Detection of Different Patterns of Genome-Wide Gene Expression Disturbance in Three Nullisomy Lines in Allotetraploid Brassica napus
Abstract
:1. Introduction
2. Results
2.1. FISH Analysis of Brassica napus Nullisomy and Euploid Oro Lines
2.2. The Morphology of Nullisomy Plants
2.3. RNA-Seq Reveals the Deletion of Chromosomes C1, C2, and C8
2.4. Overall Differential Expression of Genes Between the Aneuploid and Euploid
2.5. The Effect of Hypochromatosis on the Gene Expression of the Other Chromosomes of the Plant Genome
2.6. Perturbation of Gene Expression Due to Chromosome Deletion
2.7. Expression Changes in Homologous Chromosomes
2.8. Enrichment Analysis of DEGs
3. Discussion
3.1. Effects of Aneuploidy on Phenotypic Variation and Function
3.2. Global Perturbation of Gene Expression
3.3. Compensatory Upregulation of Chromosomes
4. Materials and Methods
4.1. Plant Materials
4.2. Cytological Analysis and Fluorescence In Situ Hybridization
4.3. RNA Extraction and cDNA Library Preparation
4.4. Differential Gene Enrichment Analysis
4.5. RT-qPCR Analysis
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
Appendix A
Genome ID | Name | Forward Primer (5′-3′) | Reverse Primer (5′-3′) |
---|---|---|---|
BnaC02g00690D | Actin-7 | GGTTCGACCATGTTCCCAGGT | GTGCTGAGGGATGCAAGGATG |
Chromosome | Number of Reference Genes | Expressed Genes | R (%) (EGs/RGs) | DEGs | R (%) (DEGs/EGs) | Group |
---|---|---|---|---|---|---|
A01 | 4296 | 2306 | 53.68 | 437 | 18.95 | Middle |
A02 | 4203 | 2121 | 50.46 | 338 | 15.94 | Low |
A03 | 5946 | 3398 | 57.15 | 546 | 16.07 | Low |
A04 | 3014 | 1579 | 52.39 | 363 | 22.99 | High |
A05 | 5002 | 2274 | 45.46 | 555 | 24.41 | High |
A06 | 4533 | 2496 | 55.06 | 457 | 18.31 | Middle |
A07 | 3904 | 2235 | 57.25 | 466 | 18.31 | Middle |
A08 | 3222 | 1824 | 46.61 | 332 | 18.20 | Middle |
A09 | 7218 | 3616 | 50.10 | 811 | 22.43 | High |
A10 | 3021 | 1762 | 58.33 | 359 | 6.92 | Low |
A | 44,359 | 23,611 | 53.23 | 4664 | 19.75 | — |
C01 | 5168 | 2527 | 48.90 | 540 | 21.37 | Middle |
C02 | 5574 | 1061 | 19.03 | 817 | 77.00 | — |
C03 | 8178 | 4124 | 50.43 | 834 | 20.22 | Middle |
C04 | 6183 | 2758 | 44.61 | 631 | 22.88 | High |
C05 | 5761 | 2951 | 51.22 | 570 | 19.32 | Middle |
C06 | 4597 | 2325 | 50.58 | 380 | 16.34 | Low |
C07 | 5507 | 2732 | 49.61 | 436 | 15.96 | Low |
C08 | 5349 | 2576 | 48.16 | 466 | 18.09 | Middle |
C09 | 6245 | 2734 | 43.78 | 585 | 21.40 | High |
C | 52,562 | 23,788 | 45.26 | 5259 | 22.11 | — |
Total | 96,924 | 47,399 | 48.90 | 9921 | 20.93 | — |
Chromosome | Number of Reference Genes | Expressed Genes | R (%) (EGs/RGs) | DEGs | R (%) (DEGs/EGs) | Group |
---|---|---|---|---|---|---|
A01 | 4296 | 2351 | 54.73 | 323 | 13.74 | Low |
A02 | 4203 | 2138 | 50.87 | 450 | 21.05 | High |
A03 | 5946 | 3373 | 56.73 | 627 | 18.59 | Middle |
A04 | 3014 | 1581 | 52.46 | 379 | 23.97 | High |
A05 | 5002 | 2305 | 46.08 | 567 | 24.60 | High |
A06 | 4533 | 2499 | 55.13 | 509 | 20.37 | High |
A07 | 3904 | 2275 | 58.28 | 300 | 13.19 | Low |
A08 | 3222 | 1832 | 56.86 | 293 | 15.99 | Middle |
A09 | 7218 | 3639 | 50.42 | 622 | 17.09 | Middle |
A10 | 3021 | 1820 | 60.24 | 194 | 10.66 | Low |
A | 44,359 | 23,813 | 53.68 | 4264 | 17.91 | — |
C01 | 5168 | 2569 | 49.71 | 361 | 14.05 | Middle |
C02 | 5574 | 2459 | 44.12 | 368 | 14.97 | Middle |
C03 | 8178 | 4188 | 51.21 | 586 | 13.99 | Middle |
C04 | 6183 | 2751 | 44.49 | 563 | 20.47 | High |
C05 | 5761 | 3019 | 52.40 | 424 | 14.04 | Middle |
C06 | 4597 | 2348 | 51.08 | 325 | 13.84 | Middle |
C07 | 5507 | 2781 | 50.50 | 382 | 13.74 | Low |
C08 | 5349 | 1093 | 20.43 | 918 | 83.99 | — |
C09 | 6245 | 2805 | 44.92 | 362 | 12.91 | Low |
C | 52,562 | 24,013 | 45.69 | 4289 | 17.86 | — |
Total | 96,924 | 47,826 | 49.34 | 8553 | 17.88 | — |
Genes | Gene ID | Gene Expression (TPM) | |
---|---|---|---|
Oro | NC1 | ||
ARF | BnaA01G0267900ZS | 8.94 | 13.08 |
BnaA02G0396100ZS | 2.82 | 2.51 | |
BnaA02G0396600ZS | 4.93 | 4.83 | |
BnaA04G0008800ZS | 6.74 | 3.94 | |
BnaA05G0014400ZS | 0.08 | 0.12 | |
BnaA09G0077100ZS | 21.69 | 16.17 | |
BnaA09G0559300ZS | 4.19 | 1.90 | |
BnaA09G0702900ZS | 3.54 | 2.14 | |
BnaC01G0174100ZS | 0.37 | 0.27 | |
BnaC01G0328100ZS | 7.26 | 1.99 | |
BnaC02G0529200ZS | 11.68 | 8.16 | |
BnaC03G0559800ZS | 21.86 | 17.08 | |
BnaC04G0014300ZS | 0.45 | 0.10 | |
BnaC04G0265800ZS | 3.71 | 0.77 | |
BnaC08G0407500ZS | 4.69 | 2.74 | |
BnaC09G0068500ZS | 3.51 | 2.52 | |
TRY | BnaA02G0140700ZS | 0.00 | 0.00 |
BnaA03G0131600ZS | 1.59 | 0.00 | |
BnaA10G0097300ZS | 0.00 | 1.57 | |
BnaC01G0222200ZS | 1.66 | 0.00 | |
BnaC01G0222400ZS | 3.82 | 0.00 | |
BnaC02G0178400ZS | 1.46 | 0.00 | |
BnaC03G0153000ZS | 0.10 | 1.98 | |
BnaC09G0353000ZS | 2.30 | 0.60 | |
R2R3 | BnaA01G0097700ZS | 0.00 | 0.00 |
BnaA08G0111700ZS | 0.00 | 0.00 | |
BnaC01G0119400ZS | 0.00 | 0.00 | |
BnaC03G0706500ZS | 0.00 | 0.02 | |
BnaC07G0425500ZS | 0.00 | 0.00 | |
EGL3 | BnaA09G0134400ZS | 0.32 | 0.41 |
BnaA09G0148900ZS | 0.90 | 0.15 | |
BnaC09G0142800ZS | 0.67 | 0.72 | |
BnaC09G0162100ZS | 0.81 | 0.21 | |
WU | BnaA06G0314000ZS | 0.00 | 0.00 |
BnaA09G0114500ZS | 0.00 | 0.00 | |
BnaC03G0508400ZS | 0.00 | 0.00 | |
BnaC09G0117600ZS | 0.00 | 0.00 | |
MYB3 | BnaA07G0121400ZS | 4.52 | 2.11 |
BnaC07G0178800ZS | 2.86 | 2.14 | |
CPC | BnaA04G0292300ZS | 0.00 | 0.00 |
BnaC04G0015600ZS | 0.00 | 0.00 | |
GL1 | BnaA09G0040500ZS | 0.00 | 0.00 |
BnaC07G0310800ZS | 0.00 | 0.00 | |
TMM | BnaA07G0224900ZS | 1.02 | 0.12 |
BnaC06G0242000ZS | 1.63 | 0.1 | |
GL2 | BnaC06G0240800ZS | 0.08 | 0.12 |
References
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Oro_vs_NC1 | Oro_vs_NC2 | Oro_vs_NC8 | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
UP | Ratio (%) | Down | Ratio (%) | Total | UP | Ratio (%) | Down | Ratio (%) | Total | UP | Ratio (%) | Down | Ratio (%) | Total | |
DEGs | 3253 | 51.41 | 3043 | 48.59 | 6296 | 6314 | 55.11 | 5144 | 44.89 | 11,458 | 4967 | 53.24 | 4363 | 46.76 | 9330 |
FC ≥ 10 | 921 | 49.84 | 927 | 50.16 | 1848 | 1932 | 61.31 | 1219 | 38.69 | 3151 | 1259 | 56.11 | 985 | 43.89 | 2244 |
FC ≥ 100 | 368 | 55.76 | 292 | 44.24 | 660 | 587 | 58.41 | 418 | 41.59 | 1005 | 269 | 44.98 | 329 | 55.02 | 598 |
FC ≥ 1000 | 46 | 63.01 | 27 | 36.99 | 73 | 110 | 62.15 | 67 | 37.85 | 177 | 32 | 33.68 | 63 | 66.32 | 95 |
Chromosome | Number of Reference Genes | Expressed Genes | R (%) (EGs/RGs) | DEGs | R (%) (DEGs/EGs) | Group |
---|---|---|---|---|---|---|
A01 | 4296 | 2350 | 54.70 | 824 | 35.06 | High |
A02 | 4203 | 2066 | 49.17 | 301 | 14.57 | High |
A03 | 5946 | 3210 | 53.99 | 421 | 13.12 | Middle |
A04 | 3014 | 1527 | 50.66 | 220 | 14.41 | High |
A05 | 5002 | 2007 | 40.12 | 256 | 12.76 | Middle |
A06 | 4533 | 2388 | 52.68 | 339 | 14.20 | High |
A07 | 3904 | 2185 | 55.97 | 185 | 8.47 | Middle |
A08 | 3222 | 1732 | 53.76 | 150 | 8.66 | Middle |
A09 | 7218 | 3479 | 48.20 | 393 | 11.30 | Middle |
A10 | 3021 | 1748 | 57.86 | 121 | 6.92 | Middle |
A | 44,359 | 22,692 | 51.16 | 3210 | 14.15 | — |
C01 | 5168 | 1509 | 29.20 | 827 | 54.80 | — |
C02 | 5574 | 2218 | 39.79 | 334 | 15.06 | High |
C03 | 8178 | 4067 | 49.73 | 232 | 5.70 | Low |
C04 | 6183 | 2841 | 45.95 | 195 | 6.86 | Middle |
C05 | 5761 | 2922 | 50.72 | 160 | 5.48 | Low |
C06 | 4597 | 2270 | 49.38 | 125 | 5.51 | Low |
C07 | 5507 | 2683 | 46.72 | 151 | 5.63 | Low |
C08 | 5349 | 2548 | 47.64 | 131 | 5.14 | Low |
C09 | 6245 | 2607 | 41.75 | 226 | 8.67 | Middle |
C | 52,562 | 23,665 | 45.02 | 2381 | 10.06 | — |
Total | 96,924 | 46,357 | 47.83 | 5591 | 12.03 | — |
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Lei, S.; Wei, B.; Hu, Q.; Liu, L.; Yu, F.; Zeng, T.; Du, X.; Gu, L.; Wang, H. Detection of Different Patterns of Genome-Wide Gene Expression Disturbance in Three Nullisomy Lines in Allotetraploid Brassica napus. Plants 2025, 14, 1434. https://doi.org/10.3390/plants14101434
Lei S, Wei B, Hu Q, Liu L, Yu F, Zeng T, Du X, Gu L, Wang H. Detection of Different Patterns of Genome-Wide Gene Expression Disturbance in Three Nullisomy Lines in Allotetraploid Brassica napus. Plants. 2025; 14(10):1434. https://doi.org/10.3390/plants14101434
Chicago/Turabian StyleLei, Shaolin, Bo Wei, Qi Hu, Lang Liu, Feng Yu, Tuo Zeng, Xuye Du, Lei Gu, and Hongcheng Wang. 2025. "Detection of Different Patterns of Genome-Wide Gene Expression Disturbance in Three Nullisomy Lines in Allotetraploid Brassica napus" Plants 14, no. 10: 1434. https://doi.org/10.3390/plants14101434
APA StyleLei, S., Wei, B., Hu, Q., Liu, L., Yu, F., Zeng, T., Du, X., Gu, L., & Wang, H. (2025). Detection of Different Patterns of Genome-Wide Gene Expression Disturbance in Three Nullisomy Lines in Allotetraploid Brassica napus. Plants, 14(10), 1434. https://doi.org/10.3390/plants14101434