (en) * | 2021-07-21 | 2021-08-27 | 江苏省家禽科学研究所 | SNP locus combination for identifying variety of Mongolian snakegourd and identification method thereof |
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| CN113308559B (en) * | 2021-07-21 | 2023-07-18 | 江苏省家禽科学研究所 | SNP locus combination for identifying royal duck variety and identification method thereof |
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