SNP (Single Nucleotide Polymorphism) marker related to cane sugar component of sugarcane

Abstract

The invention discloses an SNP (Single Nucleotide Polymorphism) marker related to cane sugar components of sugarcanes. The inventor finds that genotypes at 47469846bp positions of a sugarcane chromosome 3 are highly related to sugarcane sucrose components, and researches find that the sucrose components of sugarcanes with 91.72% of SNP genotypes AA are all higher than 15.0%, the sucrose components of sugarcanes with 72.73% of SNP genotypes AG are all higher than 15.0%, the sucrose components of sugarcanes with 0.00% of SNP genotypes GG are all higher than 15.0%, and the sucrose components of sugarcanes with 0.00% of SNP genotypes GG are all higher than 15.0%. Therefore, the genotype at the position can be used as the SNP marker of the sucrose component of the sugarcane. By utilizing the discovery, the SNP marker is applied to the detection of the sucrose content of the sugarcane, and the cultivation of a high-sugar sugarcane variety is facilitated.

Description

Technical Field

[0001] The invention belongs to the field of biotechnology, and particularly relates to SNP markers related to sucrose content in sugarcane and applications thereof. Background Art

[0002] Sugar content is one of the most important quality traits of sugarcane and is influenced by multiple factors. Not only does sugar content vary significantly between sugarcane varieties, but also the varying effective stems, planting environments, and cultivation conditions of the same material significantly impact the final sugar content, significantly increasing the difficulty of breeding high-sugar sugarcane varieties.

[0003] For a long time, one of the challenges limiting the application of sugarcane genomic selection technology has been the lack of reference genomic information. In 2018, Chinese scientists deciphered the genome of a closely related wild sugarcane species, Xanthoceras sutsugumi. In 2025, the genome code of the modern cultivated sugarcane "star" variety, New Taiwan Sugar No. 22 (XTT22), was also successfully cracked, laying the foundation for the discovery of functional genes in sugarcane and the development of corresponding molecular markers. Currently, the application of molecular markers in breeding is a key component of the selection of new sugarcane varieties. Therefore, the development of molecular markers related to the control of sugarcane sucrose content is crucial for the rapid and precise breeding of high-sugar sugarcane varieties. Summary of the Invention

[0004] One of the objectives of the present invention is to provide a SNP marker related to the sucrose content of sugarcane, which can be used to detect the sucrose content of sugarcane.

[0005] A SNP marker related to sugarcane sugar content is located at position 47469846bp on sugarcane chromosome 3.

[0006] In some embodiments, the genotype at position 47469846 bp is GG.

[0007] In some embodiments, the genotype at position 47469846 bp is AA.

[0008] In some embodiments, the genotype at position 47469846 bp is AG.

[0009] Another object of the present invention is to provide a use of a SNP marker associated with sucrose content in sugarcane in any of the following aspects:

[0010] (1) Identifying or assisting in identifying the sucrose content of sugarcane or preparing products that identify or assist in identifying the sucrose content of sugarcane;

[0011] (2) Screening sugarcane plants with high sugar content;

[0012] (3) Improved sugarcane varieties or strains;

[0013] (4) Breeding new sugarcane varieties or strains;

[0014] The SNP marker is located at the position 47469846bp of sugarcane chromosome 3; the genotype of the SNP site is GG homozygous, AA homozygous and AG heterozygous.

[0015] When the genotype of 47469846bp of sugarcane chromosome 3 is GG, the sugar content of sugarcane is low; when the genotype of 47469846bp of sugarcane chromosome 3 is AA or AG, the sugar content of sugarcane is high.

[0016] Another object of the present invention is to provide a method for detecting the sugar content of sugarcane, which comprises the step of detecting the genotype of 47469846bp of sugarcane chromosome 3.

[0017] The detection method includes direct sequencing, specific probe hybridization method, specific primer extension method or PCR method.

[0018] Another object of the present invention is to provide a kit for detecting the sugar content of sugarcane, which includes a reagent for detecting the genotype of sugarcane chromosome 3 47469846bp.

[0019] The detection adopts direct sequencing, specific probe hybridization method, specific primer extension method or PCR method.

[0020] Another object of the present invention is to provide the use of the above-mentioned detection method or kit in genetic improvement or molecular breeding of sugarcane, preferably in genetic improvement or molecular breeding to increase the sugar content of sugarcane.

[0021] Another object of the present invention is to provide a breeding method for increasing the sugar content of sugarcane, comprising the following steps: performing genotype detection on a SNP marker located at 47469846bp on chromosome 3 in a sugarcane sample, and selecting sugarcane samples with a genotype of AA or AG for breeding.

[0022] The present invention has the following beneficial effects:

[0023] The inventors discovered that the genotype at position 47469846bp on sugarcane chromosome 3 is highly correlated with sugarcane sugar content. Research revealed that 91.72% of those with the AA SNP genotype had sugar content above 15.0%, 72.73% of those with the AG SNP genotype had sugar content above 15.0%, and 0.00% of those with the GG SNP genotype had sugar content above 15.0%. The genotype at this position can be used as a SNP marker for sugarcane sugar content. Leveraging this discovery, the SNP marker can be applied to sugarcane sugar content detection, facilitating the cultivation of high-sugar sugarcane varieties. BRIEF DESCRIPTION OF THE DRAWINGS

[0024] Figure 1 Manhattan plot for GWAS analysis of sugarcane sucrose content.

[0025] Figure 2 Box plot of the distribution of sugarcane sugar content in different genotype samples. DETAILED DESCRIPTION

[0026] The following examples are provided to further illustrate the present invention, but are not intended to limit the present invention.

[0027] Unless otherwise specified, the experimental methods in the following examples are all conventional experimental methods. Unless otherwise specified, the experimental reagents and consumables described in the following examples are all from conventional biochemical reagent companies.

[0028] Example 1

[0029] 1. Research Methods

[0030] (1) Phenotypic determination

[0031] This study was conducted in Zhanjiang City, Guangdong Province, China in 2019 using a randomized complete block design, utilizing 174 domestic and international sugarcane germplasm resources. The experimental plots were 3 m long and 2 m wide, planted in three rows of 10 plants each, with a spacing of 0.3 m between plants and 0.65 m between rows. Normal irrigation was used. Upon reaching full maturity, all sugarcane stems were harvested, and the sugar content of the mature sugarcane stems was determined according to national standards. Each sample was measured in triplicate, with each replicate containing three active sugarcane stems. The average of these three replicates was used as the final sugar content. The results are shown in (Tables 1 and 3).

[0032] (2) Genotype identification

[0033] Second-generation sequencing was performed on 174 sugarcane materials. The reads obtained by sequencing were aligned to the sugarcane XTT22 reference genome (GenBank: GCA_042768165.1) using bwa software, and genotype identification was performed using GATK software.

[0034] (3) Genome-wide association study (GWAS)

[0035] First, Beagle software was used to fill in the missing SNP genotypes; then Haploview software was used to estimate the LD decay of the whole genome and the LD decay of each 1Mb region of the genome; principal component analysis of the population was performed on SNPs with a missing rate less than 50% and a minimum allele frequency greater than 0.05, using the GCTA software; the kinship between inbred lines was analyzed, and the gemma tool in the gemma software was used for kinship calculation; finally, the compressed mixed linear model (CMLM) in the GAPIT software was used for GWAS analysis.

[0036] 2. Research Results

[0037] (1) Phenotypic distribution of sugar content in sugarcane-associated populations

[0038] The present invention measured the sugar content of 174 mature sugarcane materials, and conducted qualitative and quantitative analysis of the sugarcane sugar content. The sugar content ranged from 8.60 to 18.74%, with a median of 16.30% and an average of 16.124% (Table 1).

[0039] Table 1 Phenotypic data analysis of sugarcane sucrose content-related traits

[0040]

[0041] (2) Genome-wide association analysis

[0042] Using the tens of millions of SNP markers and sugar content phenotypic data obtained, the inventors used genome-wide association analysis to find a locus at 47469846bp on sugarcane chromosome 3 that was significantly correlated with sugarcane sugar content and named it ShCd3-47469846 ( Figure 1 Table 2). ShCd3-47469846 is located in the intergenic region, and its base types (genotypes) are AA, AG, and GG. There are 157 sugarcane materials with the AA genotype, 11 with the AG genotype, and 6 with the GG genotype. Among them, 91.72% of the sugarcane with the AA SNP genotype had a sucrose content higher than 15.0%, 72.73% of the sugarcane with the AG SNP genotype had a sucrose content higher than 15.0%, and 0.00% of the sugarcane with the GG SNP genotype had a sucrose content higher than 15.0%. Figure 2 ; Tables 3 and 4).

[0043] Table 2 Description of ShCd3-47469846 position results

[0044]

[0045] Table 3 Sugarcane sugar content

[0046]

[0047]

[0048]

[0049]

[0050] Table 4 Statistics of ShCd3-47469846

[0051]

[0052] Example 2

[0053] This example uses SNP markers to detect genotypes and identify the sugar content of sugarcane.

[0054] Twenty-four sugarcane germplasm materials were randomly selected and the genotypes and sucrose content at position 47469846 on chromosome 3 at maturity were determined for these 24 natural population materials. The results are shown in Table 5.

[0055] Table 5 Sucrose content and genotypes of 24 natural sugarcane populations at maturity

[0056]

[0057] As shown in Table 5, 80.0% of the sugarcane with SNP genotype AA had a sucrose content higher than 15.0%, 83.33% of the sugarcane with SNP genotype AG had a sucrose content higher than 15.0%, and 0% of the sugarcane with SNP genotype GG had a sucrose content higher than 15.0%.

[0058] The embodiments described above are merely descriptions of preferred implementations of the present invention and are not intended to limit the scope of the present invention. Without departing from the spirit of the present invention, various modifications and improvements made to the technical solutions of the present invention by ordinary engineering technicians in this field should fall within the scope of protection determined by the claims of the present invention.

Claims

1. Application of SNP markers related to sugarcane sugar content in any of the following aspects: (1) Identifying or assisting in identifying the sucrose content of sugarcane or preparing products that identify or assist in identifying the sucrose content of sugarcane; (2) Screening sugarcane plants with high sugar content; (3) Improved sugarcane varieties or strains; (4) Breeding new sugarcane varieties or strains; The SNP marker is located at the position 47469846bp of sugarcane chromosome 3; the genotype of the SNP site is GG homozygous, AA homozygous and AG heterozygous.

2. The use according to claim 1, characterized in that When the genotype of 47469846bp of sugarcane chromosome 3 is GG, the sugar content of sugarcane is low; when the genotype of 47469846bp of sugarcane chromosome 3 is AA or AG, the sugar content of sugarcane is high.

3. A method for detecting the sucrose content of sugarcane, characterized in that: The method comprises the steps of detecting the genotype of 47469846bp of sugarcane chromosome 3.

4. The detection method according to claim 3, characterized in that When the genotype of 47469846bp of sugarcane chromosome 3 is GG, the sugar content of sugarcane is low; when the genotype of 47469846bp of sugarcane chromosome 3 is AA or AG, the sugar content of sugarcane is high.

5. The detection method according to claim 3 or 4, characterized in that The detection method includes direct sequencing, specific probe hybridization method, specific primer extension method or PCR method.

6. A kit for detecting the sucrose content of sugarcane, characterized in that: Contains reagents for detecting the genotype of sugarcane chromosome 3, 47469846bp.

7. The kit according to claim 6, characterized in that The detection adopts direct sequencing, specific probe hybridization method, specific primer extension method or PCR method.

8. Use of the detection method according to claim 3 or the kit according to claim 6 in sugarcane genetic improvement or molecular breeding.

9. The use according to claim 8, characterized in that It is used in genetic improvement or molecular breeding to increase the sugar content of sugarcane.

10. A breeding method for increasing the sugar content of sugarcane, characterized in that: The method comprises the following steps: performing genotype detection on a SNP marker located at 47469846bp on chromosome 3 in a sugarcane sample, and selecting sugarcane samples with genotypes of AA or AG for breeding.

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