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CAPS molecular marker for identifying oncidium varieties, screening method and application

A technology of molecular markers and screening methods, applied in the field of molecular biology, can solve problems such as no relevant literature reports, and achieve the effect of making up for the lack of CAPS molecular markers

Active Publication Date: 2021-10-26
CROP RES INST OF FUJIAN ACAD OF AGRI SCI
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  • Claims
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Problems solved by technology

[0004]At present, molecular marker technology has been widely used in oncidium genetic diversity analysis, genetic relationship research, such as ISSR (Inter-Simple Sequence Repeat) molecular marker and SRAP (Sequence-Related Amplified Polymorphism) molecular markers have been developed and utilized, but there is no relevant literature report on the development of Oncidium CAPS markers

Method used

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  • CAPS molecular marker for identifying oncidium varieties, screening method and application
  • CAPS molecular marker for identifying oncidium varieties, screening method and application
  • CAPS molecular marker for identifying oncidium varieties, screening method and application

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Embodiment 1

[0046] Step 1 Mining of SNP sites of oncidium cultivars and design of CAPS primers

[0047] (1) Transcriptome sequencing of Oncidium 'Jinhui', 'Perfume', 'Fenmengxiang', 'Hongmengxiang', 'Huangmengxiang' and 'Whitemengxiang'. Using tools such as samtools and picard-tools to compare and compare the results, sort the chromosome coordinates, remove duplicate reads, etc., and finally use the variation detection software GATK2 to perform SNP Calling, and filter the original results (filter out quality values ​​less than 30 and distances less than 5 SNP), get the SNP information.

[0048](2) In the oncidium transcriptome sequence, search for SNP sites in the unigene of genes related to anthocyanin biosynthesis and floral fragrance biosynthesis, and copy the 30 bp sequences upstream and downstream of the SNP site to the online enzyme recognition software dCAPS Find2 .0 (http: / / helix.wustl.edu / dcaps / dcaps.html), looking for SNP sites that can cause changes in the recognition sites of...

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Abstract

The invention discloses a CAPS molecular marker for identifying oncidium varieties. The marker comprises sequences shown as SEQIDNO.1-SEQIDNO.12. A screening method of the sequences comprises the following steps of obtaining SNP sites based on transcriptome data of six oncidium varieties, searching for SNP sites capable of causing change of restriction enzyme recognition sites, and designing a CAPS primer pair according to different SNP sites; extracting genome DNA of oncidium; carrying out PCR amplification on genome DNA of different oncidium varieties by using CAPS primers to obtain a target fragment; and performing enzyme digestion on the target fragment by using a restriction enzyme, carrying out agarose gel electrophoresis detection and enzyme digestion product polymorphism analysis on an enzyme digestion product, if the enzyme digestion product polymorphism exists between the varieties, taking the SNP site as the CAPS marker for identifying the oncidium varieties. The molecular marker can be used for identifying the oncidium varieties.

Description

technical field [0001] The invention relates to the technical field of molecular biology, and more specifically relates to a CAPS molecular marker for identifying oncidium varieties and its screening method and application. Background technique [0002] Oncidium, also known as Dancing Girl Orchid and Auspicious Orchid, belongs to the Orchidaceae (Orchidaceae) tree orchid subfamily (Epidendroideae) Oncidium (Oncidium) plant. It is native to tropical and subtropical America. With beautiful flower shape and bright colors, it is an important pot-cut dual-purpose flower in the world, with high ornamental and economic value. At present, there are more than 750 native species of oncidium plants, and most of the oncidium species in the market are hybrid species, and the genetic relationship between species is very complicated; in addition, oncidium has a long growth cycle and is closely related to species There is little difference in agronomic traits among them, and it is difficul...

Claims

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Application Information

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IPC IPC(8): C12N15/11C12Q1/6811C12Q1/6895
CPCC12Q1/6811C12Q1/6895C12Q2600/156C12Q2531/113C12Q2565/125C12Q2521/301
Inventor 孔兰钟淮钦樊荣辉林榕燕方能炎林兵罗远华黄敏玲
Owner CROP RES INST OF FUJIAN ACAD OF AGRI SCI
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