Method for genotyping forest populations on basis of gene CNV (copy number variation) sites

A technology of gene copy number and mutation site, applied in the field of molecular biology, can solve the problems of inability to accurately detect the genotype of CNV sites, difficulty in result analysis, application limitations, etc., so as to reduce the sequencing depth and reduce the algorithm complexity. , the effect of accurate typing results

Active Publication Date: 2017-03-08
BEIJING FORESTRY UNIVERSITY
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Problems solved by technology

[0003] At present, the genotyping of CNV sites using high-throughput sequencing results is mostly based on the genotypes of SNP sites near CNV sites. This method is complicated to operate, difficult to analyze results, and cannot accura...

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  • Method for genotyping forest populations on basis of gene CNV (copy number variation) sites
  • Method for genotyping forest populations on basis of gene CNV (copy number variation) sites

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Embodiment 1

[0071] (1) Acquisition of raw materials: 435 individuals were collected from the natural distribution area of ​​Populus tomentosa as research objects. After the genomic DNA of each individual strain was extracted by CTAB method, it was sent to Shanghai Bohao Biotechnology Co., Ltd. for sequencing. Two sequencing methods of pair-end of Illumina and mate-pair of 454 were used for sequencing to sequence Populus tomentosa individuals.

[0072] (2) Alignment: Using the above-mentioned alignment tools, software, and algorithms, compare the sequenced fragments (reads) obtained from each individual strain with the reference genome sequence, and remove PCR duplication, redundancy, and linker sequences introduced during the sequencing process.

[0073] (3) Statistics: use CNVnator software and its algorithm to count the relevant information of each potential CNV site area, such as the start-end coordinates of CNV, the length of CNV, type (deletion or duplication), read depth signal valu...

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Abstract

The invention provides a method for genotyping forest populations on basis of gene CNV (copy number variation) sites. Compared with published reference genome sequences of species, a large quantity of reads obtained by sequencing on different individuals is mapped to a pre-segmented reference genome for comparison; the number of reads matched in each window is taken as a read depth signal; read depth signal values are subjected to data standardized treatment according to GC content and deviation in windows and on the basis of the median value of a data set of read depth signal values of different individuals in the windows; varied copy numbers of the different individuals in the windows are predicted by means of corrected read depth signal values, and genotyping is performed on each CNV site according to the read depth signal values. The method is applicable to forests with different population sizes, genotypes of the CNV sites are determined on the basis of the read depth signals of high-throughput sequencing results, the algorithm is simple, the operation is simple and convenient, and the genotypes of the CNV sites are discovered and detected more accurately.

Description

technical field [0001] The present invention relates to the technical field of molecular biology, in particular to a genotyping method based on gene copy number variation sites, and more specifically to a method for genotyping forest natural populations based on gene copy number variation sites . Background technique [0002] Copy Number Variations (Copy Number Variations, CNVs) refer to submicroscopic chromosomal structural variations in which DNA segments ranging in length from 1 kb to several Mb in the genome of different individuals have copy number variations compared with the reference genome. In humans, CNVs have been shown to be associated with many complex diseases. In the plant genome, the existence of CNV affects the phenotypic traits, metabolic process, physiological process and adaptive evolution of the plant. Therefore, it is particularly important to conduct a comprehensive study of gene copy number variation in populations. Although in the past few years, ...

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Application Information

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IPC IPC(8): C12Q1/68
CPCC12Q1/6869C12Q2537/16C12Q2535/122
Inventor 张德强杨海娇杜庆章
Owner BEIJING FORESTRY UNIVERSITY
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