A method for obtaining high-density SNP marker loci in chicken whole genome

Abstract

The invention belongs to the technical field of genetic engineering, and provides a method for acquiring chicken whole genome high-density SNP marker sites. The method comprises the following steps: (1) predicting distribution of restriction fragments acquired from double-restriction chicken genomes of EcoRI and MseI; (2) designing a universal joint, a barcode joint and a PCR amplification primer according to the distribution characteristics of the restriction fragments of EcoRI and MseI; (3) constructing a simplified genome sequencing library; (4) sequencing by virtue of the library constructed in the step (3) through a computer; and (5) according to a sequencing result, acquiring SNP marker sites. The method disclosed by the invention provides a universal strategy for the construction of a whole genome high-density SNP map by virtue of double-restriction GBS for different varieties of chickens, so that the cost on acquiring every SNP marker site is reduced by an order of magnitude compared with a conventional chip technology; and the method is stable in technology and high in repeatability.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a method for obtaining high-density SNP marker sites in the whole genome of chickens based on sequencing genotyping technology. Background technique [0002] As a model organism of poultry, the chicken became the first agricultural economic animal to complete complete gene sequencing in 2004. Due to the huge biodiversity of different chicken breeds, it is being used more and more as a high-quality genetic model To quantitative genetics and molecular breeding, functional gene mapping, gene regulation and development and other fields. Molecular markers are an important tool for studying biological genetic variation. Single nucleotide polymorphisms (SNP), as the third generation of molecular markers, have the characteristics of large number, wide distribution, and genetic stability, and are widely used in linkage analysis , genome-wide association analysis and genome selection and othe...

AI Technical Summary

Problems solved by technology

However, different simplified genome sequencing methods are quite different in terms of library construction strategy, single-enzyme digestion / double-enzyme digestion combination selection, and sequencing platform selection, which will significantly affect the efficiency and cost of subsequent typing

For example, the library construction strategy of the RAD sequencing method is complicated, and too many steps will interfere with the results of subsequent experiments; the frequency and distribution of different restriction endonucleases on the genomes of different species are quite different. Species, which enzyme to use for experiments will become the decisive factor in determining the number and cost of SNPs obtained in experiments; 2b-RAD technology uses type IIB restriction endonucleases, but the size of the fragments cut by this enzyme is only 25-35bp, 2b-RAD Although technology can obtain genome-wide enzyme-digested fragments, according to the frequency of genome-wide variation, it is difficult for too short enzyme-digested fragments to be rich in SNP sites, resulting in a large amount of data loss. There are many errors in the alignment of repetitive regions of the genome, which greatly reduces the reliability of SNP typing and seriously interferes with downstream applications

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