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SSR primer of endangered species thuja sutchuenensis and application of SSR primer

A technology for planting thuja and endangered species, applied in the field of SSR primers, to achieve the effects of high stability, large amount of useful genetic information, co-dominant inheritance and convenient and rapid detection

Active Publication Date: 2021-01-15
CHINESE RES ACAD OF ENVIRONMENTAL SCI
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

According to the search, there is currently no SSR markers used to design primers to study the genetic diversity of Thuja japonica

Method used

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  • SSR primer of endangered species thuja sutchuenensis and application of SSR primer
  • SSR primer of endangered species thuja sutchuenensis and application of SSR primer
  • SSR primer of endangered species thuja sutchuenensis and application of SSR primer

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0031] Design and screening of embodiment 1 specific SSR primer

[0032] 1. Find sequences containing microsatellite repeat units

[0033] (1) Acquisition of the original sequence of Thuja thuja: Extract the chloroplast DNA of Thuja thuja, and use HiSeq PE150 mode (double-end sequencing) for de novo sequencing to obtain the original sequence of the chloroplast genome of Thuja japonica.

[0034] (2) Raw data preprocessing: For the raw data obtained by high-throughput sequencing obtained in the above step (1), for the quality coding mark of each base, different software adopts different schemes. The scheme used in this experiment is Phred The qualityscore value ranges from 0 to 62, the corresponding ASCII code is from 64 to 126, and the score is between 0 and 40.

[0035] (3) Raw data quality assessment: use FastQC to assess the quality of the original data, make statistics and visualize some basic information, and determine its data quality.

[0036] (4) Raw data quality cont...

Embodiment 2

[0076] Example 2 Genetic Diversity Analysis of Thuja Population

[0077] Genetic diversity indicators mainly include the number of alleles (Number of alleles, Na), the number of effective alleles (Number of effective alleles, Ne), observed heterozygosity (Observed heterozygosity, Ho), expected heterozygosity (Expected heterozygosity, He ) and inbreeding coefficient (Inbreedingcoefficient, F IS ). The number of alleles refers to the mean value of the number of allele types at all gene loci measured in the population, reflecting the level of genetic diversity of the population. The effective number of alleles is the reciprocal of the homozygous frequency in the population, which is more suitable for comparing the degree of change in the genetic diversity of the population. The observed heterozygosity refers to the ratio of the number of heterozygotes actually observed to the total population, and the expected heterozygosity refers to the theoretically calculated heterozygosity...

Embodiment 3

[0082] Example 3 Analysis of Genetic Structure of Thuja Population

[0083] We used the STRUCTURE (version 2.3.4) software to analyze 10 populations (2 wild populations in Xianyi Township, 1 wild population in Manyue Township, 1 wild population in Baiquan Township, 1 wild population in Guanmian Township, and 1 wild population in Qishu Township). Populations, 1 wild population in Mingzhong Township, 1 artificial population in Xianyi Township, 1 artificial population in Baiquan Township, 1 artificial population in Guanmian Township) were analyzed by Bayesian clustering. Set the K value from 2 to 12, the number of independent operations is 10, use the mixed ancestor model, Burn-in is set to 10000-step, and Markov chain Monte Carlo (MCMC) is set to 100000-step. After finishing the calculation results, upload them to the STRUCTURE HARVERST (version 0.6.94) website to calculate the delta K value and infer the optimal K value. We used the MEGA (version 6.0) software to establish a p...

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Abstract

The invention belongs to the field of thuja sutchuenensis research, and discloses a specific SSR primer of an endangered species thuja sutchuenensis and application of the specific SSR primer in the aspects of population genetic diversity analysis, population genetic structure analysis, population genetic differentiation analysis and the like of the endangered species thuja sutchuenensis. Geneticdifferentiation and gene flow conditions of different populations and phylogenetics and evolution relations of the populations are clarified, so that genetic variation rules of the thuja sutchuenensispopulations can be revealed, and phylogenetic evolution and geographical differentiation of the thuja sutchuenensis populations are illustrated; and therefore, very important theoretical and practical significance is achieved for mastering sources and population differentiation conditions of the thuja sutchuenensis and developing and utilizing the thuja sutchuenensis.

Description

technical field [0001] The present invention relates to SSR primers, in particular to specific SSR primers for endangered species Thuja thuja, and the present invention further relates to the use of said specific SSR primers in the analysis of genetic diversity, population genetic structure and population genetic differentiation of endangered species Thuja thuja population, etc. The application of thuja belongs to the research field of thuja. Background technique [0002] Thuja Sutchuenensis (Thuja Sutchuenensis) is an evergreen tree belonging to the genus Thuja in the family Cupressaceae, and it is a very small gymnosperm unique to China ( http: / / www.iplant.cn / rep / protlist ). Based on cpDNA, nrDNAITS, LEAFY, 4CL, etc., Cui et al. (Cui YM Sun B, Wang H F, Ferguson D K, Wang YF, Li CS, Yang J, Ma QW (2015) Exploring the Formation of a Disjunctive Pattern between Eastern Asia and North America Based on Fossil Evidence from Thuja (Cupressaceae). Plos One, 10, e0138544.) Analy...

Claims

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Application Information

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IPC IPC(8): C12Q1/6895C12Q1/6858C12N15/11
CPCC12Q1/6895C12Q1/6858C12Q2600/156C12Q2600/16C12Q2531/113C12Q2537/143
Inventor 刘勇波姚志李永华王开来王欣玉邓普荣董锦熠
Owner CHINESE RES ACAD OF ENVIRONMENTAL SCI
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