A haplotype molecular marker related to cadmium tolerance of maize and application thereof

Abstract

The application belongs to the technical field of molecular genetic markers, and specifically discloses a haplotype molecular marker related to corn cadmium tolerance and application thereof. The application takes 187 corn inbred line association population germplasm resources as materials, adopts microwave digestion-inductively coupled plasma mass spectrometry to measure the cadmium content in grains, carries out whole genome association analysis in combination with SNP typing data, screens and obtains SNP sites and related haplotypes significantly related to corn grain cadmium accumulation, and integrates eight haplotype blocks to obtain a key haplotype block Hap closely related to corn grain cadmium tolerance. The haplotype block contains two functionally differentiated haplotypes: SHap haplotype is associated with low cadmium accumulation traits, and AHap haplotype is associated with high cadmium accumulation traits. The molecular marker provided by the application can be used for corn molecular marker assisted breeding, directional breeding of cadmium tolerant and low cadmium accumulation varieties, and guaranteeing corn safe production and grain quality in cadmium contaminated farmland.

Description

Technical Field

[0001] This invention belongs to the field of molecular genetic marker technology, specifically relating to a haplotype molecular marker related to cadmium tolerance in maize and its application. Background Technology

[0002] Cadmium (Cd) is a highly toxic heavy metal classified as a Group 1 carcinogen by the International Agency for Research on Cancer. Exposure to cadmium stress in maize triggers a series of harmful physiological responses, including stunted growth, inhibited development, and chlorosis of leaves. These combined factors lead to decreased yield and impaired quality. Therefore, identifying gene loci associated with cadmium tolerance, studying the functions of candidate genes, and elucidating the molecular mechanisms controlling cadmium tolerance in maize are crucial for promoting high tolerance under cadmium conditions and ultimately increasing yield and quality.

[0003] In the field of molecular breeding, marker-assisted selection (MAS) technology has been widely used for crop trait improvement. Although some quantitative trait loci (QTLs) or molecular markers related to cadmium accumulation in crops such as rice and wheat have been reported in existing technologies, there are few cloned cadmium tolerance genes in maize, and the developed molecular markers often have problems such as low polymorphism, insufficient linkage with the target trait, and poor stability under different genetic backgrounds.

[0004] It is worth noting that most agronomic traits (including cadmium tolerance) are typical quantitative traits, controlled by multiple minor genes, and these genes often contain multiple single nucleotide polymorphisms (SNPs). Traditional molecular markers often target only a single SNP. Because a single SNP provides limited information, and complex linkage disequilibrium or epistatic effects may exist between different sites, the predictive accuracy of a single marker is often unsatisfactory. A haplotype, on the other hand, is a combination of multiple tightly linked SNPs on the same chromosome. It contains richer genetic information than a single SNP and can more accurately reflect the genetic diversity of a target gene and its association with the phenotype.

[0005] However, to date, there is a lack of stable, reliable, and commercially viable haplotype markers for cadmium accumulation in maize kernels that can be used in molecular breeding practices. There is an urgent need in this field to develop a haplotype molecular marker that can effectively distinguish between high and low cadmium accumulation phenotypes in maize kernels, in order to rapidly and accurately screen germplasm resources carrying superior alleles and accelerate the breeding process of new low-cadmium maize varieties. Summary of the Invention

[0006] To address the aforementioned technical problems, this invention aims to provide a haplotype molecular marker related to cadmium tolerance in maize and to reveal its application in the breeding of low-cadmium-accumulating maize varieties, improvement of grain quality, and identification of germplasm resources.

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

[0008] In a first aspect, the present invention provides a haplotype molecular marker associated with cadmium tolerance in maize, the haplotype molecular marker consisting of the following 56 SNP sites:

[0009] SNP1: Located at position 163131630 on chromosome 2 of the maize genome, with a variant type of A / -;

[0010] SNP2: Located at position 163131658 on chromosome 2 of the maize genome, with a variant type of - / A;

[0011] SNP3: Located at position 163131783 on chromosome 2 of the maize genome, with a variant type of C / T;

[0012] SNP4: Located at position 163131817 on chromosome 2 of the maize genome, with a variant type of C / T;

[0013] SNP5: Located at position 163131819 on chromosome 2 of the maize genome, with a variant type of - / A;

[0014] SNP6: Located at position 163131823 on chromosome 2 of the maize genome, with a variant type of A / -;

[0015] SNP7: Located at position 163131857 on chromosome 2 of the maize genome, with a variant type of - / A;

[0016] SNP8: Located at position 163131866 on chromosome 2 of the maize genome, with a variant type of C / T;

[0017] SNP9: Located at position 163132250 on chromosome 2 of the maize genome, with a variant type of C / T;

[0018] SNP10: Located at position 163132257 on chromosome 2 of the maize genome, with a variant type of - / A;

[0019] SNP11: Located at position 163140193 on chromosome 2 of the maize genome, with a variant type of C / A;

[0020] SNP12: Located at position 163140199 on chromosome 2 of the maize genome, with a variant type of - / T;

[0021] SNP13: Located at position 163140239 on chromosome 2 of the maize genome, with a variant type of A / -;

[0022] SNP14: Located at position 163140254 on chromosome 2 of the maize genome, with a variant type of - / A;

[0023] SNP15: Located at position 163140295 on chromosome 2 of the maize genome, with a variant type of T / C;

[0024] SNP16: Located at position 163140406 on chromosome 2 of the maize genome, with a variant type of C / T;

[0025] SNP17: Located at position 163140455 on chromosome 2 of the maize genome, with a variant type of - / A;

[0026] SNP18: Located at position 163140527 on chromosome 2 of the maize genome, with a variant type of - / A;

[0027] SNP19: Located at position 163140528 on chromosome 2 of the maize genome, with a variant type of T / C;

[0028] SNP20: Located at position 163,140,769 on chromosome 2 of the maize genome, with a variant type of G / T;

[0029] SNP21: Located at position 163140814 on chromosome 2 of the maize genome, with a variant type of C / T;

[0030] SNP22: Located at position 163,140,937 on chromosome 2 of the maize genome, with a variant type of T / G;

[0031] SNP23: Located at position 163,140,975 on chromosome 2 of the maize genome, with a variant type of G / T;

[0032] SNP24: Located at position 163141012 on chromosome 2 of the maize genome, with a variant type of C / T;

[0033] SNP25: Located at position 163,143,938 on chromosome 2 of the maize genome, with a C / T variant;

[0034] SNP26: Located at position 163143955 on chromosome 2 of the maize genome, with a variant type of C / T;

[0035] SNP27: Located at position 163,143,961 on chromosome 2 of the maize genome, with a variant type of - / A;

[0036] SNP28: Located at position 163,143,972 on chromosome 2 of the maize genome, with a variant type of T / C;

[0037] SNP29: Located at position 163,143,979 on chromosome 2 of the maize genome, with a variant type of T / C;

[0038] SNP30: Located at position 163,143,988 on chromosome 2 of the maize genome, with a variant type of C / T;

[0039] SNP31: Located at position 163144007 on chromosome 2 of the maize genome, with a variant type of - / A;

[0040] SNP32: Located at position 163145163 on chromosome 2 of the maize genome, with a variant type of A / -;

[0041] SNP33: Located at position 163145165 on chromosome 2 of the maize genome, with a variant type of C / T;

[0042] SNP34: Located at position 163145262 on chromosome 2 of the maize genome, with a variant type of - / A;

[0043] SNP35: Located at position 163145641 on chromosome 2 of the maize genome, with a variant type of T / G;

[0044] SNP36: Located at position 163147134 on chromosome 2 of the maize genome, with a variant type of A / -;

[0045] SNP37: Located at position 163147553 on chromosome 2 of the maize genome, with a variant type of - / A;

[0046] SNP38: Located at position 163,147,560 on chromosome 2 of the maize genome, with a C / T variant;

[0047] SNP39: Located at position 163148203 on chromosome 2 of the maize genome, with a variant type of G / C;

[0048] SNP40: Located at position 163,148,239 on chromosome 2 of the maize genome, with a variant type of G / T;

[0049] SNP41: Located at position 163,148,244 on chromosome 2 of the maize genome, with a variant type of A / -;

[0050] SNP42: Located at position 163,148,437 on chromosome 2 of the maize genome, with a variant type of G / T;

[0051] SNP43: Located at position 163,148,604 on chromosome 2 of the maize genome, with a variant type of - / A;

[0052] SNP44: Located at position 163,148,620 on chromosome 2 of the maize genome, with a variant type of - / A;

[0053] SNP45: Located at position 163,148,636 on chromosome 2 of the maize genome, with a variant type of - / A;

[0054] SNP46: Located at position 163,148,666 on chromosome 2 of the maize genome, with a variant type of - / A;

[0055] SNP47: Located at position 163,148,710 on chromosome 2 of the maize genome, with a variant type of - / A;

[0056] SNP48: Located at position 163,148,752 on chromosome 2 of the maize genome, with a variant type of - / A;

[0057] SNP49: Located at position 163,148,919 on chromosome 2 of the maize genome, with a variant type of - / A;

[0058] SNP50: Located at position 163,148,921 on chromosome 2 of the maize genome, with a variant type of - / A;

[0059] SNP51: Located at position 163,149,000 on chromosome 2 of the maize genome, with a variant type of G / C;

[0060] SNP52: Located at position 163149007 on chromosome 2 of the maize genome, with a variant type of A / -;

[0061] SNP53: Located at position 163149017 on chromosome 2 of the maize genome, with a variant type of - / A;

[0062] SNP54: Located at position 163183186 on chromosome 2 of the maize genome, with a variant type of C / G;

[0063] SNP55: Located at position 163183253 on chromosome 2 of the maize genome, with a variant type of T / C;

[0064] SNP56: Located at position 163,183,678 on chromosome 2 of the maize genome, with a C / T variant.

[0065] The physical location of the SNP sites was determined based on the maize B73 reference genome version V5.0 (B73 RefGen_v5);

[0066] The 56 SNP loci combine to form two haplotypes, SHap and AHap; the genotypes of the SHap and AHap haplotypes are as follows:

[0067] SHap: A-CC-A-CC-CA-TC--TGCTGCCC-TTC-AC-TA-CGGAG--------GA-CTC;

[0068] AHap:-ATTA-ATTAAT-ACTAACTTGTTTTACCTA-TAG-ATCT-TAAAAAAAAC-AGCT;

[0069] The SHap haplotype is associated with low cadmium accumulation in maize kernels, while the AHap haplotype is associated with high cadmium accumulation in maize kernels.

[0070] Preferably, the corn material corresponding to the SHap haplotype exhibits a significantly lower cadmium content in the kernels compared to corn material containing the AHap haplotype.

[0071] Secondly, the present invention also provides the application of the above-mentioned haplotype molecular markers in the preparation of products for predicting or identifying the cadmium content of corn kernels.

[0072] Preferably, the product includes a gene chip, a kit, or a reagent.

[0073] Thirdly, the present invention also provides the application of the above-mentioned haplotype molecular markers in the breeding of low cadmium accumulation maize varieties, the improvement of maize grain quality, and / or the identification of maize germplasm resources.

[0074] Preferably, the corn kernel quality improvement involves reducing the cadmium content in the corn kernels.

[0075] Fourthly, the present invention also provides a method for identifying or assisting in the identification of cadmium accumulation traits in maize kernels, comprising the following steps:

[0076] (1) Extract maize genomic DNA to be tested;

[0077] (2) Detect the genotype of the above haplotype molecular markers;

[0078] (3) Determine the cadmium accumulation trait in the grain based on the genotype: If the genotype is SHap haplotype, the corn is determined to have low cadmium accumulation trait; if the genotype is AHap haplotype, the corn is determined to have high cadmium accumulation trait.

[0079] Preferably, in step (2), the genotype detection method includes direct sequencing, KASP genotyping, or high-throughput chip detection based on specific probes.

[0080] Fifthly, the present invention also provides a maize breeding method, comprising the following steps: detecting haplotype molecular markers in maize germplasm resources or breeding materials, screening and retaining maize individuals containing the SHap haplotype as parents for breeding.

[0081] Preferably, the breeding method includes one or more combinations of hybridization, backcrossing, self-pollination, and recurrent selection.

[0082] The beneficial effects of this invention are as follows:

[0083] This invention utilizes genome-wide association analysis to systematically screen and identify SNP loci and their haplotypes significantly associated with cadmium accumulation in maize natural populations. Further integration yields a key haplotype block (Hap) closely related to cadmium tolerance in maize grains. This haplotype block contains two functionally differentiated haplotypes: the SHap haplotype is associated with low cadmium accumulation, and the AHap haplotype is associated with high cadmium accumulation. Based on this molecular marker, genotyping of germplasm resources can be performed in the early stages of maize breeding, effectively screening materials carrying superior haplotypes (SHap), thereby enabling the targeted breeding of cadmium-tolerant and low-cadmium-accumulation maize varieties. This invention overcomes the shortcomings of traditional breeding methods, such as long identification cycles for cadmium tolerance phenotypes and significant susceptibility to environmental factors, significantly improving breeding efficiency and selection accuracy. Applying the molecular marker-assisted selection technology of this invention, maize varieties adapted to cadmium-contaminated farmland can be bred, ensuring stable crop yields while reducing grain cadmium content, thus guaranteeing food quality and safety. This has significant application value for the safe utilization of heavy metal-contaminated farmland and sustainable agricultural development. Attached Figure Description

[0084] Figure 1 Figure 1 shows the results of genome-wide association analysis (GWAS) of cadmium content in maize kernels. Figure A is the QQ plot of the MLM_Q+K model analysis, Figure B is the Manhattan plot of the MLM_Q+K model analysis on chromosome 2, Figure C is the linkage disequilibrium decay plot, and Figure D is the Manhattan plot of the MLM_Q+K model analysis on significant loci on chromosome 2.

[0085] Figure 2 Association analysis between different haplotype blocks and cadmium content in maize kernels. Figure A is the Manhattan plot of the MLM_Q+K model analysis of significant sites; Figure B shows the relationship between the eight haplotype blocks and Cd content; Figure C shows the relationship between the number of superior sites and Cd content; Figure D shows the base composition of superior haplotypes; and Figure E shows the relationship between superior haplotypes and Cd content. Detailed Implementation

[0086] The following examples are further illustrations of the present invention, but not limitations thereof. Specific experimental conditions and methods are not specified in the following examples, and the techniques used are generally conventional methods well known to those skilled in the art.

[0087] Example 1

[0088] 1. Experimental Methods

[0089] (1) Phenotypic determination

[0090] This invention uses 187 maize inbred line related population germplasm resources as experimental materials. The field trial adopts a randomized complete block design. After harvest, the cadmium content of maize kernels is determined by microwave digestion-inductively coupled plasma mass spectrometry.

[0091] (2) Genotyping

[0092] DNA was extracted from 187 maize inbred lines and high-throughput sequencing was performed. After filtering out adapters and low-quality reads, the reads were aligned to the B73 maize reference genome (B73 RefGen_v5) using bwa software. Finally, SNP information was extracted using software to obtain the genotype of each inbred line.

[0093] (3) Genome-wide association analysis (GWAS)

[0094] The kinship matrix among inbred lines was calculated using Tassel5 software. Population structure (K value of 4) was calculated using Admixture software. A GWAS analysis was performed using a mixed linear model (MLM) based on Tassel5, with the population structure Q-value and kinship coefficient as correction factors, to identify Peak SNPs.

[0095] 2. Experimental Results

[0096] Based on the phenotypic data of cadmium content in grains and their SNP typing data of 187 maize inbred lines, genome-wide association analysis was performed using the MLM_Q+K model to identify gene loci associated with cadmium content in grains. The results showed that the expected P-value and observed P-value of the MLM_Q+K model were in good agreement, and the lambda values ​​were between 0.95 and 1.05 (Lai et al., 2024). Therefore, the reliability of using this model to identify gene loci associated with cadmium content in grains in this associated population is high. Figure 1 A). Based on this, this study identified a significant peak on chromosome 2 (P-value ≈ 0.05 / 626535) ( Figure 1 B), and LD analysis of the SNP sites on this chromosome revealed that when R² ≈ 0.17, the increase in LD decay distance tended to level off, with the corresponding LD decay distance being ~50Kb ( Figure 1 C). Therefore, this study identified Peak SNPs within 50 kb upstream and downstream of the significant peak, and a total of 56 Peak SNPs were found. Figure 1D), see Table 1 for details.

[0097] Further analysis identified a total of 8 strongly linked haplotype blocks (R² ≥ 0.8), namely:

[0098] H1 (number of Peak SNPs, 10) is located at: 2_163131630~2_163132257;

[0099] H2 (number of Peak SNPs, 5) is located at: 2_163140193~2_163140295;

[0100] H3 (number of Peak SNPs, 6) is located at: 2_163140406~2_163140814;

[0101] H4 (number of Peak SNPs, 3) is located at: 2_163140937~2_163141012;

[0102] H5 (Number of Peak SNPs, 7) is located at: 2_163143938~2_163144007;

[0103] H6 (number of Peak SNPs, 7) is located at: 2_163145163~2_163147560;

[0104] H7 (number of Peak SNPs, 15) is located at: 2_163148203~2_163149017;

[0105] H8 (number of Peak SNPs, 3) is located at: 2_163183186~2_163183678 ( Figure 2 A).

[0106] Maize materials carrying different variant sites of haplotypes H1 (SH1: A-CC-A-CC- and AH1: -ATTA-ATTA), H2 (SH2: CAT and AH2: AT-AC), H3 (SH3: C--TGC and AH3: TAACTT), H4 (SH4: TGC and AH4: GTT), H5 (SH5: CC-TTC- and AH5: TTACCTA), H6 (SH6: AC-TA-C and AH6: -TAG-AT), H7 (SH7: GGAG--------GA- and AH7: CT-TAAAAAAAAC-A), and H8 (SH8: CTC and AH8: GCT) were classified, and their kernel cadmium content was measured using a T-test. The results showed highly significant differences among these groups (P ≤ 3.5e-6). Figure 2 B). Further phenotypic effect analysis revealed that the effect values ​​of the variant sites CAT and CTC ranged from -0.0038 to -0.0054, tending to reduce cadmium accumulation in maize kernels and thus representing superior variant sites. Conversely, the phenotypic effect values ​​of the corresponding variant sites were all greater than 0.0094, tending to increase cadmium accumulation, which is unfavorable for breeding maize with low cadmium content. Furthermore, linear regression analysis showed that maize materials with more superior variant sites had lower kernel cadmium content (P=1.24e-19, r²=0.48). Figure 2 C), therefore, combining these 8 haplotypes can provide an important basis for subsequent breeding of cadmium materials. The two haplotypes formed by combining 56 variant sites are SHap (A-CC-A-CC-CA-TC--TGCTGCCC-TTC-AC-TA-CGGAG--------GA-CTC) and

[0107] AHap (-ATTA-ATTAAT-ACTAACTTGTTTTACCTA-TAG-ATCT-TAAAAAAAAC-AGCT) was analyzed. Figure 2 D), and found that there was a highly significant difference in cadmium content in maize kernels possessing these two haplotypes (P < 2.22e-16). Figure 2 The effect sizes of haplotype E, SHap (superior haplotype) and AHap (corresponding site) were -0.0044 (μg / g) and 0.0105 (μg / g), respectively. This study identified a haplotype block Hap (E) closely associated with cadmium tolerance in maize kernels. Figure 2 A, D, E).

[0108] Table 1. Data for 56 SNP sites ; ;

[0109] Example 2

[0110] To independently verify the correlation between the aforementioned haplotype molecular markers (SHap and AHap) and maize manganese uptake, an additional 100 maize inbred lines that did not overlap with the 187 maize inbred lines were used to construct a validation population for haplotype phenotypic effect verification. The results of the analysis of variance are shown in Table 2.

[0111] The results showed that compared with the population mean, the average reduction in cadmium content of haplotype SHap was -0.0048 μg / g, while the average increase in cadmium content of haplotype AHap was +0.0112 μg / g, with highly significant differences (P=3.4e-12). These results indicate that haplotypes SHap and AHap have a stable regulatory effect on cadmium accumulation in maize grains and can be used as molecular markers for the auxiliary selection of cadmium-tolerant and low-cadmium maize varieties. This provides technical support for the breeding of maize varieties adapted to cadmium-contaminated farmland and helps ensure stable crop yields and grain quality safety.

[0112] Table 2 Analysis of haplotype phenotypic effect values

[0113] The above are merely preferred embodiments of the present invention. It should be noted that the above preferred embodiments should not be considered as limitations on the present invention, and the scope of protection of the present invention should be determined by the scope defined in the claims. For those skilled in the art, several improvements and modifications can be made without departing from the spirit and scope of the present invention, and these improvements and modifications should also be considered within the scope of protection of the present invention.

Claims

1. A haplotype molecular marker associated with cadmium tolerance in maize, characterized in that, The haplotype molecular marker consists of the following 56 SNP sites: SNP1: Located at position 163131630 on chromosome 2 of the maize genome, with a variant type of A / -; SNP2: Located at position 163131658 on chromosome 2 of the maize genome, with a variant type of - / A; SNP3: Located at position 163131783 on chromosome 2 of the maize genome, with a variant type of C / T; SNP4: Located at position 163131817 on chromosome 2 of the maize genome, with a variant type of C / T; SNP5: Located at position 163131819 on chromosome 2 of the maize genome, with a variant type of - / A; SNP6: Located at position 163131823 on chromosome 2 of the maize genome, with a variant type of A / -; SNP7: Located at position 163131857 on chromosome 2 of the maize genome, with a variant type of - / A; SNP8: Located at position 163131866 on chromosome 2 of the maize genome, with a variant type of C / T; SNP9: Located at position 163132250 on chromosome 2 of the maize genome, with a variant type of C / T; SNP10: Located at position 163132257 on chromosome 2 of the maize genome, with a variant type of - / A; SNP11: Located at position 163140193 on chromosome 2 of the maize genome, with a variant type of C / A; SNP12: Located at position 163140199 on chromosome 2 of the maize genome, with a variant type of - / T; SNP13: Located at position 163140239 on chromosome 2 of the maize genome, with a variant type of A / -; SNP14: Located at position 163140254 on chromosome 2 of the maize genome, with a variant type of - / A; SNP15: Located at position 163140295 on chromosome 2 of the maize genome, with a variant type of T / C; SNP16: Located at position 163140406 on chromosome 2 of the maize genome, with a variant type of C / T; SNP17: Located at position 163140455 on chromosome 2 of the maize genome, with a variant type of - / A; SNP18: Located at position 163140527 on chromosome 2 of the maize genome, with a variant type of - / A; SNP19: Located at position 163140528 on chromosome 2 of the maize genome, with a variant type of T / C; SNP20: Located at position 163,140,769 on chromosome 2 of the maize genome, with a variant type of G / T; SNP21: Located at position 163140814 on chromosome 2 of the maize genome, with a variant type of C / T; SNP22: Located at position 163,140,937 on chromosome 2 of the maize genome, with a variant type of T / G; SNP23: Located at position 163,140,975 on chromosome 2 of the maize genome, with a variant type of G / T; SNP24: Located at position 163141012 on chromosome 2 of the maize genome, with a variant type of C / T; SNP25: Located at position 163,143,938 on chromosome 2 of the maize genome, with a C / T variant; SNP26: Located at position 163143955 on chromosome 2 of the maize genome, with a variant type of C / T; SNP27: Located at position 163,143,961 on chromosome 2 of the maize genome, with a variant type of - / A; SNP28: Located at position 163,143,972 on chromosome 2 of the maize genome, with a variant type of T / C; SNP29: Located at position 163,143,979 on chromosome 2 of the maize genome, with a variant type of T / C; SNP30: Located at position 163,143,988 on chromosome 2 of the maize genome, with a variant type of C / T; SNP31: Located at position 163144007 on chromosome 2 of the maize genome, with a variant type of - / A; SNP32: Located at position 163145163 on chromosome 2 of the maize genome, with a variant type of A / -; SNP33: Located at position 163145165 on chromosome 2 of the maize genome, with a variant type of C / T; SNP34: Located at position 163145262 on chromosome 2 of the maize genome, with a variant type of - / A; SNP35: Located at position 163145641 on chromosome 2 of the maize genome, with a variant type of T / G; SNP36: Located at position 163147134 on chromosome 2 of the maize genome, with a variant type of A / -; SNP37: Located at position 163147553 on chromosome 2 of the maize genome, with a variant type of - / A; SNP38: Located at position 163,147,560 on chromosome 2 of the maize genome, with a C / T variant; SNP39: Located at position 163148203 on chromosome 2 of the maize genome, with a variant type of G / C; SNP40: Located at position 163,148,239 on chromosome 2 of the maize genome, with a variant type of G / T; SNP41: Located at position 163,148,244 on chromosome 2 of the maize genome, with a variant type of A / -; SNP42: Located at position 163,148,437 on chromosome 2 of the maize genome, with a variant type of G / T; SNP43: Located at position 163,148,604 on chromosome 2 of the maize genome, with a variant type of - / A; SNP44: Located at position 163,148,620 on chromosome 2 of the maize genome, with a variant type of - / A; SNP45: Located at position 163,148,636 on chromosome 2 of the maize genome, with a variant type of - / A; SNP46: Located at position 163,148,666 on chromosome 2 of the maize genome, with a variant type of - / A; SNP47: Located at position 163,148,710 on chromosome 2 of the maize genome, with a variant type of - / A; SNP48: Located at position 163,148,752 on chromosome 2 of the maize genome, with a variant type of - / A; SNP49: Located at position 163,148,919 on chromosome 2 of the maize genome, with a variant type of - / A; SNP50: Located at position 163,148,921 on chromosome 2 of the maize genome, with a variant type of - / A; SNP51: Located at position 163,149,000 on chromosome 2 of the maize genome, with a variant type of G / C; SNP52: Located at position 163149007 on chromosome 2 of the maize genome, with a variant type of A / -; SNP53: Located at position 163149017 on chromosome 2 of the maize genome, with a variant type of - / A; SNP54: Located at position 163183186 on chromosome 2 of the maize genome, with a variant type of C / G; SNP55: Located at position 163183253 on chromosome 2 of the maize genome, with a variant type of T / C; SNP56: Located at position 163,183,678 on chromosome 2 of the maize genome, with a C / T variant. The physical location of the SNP sites was determined based on the maize B73 reference genome version V5.0; The 56 SNP loci combine to form two haplotypes, SHap and AHap; the genotypes of the SHap and AHap haplotypes are as follows: SHap: A-CC-A-CC-CA-TC--TGCTGCCC-TTC-AC-TA-CGGAG--------GA-CTC; AHap:-ATTA-ATTAAT-ACTAACTTGTTTTACCTA-TAG-ATCT-TAAAAAAAAC-AGCT; The SHap haplotype is associated with low cadmium accumulation in maize kernels, while the AHap haplotype is associated with high cadmium accumulation in maize kernels.

2. The haplotype molecular marker according to claim 1, characterized in that, The maize material corresponding to the SHap haplotype showed significantly lower cadmium content in the kernels compared to maize material containing the AHap haplotype.

3. The use of the haplotype molecular marker of claim 1 in the preparation of products for predicting or identifying cadmium content in maize kernels.

4. The application according to claim 3, characterized in that, The products include gene chips, kits, or reagents.

5. The application of the haplotype molecular marker as described in claim 1 in the breeding of low cadmium accumulation maize varieties, the improvement of maize grain quality, and / or the identification of maize germplasm resources.

6. The application according to claim 5, characterized in that, The improvement of corn kernel quality involves reducing the cadmium content in corn kernels.

7. A method for identifying or assisting in the identification of cadmium accumulation traits in maize kernels, characterized in that, Includes the following steps: (1) Extract maize genomic DNA to be tested; (2) Detecting the genotype of the haplotype molecular marker as described in claim 1 or 2; (3) Determine the cadmium accumulation trait in the grain based on the genotype: If the genotype is SHap haplotype, the corn is determined to have low cadmium accumulation trait; if the genotype is AHap haplotype, the corn is determined to have high cadmium accumulation trait.

8. The method for identifying or assisting in the identification of cadmium accumulation traits in maize kernels according to claim 7, characterized in that, In step (2), the genotype detection method includes direct sequencing, KASP genotyping, or high-throughput chip detection based on specific probes.

9. A method for breeding maize, characterized in that, Includes the following steps: Detect the haplotype molecular markers as described in claim 1 or 2 in maize germplasm resources or breeding materials, screen and retain maize individuals containing the SHap haplotype, and use them as parents for breeding.

10. The maize breeding method according to claim 9, characterized in that, The breeding methods include one or more combinations of hybridization, backcrossing, self-crossing, and recurrent selection.

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