Methods for constructing and predicting leaf trait of woody plant and photosynthetic characteristic model based on DNA methylation level
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A technology of leaf phenotype and photosynthetic characteristics, applied in the field of biological information, can solve the problems of huge data volume, high research cost, poor accuracy of results, etc.
Inactive Publication Date: 2018-07-24
BEIJING FORESTRY UNIVERSITY
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However, the research is still in the qualitative analysis, and there is a lack of quantitative research on DNA methylation analysis
At the same time, the current research on DNA methylation of forest plants relies on the scanning of DNA methylation of the whole genome, the research cost is high, and the huge amount of data leads to poor accuracy of results
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Embodiment 1
[0200] The following is an example of 235 individuals of Populus microphylla collected across the country.
[0201] Collection of experimental data:
[0202] Using the enzyme fragment A disclosed in Variation in genomic methylation in natural populations of Populus simonii is associated with leaf shape and photosynthetic traits (Journal of Experimental Botany, Vol.67, No.3pp.723-737, 2016) published by Dong Ci et al. The methylation data were calculated to obtain the DNA genome methylation levels of 235 Populus microphylla samples, and the results are shown in Table 1 (CC means Chicheng County: Chicheng County, ZJK: Zhangjiakou FX: Shaanxi Fu County; LY: Linyou County Linyou County; LX: Langao County, LC: Luochuan County, GQ: Gaoling Count; HZ: Huzhu County, XH: Xinghai County; W: DulanCounty, MY: Menyuan County County, SX: Song County, YC: Yichuan County, JL: Zhongning County, NM: Baotou City, NW: Ningwu County, TRT: Taoranting Park). At the same time, a portable laser leaf...
Embodiment 2
[0217] The relationship between DNA methylation level and leaf phenotype characteristics and photosynthetic characteristics of Populus microphylla.
[0218] To explore the effect of DNA methylation levels on phenotypic traits (leaf shape factor, leaf area, and net photosynthetic rate), we analyzed the numerical values of marginal utility.
[0219] In the first type of poplar samples, the DNA methylation levels of enzyme digestion combinations H31E3, H60E3, H63E10, H44E4, H80E2, H65E5, H63E11 and H60E2 had a significant marginal effect on leaf area (eg Figure 7-1 ). Leaf area decreased with the increase of the DNA methylation level of the restriction enzyme combinations H60E3, H44E4 and H60E2, and increased with the increase of the DNA methylation level of H31E3, H63E10, H80E2, H65E5 and H63E11. In the second type of poplar samples, the marginal effects of the DNA methylation levels of enzyme digestion combinations H80E13, H60E2, H82E5, H60E15, H63E11, H86E7, H80E9, H86E16,...
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Abstract
The invention provides methods for constructing and predicting the leaf trait of a woody plant and a photosynthetic characteristic model based on a DNA methylation level, and belongs to the technicalfield of biological analysis. The predicting method comprises selecting important characteristic variable embodying a geographic position difference based on a random forest, screening out 7 leaf characteristic variables, determining an optimal cluster number, and obtaining each group of cluster leaf samples by using an improved FCM clustering algorithm; according to the correlation between variables and the importance of Enzyme digestion combination obtained by a gradient boosted tree, obtaining an important enzyme digestion combination in each group of cluster leaf samples; by using the DNAmethylation level of the enzyme digestion combination as a regression variable, constructing LS-SVM regression prediction model based on Gaussian radial basis function; inputting the DNA methylation level of important enzyme digestion combination to accurately predict a leaf shape factor, leaf area and a net photosynthetic rate. The method is used for predicting the phenotypic characteristic and the photosynthetic characteristic of the woody plant, and screening individuals of woody plants with excellent traits.
Description
technical field [0001] The invention belongs to the field of biological information, and in particular relates to a construction method and a prediction method of a woody plant leaf phenotype characteristic and photosynthetic characteristic prediction model based on DNA methylation level. Background technique [0002] DNA methylation most commonly occurs at the fifth carbon atom of cytosine within a dinucleotide and is an important epigenetic modification. DNA methylation represses the expression of transposable elements, pseudogenes, repetitive sequences, and individual genes, and plays a key role in many biological processes such as gene expression, embryonic development, cell proliferation, differentiation, and chromosome stability. In plants, DNA methylation occurs at CG, CHG, CHH sites (H stands for bases other than guanine), and in higher plant cells, methylated cytosine can account for up to the total 50% of the number of cytosines. DNA methylation controls plant gr...
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