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Core SNP sites combination maizeSNP384 for building of maize DNA fingerprint database and molecular identification of varieties

A DNA fingerprinting and corn technology, applied in the biological field, can solve problems such as increasing the number of sites, difficulty in data sharing on electrophoresis platforms, and difficulty in improving site throughput.

Active Publication Date: 2015-04-22
BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, with the development of technology and the improvement of identification requirements, SSR markers have shown some disadvantages: such as difficulty in improving site throughput, increasing the number of sites, and corresponding increase in workload and cost; difficulty in data sharing between different electrophoresis platforms, etc.
Although a variety of different throughput maize SNP chips are available, the selection criteria for loci suitable for maize authenticity identification and fingerprint database construction are quite different from other research fields such as genetic diversity, association analysis, molecular breeding, etc. , and cannot directly apply the reported locus combinations to maize authenticity identification and database construction

Method used

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  • Core SNP sites combination maizeSNP384 for building of maize DNA fingerprint database and molecular identification of varieties
  • Core SNP sites combination maizeSNP384 for building of maize DNA fingerprint database and molecular identification of varieties
  • Core SNP sites combination maizeSNP384 for building of maize DNA fingerprint database and molecular identification of varieties

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Effect test

Embodiment 1

[0048] Example 1. Preparation of maizeSNP384 and its chip for maize DNA fingerprint database construction and variety molecular identification SNP core site combination

[0049] Based on the 3072 SNP locus data of 300 corn hybrids, 300 domestic and foreign inbred lines, and 240 DH line samples (see the Chinese invention patent with the patent number ZL 2012 8 0000286.2), maizeSNP3072, a general-purpose corn SNP chip product Among them, the core 384 SNP sites suitable for maize authenticity identification and fingerprint database construction were screened and determined according to the test effect, discrimination efficiency, and uniform distribution principle. The specific screening process is divided into three steps: (1) according to the following indicators "3072 SNPs are fully compatible with both GoldenGate and Infinium platforms, high data quality, MAF value ≥ 0.2" to obtain 1212 candidate SNPs; (2) according to Illumina design rank score> =0.7, AA, AB, BB three genotyp...

Embodiment 2

[0436] Example 2, using the SNP chip prepared in Example 1 to construct a corn standard DNA fingerprint

[0437] 1. DNA extraction and quality identification

[0438] The conventional CTAB method was used to extract the genomic DNA of all maize varieties used to construct the maize DNA fingerprint database, and remove the RNA. The quality of the extracted DNA was detected by agarose electrophoresis and ultraviolet spectrophotometer, and it was found that the extracted genomic DNA had reached the relevant quality requirements, that is, the agarose electrophoresis showed a single DNA band without obvious dispersion; the ultraviolet spectrophotometer detected A260 / 280 is between 1.8-2.0 (DNA sample has no protein contamination); A260 / 230 is between 1.8-2.0 (DNA sample has low salt ion concentration); 270nm has no obvious light absorption (DNA sample has no phenol contamination); DNA concentration > 50ng / μl; chip detection DNA dosage 500ng / sample. The diluted DNA concentration ...

Embodiment 3

[0443] Embodiment 3, utilizing the SNP chip prepared in embodiment 1 to identify the authenticity of corn varieties

[0444] One, utilize the SNP chip maizeSNP384 prepared in embodiment 1 to distinguish the determination of the authenticity test result judgment standard of maize variety

[0445] Different from the principle of site screening in other research fields, in addition to inbred line samples, the present invention also uses a large number of hybrids as evaluation materials to evaluate site specificity, stability and variety discrimination ability, and finally obtains 384 core SNP sites point (for the SNP site screening method, refer to Example 1 for details). The percentage analysis of 300 corn hybrids (1984-2011 nationally approved and popularized varieties) showed that the percentage of difference loci was between 40% and 75%. %; Among them, the percentage of difference loci is about 60% and occupies the most; the number of pairwise comparison samples with the per...

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Abstract

The invention discloses a core SNP sites combination maizeSNP384 for building of a maize DNA fingerprint database and molecular identification of varieties, and an application of the core SNP sites combination. The invention provides applications of 384 SNP sites in any one of the following conditions: (1) building of the maize DNA fingerprint database; (2) detecting of the authenticity of maize varieties; (3) genetic analysis of corn germplasm resources; and (4) molecular breeding of maize, wherein the physical positions of the 384 SNP sites are determined by comparison on the basis of a whole genome sequence of the maize variety B73; the version number of the whole genome sequence of the maize variety B73 is B73 RefGen V1; and the 384 SNP sites are MG001-MG384. An experiment proves that the 384 SNP sites can be applied to building of the maize variety DNA fingerprint database, identification of the variety authenticity, dividing of germplasm resource groups, and other related researches.

Description

technical field [0001] The invention belongs to the field of biotechnology, and relates to a SNP core site combination maizeSNP384 used for the construction of a corn DNA fingerprint database and the molecular identification of varieties and its application. Background technique [0002] Corn is an important crop, which is widely planted around the world due to its multiple uses in food, economy, fruit, feed and energy. According to statistics in 2012, the planting area and total output of corn ranked first in China, and it played a key role in China's agricultural economic structure. At the same time, because maize is a hybrid crop, high recombination rate, rich genetic diversity, and a good basis for genomics research, it has become a model plant for genetics research. Since the 1980s, with the development of the marketization of the seed industry, my country's corn varieties have gradually increased. As of 2013, the total number of varieties that have passed national and...

Claims

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Application Information

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IPC IPC(8): C40B40/06C40B50/06C12Q1/68
Inventor 王凤格田红丽赵久然王蕊李春辉
Owner BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
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