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InDel marker based on peanut genome, primer combination and application

A genome and peanut technology, applied in the field of InDel markers based on the peanut genome, can solve the problems of limited number of InDel markers, achieve stable amplification results, protect legitimate rights and interests, and achieve high resolution

Pending Publication Date: 2021-11-23
ZHANJIANG EXPERIMENTAL STATION CHINESE ACAD OF TROPICAL AGRI SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] Currently, the number of InDel markers developed using peanut genome information is very limited

Method used

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  • InDel marker based on peanut genome, primer combination and application
  • InDel marker based on peanut genome, primer combination and application
  • InDel marker based on peanut genome, primer combination and application

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0169] The identification and marker development of embodiment 1 peanut InDel

[0170] 1. Acquisition of peanut genome data

[0171] Download the genome of Tifrunner from the peanut database (https: / / peanutbase.org / ) as a reference genome, and download the sequencing data of Lionhead from the NCBI database (https: / / www.ncbi.nlm.nih.gov / ) ( SRA number: SRR7617991).

[0172] 2. Identification of InDel markers in peanut genome

[0173] Such as figure 1 As shown, first use the Fastp software to perform quality control on the obtained lion head enterprise resequencing data to obtain Cleanreads, then use the Tifrunner genome as the reference genome, use the mem program in the BWA software to compare the Cleanreads to the reference genome, and then use the smtools software Perform data format conversion, sort and remove marker PCR repeat sequences, and then use GATK software for variation detection and filtering, and obtain 38,777 InDel sites, and then screen for InDel sites with ...

Embodiment 2

[0184] Example 2 Utilize peanut InDel markers to carry out germplasm analysis

[0185] 1. Polymorphism analysis of InDel markers

[0186] The 13 peanut varieties shown in Table 2 were detected by polypropylene gel electrophoresis using the primers corresponding to the 3615 InDel markers obtained in Example 1.

[0187] (1) Design and synthesize common primers using InDel markers, and then analyze them by polypropylene gel electrophoresis.

[0188] The specific steps are: add 1 / 2 volume of denaturant to the PCR product, mix well, denature at 95°C for 5 minutes, immediately place it on ice to cool, then take 2 μL of the product and use 6% denaturing polyacrylamide gel electrophoresis for detection, nitric acid Silver staining, development, scanning and preservation.

[0189] (2) Organize the experimental data.

[0190] The amplification of peanut InDel markers in 13 peanut varieties was obtained. 100 InDel markers were further identified, and these 100 InDel markers were dist...

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Abstract

The invention provides a reagent for detecting InDel sites. The reagent is used for detecting one or more of InDel sites from 1 to 100. According to the invention, genome data of peanut Tifrunner and Shitouqi are utilized, information of the InDel sites in the genome is acquired through bioinformatics analysis, and 100 InDel markers are designed, synthesized and verified through electrophoresis detection according to the InDel sites. The developed InDel marker has the advantages of stable amplification result, high resolution ratio, co-dominance and detection in various modes; peanut molecular markers are further enriched; The InDel marker can be widely applied to the aspects of genetic diversity analysis, variety identification and protection, filial generation identification, construction of a DNA fingerprint and a genetic linkage map, important character positioning and the like of peanut resources.

Description

technical field [0001] The invention belongs to the technical field of molecular markers, and in particular relates to a peanut genome-based InDel marker, primer combination and application. Background technique [0002] Cultivated peanut (Arachis hypogaea) is one of the main oil crops and economic crops in China, which plays an important role in ensuring the supply of edible oil and vegetable protein in my country and increasing farmers' income. In 2019, my country's peanut planting area was 4.63 million hectares, with an output of 17.52 million tons, accounting for 36% of the world's total output, and the output value of the planting industry reached 120 billion yuan (https: / / data.stats.gov.cn / ). The output value of China's planting industry is second only to rice, wheat and corn. [0003] With the development of genomics and molecular biology, molecular marker technology has been widely used in genetic diversity of germplasm resources, variety identification, genetic dive...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6895C12N15/11C40B40/06
CPCC12Q1/6895C40B40/06C12Q2600/13C12Q2600/156
Inventor 徐志军胡小文安东升徐磊赵宝山严程明
Owner ZHANJIANG EXPERIMENTAL STATION CHINESE ACAD OF TROPICAL AGRI SCI
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