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Barley 40K SNP (Single Nucleotide Polymorphism) liquid phase chip

A liquid phase chip, barley technology, applied in the fields of instruments, nucleotide libraries, library creation, etc., can solve the problems of high cost and high technical threshold, and achieve the effect of improving efficiency

Pending Publication Date: 2022-07-29
NORTHWEST A & F UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The research on gene analysis or genetic mapping of barley mainly adopts the second-generation molecular marker technologies such as SSR (simple sequence repeat) markers and AFLP (amplified fragment length polymorphism) based on electrophoretic separation, which are distinguished by differences in the length of DNA fragments; Some studies have also used third-generation molecular marker technologies such as GBS (Genotyping by sequencing) based on single nucleotide polymorphisms (SNPs), but such technologies have high thresholds and high costs

Method used

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  • Barley 40K SNP (Single Nucleotide Polymorphism) liquid phase chip
  • Barley 40K SNP (Single Nucleotide Polymorphism) liquid phase chip
  • Barley 40K SNP (Single Nucleotide Polymorphism) liquid phase chip

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Embodiment 1

[0037] A barley 40K SNP liquid phase chip is obtained through the following main processes: based on whole-genome resequencing of barley materials from different ecological regions and different types of the world, more than 45 million SNP loci have been obtained; The index, the position of the binding site on the chromosome, analyze the upstream and downstream sequences, and select 40,519 SNP sites with strong representation, good polymorphism, and uniform chromosomal distribution that can be used for chip development; finally, targeted sequencing genes are used. Genotyping by Targeted Sequencing (GBTS) technology, which is a liquid-phase chip technology that only performs targeted deep resequencing of these 40,519 target sites, developed a 40K liquid-phase SNP chip of barley, and named the chip For the Barley SNP 40K Array.

Embodiment 2

[0039] A barley 40K SNP liquid phase chip is obtained by the following method.

[0040] (1) Barley resequencing and identification and screening of SNP loci

[0041]S1. In order to ensure the representativeness of barley materials, according to the analysis of agronomic traits combined with molecular markers of nearly 2,000 materials stored in the laboratory, and according to regional sources and types, 155 representative barley germplasms were selected as materials. These materials come from a wide range of sources. , strong representation, including 43 wild barley in different ecoregions worldwide (including South Levant, North Levant, East Levant, Iran, Caucasus, etc.), 54 barley farms (Middle East, Eastern Europe, etc.) , Australia, the United States, China, etc.), 27 cultivars (20 countries such as the United States, Canada, the United Kingdom, Germany, etc.) and 31 highland barley materials (wild, local and cultivated); select 10-15 full and complete trees of each line ...

Embodiment 3

[0061] In order to further evaluate the value of the 40K liquid-phase SNP chip in the actual molecular breeding of barley, it is now applied to the construction of high-density genetic map of barley (such as image 3 shown). The specific process and results are as follows.

[0062] The liquid phase SNP chip of the present invention was used to genotype 125 individuals of the Steptoe×Morex DH population, and a total of 16972 polymorphism sites were obtained, thereby constructing the first high-density SNP genetic map of barley; in the genetic map, The total genetic distance is 2023.33cM, including 7 linkage groups, and the average map distance is 2.10cM (such as image 3 In addition, the number of markers distributed on the 7 chromosomes of barley is also relatively average, and the number of markers on each chromosome ranges from 103 to 165. Among them, chromosome 1 is the shortest at 225.38cM, and chromosome 2 is the longest. Based on this map, QTL mapping was carried out f...

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Abstract

The invention belongs to the technical field of plant molecular markers, and relates to a barley 40K SNP (Single Nucleotide Polymorphism) liquid chip. The barley 40K SNP liquid phase chip is obtained by the following method: 1, selecting barley and highland barley as germplasm materials for re-sequencing, then performing quality control on a sequencing result, mapping with a reference genome, and identifying and screening out SNP loci; 2, according to the indexes of the SNP sites, combining the positions of the sites on chromosomes, analyzing upstream and downstream sequences of the sites, designing sequencing primers, and selecting the SNP sites which can be used for chip development; and 3, developing the barley 40K SNP liquid phase chip by using a targeted sequencing genotyping technology. The barley 40K SNP liquid phase chip belongs to an SNP chip for DNA detection, is a barley whole genome liquid phase chip which is developed based on a targeted capture high-throughput sequencing technology and contains 40519 SNP marker sites, and provides an important tool for barley high-density genetic map construction, barley germplasm identification, high-throughput genotyping, QTL positioning, whole genome association analysis and the like.

Description

technical field [0001] The invention belongs to the technical field of plant molecular markers, and relates to a barley 40K SNP liquid phase chip, in particular to a barley whole genome liquid phase chip containing 40,000 SNP marker sites developed based on targeted capture high-throughput sequencing technology. Background technique [0002] Barley is one of the important food crops in the world, and its planting area and total output ranks fourth in the world. Barley has both edible, feeding and industrial brewing value. In recent years, because of its "three highs and two lows" characteristics of "high protein, high cellulose, high vitamins, low fat and low sugar", it has become more and more popular as a health food. getting more and more attention. As a characteristic type of barley, highland barley is also a characteristic crop in Tibetan areas and plateaus in my country, and is of unique significance to the social, economic and cultural construction and development of...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6895C40B40/06C40B50/06G16B20/30G16B30/10
CPCC12Q1/6895C40B40/06C40B50/06G16B20/30G16B30/10C12Q2600/156
Inventor 聂小军杨光魏新雨宋卫宁佘奎军潘文秋艾琪
Owner NORTHWEST A & F UNIV
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