Data from: Preferential induction of Dt2 gene in the absence of E1 function enhances semi-determinate stem growth in soybean
Data files
Apr 07, 2026 version files 445.65 KB
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Expression_250425_Other.csv
3.34 KB
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Expression_Leaf_250722.csv
4.51 KB
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Expression_R1_250715.csv
2.48 KB
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Expression_R1_4DAF_250715.csv
1.31 KB
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Expression_SAM_250722.csv
7.43 KB
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Expression_V4_250715.csv
3 KB
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Expression_V4_R1_250715.csv
4.32 KB
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README.md
20.70 KB
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soybeancore.variant6b.missing025multiallelicMAF01.Gm18_impu_RegionExtra_-5000toDt2End.vcf
397.55 KB
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Transient_reporter_assay.csv
1 KB
Abstract
Suitable plant architecture is key to maximizing crop yield. Stem growth habit is a crucial characteristic of soybean plant architecture. Here, we investigated the combined effect of the Dt2 gene (producing semi-determinate growth habit) and a loss-of-function e1-nl allele of the floral repressor E1. Comparisons among near-isogenic lines with different maturity genotypes indicated that the loss or repression of E1 function enhanced the effect of Dt2 on main stem node numbers. Dt2 expression in stem tips was upregulated in early growing stages under long-day conditions (LD) by the Dt2 and e1-nl alleles in an additive manner. Additionally, an Arabidopsis APETALA1 ortholog was highly upregulated in a Dt2/e1-nl line. The electrophoretic mobility shift assay revealed that the E1 DNA-binding domain bound to several genomic sites harboring key polymorphisms differentiating Dt2 from dt2 alleles. One of these sites had different transcription activities between Dt2 and dt2 alleles, and these activities were repressed by E1. Together, our data suggest that the Dt2 allele confers semi-determinacy by being preferentially induced when released from the repression by E1. The allelic combination of Dt2 and e1-nl confers a distinct semi-determinate phenotype, which would facilitate the use of the Dt2 allele, particularly under LD at high latitudes.
Dataset DOI: 10.5061/dryad.bnzs7h4r6
Description of the data and file structure
Data for the study on the Preferential induction of Dt2 gene in the absence of E1 function enhances semi-determinate stem growth in soybean
Files and variables
File: EMSA_4.png
Description: Image of the electrophoretic mobility shift assay.
File: EMSA_5.png
Description: Image of the electrophoretic mobility shift assay.
File: EMSA_1.png
Description: Image of the electrophoretic mobility shift assay.
File: EMSA_2.png
Description: Image of the electrophoretic mobility shift assay.
File: EMSA_3.png
Description: Image of the electrophoretic mobility shift assay.
File: Fig3_A_e1as.JPG
Description: Image of soybean plants showing representative phenotypes from near-isogenic lines with different Dt2 / *e1-nl *genotypes.
File: Fig3_A_e1nl.JPG
Description: Image of soybean plants showing representative phenotypes from near-isogenic lines with different Dt2 / *e1-nl *genotypes.
File: Fig3_B.JPG
Description: Image of soybean plants showing representative phenotypes from near-isogenic lines with different Dt2 / *e1-nl *genotypes.
Note: Image files (e.g., EMSA and phenotype images) are provided as supplemental materials via Zenodo and are not included in the Dryad data files.
File: soybeancore.variant6b.missing025multiallelicMAF01.Gm18_impu_RegionExtra_-5000toDt2End.vcf
Description: Variant Call Format (VCF) file containing SNP and indel data for soybean chromosome 18, covering the Dt2 genetic locus. Used for haplotype and polymorphism analysis.
File: Expression_250425_Other.csv
Description: Gene expression values, including sample IDs, time points, and tissues.
Variables
-
Line: Soybean near-isogenic lines developed in this study
Values:- d_as: dt2 allele and e1-as allel
- d_nl: dt2 allele and e1-nl allele
- D_as: Dt2 allele and e1-as allele
- D_nl: Dt2 allele and e1-nl allele -
Day: Developmental stage
Values:
- V2: V2 stage
-
Organ: Tissue sampled for analysis
Values:- L: Leaves
- S: Shoot tips -
ID: Unique sample identifier
Unit: N/A -
Replicate: Biological replicate number
Unit: N/A -
FUL1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL3a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication)
File: Expression_Leaf_250722.csv
Description: Gene expression values, including sample IDs, time points, and tissues.
Variables
-
Line: Soybean near-isogenic lines developed in this study
Values:- d_as: dt2 allele and e1-as allel
- d_nl: dt2 allele and e1-nl allele
- D_as: Dt2 allele and e1-as allele
- D_nl: Dt2 allele and e1-nl allele -
Day: Developmental stage
Values:
- V2: V2 stage
- V4: V4 stage -
Organ: Tissue sampled for analysis
Values:- L: Leaves
-
ID: Unique sample identifier
Unit: N/A -
Replicate: Biological replicate number
Unit: N/A -
AP1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt2: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
E1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT5a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL3a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication)
File: Expression_R1_4DAF_250715.csv
Description: Gene expression values, including sample IDs, time points, and tissues.
Variables
-
Line: Soybean near-isogenic lines developed in this study
Values:- d_as: dt2 allele and e1-as allel
- d_nl: dt2 allele and e1-nl allele
- D_as: Dt2 allele and e1-as allele
- D_nl: Dt2 allele and e1-nl allele
-
Day: Developmental stage
Values:
- 4DAF: 4 days after flowering
-
Organ: Tissue sampled for analysis
Values:- S: Shoot tips
-
ID: Unique sample identifier
Unit: N/A -
Replicate: Biological replicate number
Unit: N/A -
AP1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt2: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
E1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT5a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL3a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication)
File: Expression_R1_250715.csv
Description: Gene expression values, including sample IDs, time points, and tissues.
Variables
-
Line: Soybean near-isogenic lines developed in this study
Values:- d_as: dt2 allele and e1-as allel
- d_nl: dt2 allele and e1-nl allele
- D_as: Dt2 allele and e1-as allele
- D_nl: Dt2 allele and e1-nl allele
-
Day: Developmental stage
Values:
- R1: R1 stage
- 4DAF: 4 days after flowering -
Organ: Tissue sampled for analysis
Values:- S: Shoot tips
-
ID: Unique sample identifier
Unit: N/A -
Replicate: Biological replicate number
Unit: N/A -
AP1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt2: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
E1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT5a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL3a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication)
File: Expression_SAM_250722.csv
Description: Gene expression values, including sample IDs, time points, and tissues.
Variables
-
Line: Soybean near-isogenic lines developed in this study
Values:- d_as: dt2 allele and e1-as allel
- d_nl: dt2 allele and e1-nl allele
- D_as: Dt2 allele and e1-as allele
- D_nl: Dt2 allele and e1-nl allele
-
Day: Developmental stage
Values:
- V2: V2 stage
- V4: V4 stage
- R1: R1 stage
- 4DAF: 4 days after flowering -
Organ: Tissue sampled for analysis
Values:- S: Shoot tips
-
ID: Unique sample identifier
Unit: N/A -
Replicate: Biological replicate number
Unit: N/A -
AP1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt2: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
E1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT5a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL3a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication)
File: Expression_V4_250715.csv
Description: Gene expression values, including sample IDs, time points, and tissues.
Variables
-
Line: Soybean near-isogenic lines developed in this study
Values:- d_as: dt2 allele and e1-as allel
- d_nl: dt2 allele and e1-nl allele
- D_as: Dt2 allele and e1-as allele
- D_nl: Dt2 allele and e1-nl allele
-
Day: Developmental stage
Values:
- V4: V4 stage
-
Organ: Tissue sampled for analysis
Values:- L: Leaves
- S: Shoot tips -
ID: Unique sample identifier
Unit: N/A -
Replicate: Biological replicate number
Unit: N/A -
AP1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt2: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
E1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT5a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL3a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication)
File: Transient_reporter_assay.csv
Description: Reporter activity measurements comparing Dt2 vs. dt2 allele with or without E1 co-expression.
Variables
-
Type: Experimental condition
Values: Control: Without E1 protein, E1: Add E1 protein, e1-as: Add e1-as protein -
Rep: Replicate number
Unit: N/A -
Hap:Haplotype of the Dt2 promoter used in the assay
Values: 1: dt2 allele, 2:Dt2 allele -
Type_Hap: Combination of experimental type and haplotype
-
Fluc/Rluc: Ratio of firefly luciferase activity to Renilla luciferase activity
Unit: Relative luminescence ratio
File: Expression_V4_R1_250715.csv
Description: Gene expression values, including sample IDs, time points, and tissues.
Variables
-
Line: Soybean near-isogenic lines developed in this study
Values:- d_as: dt2 allele and e1-as allel
- d_nl: dt2 allele and e1-nl allele
- D_as: Dt2 allele and e1-as allele
- D_nl: Dt2 allele and e1-nl allele
-
Day: Developmental stage
Values:
- V4: V4 stage
- R1: R1 stage -
Organ: Tissue sampled for analysis
Values:- L: Leaves
- S: Shoot tips -
ID: Unique sample identifier
Unit: N/A -
Replicate: Biological replicate number
Unit: N/A -
AP1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
Dt2: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
E1: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FT5a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL2b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
FUL3a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1a: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication) -
SOC1b: Gene expression level of measured by quantitative RT-PCR
Unit: Relative expression level (normalized value; see Methods in associated publication)