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

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

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.

Table 2.

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

1 Clean reads: The total number of entries in the sequencing data after quality control; Clean bases: Total amount of sequencing data after quality control; Error rate (%): The average error rate of sequencing bases corresponding to quality control data; Q20 and Q30 (%): respectively refer to the percentage of bases with sequencing quality above 99% and 99.9% in total bases; GC content (%): The percentage of the total number of G and C bases corresponding to the quality control data to the total number of bases.

Table 3.

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%]

1 Total number, the number of sequence entries of the assembled unigene/transcript. N50 length, sort the assembled unigene/transcript in descending order of length, and accumulate the length of the transcript to half of the total length, corresponding to the length of the transcript. BUSCO, using BUSCO to evaluate assembly integrity score, the higher the score, the better the complete (C). Complete (C) represents the proportion of sequences that reach the desired length in the assembled sequence compared to the total BUSCO sequence, consisting of two parts. S represents a sequence that can align with one gene in the database, and D represents a sequence that can align with multiple genes in the database.

Table 4.

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

1 Clean reads: the number of filtered sequencing data entries; mapped reads: the number of clean reads that can be compared to the assembled transcript; mapped ratio: the percentage of clean reads that can be located on the assembled transcript.

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.

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 (P_adjust < 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.

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 (P_adjust < 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.

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.

Table 5.

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
Gene name	Gene ID	KO name	Log₂FC	FDR	Log₂FC	FDR_t	Log₂FC	FDR_t
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

1 Control group is Control; 0.2 mmol · L⁻¹ + 15 mmol · L⁻¹ N is 0.2Se + 15 N; 0.2 mmol · L⁻¹ Na₂SeO₃ is 0.2Se. FDR < 0.05000 indicates significant differences.

1 FC, fold change.

Table 6.

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
Gene name	Gene ID	KO name	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

1 Control group is Control; 0.2 mmol · L⁻¹ + 15 mmol · L⁻¹ N is 0.2Se + 15 N; 0.2 mmol · L⁻¹ Na₂SeO₃ is 0.2Se. FDR < 0.05000 indicates significant differences.

1 FC, fold change; PAL, phenylalanine ammonia lyase.

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.

Table 7.

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
Gene name	Gene ID	KO name	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

1 Control group is Control; 0.2 mmol · L⁻¹ + 15 mmol · L⁻¹ N is 0.2Se + 15 N; 0.2 mmol · L⁻¹ Na₂SeO₃ is 0.2Se. FDR < 0.05000 indicates significant differences.

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.

Table 8.

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
Gene name	Gene ID	KO name	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

1 Control group is Control; 0.2 mmol · L⁻¹ + 15 mmol · L⁻¹ N is 0.2Se + 15 N; 0.2 mmol · L⁻¹ Na₂SeO₃ is 0.2Se. FDR < 0.05000 indicates significant differences.

1 FC, fold change.

References

Authors

Metrics

Articles in this issue

DOI: https://doi.org/10.2478/fhort-2024-0037 | Journal eISSN: 2083-5965 | Journal ISSN: 0867-1761

Journal RSS Feed

Language: English

Page range: 559 - 580

Submitted on: Jun 27, 2024

Accepted on: Jan 24, 2025

Published on: Feb 27, 2025

Published by: Polish Society for Horticultural Sciences (PSHS)

In partnership with: Paradigm Publishing Services

Publication frequency: 2 issues per year

Keywords:

grape,

Na₂SeO₃,

nitrogen,

physiological parameters,

transcriptome

Related subjects:

Life sciences,

Plant science

© 2025 Yongfu Zhang, Liling Mo, Xiaoqin Li, Kai Wang, Zuqin Qiao, Zhao Liu, published by Polish Society for Horticultural Sciences (PSHS)
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Volume 36 (2024): Issue 4 (December 2024)

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

Figures & Tables

Table 1.

Figure 1.

Table 2.

Table 3.

Table 4.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Table 5.

Table 6.

Figure 6.

Table 7.

Figure 7.

Table 8.

Paradigm

My account