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SSR core primer group developed based on whole genome data of tartary buckwheat and application thereof

A whole-genome, core primer technology, applied in the field of molecular biology, can solve the problems that cannot meet the needs of tartary buckwheat research, and the number of tartary buckwheat SSR markers is small

Active Publication Date: 2019-09-03
山西省农业科学院农作物品种资源研究所
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Compared with rice, wheat and other crops, the number of existing tartary buckwheat SSR markers is small, which cannot meet the needs of tartary buckwheat research. The development of a large number of SSR markers covering the whole genome is still one of the important tasks of tartary buckwheat research.

Method used

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  • SSR core primer group developed based on whole genome data of tartary buckwheat and application thereof
  • SSR core primer group developed based on whole genome data of tartary buckwheat and application thereof
  • SSR core primer group developed based on whole genome data of tartary buckwheat and application thereof

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Experimental program
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Effect test

Embodiment 1

[0029] High-throughput acquisition of SSR markers in tartary buckwheat genome

[0030] SSR marker search and primer design

[0031] 1. Obtain the tartary buckwheat genome sequence

[0032] The tartary buckwheat genome sequence completed by the research group was used as the template sequence.

[0033] 2. Search for genome sequences containing SSRs

[0034] Install the perl language, download the misa.pl program from http: / / pgrc.ipk-gatersleben.de / misa / misa.html, name the sequence file containing Unigene as S.fasta, and copy it to the perl\bin directory of the C drive, in Execute the command C:\perl\bin\perlmisa.plS.fasta in the perl environment, search for the SSR site in the sequence and get two files, S.fasta.misa and S.fasta.statistics. Among them, the minimum repetition numbers of 1-6 bases are 10, 6, 5, 5, 5, and 5 respectively, and the distance between two SSRs is less than 100bp, and they are merged into a composite SSR.

[0035] Table 2 SSR length statistics table ...

Embodiment 2

[0049] Example 2 Polymorphism Verification of SSR Primers

[0050] The 5 tartary buckwheat resources and 3 sweet buckwheat resources recorded in Table 3 with large phenotype differences were used for planting, and 2 g of leaves at the seedling stage were collected respectively, and the leaves were crushed with a high-throughput pulverizer, and Shanghai Sangong DNA extraction kit was used. (Ezup Column Plant Genomic DNA Extraction Kit, B518261-0050) for leaf DNA extraction, DNA quality detection and concentration determination on a microplate reader, and DNA was diluted to a final concentration of 30ng / μL, and kept at -20°C save. The polymorphisms of the primers were verified by PCR amplification using the material DNA and the randomly selected pair of SSR primers. The PCR reaction system was 10 μL in total, including 1.5 μL (30ng / μL) of genomic DNA, 5 μL of 2×TaqPCR MasterMix (Tiangen, KT: 121221), and 2 μL (0.002 nmol / μL) of forward and reverse primers in total. The PCR amp...

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Abstract

The invention discloses an SSR core primer group developed based on a whole genome sequence of tartary buckwheat and an application thereof. A development process includes the steps: (1) acquiring thetartary buckwheat genome sequence; (2) searching the genome sequence containing SSR; (3) designing an SSR primer; and (4) screening the SSR primer. The SSR core primer group comprises 12 pairs of primers having nucleotide sequences shown in SEQ No.1-24. The SSR core primer group provided by the invention has the advantages of uniform distribution, abundant polymorphism, good amplification reproducibility and clear band shape in the tartary buckwheat genome, and is suitable for detection of a common denatured polyacrylamide gel electrophoresis detection platform and a capillary fluorescence detection platform, and can be applied to tartary buckwheat genetic diversity analysis, variety identification, DNA fingerprint spectrum construction, molecular marker assisted breeding and other research fields.

Description

technical field [0001] The invention relates to tartary buckwheat SSR markers, specifically an SSR core primer set developed based on the whole genome sequence of tartary buckwheat and its application, and belongs to the technical field of molecular biology. Background technique [0002] Tartary buckwheat (Fagopyrum tartaricum L.Gertn) belongs to Polygonaceae (Polygonaceae) buckwheat (Fagopyrum Mill), an annual dicotyledonous plant. my country is the center of origin and genetic diversity of tartary buckwheat, and it is the country that grows and utilizes tartary buckwheat on a large scale in the world. Tartary buckwheat has the characteristics of self-pollination, short growth period, strong stress resistance, drought tolerance, cold tolerance, and barrenness tolerance. It has been used as a strategic reserve crop for drought situations since ancient times. [0003] Tartary buckwheat is one of the natural health foods that integrate nutrition, health care and treatment in ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6895C12Q1/6858C12N15/11
CPCC12Q1/6895C12Q1/6858C12Q2600/156C12Q2531/113C12Q2565/125
Inventor 张丽君马名川刘龙龙
Owner 山西省农业科学院农作物品种资源研究所
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