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Quinoa est-ssr molecular marker and its application

A molecular marker, quinoa technology, used in DNA/RNA fragments, recombinant DNA technology, etc., can solve the problems of difficulty in large-scale development of molecular markers and difficulty in genome sequence assembly, and achieve rich polymorphism, good versatility, high success rate

Active Publication Date: 2018-06-12
JIANGSU ACAD OF AGRI SCI
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Problems solved by technology

According to reports, the genome size of quinoa is about 967M, and it is an allotetraploid species (2n=4x=36). It is difficult to assemble the genome sequence, and there is no related report on genome sequencing. Therefore, it is difficult to develop molecular markers on a large scale

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  • Quinoa est-ssr molecular marker and its application
  • Quinoa est-ssr molecular marker and its application
  • Quinoa est-ssr molecular marker and its application

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[0016] The following examples facilitate a better understanding of the present invention, but do not limit the present invention. The experimental methods in the following examples are conventional methods unless otherwise specified. The test materials used in the following examples, unless otherwise specified, were purchased from conventional biochemical reagent stores.

[0017] 1) Acquisition of quinoa expression sequence data and unigene assembly. A total of 11.9G Illumina HiSeq 2000 RNA-Seq data (accession numbers: SRX257003 and SRX256971) and 2.1G Roche 454 EST data were obtained from NCBI's SRA database (http: / / www.ncbi.nlm.nih.gov / sra) (Accession number: SRX084791). After converting, cleaning, and filtering the original data, 19,571 unigenes were spliced ​​using Trinity software, with a total base number of 80,448,006 bp, and the average length of each unigene was about 4kb. Among them, 16,854 sequences contained SSR loci.

[0018] 2) Identification of EST-SSR loci ...

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Abstract

The invention relates to the technical field of molecular markers, in particular to a chenopodium quinoa willd EST-SSR (Expressed Sequence Tag-Simple Sequence Repeat) molecular marker, a development method of the chenopodium quinoa willd EST-SSR molecular marker and application of the chenopodium quinoa willd EST-SSR molecular marker. A group of chenopodium quinoa willd EST-SSR molecular markers comprises forward primers and reverse primers corresponding to 66 sites. The development method of the chenopodium quinoa willd EST-SSR molecular marker comprises the following steps of: 1, obtaining RNA-seq and EST sequences from an NCBI (National Center of Biotechnology Information) database; 2, using bioinformatics software to process, assemble and splice sequences into unigenes, and performing SSR site searching on the unigenes to obtain the EST-SSR; and 3, designing EST-SSR primer amplification chenopodium quinoa willd genome DNA for verifying the EST-SSR, and using the verified EST-SSR molecular marker to realize application of genetic diversity analysis in chenopodiaceae germplasm. The EST-SSR molecular marker developed on the basis of a public database has the advantages of high efficiency, high success rate, rich polymorphism and high universality.

Description

technical field [0001] The invention belongs to the technical field of molecular markers, and in particular relates to quinoa EST-SSR molecular markers and applications thereof. Background technique [0002] SSR (simple sequence repeat), also known as microsatellite DNA, is composed of 2 to 6 base unit sequence repeats in tandem. It has the characteristics of high polymorphism, co-dominance, and abundant quantity. It is widely used in the construction of genetic maps. , genetic diversity analysis, etc. Early methods of developing SSR markers are usually carried out by constructing libraries, including genomic libraries and cDNA libraries. Usually, the SSR developed based on EST (expressed sequence tag) is called EST-SSR. Compared with the genomic SSR developed through genome sequence, EST-SSR has a good conservation among different species due to the strong conservation of the flanking sequences at both ends. Versatility. In recent years, using the abundant genome sequenc...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12N15/11C12Q1/6895
Inventor 张体付赵涵戚维聪
Owner JIANGSU ACAD OF AGRI SCI
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