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InDel marker suitable for corn genotyping and application of InDel marker

A genotyping, molecular marker-assisted technology, applied in the fields of genomics, bioinformatics, molecular plant breeding, and molecular biology, it can solve problems such as the inability to guarantee coverage of the target area.

Active Publication Date: 2021-01-29
BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The downside of this approach is that there is no guarantee that all target areas will be covered

Method used

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  • InDel marker suitable for corn genotyping and application of InDel marker
  • InDel marker suitable for corn genotyping and application of InDel marker
  • InDel marker suitable for corn genotyping and application of InDel marker

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0024] Example 1 The development process of 1011 InDel markers in corn

[0025] A series of stringent quality control analyzes were performed on the MCIDP40K InDel chip containing 40,793 InDel markers using 500 corn backbone inbred lines and 500 main hybrids in the past 10 years. 24,968 polymorphic high resolution (PolyHigh Resolution, PHR) InDel markers were obtained. These PHR-like InDel markers belong to polymorphic InDel markers that have good genotyping effects on the chip and actually exist on the maize genome. Then the following steps were taken: Step by step screening assessment.

[0026] In the first step, based on the missing data rate of InDel markers, 1218 InDel markers with a missing rate of more than 5% were deleted. After this step, 23750 remaining candidate InDel markers were filtered; in the second step, redundant InDel markers were removed by linkage disequilibrium (LD) Markers, InDel markers belonging to the same linkage disequilibrium segment provide redun...

Embodiment 2

[0053] Example 2 The method of using Ampliseq technology to carry out maize InDel marker genotyping

[0054] (1) Using the CTAB method to extract the genomic DNA of the corn samples to be tested (Jingke 968, Jundan 20, Xianyu 335, Zhengdan 958);

[0055] (2) Construction of multiplex amplification targeted capture sequencing library:

[0056] use The fluorometer quantifies the genomic DNA of the sample to be tested. In the experiment, only 10ng of DNA was needed for each sample, so the DNA solution of the sample to be tested was diluted to 2.5ng / μL as the genomic DNA working solution. The multiplex amplification targeted capture uses the reagent Ion AmpliSeqTM Library Kit 2.0 produced by Thermo Fisher Scientific. The multiple amplification target capture system is 20 μL, add 4 μL 5×Ion AmpliSeq HiFi Master Mix, 10 μL 2×GBTS-InDel1011 multiplex amplification premix primers, 4 μL prepared genomic DNA working solution and 1 μL nuclease-free water, put SimpliAmp TM Thermal c...

Embodiment 3

[0077] Example 3 Construction of Maize DNA Fingerprint Using Multiple Amplification Targeted Capture Sequencing Genotyping InDel Marker Combination

[0078] 1. DNA extraction and quality identification

[0079] 300 maize varieties were selected, and the genomic DNA was extracted by the conventional CTAB method, and the RNA was removed. The quality of the extracted DNA was detected by agarose electrophoresis, and the results showed that the extracted genomic DNA had reached the relevant quality requirements, that is, the agarose electrophoresis showed that the DNA band was single and there was no obvious dispersion; A fluorometer was used to quantify genomic DNA, and the genomic DNA of all corn samples was diluted to 2.5 ng / μL as a DNA working solution for later use.

[0080] 2. Corn DNA fingerprint library construction InDel marker selection

[0081] From the 1011 InDel markers, 384 InDel markers were selected based on the uniform distribution on the chromosome, high stabil...

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Abstract

The invention provides an InDel marker suitable for corn genotyping and an application of the InDel marker. The InDel marker has information as shown in a table 1. The 1011 InDel markers and the combination thereof can be applied to corn variety DNA fingerprint database construction, corn variety authenticity identification, corn variety purity detection, corn germplasm resource clustering analysis, corn new breeding material genetic background analysis and screening, corn molecular marker assisted breeding and corn agronomic trait related gene genetic analysis, and wide application prospectsare realized.

Description

technical field [0001] The invention relates to the fields of genomics, molecular biology, bioinformatics and molecular plant breeding, in particular to an InDel marker suitable for maize genotyping and its application. Background technique [0002] Insertion / deletion (insertion-deletion, InDel) refers to the insertion or deletion of nucleotide fragments of different sizes in the sequence of the same site in the genome between close relatives or different individuals of the same species, that is, a certain site in a sequence One or more bases are inserted or deleted compared to another sequence of homology. As a new generation of genetic markers, InDel has the advantages of both SSR and SNP markers. Compared with SSR, InDel is essentially a length polymorphism, which can be applied to analysis on the capillary electrophoresis technology platform popularized in maize genetic research and variety identification laboratories. The typing technology is easy to master and popular...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6895C12N15/11
CPCC12Q1/6895C12Q2600/156
Inventor 王凤格许理文易红梅田红丽赵久然张云龙
Owner BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
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