Use of pto-RAD50 gene haplotype in evaluation of plant photosynthetic efficiency

Abstract

Use of a Pto-RAD50 gene haplotype in the evaluation of plant photosynthetic efficiency. The present invention belongs to the technical field of plant molecular breeding. The nucleotide sequence of the Pto-RAD50 gene is set forth in SEQ ID NO: 1. The Pto-RAD50 gene haplotype is determined according to nucleotides of SNP1, SNP2, and InDel. The SNP1 is a nucleotide at position 172 of SEQ ID NO: 1, the nucleotide being C or A; the SNP2 is a nucleotide at position 442 of SEQ ID NO: 1, the nucleotide being A or G; and the InDel is nucleotides after position 422 of SEQ ID NO: 1, and is ATTATTTTAATA or a deletion of ATTATTTTAATA. By means of determining the genotype combination of the three described sites, the photosynthetic efficiency of poplar trees can be accurately judged, and optimal strains with high photosynthetic efficiency can be accurately and efficiently screened in the early growth stage of poplar trees, thereby effectively shortening the breeding period.

Description

Application of a Pto-RAD50 haplotype in evaluating plant photosynthetic efficiency

[0001] Cross-referencing

[0002] This application claims priority to Chinese Patent Application No. 2024106663168, filed on May 27, 2024, entitled “Application of a Pto-RAD50 gene haplotype in evaluating plant photosynthetic efficiency”, the entire disclosure of which is incorporated herein by reference. Technical Field

[0003] This invention belongs to the field of plant molecular breeding technology, and in particular relates to the application of a Pto-RAD50 gene haplotype in evaluating plant photosynthetic efficiency. Background Technology

[0004] Populus tomentosa is a dominant native species, a key tree species for renewable biological resources and forest carbon sinks, and a major source of timber and pulp raw materials, possessing significant economic and ecological value. Photosynthetic efficiency directly affects carbon input, and consequently timber volume, making it one of the most important physiological processes determining forest productivity. Therefore, improving photosynthetic efficiency is a crucial goal for enhancing forest productivity.

[0005] Photosynthetic efficiency is a complex quantitative trait controlled by multiple genes. In the breeding of superior poplar varieties, photosynthetic indicators significantly correlated with photosynthetic efficiency, such as net photosynthetic rate, transpiration rate, intercellular carbon dioxide concentration, and electron transport rate, are the main reference factors for evaluating photosynthetic efficiency. Currently, the selection of individuals with high photosynthetic efficiency is mainly based on phenotypic measurements. However, since photosynthetic efficiency is affected by various environmental factors during poplar growth and development, this method, relying solely on phenotypic observation, has low accuracy and limitations. With the continuous development of modern molecular breeding technology, developing key molecular markers that can influence photosynthetic efficiency and determining the genetic effects of key molecular marker combinations on tree photosynthetic efficiency can enable rapid and precise screening of new forest tree germplasm with strong photosynthetic capabilities. This has significant application value for evaluating photosynthetic efficiency in the seedling stage. Summary of the Invention

[0006] In view of this, the purpose of this invention is to provide an application of the Pto-RAD50 gene haplotype in evaluating plant photosynthetic efficiency, which can quickly screen plants with high photosynthetic efficiency.

[0007] To achieve the above-mentioned objectives, the present invention provides the following technical solution:

[0008] The application of a Pto-RAD50 gene haplotype in evaluating plant photosynthetic efficiency, wherein the nucleotide sequence of the Pto-RAD50 gene is shown in SEQ ID NO: 1; the Pto-RAD50 gene haplotype is determined based on the nucleotides of SNP1, SNP2, and InDel, wherein SNP1 is the nucleotide at position 172 of SEQ ID NO: 1, and the nucleotide is C or A; SNP2 is the nucleotide at position 442 of SEQ ID NO: 1, and the nucleotide is A or G; and InDel is the nucleotide after position 422 of SEQ ID NO: 1, which is ATTATTTATAATA or ATTATTTATAATA is deleted.

[0009] Preferably, the nucleotide of SNP1 is C, the nucleotide of SNP2 is A, and when the nucleotide of InDel is missing ATTATTTTAATA, the photosynthetic efficiency of the plant is low.

[0010] Preferably, when the nucleotide of SNP1 is A, the nucleotide of SNP2 is G, and the nucleotide of InDel is ATTATTTTAATA, the photosynthetic efficiency of the plant is high.

[0011] Preferably, the plant is a poplar.

[0012] Another object of the present invention is to provide a primer set for detecting photosynthetic efficiency in plants, characterized in that it includes a primer set for detecting the SNP1 genotype: the nucleotide sequences are shown in SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4, respectively;

[0013] Primer set for detecting SNP2 genotype: nucleotide sequences are shown in SEQ ID NO: 5, SEQ ID NO: 6, and SEQ ID NO: 7, respectively;

[0014] Primer sets used for detecting the InDel genotype: nucleotide sequences are shown in SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, respectively.

[0015] Another object of the present invention is to provide a kit for detecting the photosynthetic efficiency of poplar trees, comprising the above-mentioned primer set.

[0016] Another object of the present invention is to provide the application of the said application, the said primer set, or the said kit in poplar breeding.

[0017] Compared with the prior art, the present invention has the following beneficial effects:

[0018] This invention provides an application of the Pto-RAD50 gene haplotype in evaluating plant photosynthetic efficiency. Based on a genome-wide association analysis strategy, and relying on a population of Populus tomentosa germplasm resources, a mixed linear model in EMMAX software was used to detect SNP sites significantly associated with the net photosynthetic rate of Populus tomentosa at the genome-wide level. SNP1 (P = 9.02 × 10⁻⁶) was detected. -8 ) and SNP2 (P = 7.31 × 10 -9 These two SNP sites were significantly associated with net photosynthetic rate, and gene annotation showed that these two SNP sites were located in the promoter region of the Pto-RAD50 gene. Using SNP and InDel variation information within the Pto-RAD50 gene, association analysis based on candidate genes revealed that, in addition to the two SNPs significantly associated with net photosynthetic rate, an InDel located in the Pto-RAD50 promoter region was also significantly associated with net photosynthetic rate (P = 7.25 × 10⁻⁶). -8 Furthermore, InDel exhibits a high degree of linkage with SNP1 and SNP2 (R... 2 >0.8), forming a stable haplotype module. SNP1, located at position 172 in the Pto-RAD50 gene promoter region, exhibits three genotypes (CC, CA, and AA) in the Populus tomentosa germplasm resource population. SNP2, located at position 442 in the Pto-RAD50 gene promoter region, exhibits only two homozygous genotypes (AA and GG) in the Populus tomentosa germplasm resource population. InDel, located after position 422 in the Pto-RAD50 gene promoter region, exhibits only two genotypes (DD (homozygous deletion) and II (homozygous insertion) in the Populus tomentosa germplasm resource population. By determining the genotype combinations at these three loci, the photosynthetic efficiency of poplar trees can be accurately determined, enabling accurate and efficient screening of superior trees with high photosynthetic efficiency in the early stages of poplar growth, effectively shortening the breeding cycle. Attached Figure Description

[0019] Figure 1: LD linkage map of the Pto-RAD50 gene haplotype module, including two SNPs and one InDel;

[0020] Figure 2: Genotypic effect of different genotype combinations on photosynthetic efficiency of Populus tomentosa in the Pto-RAD50 gene haplotype module. Detailed Implementation

[0021] This invention provides an application of the Pto-RAD50 gene haplotype in evaluating plant photosynthetic efficiency. The nucleotide sequence of the Pto-RAD50 gene is shown in SEQ ID NO: 1. The Pto-RAD50 gene haplotype is determined based on the nucleotides of SNP1, SNP2, and InDel. SNP1 is the nucleotide at position 172 of SEQ ID NO: 1, and the nucleotide is C or A. SNP2 is the nucleotide at position 442 of SEQ ID NO: 1, and the nucleotide is A or G. InDel is the nucleotide after position 422 of SEQ ID NO: 1, which is either ATTATTTTTAATA (i.e., insertion, I) or deletion, ATTATTTTTAATA (i.e., deletion, D).

[0022] In this invention, the nucleotide sequence shown in SEQ ID NO: 1 is as follows:

[0023] In this context, the underlined uppercase base C represents the site before the SNP1 mutation, the underlined uppercase base A represents the site before the SNP2 mutation, and the underlined uppercase base sequence ATTATTTAATA represents the insertion sequence.

[0024] In this invention, the nucleotide of SNP1 is C (i.e., the genotype is CC), the nucleotide of SNP2 is A (i.e., the genotype is AA), and when the nucleotide of InDel is missing ATTATTTTAATA (i.e., the genotype is DD), that is, when the genotype combination is CC-AA-DD, the photosynthetic efficiency of the plant is low.

[0025] In this invention, when the nucleotide of SNP1 is A (i.e., genotype AA), the nucleotide of SNP2 is G (i.e., genotype GG), and the nucleotide of InDel is ATTATTTATAATA (i.e., genotype II), that is, when the genotype combination is AA-GG-II, the photosynthetic efficiency of the plant is high.

[0026] In this invention, the plant is a poplar, preferably a white poplar.

[0027] The two SNPs at positions 172 and 442 of the Pto-RAD50 gene described in this invention were detected at the genome-wide association analysis (GWAS) level using a mixed linear model in EMMAX software, based on a population of Populus tomentosa germplasm resources. The InDel was detected using a candidate gene association strategy, based on all SNPs and InDel variants in the PtoRAD50 gene. This InDel showed a high linkage relationship with both SNP1 and SNP2 (R0). 2 >0.8), forming a stable haplotype module. The correlation between the SNPs and InDel described in this invention and the net photosynthetic rate is significant (P<1×10). -7 .

[0028] Among them, SNP1 is located at position 172 in the promoter region of the Pto-RAD50 gene, and has three genotypes (CC, CA, and AA) in the Populus tomentosa germplasm resource population. SNP2 is located at position 442 in the promoter region of the Pto-RAD50 gene, and has only two homozygous genotypes (AA and GG) in the Populus tomentosa germplasm resource population. InDel is located after position 422 in the promoter region of the Pto-RAD50 gene, and has only two genotypes (DD, homozygous deletion, and II, homozygous insertion) in the Populus tomentosa germplasm resource population. By determining the genotype combinations at these three loci, the photosynthetic efficiency of poplar trees can be accurately determined, allowing for accurate and efficient screening of superior trees with high photosynthetic efficiency in the early stages of poplar growth, effectively shortening the breeding cycle.

[0029] After determining the genotype combinations of the above-mentioned SNP and InDel loci, this invention judges the photosynthetic efficiency of poplar trees based on the genotype combinations of the above loci: when the genotype of SNP1 is CC, the genotype of SNP2 is AA, and the genotype of InDel is DD, that is, when the genotype combination of the haplotypes is CC-AA-DD, the photosynthetic efficiency of the poplar sample leaves is the lowest; when the genotype of SNP1 is AA, the genotype of SNP2 is GG, and the genotype of InDel is II, that is, when the genotype combination of the haplotypes is AA-GG-II, the photosynthetic efficiency of the poplar sample leaves is the highest.

[0030] This invention does not specify a particular method for extracting genomic DNA from the sample; conventional plant genome extraction methods in the art are sufficient. Similarly, this invention does not limit the methods for determining the InDel genotype at the 172nd, 442nd, and 422nd bases upstream of the Pto-RAD50 gene; SNP and InDel genotype detection methods well-known to those skilled in the art are acceptable. As one feasible approach, this invention employs PCR amplification.

[0031] The present invention also provides a primer set for detecting photosynthetic efficiency in plants, characterized in that it includes primer sets for detecting SNP1 genotype: Pto-RAD50-172-CF, nucleotide sequence as shown in SEQ ID NO: 2; Pto-RAD50-172-AF, nucleotide sequence as shown in SEQ ID NO: 3; and Pto-RAD50-172-R, nucleotide sequence as shown in SEQ ID NO: 4.

[0032] The primer set used for detecting SNP2 genotype is as follows: Pto-RAD50-442-AF, nucleotide sequence as shown in SEQ ID NO: 5; Pto-RAD50-442-GF, nucleotide sequence as shown in SEQ ID NO: 6; Pto-RAD50-442-R, nucleotide sequence as shown in SEQ ID NO: 7.

[0033] The primer set used to detect the InDel genotype is as follows: Pto-RAD50-422-DF, nucleotide sequence as shown in SEQ ID NO: 8; Pto-RAD50-422-IF, nucleotide sequence as shown in SEQ ID NO: 9; and Pto-RAD50-422-R, nucleotide sequence as shown in SEQ ID NO: 10.

[0034] This invention utilizes primers designed for the target SNP1, SNP2, and InDel loci for PCR amplification. The presence of the amplified products indicates the genotype of the target locus, thus evaluating the photosynthetic efficiency of poplar trees. The primer design for the two SNP loci requires a 3x3 ratio of forward primers. ， The last base at the end of the inDel locus corresponds to the functional site. The primer design for the inDel locus requires that the forward primer either contains the insertion or does not. To ensure the specificity of the amplification product, the last base of the forward primer is modified with locked nucleic acid (LNA). Using the above primer set, the genotypes of two SNPs and the inDel locus significantly associated with the photosynthetic efficiency trait of poplar can be accurately and rapidly determined. Furthermore, the photosynthetic efficiency of poplar can be judged by the determined genotype combinations, thus enabling accurate and efficient screening of superior poplar trees with high photosynthetic efficiency in the early stages of poplar growth, effectively shortening the breeding cycle.

[0035] This invention utilizes PCR amplification to identify plant genotypes, and the methods for detecting amplification products are agarose gel electrophoresis or amplicon sequencing, with agarose gel electrophoresis being preferred. In this invention, the amplification products of Pto-RAD50-172-CF and Pto-RAD50-172-R are 91 bp in size, the amplification products of Pto-RAD50-172-AF and Pto-RAD50-172-R are 91 bp in size, the amplification products of Pto-RAD50-442-AF and Pto-RAD50-442-R are 81 bp in size, the amplification products of Pto-RAD50-442-GF and Pto-RAD50-442-R are 81 bp in size, the amplification products of Pto-RAD50-422-DF and Pto-RAD50-422-R are 92 bp in size, and the amplification products of Pto-RAD50-422-IF and Pto-RAD50-422-R are 104 bp in size. If the target band is not present in the agarose gel electrophoresis results, it indicates that no corresponding amplification product was obtained.

[0036] Based on the amplification results, the genotype of the sample can be determined. Specifically, if PCR amplification of Pto-RAD50-172-CF and Pto-RAD50-172-R yields amplification products, while PCR amplification of Pto-RAD50-172-AF and Pto-RAD50-172-R does not yield amplification products, then the genotype of SNP1 in the sample is CC.

[0037] If PCR amplification of Pto-RAD50-172-CF and Pto-RAD50-172-R yields amplification products, and PCR amplification of Pto-RAD50-172-AF and Pto-RAD50-172-R also yields amplification products, then the genotype of SNP1 in the sample is CA.

[0038] If no amplification product is obtained when Pto-RAD50-172-CF and Pto-RAD50-172-R are amplified by PCR, but amplification products are obtained when Pto-RAD50-172-AF and Pto-RAD50-172-R are amplified by PCR, then the genotype of SNP1 in the sample is AA.

[0039] If PCR amplification of Pto-RAD50-442-AF and Pto-RAD50-442-R yields amplification products, while PCR amplification of Pto-RAD50-442-GF and Pto-RAD50-442-R does not yield amplification products, then the genotype of SNP2 in the sample is AA.

[0040] If no amplification product is obtained when Pto-RAD50-442-AF and Pto-RAD50-442-R are amplified by PCR, but amplification products are obtained when Pto-RAD50-442-GF and Pto-RAD50-442-R are amplified by PCR, then the genotype of SNP2 in the sample is GG.

[0041] If PCR amplification of Pto-RAD50-422-DF and Pto-RAD50-422-R yields amplification products, but PCR amplification of Pto-RAD50-422-IF and Pto-RAD50-422-R does not yield amplification products, then the genotype of sample InDel is DD, i.e. deletion type.

[0042] If no amplification product is obtained when Pto-RAD50-422-DF and Pto-RAD50-422-R are used for PCR amplification, but amplification products are obtained when Pto-RAD50-422-IF and Pto-RAD50-422-R are used for PCR amplification, then the genotype of sample InDel is II, i.e., insertion type.

[0043] This invention also provides a kit for detecting the photosynthetic efficiency of poplar trees, comprising the aforementioned primer set. The kit provided by this invention can accurately and rapidly determine the photosynthetic efficiency of poplar trees.

[0044] This invention also provides the application of the aforementioned application, primer set, or kit in poplar breeding. This invention can rapidly and accurately determine the genotypes of the SNPs and InDel sites in poplar samples, and then determine the photosynthetic efficiency of the poplar through the determined genotype combinations. This allows for accurate and efficient screening of superior white poplar trees with high photosynthetic efficiency in the early stages of poplar growth, effectively shortening the breeding cycle. By detecting the genotypes of the SNPs and InDel sites, this invention can screen poplar samples with the genotype combination AA-GG-II for subsequent breeding operations to obtain poplar varieties with high photosynthetic efficiency.

[0045] In this invention, all primers were synthesized by Sangon Biotech Co., Ltd.

[0046] Unless otherwise specified, all chemical reagents used in this invention are commercially available conventional reagents, and all technical means used are conventional technical means well known to those skilled in the art.

[0047] The technical solutions provided by the present invention will be described in detail below with reference to the embodiments, but they should not be construed as limiting the scope of protection of the present invention.

[0048] Example 1

[0049] Primer set for detecting Pto-RAD50 gene haplotype

[0050] The primer set includes: primers for identifying the genotype of nucleotide sequence SEQ ID NO.1 at position 172 (SNP1): Pto-RAD50-172-CF and Pto-RAD50-172-R, with an amplification product of 91 bp; and Pto-RAD50-172-AF and Pto-RAD50-172-R, with an amplification product of 91 bp; primers for identifying the genotype of nucleotide sequence SEQ ID NO.1 at position 442 (SNP2): Pto-RAD50-442-AF and Pto-RAD50-442-R, with an amplification product of 81 bp; and Pto-RAD50-442-GF and Pto-RAD50-442-R, with an amplification product of 81 bp; primers for identifying the genotype of nucleotide sequence SEQ ID NO.1 at position 442 (SNP2); ... The primer sets for the InDel sequence after position 422 of the nucleotide sequence shown in NO.1 are: Pto-RAD50-422-DF and Pto-RAD50-422-R, with an amplification product of 92bp; Pto-RAD50-422-IF and Pto-RAD50-422-R, with an amplification product of 104bp; the specific nucleotide sequences of the primer sets are shown in Table 1.

[0051] Table 1 Primer sets used to identify SNP and InDel genotypes.

[0052] All primers were synthesized by Sangon Biotech Co., Ltd.

[0053] Example 2

[0054] Using the primer set from Example 1, the genotypes of the SNPs and InDel in 30 individuals from a Populus tomentosa hybrid population were identified, and the photosynthetic efficiency of the samples was evaluated. The steps are as follows:

[0055] 1) Thirty individuals were randomly selected from the germplasm resource bank of the hybrid population of Populus tomentosa planted in Guanxian County, Shandong Province. Under sunny weather conditions between 8:30 am and 11:00 am, the net photosynthetic rate of any one leaf from the third to the sixth leaf was measured using the Li-6800 portable photosynthetic fluorescence measurement system. The results are shown in Table 2.

[0056] 2) After the measurement is completed, collect the leaf samples and immediately freeze them in liquid nitrogen (-196℃);

[0057] 3) Genomic DNA was extracted from leaf samples using the FastPure Universal Plant Total RNA Isolation Kit (Vazyme China, Nanjing, China);

[0058] 4) The locked nucleic acid modification method was used to determine the 172nd, 442nd, and InDel bases following the 422nd base in the promoter region of the Pto-RAD50 gene in the genomic DNA of the Populus tomentosa leaf samples. PCR amplification was performed using the primer set described in Example 1, with the genomic DNA obtained in step 3) as a template.

[0059] The PCR reaction system is as follows: 5 μL of 10×PCR amplification buffer, 1 μL of 0.01 μmol / μL dNTP mixture, 2.5 μL of 300 ng / μL genomic DNA template, 0.5 μL of 2.5 U / μL high-fidelity DNA polymerase, 0.5 μL of 1.5 mmol / μL MgCl2, 1.25 μL each of 10 μmol / L forward and reverse primers, and 38 μL of double-distilled water;

[0060] The amplification procedure is as follows:

[0061] Step 1: Pre-denaturation at 95℃ for 3 minutes;

[0062] Step 2: 95℃ denaturation for 15s, 57℃ annealing for 30s, 72℃ extension for 15s, and repeat Step 2 35 times.

[0063] Step 3: Extend thoroughly at 72℃ for 5 minutes.

[0064] After PCR amplification, the amplification products were detected by agarose gel electrophoresis. The results were then interpreted.

[0065] The genotypes of the SNPs and InDel in the candidate samples and their corresponding net photosynthetic rates are shown in Table 2.

[0066] Table 2 Genotypes and net photosynthetic rates at three predetermined loci in the tested Populus tomentosa individuals.

[0067] According to the results in Table 2, the overall net photosynthetic rate of the 30 individuals was 15.21 μmol CO2·m⁻¹. -2 ·s - 1 ±5.01 μmol CO2·m -2 ·s -1When the genotype combination of InDel at bases 172, 442, and 422 after the Pto-RAD50 promoter region was CC-AA-DD, the net photosynthetic rate of the candidate poplar individuals was the lowest, reflected in the candidate individual's net photosynthetic rate (10.79 μmol CO2·m). -2 ·s - 1 ±1.16 μmol CO2·m -2 ·s -1 ) and overall net photosynthetic rate (15.21 μmol CO2·m -2 ·s -1 ±5.01 μmol CO2·m -2 ·s -1 The net photosynthetic rate was 29.06% lower than that of the target population. The highest net photosynthetic rate was observed in candidate poplar individuals when the genotype combination of InDel at bases 172, 442, and 422 after the target population in the Pto-RAD50 promoter region was AA-GG-II, as reflected in the candidate individual's net photosynthetic rate (22.75 μmol CO2·m⁻¹). -2 ·s - 1 ±0.92 μmol CO2·m -2 ·s -1 ) and overall net photosynthetic rate (15.21 μmol CO2·m -2 ·s -1 ±5.01 μmol CO2·m -2 ·s -1 This is 49.57% higher than the previous figure.

[0068] As can be seen, the present invention can accurately and quickly determine the genotypes of two SNPs and InDel loci that are significantly related to the photosynthetic efficiency trait of poplar trees, and then determine the photosynthetic efficiency of poplar trees by determining the genotype combination. This allows for accurate and efficient screening of superior trees with high photosynthetic efficiency in the early stage of poplar growth, effectively shortening the breeding cycle of high-productivity poplar varieties.

[0069] The above description is only a preferred embodiment of the present invention. It should be noted that for those skilled in the art, several improvements and modifications can be made without departing from the principle of the present invention, and these improvements and modifications should also be considered within the scope of protection of the present invention. Industrial applicability

[0070] This invention provides an application of the Pto-RAD50 gene haplotype in evaluating plant photosynthetic efficiency, belonging to the field of plant molecular breeding technology. The nucleotide sequence of the Pto-RAD50 gene is shown in SEQ ID NO: 1; the Pto-RAD50 gene haplotype is determined based on the nucleotides of SNP1, SNP2, and InDel. SNP1 is the nucleotide at position 172 of SEQ ID NO: 1, and the nucleotide is C or A; SNP2 is the nucleotide at position 442 of SEQ ID NO: 1, and the nucleotide is A or G; InDel is the nucleotide after position 422 of SEQ ID NO: 1, which is either ATTATTTTTAATA or ATTATTTTAATA is deleted. By determining the genotype combination at these three loci, the photosynthetic efficiency of poplar trees can be accurately determined. This allows for accurate and efficient screening of superior plants with high photosynthetic efficiency in the early stages of poplar growth, effectively shortening the breeding cycle and demonstrating good economic value and application prospects.

Claims

1. Use of a Pto-RAD50 haplotype in the evaluation of photosynthetic efficiency in a plant, characterized in that, The nucleotide sequence of the Pto-RAD50 gene is shown as SEQ ID NO: 1; the Pto-RAD50 gene haplotype is determined according to SNPs 1, 2 and InDel, the SNP 1 is the nucleotide at position 172 of SEQ ID NO: 1, which is C or A; the SNP 2 is the nucleotide at position 442 of SEQ ID NO: 1, which is A or G; the InDel is the nucleotides after position 422 of SEQ ID NO: 1, which are ATTATTTTAATA or deletion of ATTATTTTAATA.

2. Use according to claim 1, characterized in that, When the nucleotide of the SNP 1 is C, the nucleotide of the SNP 2 is A, and the nucleotide of the InDel is deletion of ATTATTTTAATA, the photosynthetic efficiency of the plant is low.

3. Use according to claim 1, characterized in that, When the nucleotide of the SNP 1 is A, the nucleotide of the SNP 2 is G, and the nucleotide of the InDel is ATTATTTTAATA, the photosynthetic efficiency of the plant is high.

4. Use according to any one of claims 1 to 3, characterized in that, The plant is a poplar.

5. A primer set for detecting photosynthetic efficiency of a plant, characterized by, The primer set for detecting the genotype of SNP 1 includes: the nucleotide sequences are shown as SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4, respectively; The primer set for detecting the genotype of SNP 2 includes: the nucleotide sequences are shown as SEQ ID NO: 5, SEQ ID NO: 6, and SEQ ID NO: 7, respectively; The primer set for detecting the genotype of InDel includes: the nucleotide sequences are shown as SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, respectively.

6. A kit for detecting photosynthetic efficiency in poplar plants, characterized in that, The primer set of claim 5 is included.

7. Use of any of claims 1-4 or the primer set of claim 5 or the kit of claim 6 in poplar breeding.

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