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Malus plant whole genome InDel marker genotype database and application thereof to germplasm resource specificity identification

A technology of marking genes and whole genomes, applied in the field of molecular biology, to overcome the limitations of environmental influences

Active Publication Date: 2020-12-25
CHINA AGRI UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] At present, InDel markers have been used to identify the specificity of germplasm resources in mulberry, mustard, sorghum and other crops, and achieved ideal results, but there is no related report in apples

Method used

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  • Malus plant whole genome InDel marker genotype database and application thereof to germplasm resource specificity identification
  • Malus plant whole genome InDel marker genotype database and application thereof to germplasm resource specificity identification
  • Malus plant whole genome InDel marker genotype database and application thereof to germplasm resource specificity identification

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Experimental program
Comparison scheme
Effect test

Embodiment 1

[0280] InDel Tag Development

[0281] Illumina HiSeq2500 sequencer was used to resequence the genomes of two apple varieties 'Red Jade' and 'Golden Delicious'. The obtained sequencing data were analyzed by Delly software to obtain a total of 66,841 structural variations, including 16,130 deletions (deletion, DEL), 9,794 Insertion (INS), 430 inversions (INV), 1132 intrachromosomal translocations (ITX) and 39355 interchromosomal translocations (CTX). In order to facilitate detection of variation by PCR method, an insertion or deletion (Insertion / Deletion, InDel) with a length of 50-500 bp of the variation sequence is selected as a marker.

[0282]Among the 25,924 InDel variants mentioned above, primers were designed for InDel variant sites that were evenly distributed on the 17 chromosomes of the apple genome and were genotype-stable and widely separated in Malus plant resources. The accuracy of the predicted InDel variant sequence was verified by PCR and Sanger sequencing. Ta...

Embodiment 2

[0289] Construction of InDel Marker Genotype Database of Malus Germplasm Resources

[0290] The present invention collects altogether 1251 parts of Malus germplasm resources, including 35 species, and cultivated apples comprise 981 varieties, and there are 322 parts of bud varieties in the cultivated species (Table 2).

[0291] The invention adopts the CTAB method to extract the genome DNA of the Malus germplasm resource, and finally adjusts the concentration of the extracted DNA solution to 200ng / μL for detection.

[0292] Using the fluorescent multiplex PCR system constructed in Example 1, 1251 Malus germplasm resources were detected for InDel marker genotypes. The format of the test results is as follows: according to the format of one germplasm resource for all marker genotype results, the genotype results of all markers are sorted out, and a database containing 1251 Malus germplasm resources corresponding to 102 InDel marker genotypes is constructed. The database construc...

Embodiment 3

[0426] Germplasm-specific identification in databases

[0427] Adopt AppleParentage1.0 software to carry out specificity analysis to all germplasms in the database that embodiment 2 obtains, find that altogether 942 materials have unique genotype in 1251 germplasm resources, promptly have specificity, its InDel genotype data Use online two-dimensional code generation software to generate two-dimensional code molecular ID cards. There are 309 materials with shared InDel marker genotype data, which are divided into 76 groups, as shown in Table 4; wherein there are 197 budding varieties, that is, 107 (11 groups) of 'Fuji' line budding materials, 35 (3 Group) 'Marshal' sprouting material, 33 (6 groups) 'Gala' sprouting material, 4 (1 group) 'Jinguan' sprouting material, 7 (2 groups) 'Hongyu' sprouting material Mutation materials, 5 copies (2 groups) of 'Guoguang' bud mutation materials, 4 copies (1 group) of 'Tsugaru' bud mutation materials, 2 copies (1 group) of 'Longwei' bud mu...

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Abstract

The invention provides a malus plant whole genome InDel marker genotype database and application thereof to germplasm resource specificity identification, and belongs to the technical field of molecular biology. A construction method for the genotype database includes the following steps: performing genotyping on InDel markers of apple germplasm resource genome DNA samples by using a primer pair and multiple PCR; recording by taking genotype of InDel markers corresponding to each malus germplasm resource as a row; and summarizing all germplasm resource records to obtain the malus plant whole genome InDel marker genotype database. The database provided by the invention can simply, conveniently, efficiently and stably identify the specificity of malus germplasm, overcomes the limitation thatDUS test is easily influenced by the environment, and provides a powerful tool for apple new variety protection and germplasm resource management.

Description

technical field [0001] The invention belongs to the technical field of molecular biology, and in particular relates to a whole genome InDel marker genotype database of Malus plants and its application in the specific identification of germplasm resources. Background technique [0002] Apple is one of the five largest fruit trees in the world and has a long history of cultivation. my country is a big apple producing country, with the cultivation area, output and consumption all ranking first in the world, occupying an important position in my country's agricultural production. Since the founding of New China, through unremitting efforts, Chinese apple breeders have cultivated hundreds of new varieties. But in the selection of parents for cross breeding, 'Marshal', 'Guoguang', 'Jinguan', 'Fuji' and 'Hongyu' are the most commonly used breeding parents. Due to the repeated use of backbone parents, the genetic differences between varieties are reduced and the genetic background...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6895C12Q1/6858G16B20/20
CPCC12Q1/6895C12Q1/6858G16B20/20C12Q2600/156C12Q2600/16C12Q2531/113C12Q2537/143C12Q2563/107C12Q2600/13C12Q1/686C12Q1/6888
Inventor 张新忠王旋申飞陈瑞婷韩振海王忆吴婷许雪峰李威邱昌朋张希
Owner CHINA AGRI UNIV
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