DNA chip and application of DNA chip in corn variety identification and breeding

A technology of DNA chips and DNA molecules, which is applied in the directions of DNA/RNA fragments, DNA preparation, recombinant DNA technology, etc., can solve the problems of low genome coverage, uneven distribution of chip sites, and lack of information on corn genome diversity. Effect of low locus deletion and heterozygosity, high genome coverage

Active Publication Date: 2017-03-29
INST OF CROP SCI CHINESE ACAD OF AGRI SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0003] At present, although many kinds of corn chips have come out, these chips have some shortcomings, which limit their application in molecular breeding
These deficiencies are mainly reflected in: (1) low genome coverage and uneven distribution of microarray sites; (2) microarray design is biased towards temperate maize, not suitable for tropical maize populations; (3) excellent rare alleles are eliminated; ( 4) Taking the maize inbred line B73 as the reference genome, resulting in the loss of maize genome diversity information

Method used

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  • DNA chip and application of DNA chip in corn variety identification and breeding
  • DNA chip and application of DNA chip in corn variety identification and breeding
  • DNA chip and application of DNA chip in corn variety identification and breeding

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Experimental program
Comparison scheme
Effect test

Embodiment 1、55

[0034] Embodiment 1, the discovery process, application method and application effect of 55k chips

[0035] 1. The generation process of all SNP sites in the 55k chip

[0036] (1) Screening Europe 600K All sites in the Maize Genotyping Array were obtained to obtain 30133 SNP sites evenly distributed throughout the genome.

[0037] (2) Obtained by calculation The 10,768 loci with a deletion rate of less than 5% in MaizeSNP50BeadChip included 4,049 SNP loci with high polymorphisms in the temperate and tropical maize populations.

[0038] (3) Select 9395 SNP sites in the transcriptome sequencing data of 368 maize inbred lines.

[0039] (4) Add 451 loci related to important agronomic traits of maize.

[0040] (5) 4067 loci from the non-B73 reference genome.

[0041] (6) 734 specific loci with independent intellectual property rights for dividing heterosis groups in maize.

[0042] (7) 132 loci related to transgenic events.

[0043] After calculation, the false positive ...

Embodiment 2、1000

[0066] Embodiment 2, the development of 1000 SNP sites

[0067] When conducting maize fingerprint identification and germplasm resource evaluation, 1-3k SNP sites are most suitable considering the cost and the amount of information that the sites can provide. Based on the sequencing results of 593 maize inbred lines, the inventors of the present invention further selected a full 1000 SNPs for simplified fingerprint identification and germplasm resource evaluation. In order to select markers with uniform distribution and good polymorphism in the genome as much as possible, firstly, according to the sequencing results of 55229 SNP sites, they were divided into 1000 types. Then, based on the sequencing results of the maize inbred line B73, the entire maize genome was divided into 2000 genetic regions. Then, based on the "genetic algorithm", a group of sites is randomly selected (evenly selected according to 1000 sequencing types), and the optimal site combination that can contai...

Embodiment 3

[0068] Embodiment 3, the making and application of the chip that is used to detect 1000 SNP sites

[0069] 1. Chip preparation

[0070] The information of 1000 SNP sites is shown in Table 5.

[0071] table 5

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[0094] Note: The probes are all single-stranded DNA molecules.

[0095] The probes described in Sequence 1 to Sequence 1000 are respectively solidified on the same substrate in the form of an array to obtain a specific DNA chip (AXIOM gene chip).

[0096] 2. Chip application

[0097] The samples to be tested are: 593 corn inbred lines (the eight corn inbred lines are: corn inbred line H201, corn inbred line Ji 046, corn inbred line Ji495, corn inbred line K14, corn inbred line line B73, corn inbred line CML2...

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Abstract

The invention discloses a DNA chip and an application of the DNA chip in corn variety identification and breeding. The DNA chip is fixedly provoded with a specific probe; the specific probe is a probe used for detecting 1,000 SNP; and the 1,000 SNP loci are showed in the first line, the second line and the third line of the form 5. The application of the DNA chip is shown as follows: corn germplasm resource identification is conducted; a corn phylogenetic analysis is conducted; a corn cluster analysis is conducted; a corn variety is identified or evaluated; molecular breeding of corn is conducted; a corn DNA fingerprint database is built; corn variety authentication is detected; and a corn germplasm resource genetic analysis is conducted. The DNA chip contains specific SNP loci of tropical corn, has a higher genome coverage rate and has a lower miss rate and heterozygosis rate of loci.

Description

technical field [0001] The invention relates to a DNA chip and its application in corn variety identification and breeding. Background technique [0002] In the past decade, with the development of sequencing technology and the reduction of cost, DNA chips have been widely used in plant breeding. As an important food and feed crop, maize has rich genetic diversity, and its single nucleotide loci spread throughout the genome, which is very suitable for microarray development. [0003] At present, although many kinds of corn chips have come out, these chips all have some shortcomings, which limit their application in molecular breeding. These deficiencies are mainly reflected in: (1) low genome coverage and uneven distribution of microarray sites; (2) microarray design is biased towards temperate maize, not suitable for tropical maize populations; (3) excellent rare alleles are eliminated; ( 4) The maize inbred line B73 was used as the reference genome, resulting in the loss...

Claims

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Application Information

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IPC IPC(8): C12Q1/68C12N15/11C12N15/10C40B50/06
CPCC12N15/1093C12Q1/6895C12Q2600/156C40B50/06
Inventor 邹枨许诚徐云碧
Owner INST OF CROP SCI CHINESE ACAD OF AGRI SCI
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