Cucurbita moschata transcriptome simple sequence repeat (SSR) molecular marker primer and application thereof

A molecular marker, Chinese pumpkin technology, applied in the biological field to achieve the effect of rich types, rich and reliable marker selection

Active Publication Date: 2019-01-29
CROP RES INST OF FUJIAN ACAD OF AGRI SCI
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  • Abstract
  • Description
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  • Application Information

AI Technical Summary

Problems solved by technology

The number of existing Chinese pumpkin SSR molecular markers is far from meeting the needs of Chinese pumpkin molecular biology research, so the development of a large number of SSR markers is still one of the important tasks of Chinese pumpkin research

Method used

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  • Cucurbita moschata transcriptome simple sequence repeat (SSR) molecular marker primer and application thereof
  • Cucurbita moschata transcriptome simple sequence repeat (SSR) molecular marker primer and application thereof
  • Cucurbita moschata transcriptome simple sequence repeat (SSR) molecular marker primer and application thereof

Examples

Experimental program
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Effect test

Embodiment 1

[0012] Example 1 Analysis of SSR characteristics in Chinese pumpkin transcriptome

[0013] The transcriptome data of Chinese pumpkin came from the results of Illumina high-throughput deep sequencing in 2016 by our research group. During the sequencing, three drought-treated seedling leaves at the stage of two leaves and one heart were used, and Beijing Biomike Biotechnology Co., Ltd. was entrusted to use the Illumina HiSeqTM 2500 PE125 system to perform RNA-Seq transcriptome sequencing, and Trinity was used for sequence assembly. A total of 7.48Gb Clean Data was obtained, and the Clean Data reached 7.48Gb. A total of 61,882 Unigenes were obtained after assembly. Among them, there are 12,526 Unigenes with a length of more than 1kb. Functional annotation of Unigene, including comparison with NR, Swiss-Prot, KEGG, COG, KOG, GO and Pfam databases, obtained a total of 32,033 Unigene annotation results. The gene structure analysis based on the Unigene library was carried out, and...

Embodiment 2

[0024] Example 2 Molecular marker primer screening and its application

[0025] The materials used for SSR primer screening and usability evaluation were 30 Chinese pumpkin materials collected and preserved by the Vegetable Research Center of Fujian Academy of Agricultural Sciences (Table 3). Genomic DNA was extracted by CTAB method.

[0026] Table 3 SSR polymorphism analysis materials of Chinese pumpkin

[0027]

[0028] Use the MISA program (http: / / pgrc.ikp-gatersleben.de / misa) to search for SSR sites, and search based on the minimum repeats of two to six nucleotides being 6, 5, 5, 4 and 4 times respectively . The Primer 3.0 software was used to design and evaluate primers for the sequence before and after the SSR repeat motif, and 3 primers were generated for each SSR. The length of the primer sequence is 18~27 bp, the GC content is 40%~60%, the annealing temperature is 56~62 ℃, the difference between the Tm values ​​of the upstream and downstream primers is ≤2℃, the ...

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Abstract

The invention provides a cucurbita moschata transcriptome simple sequence repeat (SSR) molecular marker primer and application thereof. The cucurbita moschata transcriptome SSR molecular marker primercomprises 18 pairs of primer bodies, the sequences of the primer bodies are correspondingly shown in SEQ ID NO.1-36. A total of 6489 pairs of SSR primer bodies are designed by using Primer 3.0. Thirty pairs of primer bodies are randomly selected from 92 pairs of effective amplification primer bodies, and 30 cucurbita moschata germplasms are analyzed for polymorphism verification, wherein 18 pairs(account for 60%) of primer bodies show stable and repeatable polymorphism. UPGMA is used for mapping, and 30 selected materials are divided into 2 types. Cucurbita moschata transcriptome data are utilized to develop SSR markers to obtain high frequency SSR locus with rich types, and more abundant and reliable marker selection for genetic diversity analysis and genetic map construction in cucurbita moschata are provided.

Description

technical field [0001] The invention belongs to the field of biotechnology, and in particular relates to a Chinese pumpkin transcriptome SSR molecular marker primer and application thereof. Background technique [0002] Chinese Pumpkin ( Cucurbita moschata Duch. ) is Cucurbitaceae Cucurbitaceae Cucurbita ( Cucurbita spp. ), one of the three major cultivars, originated in the American continent and was introduced to China via Southeast Asia in the middle of the 16th century. Chinese pumpkin has strong adaptability, wide distribution and rich nutrition. It is a traditional vegetable loved by our people. It is planted on a large scale in my country and is the largest producer and consumer of Chinese pumpkin. There are many kinds of Chinese pumpkins with different qualities, and the characteristics of diversification are very prominent. The research on the genetic diversity of Chinese pumpkin germplasm resources is beneficial to the collection, preservation, identification,...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6895C12N15/11
CPCC12Q1/6895C12Q2600/156
Inventor 朱海生王彬叶新如刘建汀李永平陈敏氡林珲温庆放
Owner CROP RES INST OF FUJIAN ACAD OF AGRI SCI
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