Poplar SNP molecular marker combination, and whole-genome liquid-phase chip prepared therefrom and use thereof

Abstract

Disclosed in the present application are a poplar SNP molecular marker combination, and a whole-genome liquid-phase chip prepared therefrom and the use thereof. The poplar SNP molecular marker combination comprises 60,944 SNP molecular markers, and the physical positions of the 60,944 SNP molecular markers are determined by means of sequence alignment based on reference genome GCA_015852605.2 of poplar. The poplar SNP molecular markers of the present application can be used for specifically identifying five major species of poplar. By means of using the poplar SNP molecular markers to prepare a whole-genome liquid-phase chip for poplar species, low-cost, efficient and accurate genotyping detection of poplar germplasm resource populations can be realized.

Description

Populus SNP molecular marker combination and whole genome liquid chip prepared therefrom and application thereof TECHNICAL FIELD

[0001] The present application belongs to the field of biotechnology, and particularly relates to a Populus SNP molecular marker combination and whole genome liquid chip prepared therefrom and application thereof. BACKGROUND

[0002] Populus is the general term for plants of the genus Populus in the Salicaceae family. Generally, plants of the genus Populus can be divided into five major groups: Sect. Populus, Sect. Aigeiros, Sect. Tacamahaca, Sect. Leucoides and Sect. Turanga. Populus has the characteristics of fast growth, strong adaptability and easy propagation, and is one of the world's major afforestation tree species, playing an important role in industrial timber forests and ecological protection forests and the like.

[0003] Due to extreme abnormal climate changes in recent years and the promotion of national farmland rectification measures, Populus afforestation will tend to be more difficult for the restoration and utilization of difficult sites. Therefore, more multi-resistant and multi-purpose breakthrough new varieties need to be bred to meet the diversified needs in actual production. Rich germplasm resources are the basis for Populus breeding work, and genetic diversity evaluation research on specific traits of germplasm resources can better tap and utilize excellent germplasm resources.

[0004] At present, most of the Populus breeding methods use traditional breeding methods, and the combination with modern molecular techniques is weak. The existing liquid chip Populus nigra 40K only has specificity for the Sect. Aigeiros group, and has low universality and utilization rate for the Sect. Populus, Sect. Tacamahaca, Sect. Leucoides and Sect. Turanga groups, resulting in poor breeding effect, low breeding efficiency, low universality and the like. In the study of molecular markers of Populus, in addition to the use of SSR (Simple Sequence Repeat) markers, a large number of SNPs (Single Nucleotide Polymorphism) have also been tapped, but their throughput is low, the genomic coverage is narrow, and they are not suitable for large-scale breeding work. Whole genome breeding chip is a breeding tool based on high-throughput molecular marker technology, which can cover the SNP sites of the entire genome, and has the characteristics of wide coverage, high sensitivity, high detection throughput and high precision. Using the whole genome breeding chip to conduct overall evaluation of the genotype, genetic diversity and functional gene tapping of the germplasm resources of the five major groups of Populus can help to improve the efficiency of parent selection in hybrid breeding research, better utilize and tap the excellent germplasm resources of the five major groups of Populus, and promote the transformation of Populus from conventional breeding to molecular design breeding and intelligent breeding.

[0005] SUMMARY

[0006] The present application aims to at least solve one of the technical problems existing in the prior art. To this end, the present application provides a poplar SNP molecular marker combination.

[0007] The present application also provides a whole genome liquid chip for detecting the poplar SNP molecular marker combination.

[0008] The present application also provides a kit for detecting the poplar SNP molecular marker combination.

[0009] The present application also provides a screening method of the poplar SNP molecular marker combination.

[0010] The present application also provides an application of the poplar SNP molecular marker combination, the whole genome liquid chip or the kit.

[0011] The present application also provides a breeding method of poplar.

[0012] According to an aspect of the present application, a poplar SNP molecular marker combination is provided, which comprises 60,944 SNP molecular markers, the physical positions of the 60,944 SNP molecular markers are determined based on sequence alignment of poplar reference genome GCA_015852605.2, and the site information is shown in Table 1 as follows.

[0013] Table 1

[0014] In some embodiments of the present application, the SNP molecular marker 19: 17260837 T / - means that "-" represents an insertion of TATTTGAAGTTCGTCGAAGCTCCCAGTAAACATGAC.

[0015] In some embodiments of the present application, the Alt is "." which means that it has multiple mutation possibilities.

[0016] In some embodiments of the present application, when ref is A, Alt is "." which means that the mutation can be T, G, C or N; when ref is T, Alt is "." which means that the mutation can be A, G, C or N; when ref is G, Alt is "." which means that the mutation can be A, T, C or N; when ref is C, Alt is "." which means that the mutation can be A, T, G or N, wherein N is deletion.

[0017] In some embodiments of the present application, the position information of the SNP site is represented in the form of chromosome number: physical position.

[0018] In the second aspect of the present application, a whole genome liquid phase chip is provided, which comprises a primer set and / or a probe for detecting the above-mentioned Populus SNP molecular marker combination.

[0019] In a third aspect of the present application, a kit is provided, which comprises a primer set and / or a probe for detecting the above-mentioned Populus SNP molecular marker combination.

[0020] In a fourth aspect of the present application, a screening method for the above-mentioned Populus SNP molecular marker combination is provided, which comprises the following steps:

[0021] (1) After aligning and variant calling of Populus whole genome sequencing data using Sentieon software, preliminary hard filtering is performed to obtain a file containing SNP variation information of all samples;

[0022] (2) The file containing SNP variation information of all samples is mined and filtered to obtain target site SNPs; the mining and filtering parameters are: MAF≥0.05, SNP site detection rate≥80%, heterozygosity≤50%, sequencing depth≥6X;

[0023] (3) According to SNP site detection rate≥90%, heterozygosity≤50%, sequencing depth≥5X, the file containing SNP variation information of all samples is extracted to obtain SNP sites of genes related to Populus growth, resistance, wood formation, flowering regulation, flavonoid metabolism, etc.;

[0024] (4) According to the file containing SNP variation information of all samples, inter-population genetic differentiation index of each SNP variation site of different Populus species is calculated; the parameter is --weir-fst-pop, and filtering and probe design are performed according to the threshold of FST>0.5 to screen specific SNP sites of different Populus species;

[0025] (5) The target site SNPs obtained in step (2), the SNP sites of genes related to Populus growth, resistance, wood formation, flowering regulation, flavonoid metabolism, etc. obtained in step (3), and the specific SNP sites of different Populus species obtained in step (4) are combined, and probe design is performed to screen SNPs meeting the requirements to obtain a Populus SNP molecular marker combination.

[0026] In some embodiments of the present application, the resistance includes drought resistance, salt tolerance and disease resistance.

[0027] In some embodiments of the present application, the Populus species includes at least one of white poplar, green poplar, black poplar, cottonwood and large leaf poplar.

[0028] In some embodiments of the present application, aligning and variant calling of Populus resequencing data using Sentieon software specifically comprises the following steps:

[0029] (1) Using Sentieon software to align the whole genome sequencing data of the poplar to the poplar reference genome GCA_015852605.2, to perform position sorting and mark repeated reads;

[0030] (2) Using Sentieon software to perform variant site detection on each sample to obtain the gVCF of each sample;

[0031] (3) Using Sentieon to perform joint-calling, joint analysis of the gVCF of all samples to obtain the variation results of each individual in the population.

[0032] In some embodiments of the present application, the hard filtering criteria are as follows: QD < 2.0 || FS > 60.0 || MQ < 40.0 || SOR > 3.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0.

[0033] In some embodiments of the present application, the length of the probe is 80-120 bp.

[0034] In some embodiments of the present application, the length of the probe is about 100 bp.

[0035] In some embodiments of the present application, the GC content of the probe is between 20%-80%.

[0036] In some embodiments of the present application, screening probes meeting the requirements includes the following steps: sequencing the probes, removing probes that cannot be uniquely aligned on the genome, and containing repeat sequences in the flanking sequence.

[0037] In the fifth aspect of the present application, at least one of the above-mentioned poplar SNP molecular marker combination, whole genome liquid chip and kit is applied, and the application is in detecting white poplar.

[0038] In some embodiments of the present application, the application is in detecting the poplar of the white poplar.

[0039] In some embodiments of the present application, the application is in detecting the poplar of the black poplar.

[0040] In some embodiments of the present application, the application is in detecting the poplar of the black poplar.

[0041] In some embodiments of the present application, the application is in detecting the poplar of the black poplar.

[0042] In some embodiments of the present application, the application is in the whole genome selection breeding of the poplar.

[0043] In some embodiments of the present application, the application is the application in populus genome-wide association analysis.

[0044] In some embodiments of the present application, the application is the application in populus germplasm resource identification and variety authenticity identification.

[0045] In some embodiments of the present application, the application is the application in populus cluster analysis and genetic relationship identification.

[0046] In some embodiments of the present application, the application is the application in populus trait mining and identification.

[0047] In some embodiments of the present application, the application is the application in populus genotyping detection.

[0048] In some embodiments of the present application, the application is the application in populus genetic map construction and gene positioning.

[0049] In some embodiments of the present application, the application is the application in populus genetic diversity identification.

[0050] In some embodiments of the present application, the application is the application in populus molecular design breeding.

[0051] In some embodiments of the present application, the application can be specifically realized by the following method steps:

[0052] S1, using at least one of the populus SNP molecular marker combination, the whole genome liquid chip and the kit to genotype the sample to be tested, and obtaining the genotyping result; S2, analyzing the genotyping result obtained in step S1.

[0053] In the sixth aspect of the present application, a breeding method of populus is provided, which comprises the following steps: using at least one of the populus SNP molecular marker combination, the whole genome liquid chip and the kit to detect the DNA of the populus to be tested, and selecting a suitable populus species for subsequent breeding.

[0054] In some embodiments of the present application, the populus species includes at least one of white poplar, green poplar, black poplar, cottonwood and large leaf poplar.

[0055] In some embodiments of the present application, the detection is based on liquid probe capture sequencing genotyping technology.

[0056] According to some embodiments of the present application, the present application has at least the following beneficial effects:

[0057] The poplar SNP molecular marker combination of the present application can be used to specifically identify five major poplar species, and when used to prepare a poplar species whole genome liquid chip, can realize low-cost poplar germplasm resource group genotype efficient and accurate typing detection, and has specificity for the white poplar, black poplar, green poplar, large leaf poplar and hu poplar of the poplar genus. It can be applied to genotype analysis and genetic diversity evaluation of poplar germplasm resources, authenticity identification of germplasm resources and varieties, genetic map construction and functional gene positioning, whole genome association analysis, molecular design breeding, etc., and has important application value in many fields of poplar biological breeding.

[0058] Meanwhile, the poplar species whole genome liquid chip of the present application is based on the principle of liquid chip, and the site is flexible, and new marker sites can be added at any time in the later period. In addition, this chip also includes 12,287 functional sites and trait-associated sites such as growth, resistance, wood formation, flowering period regulation, flavonoid metabolism, 4,438 specific sites of white poplar, black poplar, green poplar and hu poplar of the four major poplar species, the number of sites is large, and the functional sites and trait-associated sites are rich, which is beneficial to the development and mining and utilization of poplar germplasm resources and the creation of new varieties, and provides an important tool for poplar molecular breeding, and plays an important role in the research of poplar genomic selection breeding.

[0059] Other features and advantages of the present application will be described in the subsequent description, and part of them will become apparent from the description, or can be understood by implementing the present application. BRIEF DESCRIPTION OF DRAWINGS

[0060] The present application will be further described below in combination with the drawings and examples, in which:

[0061] FIG. 1 is a chromosome density distribution diagram of the poplar 60K cGPS liquid chip in Example 1 of the present application;

[0062] FIG. 2 is a MAF distribution diagram of the poplar 60K cGPS liquid chip in Example 1 of the present application;

[0063] FIG. 3 is a schematic diagram of the cGPS liquid chip process detection in Example 2 of the present application;

[0064] FIG. 4 is a diagram of the genotype average consistency rate detection results of the technical repeat sample in Example 3 of the present application;

[0065] FIG. 5 is a principal component analysis diagram of the four major poplar species in Example 4 of the present application;

[0066] FIG. 6 is a cluster analysis diagram of the four major poplar species in Example 4 of the present application. DETAILED DESCRIPTION

[0067] The concept and the generated technical effects of the present application will be described clearly and completely in combination with the embodiments below, so as to fully understand the purposes, features and effects of the present application. Obviously, the described embodiments are only some of the embodiments of the present application, but not all the embodiments. Based on the embodiments of the present application, other embodiments obtained by those skilled in the art without creative labor are within the protection scope of the present application. The specific conditions are not indicated in the embodiments, and the conventional conditions or the conditions recommended by the manufacturer are adopted. The reagents or instruments used are not indicated by the manufacturer, and are conventional products that can be obtained by market purchase.

[0068] Embodiment 1

[0069] In this embodiment, a poplar SNP molecular marker combination and a poplar whole genome liquid chip designed according to the poplar SNP molecular marker combination are prepared.

[0070] 1. The screening process of the poplar SNP molecular marker combination is as follows:

[0071] (1) Poplar germplasm resource collection

[0072] In order to obtain poplar whole genome sites with rich genetic information, the resequencing data of 1307 samples of white poplar, 458 samples of green poplar, 635 samples of black poplar, 252 samples of Chinese poplar and 9 samples of large leaf poplar of five major poplar species in the existing database were collected and summarized, and 546 black poplar diversity materials were collected from the cooperative base of the Institute of Forestry, Chinese Academy of Forestry. The total number of samples is 3,207.

[0073] (2) Poplar whole genome resequencing and resequencing data analysis

[0074] The 546 poplar materials collected were subjected to whole genome resequencing, and the specific steps included:

[0075] 1) DNA was extracted by magnetic bead method; 2) the qualified DNA was used for DNA-seq sequencing library construction by adopting the standard method of MGI library; 3) after the library was qualified, sequencing was performed by adopting the sequencing platform (MGI) of Huada, the sequencing strategy was PE150, the sequencing depth was 20x, and the sequencing amount of each material was 9 Gb.

[0076] The 3,207 resequencing data were aligned and variant detected by Sentieon, and the analysis process was as follows:

[0077] 1) Using Sentieon to align reads to the Populus reference genome (GCA_015852605.2), position sorting and marking duplicate reads; 2) Using Sentieon to perform variant site detection for each sample, obtaining the gVCF of each sample; 3) Using Sentieon for joint-calling, joint analysis of the gVCF of all samples, and obtaining the variation results of each individual in the population. To ensure the accuracy of SNPs, the SNP sites obtained after joint analysis were subjected to preliminary hard filtering (SNP hard filtering criteria: "QD < 2.0 || FS > 60.0 || MQ < 40.0 || SOR > 3.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0").

[0078] After filtering, a.vcf file containing SNP variation information of all samples was obtained, totaling 49,998,887 SNP sites.

[0079] (3) Site screening

[0080] (1) Whole genome site

[0081] From the.vcf file containing SNP variation information of all samples, the MAF value, detection rate, heterozygosity, and sequencing depth of the site were calculated and statistically analyzed, and 419,970 Populus candidate site sets were screened according to MAF ≥ 0.2, SNP site detection rate ≥ 80%, heterozygosity ≤ 50%, and sequencing depth ≥ 6X.

[0082] Probes were designed for the target site set screened. The principle of probe design is to design probes within 100 bp on the left and right of all target sites, with a probe length of generally 100 bp and a GC content of between 20% and 80%. According to the probe design results, probes that cannot be uniquely aligned on the genome or contain repeat sequences in the flanking sequence were removed. Based on the principle of uniform distribution, 30,704 SNP sites were selected as whole genome sites.

[0083] (2) Important functional sites

[0084] Functional genes related to important economic traits such as Populus growth, resistance, wood formation, flowering regulation, and flavonoid metabolism that have been reported were collected and summarized. According to SNP site detection rate ≥ 90%, heterozygosity ≤ 50%, and sequencing depth ≥ 5X, all site information of these functional genes was extracted from the.vcf file containing SNP variation information of all samples obtained in 3), and SNP sites with higher MAF values were selected as candidate sites. According to the probe design results, probes that cannot be uniquely aligned on the genome or contain repeat sequences in the flanking sequence were removed, and finally 12,404 SNP sites were obtained (as shown in Table 2).

[0085] Table 2

[0086] (3) Four major species-specific sites

[0087] The inter-population genetic differentiation index (FST) is a measure of population differentiation and genetic distance. The greater the differentiation index, the greater the difference. Fst is between 0 and 1, and the closer to 1, the greater the degree of differentiation between the two populations, and the higher the selection degree. The closer to 0, the smaller the degree of differentiation between the two populations, and the lower the selection degree. The.vcf file of all sample SNP variation information obtained in 3) was calculated (single point calculation), the parameter was --weir-fst-pop, and finally filtered and probe designed according to the threshold of FST>0.5, and 4,438 four major species-specific sites were obtained (as shown in Table 3).

[0088] Table 3: FST site statistics

[0089] Finally, all target sites were found to have a gap region, which was filled based on the principle of uniform distribution on the chromosome, and the indicators of MAF≥0.05, SNP site detection rate≥80%, heterozygosity≤50%, and sequencing depth≥6X were used for filling. Finally, a poplar 60K liquid phase chip was constructed for probe synthesis, with a total of 60,944 sites, an average interval of 6.8Kb (as shown in Figure 1), site information is shown in Table 1, and MAF distribution map is shown in Figure 2 (functional sites do not consider MAF value).

[0090] 2. Poplar whole genome liquid phase chip

[0091] Based on the 60,944 SNP sites screened, the liquid phase capture probe was synthesized by Huazhi Biotechnology Co., Ltd., and the cGPS based on the target region genome sequence liquid phase capture precise positioning genotyping technology was used to form the system of poplar liquid phase chip, and the poplar whole genome liquid phase chip was prepared.

[0092] cGPS is based on an optimized thermodynamic stability algorithm model, which designs probes for different target regions of genome sequences, uses synthesized specific probes to capture and enrich multiple different target sequences located at different genomic positions, and then constructs sequencing library and high-throughput sequencing of the captured and enriched target genomic sequences, thereby obtaining the genotypes of all SNP / InDel sites in the target region, as shown in Figure 3.

[0093] Example 2

[0094] The embodiment provides a use method of the poplar whole genome liquid chip in the above embodiment 1, and specifically comprises the following contents:

[0095] 1. Poplar gDNA extraction and detection

[0096] 23 samples were selected as 60,944 SNP liquid chip development system verification samples, 8 fresh leaves of P. tomentosa, 7 fresh leaves of P. simonii and 8 fresh leaves of P. nigra were collected, and gDNA was extracted from the tissues by using magnetic beads. The integrity and purity of the gDNA were analyzed by 1% agarose gel electrophoresis method, and the concentration was accurately quantified by using Qubit.

[0097] 2. cGPS experimental process

[0098] (1) 200 ng of quantified and qualified gDNA was taken, and the DNA was cut into 100-500 bp fragments by using enzyme cutting reagent, and then Taq enzyme was added for end repair; (2) T4 ligase was used to connect the adapter fragments to both ends of the DNA, and fragment sorting magnetic beads were used to purify and amplify the library to complete the library construction; (3) the qualified library was placed in a PCR instrument with blocking reagent, RNAse inhibitor Rnase Block and 60K liquid chip probe for hybridization reaction, and incubated at 55°C overnight (16-24 h); (4) the hybridization product was captured by using streptavidin, and the captured library was amplified and enriched, and PE150 sequencing was performed on the Huada sequencing platform; (5) after high-throughput sequencing, the raw data was processed by quality control and filtration, and fastp software was used to remove the Reads containing adapter contamination and low-quality Reads. BWA software is used for alignment with the target genome, and GATK software is used for variant site analysis of the sequencing results to obtain the genotyping results of the target site, and the process schematic diagram is shown in Figure 3.

[0099] Example 3: Genotyping effect evaluation of poplar whole genome liquid chip

[0100] In order to verify the genotyping effect of the poplar whole genome liquid chip, 30 different poplar materials (including 7 repeated samples) were subjected to genotyping detection by using the poplar whole genome liquid chip obtained in embodiment 1 (for specific operation method, see embodiment 2).

[0101] Table 4: Site detection rate of 30 poplar samples

[0102] The results are shown in Table 4 and Figure 4. As shown in Table 4, through sequencing and data analysis, the detection rate of Populus davidiana sites is between 80.39% and 83.85%, with an average detection rate of 82.31%; the detection rate of Populus simonii sites is between 87.41% and 89.53%, with an average detection rate of 88.02%; and the detection rate of Populus nigra sites is between 98.33% and 99.18%, with an average detection rate of 98.68%. As shown in Figure 4, the genotype results of the 7 repeated samples are compared, and the consistency rate is between 98.84% and 99.47%, with an average consistency rate of 99.17%. The genotyping effect evaluation results of 60,944 SNP liquid chips show that the detection rate is the highest for Populus nigra, followed by Populus simonii and Populus davidiana, the average genotype consistency rate is high, and the genotyping results are accurate and reliable.

[0103] Example 4: Population structure analysis of Populus whole genome liquid chip

[0104] The Populus whole genome liquid chip prepared in Example 1 was used to identify the genotypes of 720 different Populus samples (including 139 Populus davidiana, 230 Populus nigra, 191 Populus simonii and 160 Populus euphratica), the PCA components of the detection materials were analyzed by using Plink software, and a PCA scatter plot was constructed. Each site in the scatter plot represents a sample, and the farther apart the two samples in the plot, the greater the genetic background difference between the two samples. Individuals with similar genetic backgrounds will be clustered in the plot.

[0105] The results are shown in Figure 5. It was found through statistics that the Populus materials were divided into 4 obvious populations, and the classification effect was consistent with the classification of tree species.

[0106] At the same time, the genetic distance matrix was calculated by using the IBS method in Plink software, and clustering analysis and phylogenetic tree construction were performed, and the results are shown in Figure 6. As shown in the figure, the Populus 60K liquid chip can effectively distinguish different Populus species, and the classification effect is consistent with the actual classification.

[0107] The above embodiments of the present application have been described in detail, but the present application is not limited to the above embodiments, and various changes can be made within the scope of knowledge possessed by those skilled in the art without departing from the purpose of the present application. In addition, the embodiments of the present application and the features in the embodiments can be combined with each other without conflict.

Claims

1. A molecular marker combination of Populus SNPs, characterized in that, The 60,944 SNP molecular markers comprise 60,944 SNP molecular markers, the physical position of which is determined based on sequence alignment of the poplar reference genome GCA_015852605.2, and the site information is specifically shown in Table 1 in the specification.

2. A whole genome liquid chip, characterized by, The whole genome liquid chip comprises a primer set and / or a probe for detecting the combination of poplar SNP molecular markers as claimed in claim 1.

3. A kit characterized in that, The kit comprises a primer set and / or a probe for detecting the combination of poplar SNP molecular markers as claimed in claim 1.

4. The screening method of the Populus SNP molecular marker combination according to claim 1, characterized in that, The screening method comprises the following steps: (1) After aligning and variant detection of poplar whole genome sequencing data using Sentieon software, preliminary hard filtering is performed to obtain a file containing SNP variation information of all samples; (2) Target site SNPs are obtained by mining and screening the file containing SNP variation information of all samples; the mining and screening parameters are: MAF≥0.05, SNP site detection rate≥80%, heterozygosity≤50%, sequencing depth≥6X; (3) According to the SNP site detection rate≥90%, heterozygosity≤50%, sequencing depth≥5X, the SNP sites of genes related to poplar growth, resistance, wood formation, flowering regulation, and flavonoid metabolism are extracted from the file containing SNP variation information of all samples; (4) According to the file containing SNP variation information of all samples, the inter-population genetic differentiation index of each SNP variation site of different poplar species is calculated; the parameter is --weir-fst-pop, and the threshold is FST>0.5 for filtering and probe design, and different poplar species specific SNP sites are screened; (5) The target site SNPs obtained in step (2), the SNP sites of genes related to poplar growth, resistance, wood formation, flowering regulation, and flavonoid metabolism obtained in step (3), and the different poplar species specific SNP sites obtained in step (4) are combined, and probes are designed to screen SNPs that meet the requirements to obtain a combination of poplar SNP molecular markers.

5. The screening method according to claim 4, characterized in that, The poplar species comprises at least one of white poplar, green poplar, black poplar, willow poplar, and large leaf poplar.

6. The screening method according to claim 4, wherein, The resistance comprises drought resistance, salt tolerance, and disease resistance.

7. The screening method according to claim 4, wherein The hard filtering criteria are as follows: QD<2.0||FS>60.0||MQ<40.0||SOR>3.0||MQRankSum<-12.5||ReadPosRankSum<-8.

0.

8. The screening method according to claim 4, wherein, The length of the probe is 80-120 bp, and the GC content is between 20%-80%.

9. Use of one of the combination of poplar SNP molecular markers of claim 1, the whole genome liquid chip of claim 2, and the kit of claim 3 in any one of the following: (1) detecting white poplar; (2) detecting green poplar; (3) detecting black poplar; (4) detecting cotton poplar; (5) detecting large leaf poplar; (6) poplar whole genome selection breeding; (7) poplar whole genome association analysis; (8) poplar germplasm resource identification and variety authenticity identification; (9) poplar cluster analysis and genetic relationship identification; (10) poplar trait mining and identification; (11) poplar genetic map construction and gene positioning; (12) poplar genetic diversity identification; or (13) poplar molecular design breeding.

10. A method of breeding a poplar tree, characterized by, The method comprises the following steps: detecting the DNA of the to-be-tested poplar by using one of the poplar SNP molecular marker combination of claim 1, the whole genome liquid chip of claim 2 and the kit of claim 3, and selecting the poplar for subsequent breeding.

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