Obtaining the QTL qWTCRFW2.1, a major inhibitor of waterlogging tolerance in maize seedlings, and developing and applying its molecular marker primers.
Patent Information
- Application Number
- CN202610777746.6
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- Filing Date
- 2026-06-01
- Publication Date
- 2026-09-25
AI Technical Summary
淹水可以破坏叶绿素的合成，淹水30d 造成叶绿素a合成受阻，光合作用也受到影响(zhang wei et al., 2017),导致严重的能量不足(Kaur et al., 2020；Tian et al., 2021)，玉米无法承受根区低氧条件从而导致产量大幅度减少(Dennis et al., 2000)
[0027]本发明首次基于全基因组关联分析对一个新的控制玉米苗期渍水根鲜重耐渍系数主效QTL进行了精细定位，将该主效QTL定位于2号染色体，该区间包含3个显著的SNP位点，总长度为400bp（Chr2：2927759-2928159），该位点均为控制耐渍表型变异的主效QTL位点，与之紧密连锁的优良单倍型SNP标记，位于玉米B73参考基因组(Zm-B73-REFERENCE-NAM-5.0)第二染色体的第2927959碱基处，解释的渍水根鲜重耐渍系数表型贡献率为5.25%，基于其最佳等位基因型开发的PARMS标记可用于分子标记辅助选择育种。
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Abstract
Description
Technical Field
[0001] This invention belongs to the field of molecular biology, specifically relating to the acquisition of the main QTL qWTCRFW2.1 for waterlogging tolerance in maize seedlings, and the development and application of its molecular marker primers. Background Technology
[0002] With the intensification of climate anomalies and uneven rainfall during the maize growing season, waterlogging stress has become one of the major natural disasters facing maize production (Zhu Shidie et al., 2024). Developing waterlogging-tolerant varieties with high yield potential is one of the main goals of maize breeding. Understanding the mechanisms of waterlogging tolerance is of great significance for breeders to develop new waterlogging-tolerant varieties with different waterlogging tolerance traits (Zaidi et al., 2004).
[0003] The severity of waterlogging damage is related to the duration of stress, soil conditions, climate, cultivation techniques, crop growth stage, and genotype (Mano et al., 2002). Studies have shown that waterlogging during the seedling stage of maize for 6 days is more severe than during the jointing and tasseling stages (Ren et al., 2023), especially from the second leaf stage (V2) to the seventh leaf stage (V7), where the root system is the first to be affected by waterlogging stress (Zaidi et al., 2004). After 6 days of waterlogging treatment, most roots, except for some adventitious roots, tend to rot, and the plants cannot absorb soil nutrients well, resulting in nitrogen deficiency, leaching, and denitrification, the latter manifesting as leaf yellowing (Ren et al., 2017). Root hypoxia leads to decreased respiration rate and root vigor, accelerating leaf senescence and reducing indicators such as photosynthetic rate, intercellular CO2 concentration, transpiration rate, and stomatal conductance. Photosynthetic indicators, such as net photosynthetic rate, decrease with prolonged flooding, and the magnitude of the decrease is directly proportional to the duration of flooding (Zhou Qingyun et al., 2020; Zhang Wei et al., 2017; Han Liangliang et al., 2011). Flooding can disrupt chlorophyll synthesis; 30 days of flooding inhibits chlorophyll a synthesis, affecting photosynthesis (Zhang Wei et al., 2017), resulting in severe energy deficiency (Kaur et al., 2020; Tian et al., 2021). Maize cannot withstand low-oxygen conditions in the root zone, leading to a significant reduction in yield (Dennis et al., 2000).
[0004] However, the current scarcity of waterlogging-tolerant maize germplasm resources, insufficient discovery of key genes, unclear molecular regulatory mechanisms, and lack of efficient molecular breeding technologies severely restrict the cultivation of new waterlogging-tolerant varieties. Discovering and effectively utilizing waterlogging-tolerant genes, exploring the molecular mechanisms of waterlogging tolerance in maize, creating new waterlogging-tolerant maize germplasm, and cultivating new waterlogging-tolerant varieties are the most economical and effective ways to reduce maize losses, increase yield per unit area, and expand the maize planting area (Zaidi et al., 2004, 2010).
[0005] Based on this, this study extensively collected 567 backbone inbred lines from maize producing areas in Southwest China and the Huang-Huai-Hai Plain, established a population of superior germplasm with different characteristics, completed whole-genome resequencing at a depth of 20X using the DNBSEQ-T7 / PE150 sequencing platform, and evaluated waterlogging at the seedling stage. Furthermore, through association analysis, superior allelic variations were identified, specific functional markers were developed and used to create intermediate breeding materials, providing superior allelic resources for carrying out molecular breeding for maize waterlogging tolerance. Summary of the Invention
[0006] The purpose of this invention is to provide a reagent for detecting the base at position 2927959 of the second chromosome of the maize genome and its application in screening breeding for waterlogging tolerance during the maize seedling stage.
[0007] Another objective of this invention is to provide the application of a reagent for detecting the base at position 2927959 of the second chromosome of the maize genome in the preparation of a screening kit for waterlogging tolerance in maize seedlings.
[0008] The final objective of this invention is to provide a method for screening and breeding maize seedlings to tolerate waterlogging.
[0009] To achieve the above objectives, the present invention is implemented through the following technical solution:
[0010] Obtaining the main QTL qWTCRFW2.1 for controlling root fresh weight and waterlogging tolerance coefficient during maize seedling waterlogging:
[0011] 1) Through genome-wide association analysis, this invention detected the QTL qWTCRFW2.1 on chromosome 2 of maize, which regulates the root fresh weight tolerance coefficient during waterlogging at the seedling stage. This region contains 3 significant SNP sites with a total length of 400 bp (Chr2: 2927759-2928159). Furthermore, a superior haplotype SNP marker closely linked to it was discovered, located at 2927959 bases on chromosome 2 of the maize B73 reference genome (Zm-B73-REFERENCE-NAM-5.0), which explained 5.25% of the phenotypic contribution rate of the root fresh weight tolerance coefficient.
[0012] 2) For the above-mentioned SNP molecular markers, the applicant has developed PARMS marker primers, which are as follows:
[0013] qWTCRFW2.1F1 (Waterlogging Resistance Haplotype C): GAAGGTCGGAGTCAACGGATTCTGCGCGGGTGCAGAC;
[0014] qWTCRFW2.1F2 (Water-sensitive haplotype T): GAAGGTGACCAAGTTCATGCTCTGCGCGGGTGCAGAT;
[0015] and qWTCRFW2.1R: GTGGACAAGACACGCAACG.
[0016] The scope of protection of this invention also includes:
[0017] Application of reagents for detecting base position 2927959 on chromosome 2 of the maize genome in screening breeding for waterlogging tolerance during maize seedling stage.
[0018] Application of reagents for detecting base position 2927959 on chromosome 2 of the maize genome in the preparation of a screening kit for waterlogging tolerance in maize seedlings.
[0019] In the above-described applications, if a homozygote is detected with a C at position 2927959 of the second chromosome of the maize genome, the maize is determined to be waterlogged tolerant during the seedling stage. If a homozygote is detected with a T at position 2927959 of the second chromosome of the maize genome, the maize is determined to be waterlogged sensitive during the seedling stage.
[0020] In the above-described applications, preferably, the reagent is a primer.
[0021] The primers described above are preferably PARMS detection primers, and more preferably the primers provided by this invention: qWTCRFW2.1F1 (waterlogging resistant haplotype C): GAAGGTCGGAGTCAACGGATTCTGCGCGGGTGCAGAC; qWTCRFW2.1F2 (waterlogging sensitive haplotype T): GAAGGTGACCAAGTTCATGCTCTGCGCGGGTGCAGAT; and qWTCRFW2.1R: GTGGACAAGACACGCAACG.
[0022] A method for screening and breeding maize seedlings for waterlogging tolerance includes detecting the 2927959th base on chromosome 2 of the maize genome using conventional methods in the art. These conventional methods include, but are not limited to, sequencing, TaqMan probe method, AS-PCR method, molecular beacon method, high-resolution melting curve method, CAPS method, SNaPshot method, KASP method, PARMS method, gene chip method, or mass spectrometry.
[0023] In the above-described applications, the root fresh weight waterlogging tolerance coefficient of the seedling-stage waterlogged tolerant corn is greater than 0.7, while the root fresh weight waterlogging tolerance coefficient of the seedling-stage waterlogged sensitive corn is less than 0.6.
[0024] The above-described applications include waterlogging resistance traits such as root fresh weight, root dry weight, seedling fresh weight, tassel main axis length, number of grains per row, ear weight, and / or single ear grain weight.
[0025] The reference genome of maize used in this invention is Zm-B73-REFERENCE-NAM-5.0.
[0026] Compared with the prior art, the present invention has the following advantages:
[0027] This invention, for the first time, finely mapped a novel major QTL controlling the waterlogging tolerance coefficient of roots during the waterlogging stage in maize seedlings based on genome-wide association analysis. The major QTL was located on chromosome 2, which contains three significant SNP loci with a total length of 400 bp (Chr2: 2927759-2928159). These loci are all major QTL loci controlling waterlogging tolerance phenotypic variation. The superior haplotype SNP marker closely linked to it is located at 2927959 bases on chromosome 2 of the maize B73 reference genome (Zm-B73-REFERENCE-NAM-5.0), explaining 5.25% of the phenotypic contribution of waterlogging tolerance coefficient to roots. The PARMS marker developed based on its optimal allele can be used for marker-assisted selection breeding.
[0028] The applicant verified, through the seedling waterlogging root fresh weight and waterlogging tolerance coefficient phenotype of 567 maize inbred lines, that the superior haplotype qWTCRFW2.1 can increase the root fresh weight and waterlogging tolerance coefficient by 33.44% in natural populations. Moreover, it has a good selection effect on traits such as root fresh weight, root dry weight, seedling fresh weight, tassel main axis length, number of kernels per row, ear weight, and single ear kernel weight under maize waterlogging stress. This superior haplotype provides genetic resources for the creation of waterlogging-tolerant maize lines. Attached Figure Description
[0029] Figure 1 Partial field photos of the seedling waterlogging tolerance assessment of 567 inbred line materials;
[0030] The control group had 3 replicates, and the waterlogging treatment group had 3 replicates.
[0031] Figure 2 The distribution of the root fresh weight tolerance coefficient of an inbred line population after two weeks of waterlogging.
[0032] Figure 3 This is a schematic diagram of the site association analysis for qWTCRFW2.1;
[0033] Association analysis of 13.2 million polymorphic variation sites with a minimum allele frequency greater than 0.05 at the qWTCRFW2.1 locus with waterlogged root fresh weight tolerance coefficient phenotype in 567 different inbred lines. Each dot represents a polymorphic site.
[0034] Figure 4 A schematic diagram for the analysis of superior haplotype effects;
[0035] Comparative analysis of root fresh weight waterlogging tolerance coefficients of 27 Hap1 inbred lines and 434 Hap2 inbred lines was conducted. Each box represents the median and interquartile range, extended to the maximum and minimum values. The significance of the differences was estimated by one-way ANOVA.
[0036] Figure 5 A schematic diagram illustrating the genetic effects of qWTCRFW2.1 on the traits of root dry weight and seedling fresh weight waterlogging tolerance coefficient.
[0037] Scatter plots represent the distribution of root dry weight and seedling fresh weight waterlogging tolerance coefficients in families. Each box represents the median and interquartile range, extended to the maximum and minimum values. Error bars represent SD. The significance of differences was estimated by one-way ANOVA.
[0038] Figure 6 A schematic diagram illustrating the genetic effects of qWTCRFW2.1 on the length of the tassel axis;
[0039] Scatter dots represent the distribution of the main axis of the tassel in the family. Each box represents the median and interquartile range and extends to the maximum and minimum values. Error bars represent the standard deviation (SD). The significance of the differences was estimated by one-way ANOVA.
[0040] Figure 7 This is a schematic diagram illustrating the genetic effects of qWTCRFW2.1 on traits such as row grain number, ear weight, and single ear grain weight waterlogging tolerance coefficient.
[0041] Scatter plots represent the distribution of row grain number, ear weight, and single ear grain weight waterlogging tolerance coefficient in families. Each box represents the median and interquartile range, extended to the maximum and minimum values. Error bars represent SD. The significance of differences was estimated by one-way ANOVA.
[0042] Figure 8 A schematic diagram illustrating the development and utilization of the optimal haplotype functional marker for qWTCRFW2.1;
[0043] In the diagram: Green: qWTCRFW2.1 type family has strong waterlogging resistance; Blue: qWTCRFW2.1 type family has weak waterlogging resistance; Red: Hybrid material. Detailed Implementation
[0044] Unless otherwise specified, the technical solutions described in this invention are conventional solutions in the field; unless otherwise specified, the reagents or materials described are all publicly available.
[0045] The reference genome for maize in this invention is Zm-B73-REFERENCE-NAM-5.0 (MaizeGDB GenomeCenter).
[0046] Example 1:
[0047] Obtaining the main active ingredient (QTL) qWTCRFW2.1 for waterlogging tolerance in maize seedlings:
[0048] 1. Materials and Methods
[0049] 1.1 Materials
[0050] A total of 567 backbone inbred lines from maize producing areas in Southwest China and the Huang-Huai-Hai Plain were collected. A population of superior germplasm with different characteristics was established. The whole genome was resequencing at a depth of 20X based on the DNBSEQ-T7 / PE150 sequencing platform, and 13.2 million high-quality SNP markers were obtained.
[0051] 1.2 Experimental Methods
[0052] 1.2.1 Phenotypic Identification
[0053] For related populations, 20 seeds from each family were planted in a rectangular plastic box (60 cm long, 25 cm deep, 35 cm wide) divided into 10 compartments, each containing 30 kg of quartz sand. Each experiment was repeated three times, with no replicates for each square box. At the two-leaf stage, 10 uniformly growing seedlings were retained from each replicate and subjected to waterlogging, with the water level maintained 5-7 cm above the quartz sand. A parallel control experiment under normal growth conditions was also conducted. After 8 days of waterlogging stress, 10 traits of seedlings under control (CK) and waterlogging (WT / R) conditions were measured, including seedling height (cm), root length (cm), seedling fresh weight (g), root fresh weight (g), seedling dry weight (g), root dry weight (g), number of adventitious roots, number of primary roots, and total number of roots (adventitious roots + primary roots). The yellowing index and survival rate were scored only under waterlogging conditions. If seedlings did not show leaf chlorosis, the yellowing index was 0; if 50% of the first leaf was chlorotic, the yellowing index was 0.5, and so on. The survival rate was the ratio of the number of surviving seedlings to the total number of seedlings, and the waterlogging tolerance coefficient was the ratio of the trait value under waterlogging conditions to the trait value under control conditions.
[0054] 1.2.2 Genome-wide association analysis of loci for waterlogging tolerance coefficient of roots during seedling stage
[0055] For the raw sequencing data after sequencing, data quality control was performed to obtain high-quality clean data. This clean data was then aligned to a reference genome for variant detection. The reference genome used was AGPv5, downloaded from http: / / plants.ensembl.org / Zea_mays / Info / Index. BWA software was used to align PE reads with the B73 reference genome sequence, obtaining alignment results in AM format. The SAM format file was converted to BAM format using samtools software. Then, the reads in the BAM file were sorted using the SortSam tool in Picard, and PCR duplicates were removed to obtain the final BAM file suitable for variant calling. Finally, the HaplotypeCaller module of GATK was used for variant detection, including SNPs and InDels. Q and K were calculated using STRUCTURE and TESSEL 5.0 software, respectively. After correction, the P-value was set to 1.0 × 10⁻⁶. -5 As a threshold for the significance of GWAS results.
[0056] 1.2.3 Development of optimal haplotype molecular markers
[0057] Based on the B73 genome and the differential site information provided by qWTCRFW2.1 sequencing, specific primers were designed. Using PARMS detection technology, the adapter sequence that matches FAM fluorescence is GAAGGTGACCAAGTTCATGCT, and the adapter sequence that matches HEX fluorescence is GAAGGTCGGAGTCAACGGATT.
[0058] 1.2.4 Genotype Analysis
[0059] Small-scale DNA extraction from maize was performed using the CTAB (Cetyltrimethyl Ammonium Bromide) method (Saghai-Maroof et al 1984), followed by PARMS SNP detection.
[0060] 2. Results and Analysis
[0061] 2.1 Evaluation of the waterlogging resistance of 567 inbred lines
[0062] At the two-leaf-one-heart stage, the plants were treated with waterlogging for two weeks. The control group grew normally. Among the population groups, the root length waterlogging tolerance coefficient was the lowest at 0.48, with a variation range of 0.17-0.99. There were highly significant differences in root length between the control group and the waterlogging treatment group. The waterlogging tolerance coefficient for fresh root weight was 0.63, with a variation range of 0.12-0.98, and the waterlogging tolerance coefficient for dry root weight was 0.76, with a variation range of 0.20-1.03. This indicates that there is relatively rich genetic variation among the populations, and root length is the most sensitive to waterlogging stress. The waterlogging tolerance coefficients for indeterminate root number and total root number were 1.06 and 1.04, respectively, indicating that waterlogging stress has a relatively small impact on the root coefficient (Table 1).
[0063] Based on the root fresh weight waterlogging tolerance coefficient after 2 weeks of waterlogging, the population was divided into 4 levels. Among them, there were 104 inbred lines with a root fresh weight waterlogging tolerance coefficient greater than 0.8, 51 inbred lines with a root fresh weight waterlogging tolerance coefficient less than 0.4, and 408 inbred lines with a root fresh weight waterlogging tolerance coefficient between 0.4 and 0.8. Figure 2 ).
[0064] Table 1. Evaluation of the waterlogging tolerance of inbred line populations
[0065] .
[0066] WT represents the waterlogged treatment group, CK represents the normal growth group, and T-test two-way ANOVA is used for significance testing.
[0067] 2.2 Identification and genetic effect analysis of the gene locus qWTCRFW2.1 for the seedling root fresh weight waterlogging tolerance coefficient
[0068] This application identifies a novel major QTL controlling the root fresh weight waterlogging tolerance coefficient in maize seedlings based on genome-wide association analysis. This major QTL is located on chromosome 2, and the region contains three significant SNP loci with a total length of 400 bp (Chr2: 2927759-2928159), named qWTCRFW2.1. Figure 3 ).
[0069] qWTCRFW2.1 locus leadSNP 2927959 (C / T) A significant association was found at P=2.34E-06, located at base 2927959 on chromosome 2 of the maize genome (maize B73 reference genome Zm-B73-REFERENCE-NAM-5.0, referred to in this invention as maize B73V5 reference genome), explaining 5.25% of the phenotypic contribution of the waterlogged root fresh weight tolerance coefficient.
[0070] PARMS primers were designed for the above SNP sites as follows:
[0071] For peak SNPs closely linked to qWTCRFW2.1, label the leadSNP. 2927959 (C / T) The sequence of 200 bp upstream and downstream of position 2927959 on chromosome 2 of the maize B73V5 reference genome was extracted. The PARMS marker detection primer sequences were obtained according to primer design principles as follows:
[0072] qWTCRFW2.1F1: GAAGGTCGGAGTCAACGGATT CTGCGCGGGTGCAGAC, as shown in SEQ ID NO.3;
[0073] qWTCRFW2.1F2: GAAGGTGACCAAGTTCATGCT CTGCGCGGGTGCAGAT, as shown in SEQ ID NO.4;
[0074] qWTCRFW2.1R: GTGGACAAGACACGCAACG, as shown in SEQ ID NO.5;
[0075] The underlined part of the forward primer is the fluorescent adapter sequence.
[0076] (2) Using the genomic DNA of the maize inbred line population as a template, the above primers were used to perform real-time PCR amplification. The FAM and HEX signals were scanned using a Tecan F200 and the results were output. Finally, the genotype was converted.
[0077] Using the primers described above, the sequence amplified in L676 (the male parent of Qinlong 13) is: CTGCGCGGGTGCAGA C TGCATTGAGCCTTCATTGTGACAAAAAAAAAGTGTGGGTCGCGTTGCGTGTCTTGTCCAC, as shown in SEQ ID NO.1;
[0078] The sequence amplified in the stain-sensitive material KA105 (the parent material of Shaanxi Dan 618) is: CTGCGCGGGTGCAGA T TGCATTGAGCCTTCATTGTGACAAAAAAAAAGTGTGGGTCGCGTTGCGTGTCTTGTCCAC, as shown in SEQ ID NO.2.
[0079] Amplification system:
[0080] .
[0081] Amplification parameters:
[0082] .
[0083] According to SNP2927959(C / T) The 567 maize inbred lines were divided into two haplotypes, named Hap1 and Hap2, and then paired to compare the differences in root fresh weight waterlogging tolerance coefficients between the two haplotypes after two weeks of waterlogging. Among these, 27 inbred lines were SNPs. 2927959(C / C) Also known as the Hap1 allele, 434 materials were SNPs. 2927959(T / T) Alternatively referred to as the Hap2 allele, other heterozygous sites were filtered out and not counted. Compared with the Hap2 haplotype, the root fresh weight waterlogging tolerance coefficient of the Hap1 haplotype inbred lines was increased by an average of 33.44% (p=7.36E-07). Figure 4 Therefore, Hap1 is a superior haplotype of qWTCRFW2.1, accounting for 5.9%, which suggests that there is still a lot of room for improvement of the waterlogging tolerance of inbred lines by using qWTCRFW2.1 in breeding practice. It can be combined with other related gene loci that regulate yield to achieve the improvement effect of waterlogging tolerance and high yield.
[0084] Meanwhile, qWTCRFW2.1 is a pleiotropic gene locus. Under waterlogging stress, its superior haplotype HAP1 can significantly improve the waterlogging tolerance coefficients of root dry weight and seedling dry weight. Compared with the Hap2 haplotype, the root dry weight waterlogging tolerance coefficient increased by an average of 0.25 (p=1.60E-04), and the seedling dry weight waterlogging tolerance coefficient increased by an average of 0.20 (p=3.37E-05). Figure 5 Regarding plant type-related traits, under waterlogging stress, the average length of the main axis of the tassel inbred line of haap1 was shortened by 2.09 cm compared to haap2 (p=8.92E-03). Figure 6 Regarding yield-related traits, the superior haplotype HAP1 significantly improved row grain number, ear weight, and single ear grain weight waterlogging tolerance coefficient, increasing by 0.11 (p=3.70E-03), 0.10 (p=8.74E-03), and 0.12 (p=3.54E-03), respectively, compared to the Hap2 haplotype. Figure 7 ).
[0085] Example 2:
[0086] Application of the superior haplotype molecular marker primer qWTCRFW2.1, a major QTL for waterlogging tolerance in maize seedlings:
[0087] In 214 maize inbred lines and 1200 local germplasm populations, after one week of waterlogging at the two-leaf stage, 12 families with a root fresh weight waterlogging tolerance coefficient greater than 0.7 and 12 families with a root fresh weight waterlogging tolerance coefficient less than 0.6 were randomly selected. Eight plants from each family were pooled, DNA was extracted, and the F1 generation was analyzed. Genotyping was performed using PARMS primers developed from the optimal allele at the qWTCRFW2.1 locus in Example 1. The results showed that 11 of the families with a root fresh weight waterlogging tolerance coefficient greater than 0.7 belonged to the Hap1 allele, and one was heterozygous. In contrast, all 12 families with a root fresh weight waterlogging tolerance coefficient less than 0.6 contained the unfavorable Hap2 allele, and the F1 generation was heterozygous (Table 2). Figure 8 These results confirm that the developed functional markers can be used for molecular marker-assisted selection in the genetic improvement of waterlogging-resistant lines, providing selection targets for creating new waterlogging-resistant maize germplasm and breeding new waterlogging-resistant varieties.
[0088] Table 2 shows that the PARMS designation qWTCRFW2.1SR can be used for stain resistance assessment.
[0089] .
[0090] Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present invention and are not intended to limit it. Although the present invention has been described in detail with reference to preferred embodiments, those skilled in the art should understand that modifications or equivalent substitutions can be made to the technical solutions of the present invention without departing from the spirit and scope of the present invention, and all such modifications or substitutions should be covered within the scope of the claims of the present invention.
Claims
1. The application of a reagent for detecting base position 2927959 on chromosome 2 of the maize genome in the screening and breeding of waterlogging tolerance traits in maize seedlings, characterized in that... If a homozygote is detected at position 2927959 of chromosome 2 of the maize genome with a base of C, the maize is determined to be a seedling-tolerant maize. If a homozygote is detected at position 2927959 of chromosome 2 of the maize genome with a base of T, the maize is determined to be a seedling-sensitive maize. The maize genome is Zm-B73-REFERENCE-NAM-5.
0.
2. The application of a reagent for detecting base position 2927959 on chromosome 2 of the maize genome in the preparation of a screening kit for waterlogging tolerance in maize seedlings, characterized in that... If a homozygote is detected at position 2927959 of chromosome 2 of the maize genome with a base of C, the maize is determined to be a seedling-tolerant maize. If a homozygote is detected at position 2927959 of chromosome 2 of the maize genome with a base of T, the maize is determined to be a seedling-sensitive maize. The maize genome is Zm-B73-REFERENCE-NAM-5.
0.
3. The application according to claim 1 or claim 2, characterized in that, The root fresh weight waterlogging tolerance coefficient of the seedling-stage waterlogged tolerant corn is greater than 0.7, while the root fresh weight waterlogging tolerance coefficient of the seedling-stage waterlogged sensitive corn is less than 0.
6.
4. The application according to claim 1 or 2, characterized in that, The reagent mentioned is a primer.
5. The application according to claim 4, wherein the primers are: qWTCRFW2.1F1: GAAGGTCGGAGTCAACGGATTCTGCGCGGGTGCAGAC, qWTCRFW2.1F2: GAAGGTGACCAAGTTCATGCTCTGCGCGGGTGCAGAT, and qWTCRFW2.1R: GTGGACAAGACACGCAACG.
6. A method for screening and breeding maize seedlings for waterlogging tolerance, comprising detecting the 2927959th base of the second chromosome of the maize genome, wherein the method is: sequencing, TaqMan probe method, AS-PCR method, molecular beacon method, high-resolution melting curve method, CAPS method, SNaPshot method, KASP method, PARMS method, gene chip method, or mass spectrometry method. If a homozygote is detected at the 2927959th base of the second chromosome of the maize genome with a C, the maize is determined to be waterlogging tolerant maize at the seedling stage; if a homozygote is detected at the 2927959th base of the second chromosome of the maize genome with a T, the maize is determined to be waterlogging sensitive maize at the seedling stage. The maize genome is Zm-B73-REFERENCE-NAM-5.
0.
7. The application according to claim 1 or 2, or the method according to claim 6, wherein the waterlogging resistance trait is root fresh weight, root dry weight, seedling fresh weight, tassel main axis length, number of grains per row, ear weight and / or single ear grain weight trait.