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Enhancing effect of Na2SeO3 on the growth and physiological parameters of Vitis vinifera × labrusca 'Shuijing' under nitrogen deficiency and underlying transcriptomic mechanisms

Yongfu Zhang

Yongfu Zhang

Department of Horticulture, School of Agriculture and Life Sciences, Kunming UniversityKunming, China
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Zhang, Yongfu
, 
Liling Mo

Liling Mo

Department of Horticulture, School of Agriculture and Life Sciences, Kunming UniversityKunming, China
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Mo, Liling
, 
Xiaoqin Li

Xiaoqin Li

Department of Horticulture, School of Agriculture and Life Sciences, Kunming UniversityKunming, China
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Li, Xiaoqin
, 
Kai Wang

Kai Wang

Department of Horticulture, School of Agriculture and Life Sciences, Kunming UniversityKunming, China
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Wang, Kai
, 
Zuqin Qiao

Zuqin Qiao

Department of Horticulture, School of Agriculture and Life Sciences, Kunming UniversityKunming, China
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Qiao, Zuqin
 und 
Zhao Liu

Zhao Liu

Department of Horticulture, School of Agriculture and Life Sciences, Kunming UniversityKunming, China
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Liu, Zhao
  
27. Feb. 2025
Enhancing effect of Na2SeO3 on the growth and physiological parameters of Vitis vinifera × labrusca 'Shuijing' under nitrogen deficiency and underlying transcriptomic mechanisms's Cover Image
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Artikel-Kategorie: ORIGINAL ARTICLE
Online veröffentlicht: 27. Feb. 2025
Seitenbereich: 559 - 580
Eingereicht: 27. Juni 2024
Akzeptiert: 24. Jan. 2025
DOI: https://doi.org/10.2478/fhort-2024-0037
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© 2024 Yongfu Zhang et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1.

Effects of Na2SeO3 treatment on the growth and physiological characteristics of grape under various nitrogen conditions. (A) The growth status of grape plants; (B) the net growth of plant height, the net growth of stem thickness, root volume and internode length of grape; (C) leaf thickness, biomass, root shoot ratio and flavonoids content of grape; (D) starch content, soluble sugar content, nitrogen content and soluble protein content of grape. The results were shown as mean ± standard deviation (n = 4), and one-way ANOVA was used to compare the significant differences among the treatments. Different lowercase letters on the bar graph indicate significant differences at the p < 0.05 level. Control group is Control; 0.1 mmol · L−1 + 15 mmol · L−1 N is 0.1Se + 15 N; 0.2 mmol · L−1 + 15 mmol · L−1 N is 0.2Se + 15 N; 0.4 mmol · L−1 + 15 mmol · L−1 N is 0.4Se + 15 N; 0.1 mmol · L−1 Na2SeO3 is 0.1Se; 0.2 mmol · L−1 Na2SeO3 is 0.2Se; 0.4 mmol · L−1 Na2SeO3 is 0.4Se.
Effects of Na2SeO3 treatment on the growth and physiological characteristics of grape under various nitrogen conditions. (A) The growth status of grape plants; (B) the net growth of plant height, the net growth of stem thickness, root volume and internode length of grape; (C) leaf thickness, biomass, root shoot ratio and flavonoids content of grape; (D) starch content, soluble sugar content, nitrogen content and soluble protein content of grape. The results were shown as mean ± standard deviation (n = 4), and one-way ANOVA was used to compare the significant differences among the treatments. Different lowercase letters on the bar graph indicate significant differences at the p < 0.05 level. Control group is Control; 0.1 mmol · L−1 + 15 mmol · L−1 N is 0.1Se + 15 N; 0.2 mmol · L−1 + 15 mmol · L−1 N is 0.2Se + 15 N; 0.4 mmol · L−1 + 15 mmol · L−1 N is 0.4Se + 15 N; 0.1 mmol · L−1 Na2SeO3 is 0.1Se; 0.2 mmol · L−1 Na2SeO3 is 0.2Se; 0.4 mmol · L−1 Na2SeO3 is 0.4Se.

Figure 2.

Transcriptome analysis of grape leaves after Na2SeO3 treatment under various nitrogen conditions. (A) Correlation between samples; (B) unigene distribution and group overlap; (C) Venn diagram displaying the number of DEGs in each comparison group and group overlap; (D–F) The DEGs in 0.2Se + 15N versus Control, 0.2Se versus Control, and 0.2Se + 15N vs 0.2Se are plotted in a volcano plot. Control group is Control; 0.1 mmol · L−1 + 15 mmol · L−1 N is 0.1Se + 15 N; 0.2 mmol · L−1 + 15 mmol · L−1 N is 0.2Se + 15 N; 0.4 mmol · L−1 + 15 mmol · L−1 N is 0.4Se + 15 N; 0.1 mmol · L−1 Na2SeO3 is 0.1Se; 0.2 mmol · L−1 Na2SeO3 is 0.2Se; 0.4 mmol · L−1 Na2SeO3 is 0.4Se.
Transcriptome analysis of grape leaves after Na2SeO3 treatment under various nitrogen conditions. (A) Correlation between samples; (B) unigene distribution and group overlap; (C) Venn diagram displaying the number of DEGs in each comparison group and group overlap; (D–F) The DEGs in 0.2Se + 15N versus Control, 0.2Se versus Control, and 0.2Se + 15N vs 0.2Se are plotted in a volcano plot. Control group is Control; 0.1 mmol · L−1 + 15 mmol · L−1 N is 0.1Se + 15 N; 0.2 mmol · L−1 + 15 mmol · L−1 N is 0.2Se + 15 N; 0.4 mmol · L−1 + 15 mmol · L−1 N is 0.4Se + 15 N; 0.1 mmol · L−1 Na2SeO3 is 0.1Se; 0.2 mmol · L−1 Na2SeO3 is 0.2Se; 0.4 mmol · L−1 Na2SeO3 is 0.4Se.

Figure 3.

GO pathway enrichment analysis of DEGs in grape after Na2SeO3 treatment under various nitrogen conditions. The numbers listed on the horizontal axis represent the top 40 GO-enriched entries in different comparison groups (Padjust < 0.05). Control group is Control; 0.2 mmol · L−1+ 15 mmol · L−1 N is 0.2 Se + 15 N; 0.2 mmol · L−1 Na2SeO3 is 0.2 Se. 1. Catalytic activity; 2. oxidoreductase activity; 3. DNA binding; 4. transferase activity, transferring acyl groups; 5. transferase activity, transferring acyl groups other than amino-acyl groups; 6. DNA-binding transcription factor activity; 7. tetrapyrrole binding; 8. heme binding; 9. lyase activity; 10. cytoskeletal protein binding; 11. extracellular region; 12. cell wall; 13. external encapsulating structure; 14. supramolecular complex; 15. plasmodesma; 16. anchoring junction; 17. cell-cell junction; 18. cell junction; 19. polymeric cytoskeletal fibre; 20. supramolecular polymer; 21. response to stimulus; 22. oxidation-reduction process; 23. response to stress; 24. transmembrane transport; 25. response to chemical; 26. cell cycle process; 27. response to abiotic stimulus; 28. lipid biosynthetic process; 29. small molecule biosynthetic process; 30. microtubule-based process; 31. response to oxygen-containing compound; 32. response to external stimulus; 33. ion transmembrane transport; 34. response to oxidative stress; 35. mitotic cell cycle process; 36. organic acid biosynthetic process; 37. carboxylic acid biosynthetic process; 38. regulation of cell cycle; 39. inorganic ion transmembrane transport; 40. cell wall organisation or biogenesis; 41. transferase activity, transferring glycosyl groups; 42. transferase activity, transferring hexosyl groups; 43. hydrolase activity, acting on glycosyl bonds; 44. UDP-glycosyltransferase activity; 45. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen; 46. hydrolase activity, hydrolysing O-glycosyl compounds; 47. monooxygenase activity; 48. iron ion binding; 49. intrinsic component of membrane; 50. integral component of membrane; 51. membrane; 52. plasma membrane; 53. Golgi apparatus; 54. carbohydrate metabolic process; 55. catabolic process; 56. protein phosphorylation; 57. polysaccharide metabolic process; 58. cellular carbohydrate metabolic process; 59. cellular polysaccharide metabolic process; 60. external encapsulating structure organisation; 61. cell wall organisation; 62. apoplast; 63. organic substance catabolic process; 64. ion transport; 65. regulation of biological quality; 66. homeostatic process; 67. cation transport; 68. metal ion transport; 69. response to inorganic substance; 70. inorganic ion homeostasis.
GO pathway enrichment analysis of DEGs in grape after Na2SeO3 treatment under various nitrogen conditions. The numbers listed on the horizontal axis represent the top 40 GO-enriched entries in different comparison groups (Padjust < 0.05). Control group is Control; 0.2 mmol · L−1+ 15 mmol · L−1 N is 0.2 Se + 15 N; 0.2 mmol · L−1 Na2SeO3 is 0.2 Se. 1. Catalytic activity; 2. oxidoreductase activity; 3. DNA binding; 4. transferase activity, transferring acyl groups; 5. transferase activity, transferring acyl groups other than amino-acyl groups; 6. DNA-binding transcription factor activity; 7. tetrapyrrole binding; 8. heme binding; 9. lyase activity; 10. cytoskeletal protein binding; 11. extracellular region; 12. cell wall; 13. external encapsulating structure; 14. supramolecular complex; 15. plasmodesma; 16. anchoring junction; 17. cell-cell junction; 18. cell junction; 19. polymeric cytoskeletal fibre; 20. supramolecular polymer; 21. response to stimulus; 22. oxidation-reduction process; 23. response to stress; 24. transmembrane transport; 25. response to chemical; 26. cell cycle process; 27. response to abiotic stimulus; 28. lipid biosynthetic process; 29. small molecule biosynthetic process; 30. microtubule-based process; 31. response to oxygen-containing compound; 32. response to external stimulus; 33. ion transmembrane transport; 34. response to oxidative stress; 35. mitotic cell cycle process; 36. organic acid biosynthetic process; 37. carboxylic acid biosynthetic process; 38. regulation of cell cycle; 39. inorganic ion transmembrane transport; 40. cell wall organisation or biogenesis; 41. transferase activity, transferring glycosyl groups; 42. transferase activity, transferring hexosyl groups; 43. hydrolase activity, acting on glycosyl bonds; 44. UDP-glycosyltransferase activity; 45. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen; 46. hydrolase activity, hydrolysing O-glycosyl compounds; 47. monooxygenase activity; 48. iron ion binding; 49. intrinsic component of membrane; 50. integral component of membrane; 51. membrane; 52. plasma membrane; 53. Golgi apparatus; 54. carbohydrate metabolic process; 55. catabolic process; 56. protein phosphorylation; 57. polysaccharide metabolic process; 58. cellular carbohydrate metabolic process; 59. cellular polysaccharide metabolic process; 60. external encapsulating structure organisation; 61. cell wall organisation; 62. apoplast; 63. organic substance catabolic process; 64. ion transport; 65. regulation of biological quality; 66. homeostatic process; 67. cation transport; 68. metal ion transport; 69. response to inorganic substance; 70. inorganic ion homeostasis.

Figure 4.

KEGG pathway enrichment analysis of DEGs in grape after Na2SeO3 treatment under various nitrogen conditions. The numbers listed on the horizontal axis represent the top 15 KEGG enrichment items in different treatment comparisons (Padjust < 0.05). Control group is Control; 0.2 mmol · L−1 + 15 mmol · L−1 N is 0.2 Se + 15 N; 0.2 mmol · L−1 Na2SeO3 is 0.2 Se. 1. Flavonoid biosynthesis; 2. phenylpropanoid biosynthesis; 3. starch and sucrose metabolism; 4. stilbenoid, diarylheptanoid, and gingerol biosynthesis; 5. glycine, serine, and threonine metabolism; 6. glycerolipid metabolism; 7. cysteine and methionine metabolism; 8. glutathione metabolism; 9. pentose and glucuronate interconversions; 10. monoterpenoid biosynthesis; 11. glycolysis/gluconeogenesis; 12. plant hormone signal transduction; 13. MAPK signalling pathway–plant; 14. circadian rhythm–plant; 15. plant-pathogen interaction; 16. glycerophospholipid metabolism; 17. amino sugar and nucleotide sugar metabolism; 18. tyrosine metabolism; 19. phagosome; 20. endocytosis; 21. protein processing in endoplasmic reticulum; 22. galactose metabolism; 23. oxidative phosphorylation.
KEGG pathway enrichment analysis of DEGs in grape after Na2SeO3 treatment under various nitrogen conditions. The numbers listed on the horizontal axis represent the top 15 KEGG enrichment items in different treatment comparisons (Padjust < 0.05). Control group is Control; 0.2 mmol · L−1 + 15 mmol · L−1 N is 0.2 Se + 15 N; 0.2 mmol · L−1 Na2SeO3 is 0.2 Se. 1. Flavonoid biosynthesis; 2. phenylpropanoid biosynthesis; 3. starch and sucrose metabolism; 4. stilbenoid, diarylheptanoid, and gingerol biosynthesis; 5. glycine, serine, and threonine metabolism; 6. glycerolipid metabolism; 7. cysteine and methionine metabolism; 8. glutathione metabolism; 9. pentose and glucuronate interconversions; 10. monoterpenoid biosynthesis; 11. glycolysis/gluconeogenesis; 12. plant hormone signal transduction; 13. MAPK signalling pathway–plant; 14. circadian rhythm–plant; 15. plant-pathogen interaction; 16. glycerophospholipid metabolism; 17. amino sugar and nucleotide sugar metabolism; 18. tyrosine metabolism; 19. phagosome; 20. endocytosis; 21. protein processing in endoplasmic reticulum; 22. galactose metabolism; 23. oxidative phosphorylation.

Figure 5.

Key DEGs involved in flavonoid and phenylpropane biosynthesis in grape after Na2SeO3 treatment under various nitrogen conditions. CYP73A: nodulation receptor kinase; CYP75A: flavonoid 3′,5′-hydroxylase; CYP75B1: flavonoid 3′-monooxygenase; CHS/ST: stilbene synthase; PGT1: UDP-glycosyltransferase; E2.3.1.133: stemmadenine O-acetyltransferase; E2.1.1.104: probable caffeoyl-CoA O-methyltransferase; DFR: dihydroflavonol 4-reductase; F3H: naringenin,2-oxoglutarate 3-dioxygenase; LAR: leucoanthocyanidin reductase; ANS: leucoanthocyanidin dioxygenase; E3.2.1.21: beta-glucosidase; E1.11.1.7: lignin-forming anionic peroxidase; CYP73A: trans-cinnamate 4-monooxygenase; CAD: probable mannitol dehydrogenase; UGT72E: anthocyanidin 3-O-glucosyltransferase; E2.3.1.133: stemmadenine O-acetyltransferase; 4CL: 4-coumarate-CoA ligase; bglX: xylan 1,4-beta-xylosidase. *FDR < 0.05, where red represents significant upregulation and green represents significant downregulation. PAL, phenylalanine ammonia lyase.
Key DEGs involved in flavonoid and phenylpropane biosynthesis in grape after Na2SeO3 treatment under various nitrogen conditions. CYP73A: nodulation receptor kinase; CYP75A: flavonoid 3′,5′-hydroxylase; CYP75B1: flavonoid 3′-monooxygenase; CHS/ST: stilbene synthase; PGT1: UDP-glycosyltransferase; E2.3.1.133: stemmadenine O-acetyltransferase; E2.1.1.104: probable caffeoyl-CoA O-methyltransferase; DFR: dihydroflavonol 4-reductase; F3H: naringenin,2-oxoglutarate 3-dioxygenase; LAR: leucoanthocyanidin reductase; ANS: leucoanthocyanidin dioxygenase; E3.2.1.21: beta-glucosidase; E1.11.1.7: lignin-forming anionic peroxidase; CYP73A: trans-cinnamate 4-monooxygenase; CAD: probable mannitol dehydrogenase; UGT72E: anthocyanidin 3-O-glucosyltransferase; E2.3.1.133: stemmadenine O-acetyltransferase; 4CL: 4-coumarate-CoA ligase; bglX: xylan 1,4-beta-xylosidase. *FDR < 0.05, where red represents significant upregulation and green represents significant downregulation. PAL, phenylalanine ammonia lyase.

Figure 6.

Key DEGs involved in plant hormone signal transduction in grape after Na2SeO3 treatment under various nitrogen conditions. ARR-A: two-component response regulator; CYCD3: cyclin-D3-1; SAUR: auxin-responsive protein; AUX1: auxin transporter-like protein; CH3: probable indole-3-acetic acid-amido synthetase; PR1: basic form of pathogenesis-related protein; IAA: auxin-induced protein; PYL: abscisic acid receptor; GID1: gibberellin receptor; NPR1: BTB/POZ domain and ankyrin repeat-containing protein; TCH4: probable xyloglucan endotransglucosylase/hydrolase protein; IRAK4: receptor-like cytosolic serine/threonine-protein kinase; AHP: histidine-containing phosphotransfer protein; JAZ: jasmonic acid protein; ETR: ethylene receptor; DELLA: DELLA protein GAI; E2.4.1.207: probable xyloglucan endotransglucosylase/hydrolase protein; TGA: transcription factor; PP2C: protein phosphatase 2C. *FDR < 0.05, where red represents significant upregulation and green represents significant downregulation.
Key DEGs involved in plant hormone signal transduction in grape after Na2SeO3 treatment under various nitrogen conditions. ARR-A: two-component response regulator; CYCD3: cyclin-D3-1; SAUR: auxin-responsive protein; AUX1: auxin transporter-like protein; CH3: probable indole-3-acetic acid-amido synthetase; PR1: basic form of pathogenesis-related protein; IAA: auxin-induced protein; PYL: abscisic acid receptor; GID1: gibberellin receptor; NPR1: BTB/POZ domain and ankyrin repeat-containing protein; TCH4: probable xyloglucan endotransglucosylase/hydrolase protein; IRAK4: receptor-like cytosolic serine/threonine-protein kinase; AHP: histidine-containing phosphotransfer protein; JAZ: jasmonic acid protein; ETR: ethylene receptor; DELLA: DELLA protein GAI; E2.4.1.207: probable xyloglucan endotransglucosylase/hydrolase protein; TGA: transcription factor; PP2C: protein phosphatase 2C. *FDR < 0.05, where red represents significant upregulation and green represents significant downregulation.

Figure 7.

Key DEGs involved in starch and sucrose metabolism in grape after Na2SeO3 treatment under various nitrogen conditions. E3.2.1.21: beta-glucosidase; WAXY: granule-bound starch synthase; TPS: alpha-trehalose-phosphate synthase; bglX: xylan 1,4-beta-xylosidase; E3.2.1.4: endoglucanase; E2.7.1.4: fructokinase; E2.4.1.13: sucrose synthase; GN4: glucan endo-1,3-beta-glucosidase; malZ: alpha-glucosidase; AMY: alpha-amylase; INV: beta-fructofuranosidase; HK: hexokinase. * FDR < 0.05, where red represents significant upregulation and green represents significant downregulation.
Key DEGs involved in starch and sucrose metabolism in grape after Na2SeO3 treatment under various nitrogen conditions. E3.2.1.21: beta-glucosidase; WAXY: granule-bound starch synthase; TPS: alpha-trehalose-phosphate synthase; bglX: xylan 1,4-beta-xylosidase; E3.2.1.4: endoglucanase; E2.7.1.4: fructokinase; E2.4.1.13: sucrose synthase; GN4: glucan endo-1,3-beta-glucosidase; malZ: alpha-glucosidase; AMY: alpha-amylase; INV: beta-fructofuranosidase; HK: hexokinase. * FDR < 0.05, where red represents significant upregulation and green represents significant downregulation.

Grape transcriptome sequencing quality data treated with Na2SeO3 and nitrogen_

Sample Raw reads Clean reads Clean bases Error rate (%) Q20 (%) Q30 (%) GC content (%)
Control-1 44342452 43068728 6392908153 0.0252 97.92 93.97 46.14
Control-2 51674990 50251708 7420078791 0.0255 97.81 93.73 46.66
Control-3 58656668 56709132 8314120252 0.0251 97.96 94.14 46.80
0.2Se + 15N-1 61956434 60368950 8886922304 0.0252 97.94 94.10 46.57
0.2Se + 15N-2 53393402 51882436 7638583022 0.0256 97.77 93.68 46.64
0.2Se + 15N-3 51910586 50527188 7411722373 0.0249 98.04 94.32 46.82
0.2Se-1 43739408 42003504 6241771742 0.0258 97.69 93.44 46.06
0.2Se-2 45886300 44202816 6568402293 0.0256 97.80 93.66 45.69
0.2Se-3 46115382 44372272 6564671570 0.0257 97.73 93.54 45.94

Differential expression results of phenylpropanoid biosynthesis_

Gene name Gene ID KO name 0.2Se + 15N versus Control 0.2Se versus Control 0.2Se versus 0.2se + 15N
Log2FC FDR Log2FC FDR Log2FC FDR
Phenylalanine ammonia lyase VIT_16s0039g01170 PAL 3.31 0.01280 –0.38 1.00000 –3.78 0.00447
Uncharacterised protein VIT_12s0055g00810 E1.11.1.7 –0.78 0.00031 –2.28 0.00000 –1.49 0.00000
Phenylalanine ammonia lyase VIT_16s0039g01100 PAL 2.40 0.03015 0.04 0.98827 –2.37 0.03448
Unnamed protein product VIT_06s0004g01430 E3.2.1.21 0.55 0.62314 3.13 0.00000 2.61 0.00000
Phenylalanine ammonia lyase VIT_16s0039g01120 PAL 2.05 0.13924 –2.61 1.00000 –4.62 0.00953
Peroxidase VIT_12s0055g00810 E1.11.1.7 –0.02 0.92531 –2.00 0.00000 –1.96 0.00000
Trans-cinnamate 4-monooxygenase VIT_06s0004g08150 CYP73A –1.24 0.00488 –0.13 0.51475 1.14 0.00104
Putative beta-glucosidase VIT_19s0014g04750 E3.2.1.21 –1.46 0.00000 –3.54 0.00000 –2.06 0.00005
Glycosyltransferase VIT_16s0022g01970 UGT72E –1.15 0.02177 –3.40 0.00000 –2.23 0.00028
Unnamed protein product VIT_13s0064g01750 E3.2.1.21 –0.89 0.10202 –1.99 0.00000 –1.08 0.00000
Probable cinnamyl alcohol dehydrogenase VIT_18s0001g14910 CAD 0.06 0.84734 –1.21 0.00000 –1.25 0.00000
Peroxidase VIT_13s0067g02360 E1.11.1.7 –2.14 0.00000 –4.01 0.00000 –1.85 0.00000
Peroxidase VIT_10s0116g01780 E1.11.1.7 –0.63 0.14670 –1.71 0.00000 –1.06 0.00000
Phenylalanine ammonia lyase VIT_16s0039g01300 PAL 1.34 0.16736 –1.43 0.36247 –2.75 0.01649
Phenylalanine ammonia lyase VIT_11s0016g01520 PAL 0.61 0.55273 –2.11 0.04852 –2.70 0.00120
Peroxidase VIT_16s0100g00090 E1.11.1.7 0.94 0.15751 –1.77 0.00308 –2.69 0.00000
Phenylalanine ammonia lyase VIT_16s0039g01110 PAL 1.78 0.11341 –1.22 0.54672 –2.99 0.01490
Unnamed protein product VIT_06s0004g01420 E3.2.1.21 –0.44 0.35440 0.82 0.12460 1.27 0.00000
Peroxidase VIT_08s0040g02200 E1.11.1.7 –1.02 0.08130 0.01 0.68626 1.06 0.04688
Peroxidase VIT_12s0055g00990 E1.11.1.7 2.58 0.10764 –2.51 1.00000 –5.02 0.00337
Cytochrome P450 CYP73A100 VIT_11s0065g00350 CYP73A 0.11 0.88529 –1.52 0.00240 –1.62 0.00002
Peroxidase VIT_16s0022g02470 E1.11.1.7 0.73 0.00275 –1.76 0.00000 –2.47 0.00000
Berberine bridge enzyme VIT_10s0003g05420 K22395 –0.63 0.26053 –2.19 0.00000 –1.54 0.00000
Peroxidase VIT_18s0072g00160 E1.11.1.7 –2.60 0.00004 –0.34 0.06431 2.28 0.00000
Peroxidase VIT_07s0191g00050 E1.11.1.7 0.01 0.98307 1.02 0.00000 1.03 0.00000
Peroxidase VIT_10s0003g00650 E1.11.1.7 –0.61 0.29475 –2.91 0.00001 –2.27 0.00104
Peroxidase VIT_12s0059g02420 E1.11.1.7 –0.69 0.05056 –1.93 0.00000 –1.22 0.00439
Unnamed protein product VIT_13s0064g01640 E3.2.1.21 –0.46 0.74547 1.16 0.15059 1.65 0.02022
Unnamed protein product VIT_11s0016g01640 PAL 2.70 0.12995 –1.38 1.00000 –4.04 0.03834
Unnamed protein product VIT_03s0038g01330 E2.3.1.133 1.20 0.00000 0.10 0.66635 –1.09 0.00000
4-coumarate – CoA ligase VIT_02s0109g00250 4CL 2.14 0.00939 0.06 0.97506 –2.07 0.01062
Uncharacterised protein VIT_06s0004g06110 bglX -0.90 0.37906 0.31 0.22344 1.23 0.00000
Peroxidase VIT_12s0055g01010 E1.11.1.7 1.89 0.32080 –2.98 1.00000 –4.86 0.02264
Probable mannitol dehydrogenase VIT_04s0044g00190 CAD 0.15 0.60019 –1.12 0.00000 –1.25 0.00000
Probable cinnamyl alcohol dehydrogenase VIT_03s0180g00250 CAD –3.13 0.00000 –6.10 0.00000 –2.98 0.01763

Assembly quality for transcript and unigene of grape_

Type Unigene Transcript
Total number 89,421 147,924
N50 length (bp) 1954 2268
BUSCO C: 73.5%[S: 70.2%; D: 3.3%] C: 89.7%[S: 64.2%; D: 25.5%]

Grape comparison and statistics of sequencing data and assembly results treated with Na2SeO3 and nitrogen_

Sample Clean reads Mapped reads Mapped ratio (%)
Control-1 43068728 38170787 88.63
Control-2 50251708 44199319 87.96
Control-3 56709132 50304056 88.71
0.2Se + 15N-1 60368950 53347721 88.74
0.2Se + 15N-2 51882436 45851321 88.27
0.2Se + 15N-3 50527188 44810011 88.34
0.2Se-1 42003504 37275528 88.37
0.2Se-2 44202816 39017275 88.38
0.2Se-3 44372272 39199620 88.68

Differential expression results of flavonoid biosynthesis_

Gene name Gene ID KO name 0.2Se + 15N versus Control 0.2Se versus Control 0.2Se versus 0.2se + 15N
Log2FC FDR Log2FC FDRt Log2FC FDRt
Trans-cinnamate 4-monooxygenase VIT_06s0004g08150 CYP73A –1.24 0.00489 –0.13 0.51476 1.14 0.00104
Chalcone synthase VIT_14s0068g00930 CHS –1.65 0.03460 –1.39 0.00004 1.28 0.01740
Dihydroflavonol reductase VIT_18s0001g12800 DFR –1.11 0.01526 0.36 0.02693 –1.49 0.00002
Stilbene synthase VIT_16s0100g01000 CHS 2.44 0.00540 –1.09 0.59531 3.67 0.00024
Stilbene synthase VIT_16s0100g00860 ST 2.15 0.00000 –0.54 0.45448 –0.27 0.10247
Flavanone 3-hydroxylase VIT_04s0023g03370 F3H –1.73 0.03047 –0.45 0.01205 1.29 0.06844
Glycosyltransferase VIT_18s0041g00830 PGT1 1.01 0.04337 0.90 0.09188 1.29 0.04528
Flavonoid-3′-hydroxylase VIT_17s0000g07200 CYP75B1 –1.20 0.03266 0.16 0.35881 1.38 0.00276
Unnamed protein product VIT_17s0000g04150 LAR –1.41 0.00198 0.11 0.55600 –1.54 0.00039
Stilbene synthase VIT_16s0100g01040 CHS 4.44 0.03436 1.01 1.00000 –3.39 0.06491
Anthocyanidin synthase VIT_02s0025g04720 ANS –1.57 0.01520 –0.41 0.01691 1.18 0.03871
Stilbene synthase VIT_16s0100g00930 CHS 1.88 0.00301 –0.61 0.60305 2.48 0.00000
Flavonoid 3′,5′-hydroxylase VIT_06s0009g02970 CYP75A –1.00 0.00000 –1.43 0.00000 1.41 0.00252
Flavonoid 3′,5′-hydroxylase VIT_06s0009g02880 CYP75A –1.22 0.00346 –1.98 0.00000 –2.73 0.38401
Anthocyanin acyltransferase VIT_03s0017g00870 E2.3.1.133 –3.60 0.00000 –4.76 0.00000 –1.14 0.12038
Stilbene synthase VIT_16s0100g00940 CHS 1.82 0.00030 –0.44 0.60887 –2.25 0.00001
Chalcone synthase isoform VIT_14s0068g00920 CHS –1.23 0.03394 –0.29 0.13223 0.96 0.038498
Unnamed protein product VIT_11s0016g02610 E2.1.1.104 –4.99 0.02208 –3.75 0.07667 1.26 1.00000
Stilbene synthase VIT_16s0100g01010 CHS 1.62 0.00326 –0.45 0.65109 –2.05 0.00075
Flavonoid 3′,5′-hydroxylase VIT_06s0009g02860 CYP75A –1.03 0.03085 –1.03 0.01032 0.02 0.94689
Flavonoid 3′-monooxygenase VIT_17s0000g07210 CYP75B1 –1.09 0.00124 0.33 0.28077 0.14 0.50203
UDP-glycosyltransferase VIT_18s0041g00800 PGT1 –5.41 0.00000 –7.00 0.00000 –1.62 1.00000
Hypothetical protein VIT_06s0009g02830 CYP75A –1.42 0.00052 –1.07 0.00000 –1.37 0.04739
UDP-glycosyltransferase VIT_18s0041g00930 PGT1 –3.30 0.03199 –0.35 0.58657 –1.09 0.00002
Unnamed protein product VIT_03s0038g01330 E2.3.1.133 1.20 0.0000 0.10 0.66635 7.94 0.00000
Stilbene synthase VIT_16s0100g00920 CHS 1.57 0.03144 –2.68 0.03760 0.92 0.07035
Stilbene synthase VIT_16s0100g00900 ST 1.68 0.02265 –1.04 0.37134 2.71 0.00043
Hypothetical protein VIT_16s0100g00950 ST 2.31 0.04592 –0.32 0.90820 –2.62 0.03463
Stilbene synthase VIT_16s0100g00840 CHS 1.58 0.00000 –1.22 0.07250 –1.78 0.00000
Chalcone synthase VIT_05s0136g00260 CHS –1.48 0.04403 0.26 0.11752 –1.92 0.05836

Differential expression results of starch and sucrose metabolism_

Gene name Gene ID KO name 0.2Se + 15N versus Control 0.2Se versus Control 0.2Se versus 0.2se + 15N
Log2FC FDR Log2FC FDR Log2FC FDR
Uncharacterised protein VIT_06s0009g00810 E3.2.1.21 –0.78 0.30589 –2.28 0.00000 –1.49 0.00000
Unnamed protein product VIT_06s0004g01430 E3.2.1.21 0.55 0.62314 3.13 0.00000 2.61 0.00000
Hypothetical protein VIT_06s0004g00720 GN4 0.23 0.32455 –0.98 0.09370 –1.20 0.00000
Starch synthase, chloroplastic/amyloplastic VIT_02s0025g02790 WAXY 0.98 0.08222 0.27 0.15132 1.28 0.00238
Alpha-trehalose-phosphate synthase VIT_10s0003g02160 TPS –0.06 0.78358 0.92 0.27515 1.00 0.00000
Endoglucanase VIT_07s0005g00740 E3.2.1.4 –1.19 0.00000 –2.27 0.00000 –1.06 0.00000
Alpha-glucosidase VIT_10s0092g00240 malZ 0.79 0.32308 –0.24 0.10826 –1.01 0.00000
Putative beta-glucosidase VIT_19s0014g04750 E3.2.1.21 –1.46 0.00000 –3.54 0.00000 –2.06 0.00006
Probable fructokinase-5 VIT_18s0089g01230 E2.7.1.4 –0.06 0.88916 –3.53 0.00000 –2.01 0.00000
Alpha-amylase VIT_18s0001g00560 AMY –0.82 0.73105 0.63 0.58606 1.48 0.00000
Beta-fructofuranosidase, soluble isoenzyme I isoform X1 VIT_16s0022g00670 INV –0.35 0.19816 –2.12 0.00000 –1.75 0.00000
Unnamed protein product VIT_13s0064g01750 E3.2.1.21 –0.89 0.41109 –1.99 0.00000 –1.07 0.00000
Putative alpha,alpha-trehalose-phosphate synthase VIT_01s0026g00280 TPS 1.37 0.00000 –0.43 0.00279 –1.07 0.00000
Phosphotransferase VIT_09s0002g03390 HK 0.97 0.48252 –2.70 0.23476 –3.66 0.027023
Sucrose synthase VIT_11s0016g00470 E2.4.1.13 –0.39 0.23845 –1.80 0.00000 –1.40 0.00000
Endoglucanase VIT_04s0008g02010 E3.2.1.4 1.03 0.08715 –0.14 0.88231 –1.15 0.04076
Sucrose synthase VIT_17s0053g00700 E2.4.1.13 0.20 0.36444 –1.60 0.00000 –1.78 0.00000
Probable fructokinase VIT_05s0102g00710 E2.7.1.4 –0.50 0.18347 –1.62 0.00000 –1.11 0.00000
Probable alpha,alpha-trehalose-phosphate synthase VIT_12s0028g01670 TPS –0.03 0.96391 –1.21 0.00261 –1.16 0.00280
Unnamed protein product VIT_06s0004g01420 E3.2.1.21 –0.48 0.35446 0.82 0.11907 1.27 0.00000
Sucrose synthase VIT_07s0005g00750 E2.4.1.13 0.68 0.06330 –0.34 0.15054 –1.00 0.00000
Unnamed protein product VIT_07s0005g06660 WAXY –1.61 0.57698 1.65 0.22606 3.25 0.03323
Probable alpha,alpha-trehalose-phosphate synthase VIT_17s0000g08010 TPS 3.15 0.00000 –0.11 0.88102 3.26 0.00000
Putative alpha,alpha-trehalose-phosphate synthase VIT_06s0009g01650 TPS 1.20 0.18780 –0.97 0.51346 –2.15 0.02419
Unnamed protein product VIT_13s0064g01640 E3.2.1.21 –0.46 0.74547 1.16 0.15059 1.65 0.02022
Uncharacterised protein VIT_06s0004g06110 bglX –0.90 0.37906 0.31 0.22344 1.23 0.00000
Probable fructokinase-7 isoform XI VIT_15s0048g01260 E2.7.1.4 0.77 0.29019 –0.75 0.06879 –1.50 0.00000
Sucrose synthase VIT_04s0079g00230 E2.4.1.13 0.24 0.33133 –1.83 0.00000 –2.05 0.00000

Experimental treatment reagent formula_

Solution Control/mL 0.1 mmol · L−1 Na2SeO3+ 15 mmol · L−1, NO3–, (0.1Se + 15N)/mL 0.2 mmol · L−1 Na2SeO3 + 15 mmol · L−1, NO3– (0.2Se + 15N)/mL 0.4 mmol · L−1 Na2SeO3 + 15 mmol · L−1, NO3–, (0.4Se + 15N)/mL 0.1 mmol · L−1 Na2SO3 (0.1Se)/mL 0.2 mmol · L−1 Na2SeO3 (0.2Se)/mL 0.4 mmol · L−1 Na2SeO3 (0.4Se)/mL
1.0 mol/L Ca(NO3)2 0 5 5 5 0 0 0
1.0 mol/L KNO3 0 5 5 5 0 0 0
0.5 mol/L K2SO4 5 0 0 0 5 5 5
1.0 mol/L CaCl2 5 0 0 0 5 5 5
1.0 mol/L MgSO4 2 2 2 2 2 2 2
1.0 mol/L KH2PO4 1 1 1 1 1 1 1
20.0 nimol/L FeSO4 1 1 1 1 1 1 1
20.0 nimol/L MnSO4 1 1 1 1 1 1 1
10.0 nimol/L ZnSO4 1 1 1 1 1 1 1
1.0 nimol/L Na2MoO4 1 1 1 1 1 1 1
0.1 mol/L H3BO3 1 1 1 1 1 1 1
0.01 mol/L CuSO4 1 1 1 1 1 1 1
0.01 mol/L Na2SeO3 0 10 20 30 10 20 30
Deionised water 981 971 961 951 971 961 951

Differential expression results of plant hormone signal transduction_

Gene name Gene ID KO name 0.2Se + 15N versus Control 0.2Se versus Control 0.2Se versus 0.2se + 15N
Log2FC FDR Log2FC Log2FC FDR Log2FC
Two-component response regulator VIT_13s0067g03510 ARR-A –0.18 0.83317 2.04 0.00000 2.24 0.00000
Cyclin-D3-1 VIT_18s0001g09920 CYCD3 –0.05 0.89851 –2.63 0.00000 –2.56 0.00000
Unnamed protein product VIT_07s0129g01100 CYCD3 –0.79 0.00000 –1.32 0.00000 –0.51 0.25060
Gibberellin receptor GID1B VIT_07s0104g00930 GID1 –0.48 0.06023 1.42 0.00000 1.92 0.00000
Regulatory protein NPR5 VIT_08s0007g05740 NPR1 –0.86 0.34463 –2.23 0.00791 –1.35 0.23369
Auxin-responsive protein SAUR71 VIT_01s0146g00180 SAUR 1.37 0.00002 1.14 0.00003 –0.22 0.54304
Unnamed protein product VIT_03s0038g02140 AUX1 –0.53 0.07953 –2.14 0.00000 –1.59 0.00000
Basic form of pathogenesis-related protein VIT_03s0088g00780 PR1 1.42 0.00000 1.18 0.00099 –0.22 0.29702
Auxin transporter VIT_13s0067g00330 AUX1 –1.64 0.00000 –1.76 0.00000 –0.11 0.69752
Indole-3-acetic acid-amido synthetase VIT_19s0014g04690 GH3 –0.65 0.17485 –1.06 0.02835 –0.40 0.52344
Xyloglucan endotransglucosylase/hydrolase VIT_11s0052g01200 TCH4 –1.45 0.00058 –2.11 0.00000 –0.64 0.22629
Hypothetical protein DKX38 VIT_03s0088g00910 IRAK4 1.03 0.00000 1.32 0.00000 0.31 0.16875
Auxin-induced protein 6B VIT_03s0038g00940 SAUR –0.91 0.15417 –1.17 0.04523 –0.25 0.78689
Histidine-containing phosphotransfer protein VIT_04s0008g00210 AHP 6.05 0.00000 3.12 0.01971 –2.92 0.00000
Auxin transporter VIT_18s0001g03540 AUX1 –1.34 0.00000 –1.04 0.00000 0.31 0.07698
Auxin-responsive protein SAUR36 VIT_15s0048g00530 SAUR –0.34 0.12180 1.35 0.00000 1.71 0.00000
Cyclin-D3-1 VIT_03s0180g00040 CYCD3 –2.26 0.00000 –2.19 0.00000 0.08 0.87093
Basic form of pathogenesis-related protein VIT_03s0097g00700 PR1 –0.27 0.93243 –2.22 0.00000 –1.94 0.28237
Pathogenesis-related protein VIT_03s0088g00810 PR1 0.82 0.00000 1.21 0.00000 0.41 0.02667
Two-component response regulator ORR9 isoform X1 VIT_13s0067g03490 ARR-A 0.51 0.00025 1.05 0.00000 0.56 0.05015
Basic form of pathogenesis-related protein VIT_03s0088g00710 PR1 0.47 0.84569 2.85 0.00775 2.40 0.00982
Auxin-responsive protein IAA9 isoform X1 VIT_11s0016g05640 IAA 0.52 0.41001 1.93 0.00000 1.43 0.000000
Jasmonate-zim-domain protein VIT_01s0146g00480 JAZ –0.38 0.37895 –1.53 0.00028 –1.13 0.00697
Ethylene receptor VIT_05s0049g00090 ETR –0.02 0.96813 –1.35 0.00000 –1.32 0.00000
DELLA protein SLR1 VIT_11s0016g04630 DELLA –0.49 0.00519 –1.16 0.00000 –0.65 0.00003
Xyloglucan endotransglucosylase/hydrolase VIT_11s0052g01270 E2.4.1.207 –0.87 0.26567 –2.51 0.00023 1.62 0.08526
Transcription factor TGA9 VIT_06s0080g00360 TGA –0.05 0.94243 1.17 0.00036 1.24 0.00002
Two-component response regulator ORR9 VIT_13s0067g03430 ARR-A 0.53 0.76430 1.96 0.00000 1.45 0.00000
Two-component response regulator ARR6 VIT_01s0026g00940 ARR-A –0.07 0.86455 1.46 0.00000 1.55 0.00000
Auxin-responsive protein SAUR32 VIT_15s0048g02860 SAUR 0.59 0.32414 1.03 0.00000 0.46 0.11100
Auxin-responsive protein SAUR50 VIT_04s0023g03230 SAUR 0.14 0.87585 1.25 0.00574 1.13 0.00406
Auxin-responsive protein VIT_07s0141g00270 IAA 0.03 0.93143 1.42 0.00000 1.41 0.00000
Auxin-responsive protein SAUR36 VIT_02s0154g00010 SAUR 0.38 0.32725 1.02 0.00028 0.65 0.20123
Unnamed protein product VIT_02s0012g01270 PYL 0.58 0.24239 –1.04 0.00037 –1.61 0.00000
Auxin-induced protein 6B VIT_03s0038g00930 SAUR –2.16 0.00509 –3.62 0.00014 –1.45 0.34481
Abscisic acid receptor PYL4 VIT_13s0067g01940 PYL 0.89 0.01109 –1.46 0.00418 –2.34 0.00000
Probable indole-3-acetic acid-amido synthetase VIT_07s0129g00660 GH3 –0.13 1.00000 4.03 0.04928 4.18 0.03700
Auxin-induced protein VIT_08s0007g03120 SAUR –0.82 0.54502 –2.97 0.04849 –2.14 0.23987
Unnamed protein product VIT_06s0004g05460 PP2C –0.16 0.88910 1.24 0.00000 1.42 0.00771
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