SNP molecular marker combination for identification of genetic relationship of pigs, application and method
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A technology of kinship and molecular markers, applied in the field of molecular genetics, to achieve accurate and reliable typing results, complete and accurate pedigree, and guaranteed accuracy
Pending Publication Date: 2022-01-28
北京康普森农业科技有限公司
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[0004] At present, there is no report on genetic relationship identification of Du, Chang and Da commercial pig breeds using SNP markers
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Embodiment 1
[0263] Embodiment 1: the selection of SNP marker combination;
[0264] The present invention has gone through 3 processes for the SNP marker selection of the paternity identification system for Du, Chang, and large commercial breed pig herds, specifically as follows:
[0265] (1) Group division
[0266] The Du, Long and large commercial pig populations were divided into marker screening population and marker verification population, the screening population was used for screening and verification, and the marker verification population was only used for marker verification.
[0267] (2) Marker screening
[0268] For the genotype data of CMIC-1 in different populations, firstly, according to callrate (>0.95), Harwin equilibrium (p>10 -6 ) to filter out the SNP markers that do not meet the requirements, and then screen out the SNP markers with MAF>0.3. Finally find out the intersection of SNP markers that meet the requirements of all groups. Finally, LD filtering was perform...
Embodiment 2
[0280] Embodiment 2: Sampling and targeted capture sequencing technology SNP polymorphism analysis and paternity identification and inference are carried out in pig herds; specifically, the following steps are included:
[0281] Step S1, preparing a porcine 200SNP-labeled liquid chip based on targeted capture sequencing;
[0282] In this step, the porcine 200SNP-labeled liquid chip is composed of independently packaged probes and hybrid capture reagents. The pig 200SNP labeled probe is a single-stranded RNA probe, which is a nucleotide sequence designed and synthesized according to the screened SNP site. The design principle of the probe is that the length of the probe is 120bp, the GC content of the probe is between 25% and 75%, and the number of homology comparisons is less than or equal to 10. According to the SNP sites obtained by screening, two oligonucleotide sequences covering the SNP sites were designed, and the 5' short nucleotide sequences were modified with biotin ...
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Abstract
The invention provides an SNP molecular marker combination for identification of a genetic relationship of pigs, application and a method. The SNP molecular marker combination comprises 200 SNP markers on 18 autosomes of pigs, wherein the SNP molecular marker combination can be applied to identification of the genetic relationship of Duroc pigs, landrace pigs and large white pigs. The identification method comprises the following steps: preparing a liquid phase chip of the 200 SNP markers; constructing a high-throughput sequencing library by using genome DNA of a to-be-detected pig; mixing the liquid chip with the high-throughput sequencing library, capturing a DNA fragment containing a target SNP site in the pig DNA high-throughput sequencing library, carrying out amplifying and purifying to obtain the genotype of the individual to-be-detected pig, and performing paternity test inference according to the genotype. The invention provides a probe and a kit for identifying SNP site information. According to the invention, SNP polymorphism is detected through targeted capture sequencing; and through high-depth sequencing, a typing result is accurate and reliable, and the accuracy of a parent-child relationship is ensured.
Description
technical field [0001] The application relates to the technical field of molecular genetics, in particular to a combination, application and method of SNP molecular markers for identification of porcine kinship. Background technique [0002] Pedigree information plays a very important role in breeding. Pedigree errors will greatly reduce the accuracy of genetic evaluation, affect the effect of selection and matching, reduce the genetic progress of the population, and bring huge economic impact to the enterprise. However, in actual production, pedigree errors are unavoidable, and it is affected by many factors, such as breeding records, calving records, human errors in the pedigree entry and sorting process, and so on. At present, the methods for identification of pig kinship are basically established based on microsatellite methods. For example, patent CN102154280A discloses a method for compound amplification of pig microsatellite markers and its special primers, and patent...
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