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Corn chloroplast genome SSR site and application in variety identification

A genome and corn leaf technology, applied in the field of crop molecular biology, can solve problems such as unrecorded SSR polymorphic sites

Active Publication Date: 2018-10-19
BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

There is no SSR polymorphic site for chloroplast genome development in the existing maize genome polymorphic site collection

Method used

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  • Corn chloroplast genome SSR site and application in variety identification
  • Corn chloroplast genome SSR site and application in variety identification
  • Corn chloroplast genome SSR site and application in variety identification

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0030] Example 1 Using the combination of SSR polymorphic sites provided by the present invention to construct a corn variety chloroplast DNA-SSR fingerprint database

[0031] DNA extraction of corn varieties: Each sample was seeded with seeds, given light, and formed green shoots. The method of DNA extraction was mixed plant DNA extraction, and the green leaves of 30 individual plants were mixed. The specific steps of DNA extraction were carried out according to the molecular identification standard of maize DNA (Wang Fengge et al., 2014). Dilute the DNA to form a working solution with a concentration of 20ng / μL.

[0032] Design and synthesis of primers: The 13 SSR sites (Table 1) provided by the present invention are single base length polymorphisms, so primers can be designed for this set of sites based on the fluorescent capillary electrophoresis platform. A pair of primers was designed for each site based on its flanking sequence, and the 5' end of one primer was labeled...

Embodiment 2

[0035] Example 2 Using the maize chloroplast genome SSR polymorphic sites provided by the present invention to perform maternal traceability analysis

[0036] For the maize hybrid A to be identified, DNA is extracted from the green leaves formed by seedlings, and the 13 SSR sites provided in the present invention are used for PCR amplification and fluorescent capillary electrophoresis to obtain fingerprint data. Concrete method is with embodiment 1. Based on the comparison of the SSR fingerprint data of sample A (Jingke 968) with the chloroplast SSR marker fingerprint database of known maize inbred varieties (refer to the external platform of the Chinese maize standard DNA fingerprint database, the website is: www.maizedna.org), determine The chloroplast fingerprint information of the sample to be tested is the same as that of the B inbred line (Jing 724), and it is speculated that the female parent of the hybrid A (Jingke 968) is B (Jing 724).

Embodiment 3

[0037] Example 3 Using the SSR polymorphic sites of the maize chloroplast genome provided by the present invention to identify the reciprocal cross of maize samples

[0038] For the reciprocal hybrid sample C (Zhengdan 958) to be identified, the DNA was extracted from the green leaves of the seeds. Based on the DNA fingerprint data of the parental parents of Zhengdan 958 in the chloroplast SSR marker fingerprint database of known maize inbred varieties, the polymorphic positions in the parental parents of the sample Zhengdan 958 were selected from 13 polymorphic SSR sites. Point PCR amplification, after fluorescence electrophoresis data analysis, obtain the fingerprint of sample C, the specific method is the same as embodiment 1. The fingerprint data of sample C to be tested was compared with the fingerprint data of its female parent (sample D, Zheng 58) and male parent (sample E, Chang 7-2). If the fingerprint data of sample C is the same as that of the female parent of samp...

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Abstract

The invention provides a corn chloroplast genome SSR site and application in variety identification. According to the corn chloroplast genome SSR site disclosed by the invention, accuracy and high efficiency of an obtained chloroplast polymorphic site are ensured by representative sample selection, high-quality sequencing data and accurate data analysis; 13 chloroplast SSR polymorphic sites can befinally determined by choosing a corn material with a wide source and rich phenotypes and gene types, based on a spliced corn material chloroplast genome sequence and by adoption of MISA software tosearch SSR. When the SSR sites are utilized, (1) a corn variety chloroplast DNA-SSR fingerprint database can be constructed, (2) a corn sample maternal line can be traced and analyzed, and (3) a cornsample can be reciprocally crossed and identified. When the chloroplast SSR site disclosed by the invention is used, a usable marker site range of corns can be expanded on the genome level; thus, a novel idea and a novel method are provided for researches on corn variety and germplasm resource identification, genetic relationship evaluation, cytoplasmic inheritance characteristics and the like.

Description

technical field [0001] The invention belongs to the technical field of crop molecular biology, and in particular relates to a corn chloroplast SSR molecular marker and an application thereof. Background technique [0002] Chloroplast is the organelle of photosynthesis in green plants, and has its own complete set of genome, called chloroplast genome. Due to the following advantages, chloroplast genome information is widely used in the research and application of plant varieties, germplasm resource identification, genetic relationship evaluation, phylogenetic evolution, and cytoplasmic genetic characteristics. (1) The chloroplast genome is small and relatively conserved, and its full sequence is easy to obtain; (2) The chloroplast genome is inherited from the maternal line, and gene exchange and fusion between different individuals rarely occur, and there is good collinearity among chloroplast genes; ( 3) The chloroplast genome is a single-copy gene except for the inverted r...

Claims

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Application Information

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IPC IPC(8): C12Q1/6895C12N15/11
CPCC12Q1/6895C12Q2600/156
Inventor 王凤格田红丽赵涵易红梅赵久然王蕊杨扬许理文葛建镕任洁王璐
Owner BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
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