Development and application of molecular marker for main-effect qwtc LL10.1 of maize tolerance to waterlogging
Patent Information
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- INST OF FOOD CROPS HUBEI ACAD OF AGRI SCI
- Filing Date
- 2026-07-10
- Publication Date
- 2026-08-07
AI Technical Summary
不同学者所采用的涝渍胁迫处理时长、胁迫强度、胁迫时期存在差异，加之玉米各类性状的变异幅度不同、不同遗传背景的玉米自交系对涝渍胁迫的响应特征差异显著，导致目前尚未形成统一规范的玉米耐淹性评价标准
[0029]本发明首次基于全基因组关联分析对一个新的控制玉米叶长耐渍系数主效QTL进行了精细定位，将该主效QTL定位于10号染色体，该区间包含4个显著的SNP位点，总长度为0.2Mb（Chr10：4294113-4294313），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)第十染色体第4294213碱基处，解释的叶长耐渍系数表型贡献率为6.54%，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 maize waterlogging-resistant major QTL qWTCLL10.1, and the development and application of its molecular marker primers. Background Technology
[0002] Maize is a globally important food and economic crop. As a typical dryland crop, it has a weak tolerance to waterlogging stress and is highly susceptible to its damage. Waterlogging stress occurs at every stage of maize's growth, leading to deterioration of plant traits and reduced yield. Waterlogging is a core abiotic stress factor restricting global maize production capacity. Data shows that approximately 15% of maize's planting area in Southeast Asia is affected by waterlogging stress annually, with yield reductions reaching 25%-30%. Therefore, clarifying the genetic regulation of waterlogging tolerance in maize and accelerating the breeding process of new waterlogging-tolerant maize varieties are crucial for effectively mitigating the growth-inhibiting effects of waterlogging stress on maize.
[0003] In maize cultivation, factors such as poor field drainage and prolonged periods of rainfall can trigger waterlogging stress, harming the growth and development of maize throughout its entire growth cycle. Water requirements vary significantly across different growth stages of maize, with daily water requirements decreasing in the following order: flowering to silking stage, tasseling to flowering stage, jointing to tasseling stage, and silking to harvest stage, with the lowest daily water requirement from sowing to emergence. In terms of stress response characteristics, waterlogging during the jointing stage has the most significant negative impact on maize growth, development, and plant traits, followed by the seedling, tasseling, and milk stages. The number of grains per ear and the 100-grain weight are core traits determining maize yield and plant architecture, and the severity of waterlogging stress gradually increases with the duration of stress. In planting environments with poor irrigation and drainage facilities and high groundwater levels, maize roots are chronically hypoxic, and waterlogging stress significantly inhibits the absorption and utilization of soil nutrients by maize roots. Existing research confirms that flooding during the jointing stage causes more severe damage to maize plant traits than flooding during the tasseling stage. The core mechanism is that flooding during the jointing stage inhibits ear differentiation, resulting in a significant reduction in the number of kernels per ear and ultimately leading to a decrease in yield. The impact of this stress on thousand-kernel weight is relatively minor. Furthermore, maize's tolerance to waterlogging varies depending on the variety and planting method. Tall varieties and maize plants grown in high-density planting patterns are more sensitive to waterlogging stress and suffer greater damage. In addition, flooding during the seedling, jointing, and tasseling stages for more than 4 days, or flooding during the grain-filling stage for more than 6 days, will cause irreversible and severe negative impacts on maize plant architecture and yield traits.
[0004] Screening and breeding maize varieties with excellent flood tolerance is a core means to enhance maize's waterlogging tolerance and reduce agricultural production losses caused by extreme rainy weather. While numerous studies have been conducted both domestically and internationally on maize's flood tolerance characteristics, research focusing on the screening of evaluation indicators for flood tolerance in maize inbred lines and systematic comprehensive evaluation remains lacking. Differences exist in the duration, intensity, and timing of waterlogging stress treatments used by different researchers. Furthermore, the varying variability of different maize traits and the significant differences in the response characteristics of maize inbred lines with different genetic backgrounds to waterlogging stress have resulted in the absence of a unified and standardized standard for evaluating maize flood tolerance. Genetic studies have shown that superior maize germplasm resources possess rich genetic potential for flood tolerance, and that maize flood tolerance is a quantitative trait regulated by multiple genes, jointly controlled by multiple quantitative trait loci (QTLs). Under flood stress, the heritability of maize yield and plant type-related agronomic traits is generally low, and the evaluation of flood tolerance is highly susceptible to interference from external environmental conditions. Therefore, marker-assisted selection (MAS) can serve as an efficient and precise breeding strategy in maize flood tolerance breeding. In summary, identifying key genes for waterlogging tolerance in maize, elucidating the molecular regulatory mechanisms of waterlogging tolerance in maize, creating new waterlogging-tolerant germplasm, and cultivating new waterlogging-tolerant varieties are the most economical and efficient technical approaches to reduce losses from waterlogging disasters in maize, increase yield per unit area, and expand the suitable planting range of maize.
[0005] Plant architecture traits are crucial agronomic traits in maize production, directly determining yield formation and field adaptability. Different genotypes of maize materials exhibit significant differentiation in their responses to waterlogging stress, with marked differences in the degree of damage to core plant architecture traits. Therefore, this study introduces the Waterlogging Tolerance Coefficient (WTC) to quantitatively evaluate the tolerance of various maize traits to waterlogging stress. This index is obtained by calculating the relative phenotypic values of traits under waterlogging stress and normal growth conditions, objectively reflecting the waterlogging tolerance characteristics of maize materials.
[0006] Based on the aforementioned research status and challenges, this study collected 567 backbone inbred lines from the two major maize-producing regions of Southwest my country and the Huang-Huai-Hai Plain as experimental germplasm materials to construct a genetically diverse and superior germplasm-associated population. Using the DNBSEQ-T7 / PE150 sequencing platform, 20X depth whole-genome resequencing was completed for all germplasm materials, along with field waterlogging stress identification experiments. Based on the sequencing and phenotypic identification data, genome-wide association analysis was used to identify superior allelic variations in maize waterlogging tolerance, develop corresponding superior haplotype functional markers, and evaluate their breeding effects. The aim is to provide precise breeding targets and theoretical support for the genetic improvement of maize waterlogging tolerance, create high-quality intermediate materials for waterlogging-tolerant breeding, and lay a solid theoretical and material foundation for the breeding of new waterlogging-tolerant maize varieties. Summary of the Invention
[0007] The purpose of this invention is to provide a reagent for detecting the base at position 4294213 of chromosome 10 of the maize genome in the application of maize waterlogging tolerance screening breeding.
[0008] Another objective of this invention is to provide the application of a reagent for detecting base 4294213 on chromosome 10 of the maize genome in the preparation of a screening kit for maize waterlogging tolerance.
[0009] The final objective of this invention is to provide a method for screening and breeding maize with waterlogging tolerance traits.
[0010] To achieve the above objectives, the present invention is implemented through the following technical solution:
[0011] Obtaining the main effective QTL qWTCLL10.1 for controlling maize leaf length waterlogging tolerance coefficient:
[0012] 1) Through genome-wide association analysis, this invention detected the QTL qWTCLL10.1, which regulates leaf length waterlogging tolerance coefficient, on chromosome 10 of maize. This region contains 4 significant SNP sites with a total length of 0.2 Mb (Chr10: 4294113-4294313). Furthermore, a superior haplotype SNP marker closely linked to it was discovered, located at base 4294213 on chromosome 10 of the maize B73 reference genome (Zm-B73-REFERENCE-NAM-5.0), which explained 6.54% of the phenotypic contribution rate of leaf length waterlogging tolerance coefficient.
[0013] 2) For the above-mentioned SNP molecular markers, the applicant has developed PARMS marker primers, which are as follows:
[0014] qWTCLL10.1F1 (waterlogging resistance haplotype A): GAAGGTGACCAAGTTCATGCTCCTCCTGCTCCTTACACAAGTT, as shown in SEQ ID NO.3;
[0015] qWTCLL10.1F2 (waterlogging-sensitive haplotype G): GAAGGTCGGAGTCAACGGATTCCTCCTGCTCCTTACACAAGTC, as shown in SEQ ID NO.4;
[0016] And qWTCLL10.1L:GCTTAGCTTGCAGATGAACACTAG, as shown in SEQ ID NO.5.
[0017] The scope of protection of this invention also includes:
[0018] Application of reagents for detecting base position 4294213 on chromosome 10 of the maize genome in screening breeding for waterlogging tolerance.
[0019] Application of reagents for detecting base position 4294213 on chromosome 10 of the maize genome in the preparation of a screening kit for maize waterlogging tolerance.
[0020] In the above-described applications, if a homozygote is detected with a base A at position 4294213 on chromosome 10 of the maize genome, the maize is determined to be waterlogged tolerant maize; if a homozygote is detected with a base G at position 4294213 on chromosome 10 of the maize genome, the maize is determined to be waterlogged sensitive maize.
[0021] In the above-described applications, preferably, the reagent is a primer.
[0022] The primers described above are preferably PARMS detection primers, and more preferably the primers provided by this invention:
[0023] qWTCLL10.1F1 (waterlogging resistant haplotype A): GAAGGTGACCAAGTTCATGCTCCTCCTGCTCCTTACACAAGTT, as shown in SEQ ID NO.3; qWTCLL10.1F2 (waterlogging sensitive haplotype G): GAAGGTCGGAGTCAACGGATTCCTCCTGCTCCTTACACAAGTC, as shown in SEQ ID NO.4; and qWTCLL10.1L: GCTTAGCTTGCAGATGAACACTAG, as shown in SEQ ID NO.5.
[0024] In the above-described applications, the leaf length waterlogging tolerance coefficient of the waterlogging-resistant corn is greater than 0.87, while the leaf length waterlogging tolerance coefficient of the waterlogging-sensitive corn is less than 0.77.
[0025] A method for screening and breeding maize with waterlogging tolerance includes detecting base 4294213 on chromosome 10 of the maize genome using conventional methods in the art. The 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 method.
[0026] The above-described applications or methods include waterlogging tolerance traits such as plant height waterlogging tolerance coefficient, tassel main axis length waterlogging tolerance coefficient, and / or yield waterlogging tolerance coefficient.
[0027] The reference genome of maize used in this invention is Zm-B73-REFERENCE-NAM-5.0.
[0028] Compared with the prior art, the present invention has the following advantages:
[0029] This invention provides the first fine mapping of a novel major QTL controlling leaf length waterlogging tolerance in maize based on genome-wide association analysis. The major QTL is located on chromosome 10, which contains four significant SNP loci with a total length of 0.2 Mb (Chr10: 4294113-4294313). These loci are all major QTL loci controlling waterlogging tolerance phenotypic variation. The closely linked superior haplotype SNP marker is located at 4294213 bases on chromosome 10 of the maize B73 reference genome (Zm-B73-REFERENCE-NAM-5.0), explaining 6.54% of the leaf length waterlogging tolerance phenotypic contribution. The PARMS marker developed based on its optimal allele can be used for marker-assisted selection breeding.
[0030] The applicant verified, through the leaf length phenotype of 567 maize inbred lines in the field, that the superior haplotype qWTCLL10.1 can increase the leaf length waterlogging tolerance coefficient by 5.48% in natural populations. Furthermore, it exhibits good selection effects on waterlogging tolerance coefficients for traits such as plant height, tassel axis length, and 100-kernel weight under maize waterlogging stress, and has been strongly selected in breeding practices. This superior haplotype provides genetic resources for the creation of waterlogging-tolerant maize lines. Attached Figure Description
[0031] Figure 1 These are some field photos from the first domestic field waterlogging tolerance test of maize with 567 inbred lines.
[0032] The control group had 2 replicates, and the waterlogging treatment group had 3 replicates.
[0033] Figure 2 Distribution of leaf length waterlogging tolerance coefficient during the first week of waterlogging in the field for inbred line populations at the jointing stage.
[0034] Figure 3 This is a schematic diagram of the qWTCLL10.1 site association analysis;
[0035] Association analysis of 13.2 million polymorphic variation sites with a minimum allele frequency greater than 0.05 at the qWTCLL10.1 locus with leaf length and waterlogging tolerance phenotype in 567 different inbred lines. Each dot represents a polymorphic site.
[0036] Figure 4 A schematic diagram for the analysis of superior haplotype effects;
[0037] Comparative analysis of leaf length waterlogging tolerance coefficients of 313 Hap1 inbred lines and 194 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.
[0038] Figure 5A schematic diagram illustrating the genetic effects of qWTCLL10.1 on traits such as plant height and waterlogging tolerance coefficient and tassel main axis length and waterlogging tolerance coefficient.
[0039] The scatter plots represent the distribution of the stain resistance coefficient, each box represents the median and interquartile range and extends to the maximum and minimum values, and the error bars represent the SD. The significance of the differences was estimated by one-way ANOVA.
[0040] Figure 6 A schematic diagram illustrating the genetic effect evaluation of qWTCLL10.1 in the trait of 100-grain weight water resistance coefficient;
[0041] The scatter plots represent the distribution of the stain resistance coefficient, each box represents the median and interquartile range and extends to the maximum and minimum values, and the error bars represent the SD. The significance of the differences was estimated by one-way ANOVA.
[0042] Figure 7 A schematic diagram illustrating the development and utilization of the optimal haplotype functional marker for qWTCLL10.1;
[0043] In the figure: Blue: qWTCLL10.1 type has strong resistance to waterlogging; Green: qWTCLL10.1 type has weak resistance to waterlogging; Gray: Negative control, the substrate for spotting is blank. 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 effect QTL qWTCLL10.1 for corn leaf length waterlogging tolerance coefficient:
[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] The first domestic field flood resistance trial of related populations was conducted at the experimental base of the Agricultural Science Research Institute in Gucheng County, Hubei Province. Under actual production conditions, the flood resistance of core maize germplasm resources was assessed through field trials. In early April 2024, 567 related populations were sown, divided into a control group and a flood-treated group. The control group contained two biological replicates, with each seed sample planted in a single row; the flood-treated group contained three biological replicates, also with each seed sample planted in a single row. After sowing, when the maize plants reached the spikelet differentiation stage (jointing stage), the flood-treated group was flooded for one week, with the water level in the flood-treated group approximately 10 cm high, submerging the first leaf of the plant; while the control group received no treatment and was allowed to grow normally. After the maize plants have completed their growth period, the agronomical traits of maize plant type were measured and recorded under control (CK) and waterlogging (WT) conditions, including plant height (cm), ear height (cm), length of leaves above the ear (cm), width of leaves above the ear (cm), number of tassel branches, length of the main axis of the tassel (cm), and number of leaves above the ear. After the maize plants matured, the agronomical traits of maize yield in the field were measured and recorded under control (CK) and waterlogging (WT) conditions, including ear length (cm), ear diameter (cm), ear weight (g), 100-kernel weight (g), weight of kernels per ear (g), number of rows per ear, and number of kernels per row per ear. Subsequently, the waterlogging tolerance coefficient (WTC) for each trait was calculated; the waterlogging tolerance coefficient is the ratio of the trait value under waterlogging conditions to that under control conditions.
[0054] 1.2.2 Genome-wide association analysis of trait loci related to waterlogging tolerance coefficient in maize plant architecture
[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 qWTCLL10.1 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] During spikelet differentiation (jointing stage), the field waterlogging group was treated with waterlogging for one week, while the control group grew normally. At the population level, the waterlogging tolerance coefficient for plant height was 0.83, with a variation range of 0.30-0.99, showing a significant difference in plant height between the control and waterlogged groups. The waterlogging tolerance coefficient for tassel length was 0.78, with a variation range of 0.20-0.99, exhibiting rich variation. The waterlogging tolerance coefficient for leaf length was 0.76, with a variation range of 0.39-0.99, and the waterlogging tolerance coefficient for leaf width was... The number was 0.76, with a variation range of 0.29-0.99; the overall value was similar to the leaf length; the waterlogging tolerance coefficient of tassel branching was 0.70, with a variation range of 0.07-0.99, and the waterlogging tolerance coefficient of ear height was 0.71, with a variation range of 0.34-0.99. Among the field plant type traits, tassel branching and ear height were the most sensitive to waterlogging stress, while plant height and tassel length were relatively less affected by waterlogging stress, but all of their phenotypic variations were very rich (Table 1).
[0063] Based on the leaf length tolerance coefficient after one week of waterlogging, the population was divided into 5 levels. Among them, there were 306 inbred lines with a tolerance coefficient greater than 0.85, 24 inbred lines with a tolerance coefficient less than 0.65, and 212 inbred lines with a tolerance coefficient between 0.65 and 0.85. Figure 2 ).
[0064] Table 1. Evaluation of waterlogging tolerance related traits in inbred line populations based on plant type.
[0065] .
[0066] CK represents the normal growth group, WT represents the waterlogged treatment group, and T-test two-way ANOVA is used for significance testing.
[0067] 2.2 Identification and genetic effect analysis of the leaf length waterlogging tolerance gene locus qWTCLL10.1
[0068] This application identifies a novel major QTL controlling maize leaf length waterlogging tolerance based on genome-wide association analysis. This major QTL is located on chromosome 10, and the region contains four significant SNP loci with a total length of 0.2 Mb (Chr10: 4294113-4294313), named qWTCLL10.1. Figure 3 ).
[0069] qWTCLL10.1 locus lead SNP 4294213 (A / G) A significant association was found at P = 1.14E-8, located at base 4294213 on chromosome 10 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 6.54% of the phenotypic contribution of the leaf length waterlogging tolerance coefficient.
[0070] PARMS primers were designed for the above SNP sites as follows:
[0071] For peak SNPs closely linked to qWTCLL10.1, label the leadSNP. 4294213 (A / G) A 200 bp sequence was extracted from each of the bases upstream and downstream of position 4294213 on chromosome 10 of the maize B73V5 reference genome. Following primer design principles, the PARMS marker detection primer sequences were obtained as follows:
[0072] qWTCLL10.1F1: GAAGGTGACCAAGTTCATGCT CCTCCTGCTCCTTACACAAGTT, as shown in SEQ ID NO.3;
[0073] qWTCLL10.1F2: GAAGGTCGGAGTCAACGGATT CCTCCTGCTCCTTACACAAGTC, as shown in SEQ ID NO.4;
[0074] qWTCLL10.1L: GCTTAGCTTGCAGATGAACACTAG, 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, quantitative real-time PCR amplification was performed using the primers described above. The amplification system and parameters are shown in Tables 2 and 3. The FAM and HEX signals were scanned using a Tecan F200 scanner, and the results were output and finally converted into genotypes.
[0077] Using the primers described above, the sequence amplified in the stain-resistant material Xun92-6 (parent of Jundan 18) is: GCTTAGCTTGCAGATGAACACTAGTAAAATACACTTGCTGCTGAAACCTGAAAGGCA A ACTTGTGTAAGGAGCAGG, as shown in SEQ ID NO.1;
[0078] The sequence amplified in the stain-resistant material PH11VR (parent of Xianyu 1140) is: GCTTAGCTTGCAGATGAACACTAGTAAAATACACTTGCTGCTGAAACCTGAAAGGCA G ACTTGTGTAAGGAGCAGG, as shown in SEQ ID NO.2.
[0079] Table 2 Amplification System
[0080] .
[0081] Table 3 Amplification Parameters
[0082] .
[0083] According to SNP 4294213 (A / G) The 567 maize inbred lines were divided into two haplotypes, named Hap1 and Hap2, and then further divided into two groups to compare the differences in leaf length waterlogging tolerance coefficients between the two haplotypes after one week of field flooding. Among these, 313 inbred lines were SNPs. 4294213 (A / A) Also known as the Hap1 allele, 194 materials were SNPs. 4294213 (G / G) Alternatively referred to as the Hap2 allele, other heterozygous loci were filtered out and not counted. Compared with the Hap2 haplotype, the Hap1 haplotype inbred lines showed an average increase of 5.48% in the field waterlogging tolerance coefficient (P = 1.14E-08). Figure 4 Therefore, Hap1 is a superior haplotype of qWTCLL10.1, accounting for 61.74%.
[0084] Meanwhile, qWTCLL10.1 is a pleiotropic gene locus; under waterlogging stress, its superior haplotype Hap1 significantly enhances the waterlogging tolerance coefficients for plant height, tassel main axis length, and 100-grain weight. Regarding plant type-related traits, compared to the Hap2 haplotype, the Hap1 haplotype inbred lines showed an average increase of 0.023 in plant height waterlogging tolerance coefficients (p=0.0025) and an average increase of 0.055 in tassel main axis length waterlogging tolerance coefficients (p=3.09E-06). Figure 5 Regarding yield-related traits, under waterlogging stress, the waterlogging tolerance coefficient of the 100-grain weight per ear of the Hap1 haplotype inbred line decreased by an average of 0.018 compared to the Hap2 haplotype (p = 0.031). Figure 6 This indicates that this locus positively regulates other plant type-related traits, suggesting to some extent that there is a certain linkage burden between superior alleles related to plant type and yield-related traits in the field. Furthermore, the frequency of Hap1 in inbred lines is 61.74%, further implying that there is considerable potential in breeding practice to improve the waterlogging tolerance of inbred lines using qWTCLL10.1, which can aggregate other gene loci related to plant type regulation to achieve the improvement effect of waterlogging tolerance and high yield.
[0085] Example 2:
[0086] Application of the superior haplotype molecular marker primer qWTCLL10.1, which is the major QTL for maize leaf length waterlogging tolerance:
[0087] In field trials, 567 inbred line samples and leaf length waterlogging tolerance coefficient data were collected. Subsequently, DNA was extracted from 21 inbred lines, and genotyping was performed using PARMS primers developed from the optimal allele at the qWTCLL10.1 locus in Example 1. The results showed that 12 inbred lines with leaf length waterlogging tolerance coefficients greater than 0.87 belonged to the Hap1 allele, while the 9 inbred lines with leaf length waterlogging tolerance coefficients less than 0.77 all contained the unfavorable Hap2 allele (Table 4). These results confirm that the developed functional markers can be used for marker-assisted selection in the genetic improvement of waterlogging-tolerant lines, providing selection targets for creating new waterlogging-tolerant maize germplasm and breeding new waterlogging-tolerant varieties. Figure 7 ).
[0088] Table 4 shows that the PARMS designation qWTCLL10.1 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 4294213 on chromosome 10 of the maize genome in the screening and breeding of maize for waterlogging tolerance, characterized in that... If a homozygote is detected at position 4294213 of chromosome 10 of the maize genome with a base of A, the maize is determined to be waterlogged tolerant maize; if a homozygote is detected at position 4294213 of chromosome 10 of the maize genome with a base of G, the maize is determined to be waterlogged sensitive maize. The maize genome is Zm-B73-REFERENCE-NAM-5.
0.
2. The application of a reagent for detecting base position 4294213 on chromosome 10 of the maize genome in the preparation of a maize waterlogging tolerance screening kit, characterized in that... If a homozygote is detected at position 4294213 of chromosome 10 of the maize genome with a base of A, the maize is determined to be waterlogged tolerant maize; if a homozygote is detected at position 4294213 of chromosome 10 of the maize genome with a base of G, the maize is determined to be waterlogged sensitive maize. The maize genome is Zm-B73-REFERENCE-NAM-5.
0.
3. The application according to claim 1 or 2, characterized in that, The reagent mentioned is a primer.
4. The application according to claim 3, wherein the primers are: qWTCLL10.1F1: GAAGGTGACCAAGTTCATGCTCCTCCTGCTCCTTACACAAGTT, as shown in SEQ ID NO.3; qWTCLL10.1F2: GAAGGTCGGAGTCAACGGATTCCTCCTGCTCCTTACACAAGTC, as shown in SEQ ID NO.4; and qWTCLL10.1L: GCTTAGCTTGCAGATGAACACTAG, as shown in SEQ ID NO.
5.
5. The application according to claim 1 or claim 2, characterized in that, The waterlogging-resistant corn has a leaf length waterlogging tolerance coefficient greater than 0.87, while the waterlogging-sensitive corn has a leaf length waterlogging tolerance coefficient less than 0.
77.
6. A method for screening and breeding maize with waterlogging tolerance, comprising detecting the base at position 4294213 of chromosome 10 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 position 4294213 of chromosome 10 of the maize genome with base A, the maize is determined to be waterlogging tolerant maize; if a homozygote is detected at position 4294213 of chromosome 10 of the maize genome with base G, the maize is determined to be waterlogging sensitive maize, wherein 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 the waterlogging resistance coefficient of plant height, the waterlogging resistance coefficient of tassel main axis length, and / or the waterlogging resistance coefficient of yield.