Pig genome molecular marker excavation method based on combination of LINE1 transposon and microsatellite primer

Abstract

The invention relates to a pig genome molecular marker excavation method based on combination of LINE1 transposon and a microsatellite primer. The method uses a 5'-terminal nucleotide sequence or a 3'-terminal nucleotide sequence of LINE1 to design a specific primer; according to bioinformatic analysis, the microsatellite sequences widely distributed in the pig genome are obtained to design the microsatellite primer; two primers are combined, and the different types of the pig genomes can be taken as a template for amplification; an amplification strip having clearness, high polymorphism and good repeatability is screened, and clone sequencing is carried out; a sequencing result is subjected to comparative analysis, combination of a side specific primer and a retrotransposon LINE1 specificprimer can be designed, a to-be-verified molecule-labeled primer is used for PCR amplification of different types of individual genome samples, the primer combination capable of clearly amplifying the strip and having polymorphism can be selected, and the molecular marker can be obtained. The method can provides the useful molecular marker for marker auxiliary selection in pig lines identification and breeding.

Description

technical field [0001] The invention relates to the fields of molecular biology and bioinformatics, in particular to a porcine genome molecular marker mining method based on the combination of LINE1 transposon and microsatellite primers. Background technique [0002] The existing genetic markers mainly include morphological markers, cell markers, biochemical markers and molecular markers. Morphological markers are based on individual shape descriptions, and the conclusions obtained are often incomplete and easily affected by the environment, and some markers are linked to bad shapes. Cytological markers are based on chromosomal structural variation and are not easily affected by the environment. However, cytogenetic markers are often accompanied by phenotypic effects that are harmful to organisms, and it is difficult to obtain corresponding marker materials, or difficult to observe and identify. Biochemical markers are detected by a series of proteins and isozymes. However,...

AI Technical Summary

Problems solved by technology

Disadvantages: Species-specific, limited in practical application; radioactive probes and Southern transfer, hybridization, and autoradiography are required, so time-consuming, cumbersome, and polluting, causing adverse effects on the environment and human body; affecting DNA content with high purity requirements and low polymorphism levels

Disadvantages: dominant inheritance, can not identify heterozygous loci, the genetic analysis of this matter is relatively complicated, when doing gene mapping, when making a linkage genetic map, the accuracy of calculating the genetic distance between loci will be reduced due to the dominance masking effect; Secondly, RAPD is quite sensitive to reaction conditions, including template concentration and Mg2+ concentration, so the repeatability of the experiment is poor

Disadvantages: slow response to templates, possible mismatch and deletion of bands, high cost, demanding technical requirements

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

[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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