A method for developing novel molecular markers based on insertion polymorphism of porcine sine transposon
A technology of molecular markers and transposons, applied in the fields of molecular biology and bioinformatics, can solve the problems of genome purity and high reaction conditions, decreased accuracy, and incomplete genome information
Active Publication Date: 2020-07-03
YANGZHOU UNIV
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Problems solved by technology
Disadvantages: When performing RFLP analysis, the DNA fragment at this site is required as a probe, and radioisotope and nucleic acid hybridization techniques are neither safe nor easy to automate
Disadvantages: RAPD technology is affected by many factors, and the stability and repeatability of the experiment are poor. First, it is dominant inheritance, and it cannot identify heterozygous sites. The accuracy of calculating the genetic distance between loci is reduced due to the dominant covering effect; secondly, RAPD is quite sensitive to reaction conditions, including template concentration, Mg 2+ Concentration, so the repeatability of the experiment is poor
Disadvantages: AFLP has high genome purity and reaction conditions, is easily contaminated by DNA, and is difficult to operate
Disadvantages: heavy workload, high cost, less practical application
Disadvantages: high chip cost, due to the complexity of DNA samples, some SNPs cannot be picked up
Disadvantages: The genome information obtained is incomplete, such as introns, regulatory sequences and other important information in gene expression regulation cannot be reflected
[0005] The main challenge currently facing porcine genomics research is that although a large number of QTLs for quantitative trait variation have been obtained, there is a lack of sufficient density of molecular markers, making it difficult to fine-map genes and effectively carry out molecular marker-assisted selection
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[0031] 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.
[0032] 1. Obtain the sequence of the LINE1 insertion site in the reference genome, the specific process is as follows:
[0033] 1. Retrieval of insertion sites of SINE transposons in the genome: use the SINE nucleotide sequence SEQ ID No.1 as the query sequence in Ensembl database (http: / / www.ensembl.org / ) and UCSC database (http: / / genome.ucsc.edu / ) uses the Blat program to compare and search the pig reference genome (SGCG Sscrofa10.2 / susScr3), and use the default settings in the database to search for the insertion site of LINE1 on the genome. . ...
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The invention relates to the fields of molecular biology and bioinformatics, in particular to a method for developing novel molecular markers based on insertion polymorphisms of pig SINE transposons. The method is to use the nucleotide sequence of SINE as the query sequence to find the insertion site in the pig genome; according to each insertion site found, extend 300-500 nucleotide sequences upstream and downstream respectively, and download each Remove redundancy from the obtained sequence; design detection primers according to the obtained sequence information; use the obtained molecular marker primers to be verified to PCR amplify different varieties, or different individual genome samples of the same variety, and select bands that can be clearly expanded and Polymorphic primer combinations to obtain molecular markers. The method of the invention can provide useful molecular markers for pig strain identification and marker-assisted selection in breeding.
Description
technical field [0001] The invention relates to the fields of molecular biology and bioinformatics, in particular to a method for developing novel molecular markers based on insertion polymorphisms of pig SINE transposons. Background technique [0002] DNA molecular marker technology is a new type of genetic marker technology based on genomic DNA polymorphism, which is a direct reflection of genetic variation at the DNA level. Compared with morphological markers, biochemical markers, and cytological markers, DNA molecular markers have the following advantages: most molecular markers are co-dominant, and it is very convenient to select recessive traits; The number is almost unlimited; at different stages of biological development, DNA from different tissues can be used for marker analysis; molecular markers reveal variation from DNA; appear neutral, do not affect the expression of target traits, and are not linked to undesirable traits; detect The means are simple and fast. ...
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IPC IPC(8): C12Q1/6806C12Q1/6888C12N15/10G16B30/00
CPCC12Q1/6806C12Q1/6888C12Q2600/124C12Q2600/156G16B30/00C12Q2531/113
Inventor 宋成义陈才王伟杨昆仑张丽沈丹王赛赛王宵燕高波
Owner YANGZHOU UNIV