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Method for mining transposon insertion polymorphisim TIP molecular markers based on comparative genomics

A comparative genomics and molecular marker technology, applied in the field of animal genetics and breeding, can solve the problem of lack of molecular markers in fine positioning, and achieve the effect of clear and easy judgment of test results, clear results, and convenient marker detection.

Active Publication Date: 2019-09-20
YANGZHOU UNIV
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Problems solved by technology

It can well solve the problem of lack of molecular markers in QTL fine-mapping

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  • Method for mining transposon insertion polymorphisim TIP molecular markers based on comparative genomics
  • Method for mining transposon insertion polymorphisim TIP molecular markers based on comparative genomics
  • Method for mining transposon insertion polymorphisim TIP molecular markers based on comparative genomics

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Embodiment Construction

[0028] Before further describing the specific embodiments of the present invention, it should be understood that the protection scope of the present invention is not limited to the following specific specific embodiments; it should also be understood that the terms used in the examples of the present invention are to describe specific specific embodiments, It is not intended to limit the protection scope of the present invention.

[0029] The following is a detailed description in conjunction with the development of the TIP molecular marker in the porcine GHR gene.

[0030] 1. Sequence acquisition

[0031]The reference sequence of the GHR gene (Gene ID: 397488) was obtained from the NCBI database (https: / / www.ncbi.nlm.nih.gov / ). Then use the reference sequence to compare with the genome sequencing data of different breeds of pigs in NCBI's WGS database, so as to obtain the sequences of GHR genes (including reference sequences) in 15 sequenced genomes, and the GHR sequences of...

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Abstract

The invention discloses a method for mining transposon insertion polymorphisim TIP molecular markers based on comparative genomics, wherein the method includes the following steps: (1) selecting target genes or genomic fragments to be studied as reference sequences; (2) carrying out Blast alignment on porcine genome sequencing data of the reference sequences in an NCBI WGS database to obtain homologous sequences in genomes of different varieties, and manually collating and splicing the sequences; (3) carrying out transposon annotation and multi-sequence alignment of the reference sequences and the splicing sequences according to the porcine transposon data; (4) selecting Indel loci existing in the sequences, having more than 100 bases and corresponding to transposons as candidate TIP loci; and (5) detecting with pooled DNA of different varieties as a template by PCR amplification, and selecting the TIP loci with clear bands and polymorphism. The method can quickly find out molecular markers, which are easy to detect and have clear and easy-to-judge results, in target regions or genes.

Description

technical field [0001] The invention belongs to the field of animal genetics and breeding, and relates to the fields of bioinformatics and molecular biology, in particular to a method for mining transposon insertion polymorphisms (Transposon insertion polymorphisims, TIP) molecular markers based on comparative genomics. Background technique [0002] Genome annotation of pigs showed that transposons accounted for 39.40% of the whole genome. Transposons are widely distributed in the genomes of mammals such as pigs, and it is predicted that transposon insertion sites almost cover more than 80% of the genes on the genome. Because transposons can be transferred between species and within species, transposons, like other sources of mutation, not only promote the differentiation of genomes between species, but also generate rich genetic diversity within species. Variety, subspecies, strain formation played an important role. [0003] Relevant studies have shown that transposons a...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6809
CPCC12Q1/6809C12Q2531/113C12Q2539/10Y02A90/10
Inventor 陈才宋成义王宵燕高波沈丹王赛赛王亚丽李奎
Owner YANGZHOU UNIV
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