Screening method and application of SSR loci for paternity testing

A screening method and paternity testing technology, applied in the field of biology, can solve problems such as breeding deviation, economic loss, and unknown pedigree records, and achieve the effects of high accuracy, high screening efficiency, and a wide range of applications

Active Publication Date: 2019-01-15
SOUTHWEST UNIVERSITY FOR NATIONALITIES
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Incorrect pedigree information can lead to breeding bias and lead to huge economic losses
In actual production, pedigree records will be unknown due to various reasons, resulting in the inability to determine good breeding males for breeding selection. Animal paternity identification is very important

Method used

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  • Screening method and application of SSR loci for paternity testing
  • Screening method and application of SSR loci for paternity testing
  • Screening method and application of SSR loci for paternity testing

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Experimental program
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Effect test

Embodiment 1

[0084] The present invention will be further explained below by taking the screening of SSR molecular markers for yak paternity identification as an example.

[0085] (1) Public data selection

[0086] Public data selection: From the NCBI SRA database, screen the whole genome sequencing data using yak genomic DNA sequencing as the data source, including whole genome sequencing projects and resequencing projects, a total of 114 samples, 126 Runs (one in the sequencing process) . In order to avoid the specificity of short sequence fragment recognition between different platforms, a total of 75 sequencing samples with the same platform-Hiseq2000 sequencing platform and uniform sequencing data quality were randomly selected.

[0087] (2) Data calibration and data collation

[0088] Data calibration and collation: the collected SRA data is first converted to FASTQ data format with the "fastq-dump-split-3" command of sra-tool kit (v2.5.2), and cutadapt (v.1.8.1) program (Default ...

Embodiment 2

[0177] Sample collection: Blood samples from live yaks were collected from the jugular vein, added with blood anticoagulant EDTA, and stored in a -80°C ultra-low temperature refrigerator. The samples are positive samples with clear records. There are 6 families with a total of 18 heads (samples include father, mother, and offspring) from the Longri species storage farm in Sichuan Province. These samples are used for parental analysis and clinical testing.

[0178]从筛选出的50个SSR位点中选择如下20个SSR位点,SSR geneID为scaffold2072_1、scaffold341_1、scaffold1139_1、scaffold879_1、 scaffold2036_1、scaffold2058_1、scaffold1000_1、scaffold1649_1、 scaffold4112_1、scaffold506_1、scaffold1645_1、scaffold2687_1、 scaffold1210_1、scaffold547_1、scaffold1214_1 , scaffold1343_2, scaffold1141_1, scaffold94_1, scaffold738_1, and scaffold629_1.

[0179] Design of microsatellite primers: Design PCR amplification primers for 20 yak paternity identification microsatellite loci, and modify the 5' end of each forward primer w...

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Abstract

The invention provides a screening method and application of SSR loci for paternity testing, which relates to the field of biotechnology. Firstly, all the potential SSR loci are identified from the whole genome sequence of the species to be screened, and then the candidate SSR loci are screened and filtered in turn. Then, according to the genetic characteristics of the SSR loci to be screened, thesimulated parents are constructed and hybridized to produce offsprings to verify the characteristics of the SSR loci that can be used for paternity testing. Then, the candidate SSR loci are sorted according to PE values, and the SSR loci are selected according to the following conditions: (b1) MAF value <= M, (b2) that proportion of missing value is less than 10%; (b3) the distance between any two SSR loci is greater than the LD attenuation distance; (b4) the repeat unit is not less than N. SSR loci satisfying the above conditions can be used for paternity testing.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a screening method and application of SSR sites for parentage identification. Background technique [0002] Parentage testing, also known as paternity testing, combines biology, molecular genetics, and medical methods to determine the relationship between parents and offspring by analyzing the genetic similarity based on the morphological structure and genetic material of parents and offspring. The basic principle of paternity testing is the application of genetic rules, that is, the genetic markers of offspring must be 50 and 50 from both parents. The genetic basis of paternity test is Mendel's law of separation and law of free combination. Forensic identification was first applied, and now it is gradually being applied to genetic breeding and protection of endangered animals. [0003] Genetic pedigrees have received extensive attention during the development of modern animal husba...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6888C12N15/11
CPCC12Q1/6888C12Q2600/156
Inventor 兰道亮陈通吉文汇李键朱育星蔡雯祎熊显荣张大伟
Owner SOUTHWEST UNIVERSITY FOR NATIONALITIES
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