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Ginkgo polymorphic EST-SSR (expressed sequence tag-simple sequence repeat) molecular marker primer and application thereof

A polymorphic primer and molecular marker technology, which is applied in the fields of bioinformatics, biochemical equipment and methods, and microbial determination/inspection, etc. Simple operation, wide coverage effect

Pending Publication Date: 2022-08-09
CENTRAL SOUTH UNIVERSITY OF FORESTRY AND TECHNOLOGY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At present, for the construction of ginkgo core germplasm, mainly ISSR, AFLP and other dominant marker data, there is no research report on the construction of ginkgo core germplasm using SSR molecular marker data

Method used

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  • Ginkgo polymorphic EST-SSR (expressed sequence tag-simple sequence repeat) molecular marker primer and application thereof
  • Ginkgo polymorphic EST-SSR (expressed sequence tag-simple sequence repeat) molecular marker primer and application thereof
  • Ginkgo polymorphic EST-SSR (expressed sequence tag-simple sequence repeat) molecular marker primer and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0080] Embodiment 1: Development of Ginkgo biloba transcriptome EST-SSR molecular marker primers

[0081] 1 Materials and methods

[0082] 1.1 Materials

[0083]Based on the Ginkgo biloba transcriptome database of our group, the SSR loci were screened and analyzed. In the present invention, a total of 141 ginkgo germplasm resources are collected for the screening of polymorphic EST-SSR primers, of which 101 germplasm resources are known varieties (lines), and the remaining 40 are unknown varieties, according to "Huanglongxian No. 1-40" " to name it. 11 ginkgo varieties (strains) from Hunan were planted in the Ginkgo Experimental Demonstration Base of Xiling Industrial Zone, Damiaokou Forest Farm, Dong'an County, Hunan Province, and the remaining 90 varieties (series) of ginkgo were planted in the National Ginkgo Advanced Breed Base in Pizhou City, Jiangsu Province, with 40 copies. An unknown variety (strain) of ginkgo was planted in Huanglongxian Village, Jiangning District...

Embodiment 2

[0115] Embodiment 2: Genetic diversity analysis of ginkgo germplasm resources

[0116] 1 Materials and methods

[0117] 1.1 Materials

[0118] The test materials were the same as those in Example 1, and were 141 ginkgo germplasm resources.

[0119] 1.2 Methods

[0120] The 20 pairs of polymorphic EST-SSR molecular marker data obtained above were input into Popgene 32 software, and the average expected heterozygosity or gene diversity index (H) was calculated. e ), Shannon diversity index (I), genetic differentiation coefficient (G st ) and gene flow (N m ). Molecular variance analysis was performed by GenAlE_v6.502 software, and UPGMA cluster analysis was performed by NTSYS software.

[0121] 2 Test results

[0122] 2.1 Genetic diversity analysis of ginkgo germplasm resources

[0123] The results of genetic diversity analysis showed that (Table 5), 141 Ginkgo germplasm resources had a high level of genetic diversity. Gene Diversity Index (H e ) was between 0.328 and ...

Embodiment 3

[0138] Example 3: Construction of Ginkgo Core Germplasm

[0139] 1 Materials and methods

[0140] 1.1 Materials

[0141] The test materials were the same as those in Example 2, and were 141 ginkgo germplasm resources.

[0142] 1.2 Methods

[0143] 1.2.1 Construction of core germplasm

[0144] In order to compare the differences between different sampling methods and obtain the best sampling strategy, two grouping principles (grouping by origin, completely random without grouping), four in-group sampling ratios (simple ratio, logarithmic ratio, square root ratio and genetic diversity) were analyzed. sex ratio), 2 sampling methods (site-priority cluster sampling, random cluster sampling), 6 overall sampling ratios (5%, 10%, 15%, 20%, 25%, 30%, 35% , 40%) in any combination to form a total of 72 sampling schemes. The genetic distance is calculated based on the SM similarity coefficient.

[0145] 1.2.2 Evaluation of core accessions

[0146] By the number of alleles, the num...

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Abstract

The invention discloses a ginkgo polymorphic EST-SSR molecular marker primer and application thereof, and belongs to the field of molecular marker development technology and application thereof. According to the invention, EST-SSR sites are screened from ginkgo transcriptome data, 100 pairs of primers are designed and synthesized, and 20 pairs of specific EST-SSR molecular marker primers with good stability and high polymorphism are finally obtained by taking 141 parts of ginkgo germplasm genome DNA in China as a template through validity verification and polymorphism screening. The invention further discloses application of the independently developed molecular marker primer in the aspects of genetic diversity analysis, core germplasm construction and the like of ginkgo biloba. The EST-SSR molecular marker primer provided by the invention provides theoretical and technical support for research on genetic evolution analysis, genetic relationship identification, improved variety breeding and the like of gingko, and has important value for reasonable utilization, preservation and protection of gingko germplasm resources.

Description

technical field [0001] The invention belongs to the field of EST-SSR molecular marker development and its application, in particular to EST-SSR-specific molecular marker primers for transcriptome polymorphisms of Ginkgo biloba, and further to the genetic diversity analysis and core germplasm construction of the molecular marker primers in Ginkgo biloba, etc. aspects of applications. Background technique [0002] Ginkgo biloba (Ginkgo biloba L.) is one of the oldest extant relict gymnosperms in the world and is known as a "living fossil". As a unique native tree species in my country, Ginkgo not only contains rich genetic resources, but also is an important economic tree species. At present, my country's ginkgo resources account for about 90% of the world's total, and are distributed in more than 20 provinces and regions in my country. Among them, the middle and lower reaches of the Yangtze River south of the Huaihe River and the vast areas of the Nanling Mountains, includi...

Claims

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Application Information

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IPC IPC(8): C12Q1/6895C12N15/11C12Q1/6858G16B20/30G16B20/40
CPCC12Q1/6895C12Q1/6858G16B20/30G16B20/40C12Q2600/13C12Q2600/156C12Q2525/151C12Q2531/113
Inventor 王义强吴春文冯致李萌张双全范开范唐建露姚志王惠孙全周涛
Owner CENTRAL SOUTH UNIVERSITY OF FORESTRY AND TECHNOLOGY
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