Lithocarpus litseifolius leaf character related SNP (Single Nucleotide Polymorphism) site and application thereof

Abstract

The invention belongs to the technical field of biology, relates to an SNP (Single Nucleotide Polymorphism) site obviously related to the leaf morphology of Lithocarpus litseifolius, and particularly provides an SNP site physical position determined by comparison according to a reference genome with the login number of GCA040182985.1. The invention also provides specific SNP sites which are obviously related to the petiole length, the leaf length, the leaf width, the leaf area, the leaf color and the bud and leaf color and luster characters respectively, and the physical positions and variation information of the specific SNP sites are shown in a table 8. The SNP site provided by the invention can be used for further developing a detection reagent for site development, so that germplasm resources of lithocarpus litseifolius can be evaluated or bred, and the breeding process is accelerated.

Description

Technical Field

[0001] The present invention belongs to the field of biotechnology and relates to SNP loci significantly related to the leaf traits of Lithocarpus litseifolius and their applications. Background Art

[0002] Lithocarpus litseifolius [Hance] Chun is an evergreen tree of the genus Lithocarpus in the Fagaceae family and is a characteristic plant resource of new food raw materials that widely distributes in the Hunan Xuefeng Mountain range area and uses young leaves as tea beverages (commonly known as sweet tea and Yao tea). Lithocarpus litseifolius is rich in flavonoids and has effects such as lowering blood sugar, lowering blood pressure, and antioxidant.

[0003] Lithocarpus litseifolius has strong adaptability, a large biomass, and strong plant germination ability. New leaves germinate in spring, summer, and autumn, and mature leaves can be picked throughout the year. After being picked, new branches can grow from the leaf axils. Even if the whole plant is cut down, multiple new branches can germinate from the roots. It is a very characteristic resource. It is mainly distributed in mountain forests at an altitude of 200 - 2,000 m south of the Yangtze River, likes sunlight and is drought-tolerant, and the resources in Hunan, Jiangxi and other provinces are particularly rich. According to incomplete statistics, the distribution area of Lithocarpus litseifolius in Hunan Province is about 133,000 hm 2 2, and the area of Lithocarpus litseifolius in Xupu County is about 0.53 hm 2 2. The annual output of fresh young leaves of wild Lithocarpus litseifolius in the whole country is about 8,000 tons, and the annual output of fresh young leaves in the Xuefeng Mountain area of Hunan is 1,600 tons.

[0004] At the present stage, the collection of Lithocarpus litseifolius mainly relies on wild plants, and the artificial cultivation is relatively less. With the development of the Lithocarpus litseifolius industry, the demand for its leaves has increased significantly. If only a large number of wild resources are continuously cut down to obtain young leaves, along with the continuous reduction of the wild distribution area, the population and its individual numbers will gradually decrease, and then the loss of genetic diversity within the species will be caused. Therefore, it is particularly important to establish a germplasm resource nursery for Lithocarpus litseifolius to protect the genetic diversity of Lithocarpus litseifolius, especially to screen excellent Lithocarpus litseifolius germplasms. Germplasm resource evaluation, from traditional morphological characteristics, cytological structure, physiological and biochemical indexes to modern molecular marker technology, is committed to revealing the diversity and variation of genetic materials.

[0005] Molecular markers are a type of genetic markers that display genetic diversity at the nucleic acid molecular level based on DNA sequence differences. They have the advantages of a large number, large amount of information, high diversity, and being unaffected by the environment, and the results have high stability and reliability. They are powerful tools in the study of genetic diversity of plant germplasm resources. Summary of the Invention

[0006] In view of this, the purpose of the present invention is to provide SNP loci related to the leaf traits of Lithocarpus litseifolius and their applications.

[0007] To achieve the above object, the present invention provides the following technical solutions:

[0008] 1. Provide an SNP locus significantly related to the leaf morphology of Lithocarpus litseifolius, including the position information of the SNP locus and its significance level (p-value). The physical position of the SNP locus is determined by alignment with the reference genome with the accession number GCA_040182985.1. It also includes the variation information (reference genotype / allele genotype) corresponding to the specific SNP locus significantly related to the leaf morphology of Lithocarpus litseifolius. The information related to the SNP locus is as follows:

[0009] SNP ID Chromosome Position (bp) REF ALT p Associated Trait Chr10_6038227 10 6038227 T C 1.58E-05 Leaf Color Chr8_24865452 8 6038227 C T 2.98E-09 Leaf Color Chr4_66105620 4 66105620 T C 3.73E-06 Leaf Length Chr11_54116311 11 54116311 A G 7.69E-07 Leaf Width Chr11_40703521 11 40703521 G A 6.65E-06 Leaf Width Chr5_72562190 5 72562190 G A 7.67E-06 Leaf Width Chr4_66105620 4 66105620 T C 7.32E-06 Leaf Area Chr10_32223744 10 32223744 T C 3.01E-06 Petiole Length Chr11_15079523 11 15079523 G A 5.00E-06 Petiole Length Chr4_56044239 4 56044239 G A 5.21E-06 Petiole Length Chr9_54196508 9 54196508 A G 1.85E-08 Bud Leaf Color and Luster Chr10_39138077 10 39138077 C T 2.45E-08 Bud Leaf Color and Luster Chr7_4428839 7 4428839 T C 1.05E-07 Leaf Thickness Chr5_88247387 5 88247387 C T 8.34E-06 Leaf Thickness Chr2_21323826 2 21323826 G T 3.10E-05 Leaf Thickness Chr6_50047354 6 50047354 A G 3.54E-05 Leaf Thickness Chr6_50047558 6 50047558 A G 3.54E-05 Leaf Thickness Chr6_50047564 6 50047564 T A 3.54E-05 Leaf Thickness 。

[0010] The leaf morphology is petiole length, leaf length, leaf width, leaf area, leaf color, leaf thickness, and / or the color of bud leaves.

[0011] 2. A reagent for detecting the SNP locus significantly related to the leaf morphology of Lithocarpus litseifolius described above.

[0012] Furthermore, the reagent includes a molecular probe or a liquid chip.

[0013] 3. An application of a reagent for detecting the SNP locus significantly related to the leaf morphology of Lithocarpus litseifolius described above in identifying the leaf morphological traits of Lithocarpus litseifolius.

[0014] 4. An application of a reagent for detecting the SNP locus significantly related to the leaf morphology of Lithocarpus litseifolius described above in screening the germplasm resources of Lithocarpus litseifolius or artificial assisted breeding.

[0015] The present invention also studied the correlation between the sweet substances and morphological characteristics of different Lithocarpus litseifolius germplasm resources. There was a very significant positive correlation between leaf area and trilobatin, with a correlation coefficient of 0.50. There was a significant positive correlation between the color of bud leaves and neohesperidin dihydrochalcone, with a correlation coefficient of 0.41.

[0016] Compared with the prior art, the beneficial effects achieved by the present invention are as follows: The present invention has carried out research on the leaf morphological characteristics and the variation law of the content of sweet substances in the germplasm resources of Lithocarpus litseifolius in different regions of the country, and conducted simplified genome sequencing. On the basis of obtaining a large number of high-quality SNPs, further GWAS analysis was carried out with 14 leaf morphologies, and multiple SNP loci significantly related to leaf morphologies such as petiole length, leaf length, leaf width, leaf area, leaf color, leaf thickness, and bud leaf color were obtained. In particular, leaf thickness was also significantly correlated with the sweet substances in Lithocarpus litseifolius. This study also analyzed the correlation between the sweet substances and morphological characteristics of different Lithocarpus litseifolius germplasm resources, and it is feasible to evaluate the sweet substances in Lithocarpus litseifolius using leaf morphological traits. The excellent Lithocarpus litseifolius germplasm resources can be evaluated by measuring the genotypes of these SNP loci, or they can be applied to the molecular assisted breeding of Lithocarpus litseifolius, which is beneficial to the industrial development of the artificial cultivation of Lithocarpus litseifolius and the protection of wild resources. BRIEF DESCRIPTION OF THE DRAWINGS

[0017] In order to make the objectives, technical solutions, and beneficial effects of the present invention clearer, the following drawings are provided for illustration:

[0018] Figure 1 It is a DNA agarose gel electrophoresis diagram.

[0019] Figure 2 It is a diagram showing the main leaf morphological traits of Lithocarpus litseifolius germplasm resources.

[0020] Figure 3 It is a clustering diagram of different Lithocarpus litseifolius germplasm resources based on leaf morphological characteristics.

[0021] Figure 4 It is a correlation analysis diagram of the sweet substances and morphological characteristics of different Lithocarpus litseifolius germplasm resources.

[0022] Figure 5 It is the GWAS analysis result of the leaf color trait of Lithocarpus litseifolius.

[0023] Figure 6 It is the GWAS analysis result of the leaf length trait of Lithocarpus litseifolius.

[0024] Figure 7 It is the GWAS analysis result of the leaf width trait of Lithocarpus litseifolius.

[0025] Figure 8 It is the GWAS analysis result of the leaf area trait of Lithocarpus litseifolius.

[0026] Figure 9 It is the GWAS analysis result of the petiole length trait of Lithocarpus litseifolius.

[0027] Figure 10 It is the GWAS analysis result of the bud leaf color trait of Lithocarpus litseifolius.

[0028] Figure 11 The results of GWAS analysis for the thick trait of Lithocarpus litseifolius leaves. Specific implementation manners

[0029] The following will clearly and completely describe the technical solutions of the preferred embodiments of the present invention with reference to the accompanying drawings in the embodiments of the present invention. Obviously, the described embodiments are only a part of the embodiments of the present invention, rather than all the embodiments. All other embodiments obtained by those of ordinary skill in the art based on the embodiments of the present invention without making creative efforts belong to the scope of protection of the present invention. For the experimental methods without specific conditions noted in the embodiments, they are usually in accordance with conventional conditions or the conditions recommended by the manufacturers.

[0030] Example 1

[0031] Materials: The standardized planting base of Lithocarpus litseifolius of Hunan Aokang Biotechnology Co., Ltd. and the surrounding wild Lithocarpus litseifolius were used as test materials, which were identified as Lithocarpus litseifolius [Hance] Chun of the genus Lithocarpus in the Fagaceae family. The standardized planting base of Lithocarpus litseifolius is located in Heiniutian Village, Yanxi Township, Liangyaping Town, Xupu County, Hunan Province (110.58°E, 27.74°N), with an altitude of about 676 m, an average annual temperature of 16.9 °C, an average annual rainfall of 1539.1 mm, and an average annual frost-free period of 286 days.

[0032] In the early stage of the present invention, the variation rules of the contents of five sweet substances, such as phloridzin, phloretin, 3-hydroxyphloretin, neohesperidin dihydrochalcone, and phloretin, in Lithocarpus litseifolius with different parts (the results are shown in Table 1), tree ages, leaf ages, harvesting periods, and processing technologies were systematically studied. The results showed that phloridzin and phloretin are the two sweet substances with the highest proportions.

[0033] Table 1 Variation of the contents of different sweet substances in different parts of Lithocarpus litseifolius

[0034]

[0035] Note: Different lowercase letters in the same column indicate significant differences in different treatments of the same substance (P<0.05), and the same below.

[0036] Example 2

[0037] The 38 germplasm resources of Lithocarpus litseifolius in this study were collected from 12 provinces such as Yunnan, Sichuan, Hunan, and Guizhou, and transplanted into the germplasm resource nursery of Lithocarpus litseifolius of Hunan Yaocha Engineering Technology Research Center (110.58°E, 27.74°N). The specific germplasm resource information is shown in Table 2.

[0038] The leaf morphological characteristics of 38 Lithocarpus litseifolius germplasm resources were evaluated according to the "Descriptive Specification and Data Standard for Tea Germplasm Resources" and the "Technical Regulations for Identification of Crop Germplasm Resources - Tea". Fourteen leaf morphological characteristics were investigated in this experiment. The standardized assignment of descriptive traits and the measurement methods of numerical traits are shown in Table 3.

[0039] Table 2 Germplasm Resource Information

[0040]

[0041]

[0042] Table 3 Leaf Morphological Characteristics and Codes of Lithocarpus litseifolius Germplasm Resources

[0043]

[0044]

[0045] Example 3

[0046] Reduced-representation genome sequencing

[0047] (1) DNA extraction and detection

[0048] CTAB method was used for DNA extraction. Preliminary DNA detection: agarose gel electrophoresis for quantification, One drop; concentration: Onedrop; purity: One drop, agarose gel electrophoresis. DNA agarose gel electrophoresis detection parameters: gel concentration: 1%; voltage: 120v; electrophoresis time: 25min. The DNA quality inspection results are as Figure 1 shown.

[0049] (2) Reduced-representation genome sequencing and genetic diversity analysis

[0050] First, a double-digestion experiment was carried out to construct a pair-end library for the DNA samples with qualified quality inspection, and then Illumina HiSeq PE150 sequencing was used to search for SNP molecular markers. Filter the SNPs to obtain high-quality SNPs for PCA, phylogenetic tree, population structure and other analyses.

[0051] After sequencing on the Illumina platform, a total of 61.19 Gb of clean reads were obtained from 38 Litsea elongata germplasm samples, and the Q30 reached over 91.83%. The number of reads for each sample was between 3,761,362 and 8,036,446, and the GC content was between 35.05% and 36.34%. Among them, HH3 obtained the largest amount of data (8,036,446 reads), and GQ1 obtained the smallest amount of data (3,761,362 reads). The number of assembled sequences was between 363,163 and 491,389, the total depth of sequence coverage was between 5,843,978 and 13,285,337, and the average depth of the sequences was between 14.95 and 28.18, indicating high sequencing quality.

[0052] Genetic Diversity Analysis of Litsea elongata Populations

[0053] Analysis of population genetic diversity: The variation information at the population level obtained by the populations program showed that the number of SNPs was between 311,516 and 439,710, the number of SNPs of the transition type was between 215,167 and 302,767, the number of SNPs of the transversion type was between 97,836 and 136,943, the ratio of transition to transversion types was between 2.09 and 2.22, the number of heterozygous SNPs was between 175,601 and 25,461, the number of homozygous SNPs was between 109,674 and 202,912, the average depth was between 13.77 and 25.60, the number of SNPs with genotype missing was between 1,837,029 and 2,278,818, and the number of SNPs identical to the reference was between 1,788,219 and 2,163,084. The genomic data can be obtained from GenBank, and the accession number is PRJNA1055704.

[0054] The main leaf morphological traits of Litsea elongata germplasm resources are as Figure 2 shown. The leaf tips include acuminate, attenuate, acute, and obtuse; the leaf colors include yellowish-green, light green, green, and dark green; the leaf shapes include ovate, elliptical, oblong, and lanceolate; the leaf sizes include extra-large leaves, large leaves, medium leaves, and small leaves; the bud leaves include yellowish-green and purple-green; and the leaf surface elevation has three types: flat, slightly elevated, and elevated.

[0055] The morphological characteristics of the Litsea elongata germplasm resources from different sources are described in Tables 4 and 5. The largest petiole angle is 69.74° for ZL1, the smallest is 22.40° for YA1, and the average is 58.61°. The largest leaf area is 37.63 cm² for HX2, the smallest is 7.45 cm² for GQ4, and the average is 19.29 cm². The longest petiole length is 1.65 cm for HR2, the shortest is 0.31 cm for GQ4, and the average is 0.92 cm. The longest leaf length is 12.20 cm for SH1, the shortest is 6.18 cm for GQ4, and the average is 9.54 cm. The widest leaf width is 5.58 cm for JS1, the narrowest is 1.71 cm for GQ4, and the average is 3.63 cm. The largest leaf length-width ratio is 3.61 for GQ4, the smallest is 2.26 for HZ1, and the average is 2.75. The thickest leaf is 0.44 mm for HX2, the thinnest is 0.23 mm for FA2, and the average is 0.31 mm. The largest leaf tip angle is 37.09° for HE1, the smallest is 2.43° for YA1, and the average is 28.28°.

[0056] Table 4 Leaf shape, leaf margin, leaf tip, leaf surface bulge, leaf color, bud leaf color, and petiole angle characteristics of Litsea elongata germplasm resources

[0057]

[0058]

[0059] Table 5 Leaf area, petiole length, leaf length, leaf width, leaf length-width ratio, leaf thickness, and leaf tip angle characteristics of Litsea elongata germplasm resources

[0060]

[0061]

[0062] The diversity description of the leaf morphological characteristics of Lithocarpus litseifolius germplasm is shown in Table 6 and Table 7. The leaf shapes are mainly long oval and oval. Most of the leaf margins are flat. The leaf tips are mainly acute and acuminate. The leaf surface bulges are mainly flat and slightly bulging. The leaf colors are mainly green and dark green. The colors of the bud leaves are yellow-green and purple-green. The maximum petiole angle is 69.74°, the minimum is 22.40°, and the average value is 58.61°. The maximum leaf area is 37.63 cm², the minimum is 7.45 cm², and the average value is 19.29 cm². The longest petiole length is 1.65 cm, the shortest is 0.31 cm, and the average value is 0.92 cm. The longest leaf length is 12.20 cm, the shortest is 6.18 cm, and the average value is 9.54 cm. The widest leaf width is 5.58 cm, the narrowest is 1.71 cm, and the average value is 3.63 cm. The maximum leaf length-width ratio is 3.61, the minimum is 2.26, and the average value is 2.75. The thickest part of the leaf is 0.44 mm, the thinnest is 0.23 mm, and the average value is 0.31 mm. The maximum leaf tip angle is 37.09°, the minimum is 2.43°, and the average value is 28.28°.

[0063] The coefficient of variation of 14 leaf morphological traits of 38 Lithocarpus litseifolius ranges from 0.12 to 39.50. The coefficient of variation of the leaf area is the largest, followed by the petiole length (36.96) and the leaf length (17.40), and the smallest is the leaf margin (0.02), indicating that the leaf margin trait is relatively stable in this study, while the traits of leaf area, petiole length and leaf length have relatively large variations. The diversity index ranges from 0.19 to 0.47. The diversity index of the leaf width is the largest, and the smallest is the leaf margin.

[0064] Table 6 Diversity analysis of descriptive traits of Lithocarpus litseifolius leaves

[0065]

[0066] Table 7 Description of quantitative traits of Lithocarpus litseifolius leaves

[0067]

[0068]

[0069] The clustering results of Lithocarpus litseifolius germplasm resources based on different leaf morphological characteristics are as Figure 3As shown in the figure, the tested Litsea coreana var. lanuginosa germplasm resources can be preliminarily divided into three categories. The first category includes 14 germplasm resources, namely YA1, YA2, SP2, HZ2, JD1, HZ1, HR2, JL1, HE1, CY1, GQ1, GQ2, SH1, and SP1. The second category includes 5 germplasm resources, namely HR1, HX2, HX3, HX4, and HX5. The third category includes 19 germplasm resources, namely GQ3, CL3, HH2, JZ1, HX1, GB2, GB1, FA2, SH2, GQ4, CL3, CL2, HH3, GH1, ZL1, HS1, HH1, and FA1. Analysis of the leaf morphological traits of the three groups found that the main characteristics of the materials in the first group are medium leaf area, medium leaf length, and medium leaf thickness. The main characteristics of the materials in the second group are large leaf area, long leaf length, and thick leaf. The main characteristics of the materials in the third group are small leaf area, short leaf length, and thin leaf.

[0070] Analysis of the correlation between the sweet substances and morphological characteristics of different Litsea coreana var. lanuginosa germplasm resources is as Figure 4 shown. When the leaves are young, there are 2 pairs with extremely significant (P<0.01) correlations. Among them, the extremely significant positive correlation is between the leaf margin and phloretin (0.47), and the extremely significant negative correlation is between the leaf tip angle and neohesperidin dihydrochalcone (0.51). There are 5 pairs with significant correlations. Among them, the significant positive correlations are between trilobatin and leaf thickness (0.38), 3-hydroxyphloridzin and leaf thickness (0.33), leaf shape and phloridzin (0.33), bud leaf color and neohesperidin dihydrochalcone (0.41), and the significant negative correlation is between 3-hydroxyphloridzin and the leaf length-width ratio (-0.32). When the leaves are mature, there are 6 pairs with extremely significant correlations. Among them, the extremely significant positive correlations are between trilobatin and leaf area (0.50), trilobatin and leaf thickness (0.56), trilobatin and leaf tip (0.53), and the extremely significant negative correlations are between phloridzin and leaf thickness (-0.42), phloretin and leaf shape (-0.58), phloridzin and leaf tip (-0.48).

[0071] Leaf phenotypic characteristics and chemical components both belong to the aspects of plant phenotypic characteristics. The level of chemical component content is an important indicator to measure quality. Characteristics are closely related to components. Characteristics are the external manifestations, and components are the material basis of characteristics. Clarifying the correlation between characteristics and components has important guiding significance for constructing an evaluation system. Therefore, further exploring the SNP loci significantly related to leaf traits lays a solid foundation for the screening of Litsea coreana var. lanuginosa germplasm resources or molecular-assisted breeding and whole-genome breeding. Developing molecular markers for detecting SNP loci can accelerate the breeding process.

[0072] Example 4

[0073] Method

[0074] Clean reads were aligned to the reference genome GCA_040182985.1_ASM4018298v1_genomic using the Burrows-Wheeler Aligner (BWA) version 0.7.17 (Li and Durbin, 2009) software. The SAM file input to the BWA software was converted to a bam file and sorted using SAMtools version 1.11 (Li et al., 2009). Picard's MarkDuplicates utility ( https: / / github.com / broadinstitute / picard / releases ) was used to remove potential PCR biases. The Bcftools (Danecek and McCarthy, 2017) software was used to genotype all loci in the genome based on the BAM file and combine the genotype information of all individuals. Then, the bcftools software was used to retain loci with an individual genotyping rate greater than 90% and a minor allele frequency (MAF) greater than 0.05. A generalized linear model (GLM) was used to perform linear regression on the quality-controlled data, with seven phenotypes such as petiole length, leaf length, leaf width, leaf area, leaf color, leaf thickness, and / or bud leaf color as the dependent variables and PCA as the covariate for population stratification correction.

[0075] The GWAS analysis in this study covered seven phenotypes, and the results revealed multiple SNP loci significantly associated with these phenotypes. Figures 5 to 11 The GWAS analysis results for each phenotype are shown separately, while Table 8 details information such as the SNP loci associated with each phenotype and their significance levels (p-values).

[0076] Table 8 SNP information associated with leaf morphological trait

[0077]

[0078]

[0079] The GWAS analysis results for the leaf color trait are as Figure 5 shown. The SNP loci significantly associated with this trait are listed in Table 8, including Chr10_6038227 (p = 1.58E-05) on chromosome 10, showing a base substitution of T→C, and Chr8_24865452 (p = 2.81E-05) on chromosome 8, showing a base substitution of C→T. This trait corresponds to the color of the leaf.

[0080] The GWAS analysis results for the leaf length trait are as Figure 6As shown in the figure. In the Leaf length trait, a significant SNP locus located on chromosome 4 was found. The locus on chromosome 4 (Chr4_66105620) showed a relatively high significance (p = 3.73E-06), with a base substitution of T→C. This trait corresponds to the length of the leaf.

[0081] The GWAS analysis results of the Leaf width trait are as Figure 7 shown in the figure. For the Leaf width trait, significant SNP loci are distributed on chromosomes 11 and 5. Among them, the locus on chromosome 11 (Chr11_54116311) showed a relatively high significance (p = 7.69E-07), with a base substitution of A→G; the significance of the locus on chromosome 5 (Chr5_72562190) was slightly lower (p = 7.67E-06), with a base substitution of G→A; another locus on chromosome 11 (Chr11_40703521) also showed a certain significance (p = 6.65E-06), with a base substitution of G→A. This trait corresponds to the width of the leaf.

[0082] The GWAS analysis results of the Leaf area trait are as Figure 8 shown in the figure. In the Leaf area trait, a significant SNP locus located on chromosome 4 was found. Specifically, the locus on chromosome 4 (Chr4_66105620) showed a relatively high significance (p = 7.32E-06), with a base substitution of T→C. This trait corresponds to the size of the leaf area.

[0083] The GWAS analysis results of the Petiole length trait are as Figure 9 shown in the figure. In the Petiole length trait, significant SNP loci located on chromosomes 10 and 11 were found. Among them, the locus on chromosome 10 (Chr10_32223744) showed a relatively high significance (p = 3.01E-06), with a base substitution of T→C; the significance of the locus on chromosome 11 (Chr11_15079523) was slightly lower (p = 5.00E-06), with a base substitution of G→A; the locus on chromosome 4 (Chr4_56044239) also showed a certain significance (p = 5.21E-06), with a base substitution of G→A. This trait corresponds to the petiole length.

[0084] The GWAS analysis results of the Young Leaf color trait are as Figure 10As shown in Table 8, the SNP loci significantly associated with this trait are listed, including Chr9_54196508 located on chromosome 9 (p = 1.43E-06), showing a base substitution of A→G, and Chr10_39138077 on chromosome 10 (p = 1.66E-06), showing a base substitution of C→T. This trait corresponds to the color of the bud leaves.

[0085] The results of the GWAS analysis of the leaf thickness trait are as Figure 11 shown. In the leaf thickness trait, significant SNP loci located on multiple chromosomes were found. Specifically, the locus on chromosome 7 (Chr7_4428839) showed the highest significance (p = 1.05E-07), suggesting that this locus may be a key genetic factor for the leaf thickness trait. The locus on chromosome 5 (Chr5_88247387) also showed relatively high significance (p = 8.34E-06). In addition, the locus on chromosome 2 (Chr2_21323826) and multiple loci on chromosome 6 (Chr6_50047354, Chr6_50047558, and Chr6_50047564) also showed certain significance (p values between 3.10E-05 and 3.54E-05).

[0086] Finally, it should be noted that the above preferred embodiments are only used to illustrate the technical solutions of the present invention and not to limit them. Although the present invention has been described in detail through the above preferred embodiments, those skilled in the art should understand that various changes can be made in form and details without departing from the scope defined by the claims of the present invention.

Claims

1. SNP loci significantly related to the leaf morphology of Lithocarpus litseifolius, characterized in that, The location information of the SNP locus is as follows: The physical location of the SNP locus is determined by alignment with the reference genome with the accession number GCA_040182985.

1.

2. The SNP locus significantly related to the leaf morphology of Lithocarpus litseifolius according to claim 1, characterized in that The variant information corresponding to the SNP locus is as follows:

3. The SNP locus significantly related to the leaf morphology of Lithocarpus litseifolius according to claim 1, characterized in that The leaf morphology is petiole length, leaf length, leaf width, leaf area, leaf color, leaf thickness, and / or bud leaf color.

4. The SNP locus significantly related to the leaf morphology of Lithocarpus litseifolius according to claim 3, characterized in that The SNP locus information corresponding to each leaf morphology is as follows:

5. A reagent for detecting the SNP locus recited in claim 1.

6. The reagent according to claim 5, wherein The reagent is a molecular probe or a liquid chip.

7. Use of the reagent for detecting the SNP locus recited in claim 1 in identifying the leaf morphological traits of Lithocarpus litseifolius.

8. Use of the reagent for detecting the SNP locus recited in claim 1 in screening the germplasm resources of Lithocarpus litseifolius or artificial assisted breeding.

Images