Chinese pumpkin transcriptome ssr molecular marker primers and their applications

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

Active Publication Date: 2021-09-21
CROP RES INST OF FUJIAN ACAD OF AGRI SCI
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  • Abstract
  • Description
  • Claims
  • 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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  • Chinese pumpkin transcriptome ssr molecular marker primers and their applications
  • Chinese pumpkin transcriptome ssr molecular marker primers and their applications
  • Chinese pumpkin transcriptome ssr molecular marker primers and their applications

Examples

Experimental program
Comparison scheme
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 primer sequence length is 18~27 bp, the GC content is 40%~60%, the annealing temperature is 56~62 ℃, the Tm value difference between the upstream and downstream primers is ≤2℃, and the expected leng...

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Abstract

The present invention provides Chinese pumpkin transcriptome SSR molecular marker primers and applications thereof. The molecular marker primers comprise 18 pairs of primers, the sequences of which are respectively shown in SEQ ID NO.1-36. A total of 6489 pairs of SSR primers were designed using Primer 3.0. 30 pairs of primers were randomly selected from 92 pairs of effective amplification primers, and polymorphism analysis was carried out on 30 Chinese squash germplasms, among which 18 pairs (accounting for 60%) showed stable and reproducible polymorphisms. Using UPGMA to plot, the 30 test materials were divided into 2 categories. Using Chinese pumpkin transcriptome data for SSR marker development can obtain a higher frequency of SSR loci, and the types are rich, providing more abundant and reliable marker selection for the analysis of genetic diversity and genetic map construction of Chinese squash.

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 Patents(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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