Mapping of Quantitative Trait Loci Underlying Nodule Traits in Soybean (Glycine max (L.) Merr.) and Identification of Genes Whose Expression Is Affected by the Sinorhizobium fredii HH103 Effector Proteins NopL and NopT
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strains, Plasmids, and Plant Material
2.2. Generation of the S. fredii HH103ΩNopLΩNopT Mutant
2.3. Nodulation Tests
2.4. QTL Analysis
2.5. Annotation of Genes in QTL Regions
2.6. RNA-Seq KEGG Enrichment Analyses
2.7. RT-qPCR Analysis of Candidate Genes
3. Results
3.1. Effect of NopL and NopT on Various Soybean Germplasms
3.2. Phenotypic Analysis
3.3. QTL Mapping of Nodulation-Related Traits
3.4. Analysis of Candidate Genes
3.5. Differentially Expressed Genes (DEGs) Are Related to the Effectors
3.6. Validation of Candidate Gene Expression by RT-qPCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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CSSLs (n = 213) | Parents (Average) | |||||
---|---|---|---|---|---|---|
Traits | Average | Standard Deviation | Coefficient of Variation | Suinong14 | ZYD00006 | |
HH103 | Nodule number | 48.57 | 38.56 | 0.79 | 21.20 ± 19.88 | 14.67 ± 6.51 * |
Nodule dry weight (g) | 0.04 | 0.03 | 0.69 | 0.03 ± 0.03 | 0.0013 ± 0.0038 | |
HH103ΩNopL | Nodule number | 13.65 ** | 8.03 | 0.58 | 17.00 ± 6.67 | 10.00 ± 1.00 |
Nodule dry weight (g) | 0.02 ** | 0.03 | 1.63 | 0.04 ± 0.02 | 0.0077 ± 0.0011 | |
HH103ΩNopT | Nodule number | 14.01 ** | 10.77 | 0.77 | 15.00 ± 3.61 | 8.33 ± 1.53 |
Nodule dry weight (g) | 0.02 ** | 0.02 | 1.28 | 0.02 ± 0.02 | 0.0074 ± 0.0038 | |
HH103ΩNopLΩNopT | Nodule number | 16.77 ** | 11.56 | 0.69 | 12.20 ± 4.71 | 9.00 ± 6.08 |
Nodule dry weight (g) | 0.02 ** | 0.01 | 0.70 | 0.03 ± 0.02 | 0.0103 ± 0.0075 |
Strain | Trait | Gm | Start Position | End Position | PVE (%) | LOD | Additive Effect |
---|---|---|---|---|---|---|---|
HH103 | NN | 5 | 39,670,584 | 39,726,296 | 7.80 | 37.9 | 0.053 |
5 | 3,976,808 | 39,891,168 | 5.19 | 28.4 | −0.044 | ||
NDW | 2 | 7,376,054 | 7,504,904 | 8.52 | 12.3 | −0.040 | |
2 | 8,200,157 | 8,248,549 | 15.60 | 20.4 | 0.051 | ||
3 | 1933 | 234,034 | 4.32 | 6.8 | 0.015 | ||
HH103ΩNopL | NN | 15 | 4,637,363 | 4,716,807 | 7.40 | 3.4 | 7.851 |
NDW | 15 | 4,119,708 | 4,302,572 | 1.75 | 2.5 | 0.011 | |
19 | 39,031,608 | 39,097,776 | 7.64 | 10.4 | −0.028 | ||
19 | 39,194,300 | 39,293,776 | 17.05 | 20.6 | 0.044 | ||
HH103ΩNopT | NN | 3 | 6,743,461 | 6,777,452 | 17.00 | 8.6 | 5.881 |
NDW | 1 | 55,304,920 | 55,503,928 | 1.46 | 7.7 | 0.048 | |
3 | 2,244,023 | 2,274,724 | 1.18 | 5.8 | 0.010 | ||
10 | 39,447,660 | 39,504,396 | 11.34 | 40.2 | 0.067 | ||
10 | 39,660,168 | 39,754,196 | 12.85 | 43.2 | 0.058 | ||
10 | 40,496,720 | 40,586,292 | 31.55 | 70.7 | −0.128 | ||
11 | 10,234,170 | 10,395,019 | 1.04 | 5.7 | 0.009 | ||
HH103ΩNopLΩNopT | NN | 3 | 1933 | 234,034 | 8.44 | 4.2 | 4.720 |
4 | 8,807,067 | 8,829,123 | 5.55 | 2.8 | 5.273 | ||
18 | 57,614,440 | 57,682,792 | 4.98 | 2.6 | 4.591 | ||
NDW | 9 | 41,985,024 | 42,131,960 | 3.55 | 14.7 | 29.446 | |
14 | 1,346,935 | 1,422,699 | 1.47 | 6.7 | −23.711 | ||
14 | 4,751,415 | 4,955,219 | 22.95 | 56.3 | 104.814 | ||
14 | 4,956,367 | 5,109,562 | 17.36 | 47.7 | −104.991 |
Rhizobium | Chrom. | Gene | Predicted Function |
---|---|---|---|
HH103 | 05 | Glyma05g36870 | Zinc finger, RING-type |
Glyma05g36810 | Phosphatidylinositol 3-/4-kinase, catalytic domain | ||
Glyma05g36700 | Development/cell death domain | ||
Glyma05g36665 | Domain of unknown function DUF2439 | ||
HH103ΩNopL | 15 | Glyma15g06540 | Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB |
Glyma15g06560 | NET domain | ||
Glyma15g06590 | PB1 domain | ||
Glyma15g06630 | CTLH/CRA C-terminal to LisH motif domain | ||
HH103ΩNopT | 03 | Glyma03g06640 | Concanavalin A-like lectin/glucanase domain |
HH103ΩNopLΩNopT | 03 | Glyma03g24141 | Nodulin-like |
Glyma03g00280 | GOLD domain | ||
Glyma03g00370 | K Homology domain | ||
Glyma03g00380 | Acid phosphatase (Class B) | ||
Glyma03g00410 | Thioredoxin | ||
Glyma03g00420 | TAFII28-like protein | ||
Glyma03g00470 | RNA recognition motif domain | ||
Glyma03g00460 | WRKY domain |
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Ni, H.; Peng, Y.; Wang, J.; Wang, J.; Yuan, Y.; Fu, T.; Zhu, Z.; Zhang, J.; Pan, X.; Cui, Z.; et al. Mapping of Quantitative Trait Loci Underlying Nodule Traits in Soybean (Glycine max (L.) Merr.) and Identification of Genes Whose Expression Is Affected by the Sinorhizobium fredii HH103 Effector Proteins NopL and NopT. Agronomy 2022, 12, 946. https://doi.org/10.3390/agronomy12040946
Ni H, Peng Y, Wang J, Wang J, Yuan Y, Fu T, Zhu Z, Zhang J, Pan X, Cui Z, et al. Mapping of Quantitative Trait Loci Underlying Nodule Traits in Soybean (Glycine max (L.) Merr.) and Identification of Genes Whose Expression Is Affected by the Sinorhizobium fredii HH103 Effector Proteins NopL and NopT. Agronomy. 2022; 12(4):946. https://doi.org/10.3390/agronomy12040946
Chicago/Turabian StyleNi, Hejia, Yang Peng, Jinhui Wang, Jing Wang, Yantong Yuan, Tingting Fu, Zikun Zhu, Jialin Zhang, Xipeng Pan, Zhuoling Cui, and et al. 2022. "Mapping of Quantitative Trait Loci Underlying Nodule Traits in Soybean (Glycine max (L.) Merr.) and Identification of Genes Whose Expression Is Affected by the Sinorhizobium fredii HH103 Effector Proteins NopL and NopT" Agronomy 12, no. 4: 946. https://doi.org/10.3390/agronomy12040946