SNP markers related to trace element Zn content in maize kernels and their application

Abstract

The present invention discloses a SNP marker associated with the trace element Zn content in corn kernels and its application. The inventors discovered that the genotype at position 176582219bp on corn chromosome 7 is significantly associated with the Zn content in corn kernels. The SNP genotype AA results in lower Zn content in the kernels, while the SNP genotype GG results in higher Zn content. The genotype at this position can be used as a SNP marker to identify Zn content in corn kernels. This SNP marker can be used to breed corn inbred lines enriched in the trace element Zn.

Description

Technical Field

[0001] The invention belongs to the field of biotechnology, and particularly relates to a SNP marker related to Zn content in corn kernels and an application thereof. Background Art

[0002] Since the 21st century, micronutrient deficiencies have been a global health concern, often referred to as hidden hunger. Nutritional imbalances and hidden hunger have become global health issues, as they can lead to stunted growth, intellectual impairment, and increased morbidity and mortality.

[0003] Biological processes throughout the human body require the participation of multiple trace elements, including zinc (Zn), iron (Fe), selenium (Se), and copper (Cu). These are essential trace elements for the human body and play a vital role in human health. Insufficient or excessive intake of trace elements from food can affect human health. Zinc is involved in the regulation of a large number of metabolism-related genes through the action of multiple transcription factors. Corn is a staple food crop that plays an important role in ensuring food security and is the main dietary source of calories, protein, and trace elements. Different corn varieties have significant differences in their absorption of Zn. Therefore, cultivating high-quality corn varieties rich in Zn is crucial to ensuring food security. Summary of the Invention

[0004] One of the objectives of the present invention is to provide a SNP marker related to the Zn content of corn kernels, which can be used for the detection of Zn content in corn kernels and corn breeding, especially the breeding of Zn-rich corn inbred lines.

[0005] A SNP marker related to Zn content in maize kernels is located at position 176582219bp on maize chromosome 7.

[0006] In some embodiments, the genotype at position 176582219 bp is AA.

[0007] In some embodiments, the genotype at position 176582219 bp is GG.

[0008] Another object of the present invention is to provide a method for detecting the Zn content of corn kernels.

[0009] A method for detecting the Zn content of corn kernels is provided, which identifies the Zn content of corn kernels by detecting the genotype at the 176582219bp position of corn chromosome 7.

[0010] In some embodiments, when the genotype at the position 176582219 bp is AA, the Zn content of corn kernels is low.

[0011] In some embodiments, when the genotype at the position 176582219 bp is GG, the Zn content of corn kernels is higher.

[0012] In some embodiments, the detection method is any one of direct sequencing, specific probe hybridization, specific primer extension or PCR.

[0013] Another object of the present invention is to provide a kit for detecting the Zn content of corn kernels.

[0014] A kit for detecting the Zn content of corn kernels comprises a reagent for detecting the genotype at the 176582219bp position of corn chromosome 7.

[0015] Preferably, the kit is used for direct sequencing, specific probe hybridization, specific primer extension or PCR detection.

[0016] Another object of the present invention is to provide the use of the above-mentioned detection method and the above-mentioned kit in detecting the Zn content of corn kernels.

[0017] Another object of the present invention is to provide the use of the above-mentioned detection method and the above-mentioned kit in cultivating Zn-enriched corn inbred lines.

[0018] Another object of the present invention is to provide a breeding method for increasing the Zn content of corn, which comprises the following steps: performing genotype detection on the SNP marker located at position 176582219bp of chromosome 7 in the corn sample, and selecting corn samples with genotype GG for breeding.

[0019] The present invention has the following beneficial effects:

[0020] The inventors discovered that the genotype at position 176582219 on maize chromosome 7 is highly correlated with the Zn content of maize kernels. When the SNP genotype is AA, the kernel Zn content is low, while when the SNP genotype is GG, the kernel Zn content is high. The genotype at this position can be used as a SNP marker for maize kernel Zn content. This SNP can be used to breed maize inbred lines enriched in Zn. BRIEF DESCRIPTION OF THE DRAWINGS

[0021] Figure 1 Manhattan plot for GWAS analysis of Zn in maize kernels.

[0022] Figure 2 Box plot of the Zn content distribution of samples with different genotypes. DETAILED DESCRIPTION

[0023] The following are specific examples of the present invention. It should be noted that these examples are merely exemplary and do not constitute any limitation on the scope of the present invention. Modifications and replacements of the details and forms of the embodiments within the scope of the present invention fall within the scope of protection of the present invention.

[0024] Unless otherwise defined, the technical terms used in the following examples have the same meanings as those generally understood by those skilled in the art to which the present invention belongs. The experimental reagents used in the following examples, unless otherwise specified, are all conventional biochemical reagents.

[0025] Example 1

[0026] 1. Research Methods

[0027] (1) Phenotypic determination

[0028] In 2021, the inventors planted 244 corn inbred line-related population germplasm resources (provided by the laboratory of Professor Lai Jinsheng of China Agricultural University) in Jiangmen City, Guangdong, China, and used microwave digestion-inductively coupled plasma mass spectrometry to detect the Zn content of grains of different inbred lines.

[0029] (2) Genotype identification

[0030] DNA was extracted from 244 maize inbred lines and subjected to high-throughput sequencing. After filtering out the adapters and low-quality reads of the sequenced reads, the DNA was aligned to the B73 maize reference genome (B73 RefGen_v4) using bwa software. Finally, SNP information was extracted using GATK software to obtain the genotype of each inbred line.

[0031] (3) Genome-wide association study (GWAS)

[0032] The kinship matrix between inbred lines was calculated using Tassel5 software. The population structure was calculated using Admixture software (K value was 4). Finally, GWAS analysis was performed using the mixed linear model (MLM) of Tassel5 to obtain the p-value of each SNP locus.

[0033] 2. Research Results

[0034] (1) Phenotypic distribution of Zn content in maize-associated populations

[0035] The present invention studies the Zn content in the kernels of maize inbred lines and conducts qualitative and quantitative analysis of the Zn content in maize (Table 1).

[0036] Table 1 Analysis of Zn-related phenotypic data

[0037]

[0038] (2) Genome-wide association analysis

[0039] Combining the obtained tens of millions of SNP markers and maize kernel Zn content data (Table 2), the inventors used the whole genome association analysis method to identify a SNP marker located at position 176582219bp on maize chromosome 7 that was significantly associated with the Zn content of maize inbred lines ( Figure 1 ; Table 3), the allele types are AA and GG. Among them, the Zn content of the maize inbred line with the genotype of AA is low, and the Zn content of the maize inbred line with the genotype of GG is high ( Figure 2 ).

[0040] Table 2 Zn component contents of samples measured

[0041]

[0042]

[0043]

[0044]

[0045]

[0046]

[0047]

[0048]

[0049]

[0050]

[0051] Table 3 Result description of position 2_176582219bp

[0052]

[0053] 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 a reagent for detecting SNP markers related to the trace element Zn content in corn kernels in corn breeding. The SNP marker is located at position 176582219bp on chromosome 7 of the corn reference genome B73 RefGen_v4. When the genotype of the SNP marker is AA, the Zn content of the corn kernels is low; when the genotype of the SNP marker is GG, the Zn content of the corn kernels is high.

2. The use according to claim 1, characterized in that The breeding is to develop Zn-enriched corn inbred lines.

3. A method for detecting Zn content in corn kernels, characterized in that: The Zn content of corn kernels is determined by detecting the genotype of a SNP marker related to the trace element Zn content of corn kernels; the SNP marker is located at position 176582219bp of chromosome 7 of the corn reference genome B73 RefGen_v4. When the genotype of the SNP marker is AA, the Zn content of the corn kernels is low; when the genotype of the SNP marker is GG, the Zn content of the corn kernels is high.

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

5. A kit for detecting Zn content in corn kernels, characterized in that: A reagent for detecting the genotype of the SNP marker according to claim 1 is included.

6. Use of the detection method according to any one of claims 3 to 4 or the kit according to claim 5 in detecting the Zn content of corn kernels.

7. Use of the detection method according to any one of claims 3 to 4 or the kit according to claim 5 in breeding Zn-enriched maize inbred lines.

8. A breeding method for increasing the Zn content of corn, characterized in that: The method comprises the following steps: performing genotype detection on a SNP marker in a corn sample, and selecting a corn sample with a genotype of the SNP marker being GG for breeding; the SNP marker is located at a position of 176582219 bp on chromosome 7 of the corn reference genome B73 RefGen_v4, and when the genotype of the SNP marker is AA, the Zn content of the corn kernel is low; and when the genotype of the SNP marker is GG, the Zn content of the corn kernel is high.

Images