DNA甲基化参与调控马铃薯响应干旱胁迫的关键基因挖掘

doi:10.3724/SP.J.1006.2021.04152

Abstract

Abstract:

When plants are subjected to water stress, they will make a rapid response to drought stress through DNA methylation. In order to study how DNA methylation affects the transcriptional expression of genes under drought stress in potato, comparative transcriptomic analysis was carried out on two potato varieties with different drought resistances, which were planted under mannitol simulated drought and 5-azadC treatments. The differentially expressed genes (DEGs) were identified by Fold-change > 2 and corrected P < 0.01. Then DEGs were subjected to GO enrichment analysis. The results showed that these DEGs were enriched in the oxidative stress and carbohydrate metabolism, suggesting these GO term-related genes were also regulated by DNA demethylation, responded to drought stress in different drought-tolerant potatoes. The common 1345 DEGs both responding to drought stress and DNA demethylation were functionally enriched by KEGG pathway. The results showed that plant MAPK signal pathway, plant hormone signal transduction pathway, plant glutathione metabolism pathway, glycolysis and glutathione metabolism pathway and inositol phosphate metabolism pathway were related to plant drought resistance. It was suggested that the sensitivity of these pathway-related genes responding to drought stress were regulated by DNA methylation in Atlantic and Qingshu 9. The cis-acting elements and methylated CpG islands were analyzed in the 1500 bp promoter region of DEGs. The results showed that the methylation level of ABRE and CAAT-box acting elements in the promoter region of GST gene involved in plant glutathione metabolism were reduced through DNA demethylation under drought stress. Then the expression was activated in response to drought stress. Therefore, DEGs under drought and DNA demethylation treatments could be analyzed using comparative transcriptomic, and then the genes related to DNA methylation involved in regulating drought stress response in potato could be found. These results provide a new idea for further studying the epigenetic mechanism of drought stress response in potato.

Key words: potato, drought stress, DNA methylation, transcriptome, glutathione S transferase

LI Peng-Cheng, BI Zhen-Zhen, SUN Chao, QIN Tian-Yuan, LIANG Wen-Jun, WANG Yi-Hao, XU De-Rong, LIU Yu-Hui, ZHANG Jun-Lian, BAI Jiang-Ping. Key genes mining of DNA methylation involved in regulating drought stress response in potato[J].Acta Agronomica Sinica, 2021, 47(4): 599-612.

Figures/Tables 17

Table 1

Table 2

Table 3

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Table 4

Functional annotation of drought-related co-enrichment KEGG pathway genes"

KEGG通路ID KEGG ID	基因ID Gene ID	对应拟南芥基因ID Gene in A. thaliana	基因功能 Gene function
KO04016	PGSC0003DMG400000193	AT3G61510	1-氨基环丙烷-1-羧酸合酶2 1-aminocyclopropane-1-carboxylate synthase 2
KO04016	PGSC0003DMG400006639	AT3G25250	类丝氨酸/苏氨酸蛋白激酶 OXI1 serine/threonine-protein kinase OXI1-like
KO04016	PGSC0003DMG400001333	AT5G39670	Ca²⁺结合蛋白 Ca²⁺ binding protein
KO04016	PGSC0003DMG400001529	AT3G12500	酸性27-kD内切酶 Acidic 27-kD endochitinase
KO04016	PGSC0003DMG400005108	AT3G19690	致病相关蛋白1 pathogenesis-related protein 1-like
KO04016	PGSC0003DMG400005112	AT4G33720	碱性PR-1蛋白 Basic PR-1 protein
KO04016	PGSC0003DMG400005116	AT2G14580	PR1蛋白 PR1 protein
KO04016	PGSC0003DMG400017231	AT3G23240	转录因子TSRF1 Transcription factor TSRF1
KO04016	PGSC0003DMG400001204	AT5G49480	Ca²⁺结合蛋白1 Ca²⁺-binding protein 1
KO04016	PGSC0003DMG400005110	AT3G19690	PR1蛋白 PR1 protein
KO04016	PGSC0003DMG400023921	AT2G14610	细胞质小热休克蛋白I类 Cytoplasmic small heat shock protein class I
KO00480	PGSC0003DMG400031091	AT1G17180	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400024232	AT1G23820	亚精胺合成酶1 Spermidine synthase 1
KO00480	PGSC0003DMG400011012	AT2G29490	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400016722	AT3G03190	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400004977	AT5G41210	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400002169	AT3G09270	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400002176	AT3G09270	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400020253	AT3G27060	核糖核苷二磷酸还原酶小链 Ribonucleoside-diphosphate reductase small chain
KO00010	PGSC0003DMG400009472	AT1G22170	磷酸甘油酸变位酶 Phosphoglycerate mutase
KO00010	PGSC0003DMG400006270	AT4G33070	丙酮酸脱羧酶 Pyruvate decarboxylase
KO00010	PGSC0003DMG400030038	AT1G09870	多肌醇多磷酸磷酸酶1 Multiple inositol polyphosphate phosphatase 1
KO00010	PGSC0003DMG400030624	AT4G37840	己糖激酶 Hexokinase
KO00010	PGSC0003DMG400018084	AT3G47800	醛糖-1-表异构酶 Aldose-1-epimerase
KO00010	PGSC0003DMG403001316	AT5G15140	非细胞自主蛋白途径2 Non-cell-autonomous protein pathway 2
KO00010	PGSC0003DMG400012308	AT5G57330	醛糖1-表异构酶 Aldose 1-epimerase
KEGG通路ID KEGG ID	基因ID Gene ID	对应拟南芥基因ID Gene in A. thaliana	基因功能 Gene function
KO00010	PGSC0003DMG400004800	AT4G17260	L-乳酸脱氢酶B L-lactate dehydrogenase B
KO00562	PGSC0003DMG400022715	AT2G26870	磷酸酯酶家族蛋白 Phosphoesterase family protein
KO00562	PGSC0003DMG401000287	AT4G26260	肌醇加氧酶 Myo-inositol oxygenase
KO00562	PGSC0003DMG400004872	AT1G14520	肌醇加氧酶 Myo-inositol oxygenase
KO00562	PGSC0003DMG400030038	AT1G09870	多肌醇多磷酸磷酸酶1 Multiple inositol polyphosphate phosphatase 1
KO00562	PGSC0003DMG401023603	AT3G02870	肌醇单磷酸酶1 Inositol monophosphatase 1
KO04075	PGSC0003DMG400019274	AT5G54510	吲哚-3-乙酸酰胺合成酶GH3.6 Indole-3-acetic acid-amido synthetase GH3.6
KO04075	PGSC0003DMG400005108	AT3G19690	致病相关蛋白1 pathogenesis-related protein 1-like
KO04075	PGSC0003DMG400005112	AT4G33720	碱性PR-1蛋白 Basic PR-1 protein
KO04075	PGSC0003DMG400021210	AT5G45110	NIM1 1
KO04075	PGSC0003DMG400020139	AT5G43700	生长素诱导蛋白22B Auxin-induced protein 22B
KO04075	PGSC0003DMG400005116	AT2G14580	PR1蛋白 PR1 protein
KO04075	PGSC0003DMG400017231	AT3G23240	转录因子TSRF1 Transcription factor TSRF1
KO04075	PGSC0003DMG400005110	AT3G19690	PR1蛋白 PR1 protein
KO04075	PGSC0003DMG400021676	AT4G03400	吲哚-3-乙酸酰胺合成酶GH3.5 Indole-3-acetic acid-amido synthetase GH3.5
KO04075	PGSC0003DMG400025856	AT2G14960	生长素和乙烯响应性GH3 Auxin and ethylene responsive GH3
KO04075	PGSC0003DMG400023921	AT2G14610	细胞质小热休克蛋白I类 Cytoplasmic small heat shock protein class I
KO04075	PGSC0003DMG400026261	AT5G47220	ATERF-2/ATERF2/ERF2
KO04075	PGSC0003DMG400024978	AT2G14960	吲哚-3-乙酸酰胺合成酶GH3.3 Indole-3-acetic acid-amido synthetase GH3.3
KO04075	PGSC0003DMG400013765	AT4G32280	ATP结合蛋白 ATP binding protein

Table 4

Table 4

Functional annotation of drought-related co-enrichment KEGG pathway genes"

KEGG通路ID KEGG ID	基因ID Gene ID	对应拟南芥基因ID Gene in A. thaliana	基因功能 Gene function
KO04016	PGSC0003DMG400000193	AT3G61510	1-氨基环丙烷-1-羧酸合酶2 1-aminocyclopropane-1-carboxylate synthase 2
KO04016	PGSC0003DMG400006639	AT3G25250	类丝氨酸/苏氨酸蛋白激酶 OXI1 serine/threonine-protein kinase OXI1-like
KO04016	PGSC0003DMG400001333	AT5G39670	Ca²⁺结合蛋白 Ca²⁺ binding protein
KO04016	PGSC0003DMG400001529	AT3G12500	酸性27-kD内切酶 Acidic 27-kD endochitinase
KO04016	PGSC0003DMG400005108	AT3G19690	致病相关蛋白1 pathogenesis-related protein 1-like
KO04016	PGSC0003DMG400005112	AT4G33720	碱性PR-1蛋白 Basic PR-1 protein
KO04016	PGSC0003DMG400005116	AT2G14580	PR1蛋白 PR1 protein
KO04016	PGSC0003DMG400017231	AT3G23240	转录因子TSRF1 Transcription factor TSRF1
KO04016	PGSC0003DMG400001204	AT5G49480	Ca²⁺结合蛋白1 Ca²⁺-binding protein 1
KO04016	PGSC0003DMG400005110	AT3G19690	PR1蛋白 PR1 protein
KO04016	PGSC0003DMG400023921	AT2G14610	细胞质小热休克蛋白I类 Cytoplasmic small heat shock protein class I
KO00480	PGSC0003DMG400031091	AT1G17180	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400024232	AT1G23820	亚精胺合成酶1 Spermidine synthase 1
KO00480	PGSC0003DMG400011012	AT2G29490	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400016722	AT3G03190	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400004977	AT5G41210	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400002169	AT3G09270	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400002176	AT3G09270	谷胱甘肽S转移酶 Glutathione S-transferase
KO00480	PGSC0003DMG400020253	AT3G27060	核糖核苷二磷酸还原酶小链 Ribonucleoside-diphosphate reductase small chain
KO00010	PGSC0003DMG400009472	AT1G22170	磷酸甘油酸变位酶 Phosphoglycerate mutase
KO00010	PGSC0003DMG400006270	AT4G33070	丙酮酸脱羧酶 Pyruvate decarboxylase
KO00010	PGSC0003DMG400030038	AT1G09870	多肌醇多磷酸磷酸酶1 Multiple inositol polyphosphate phosphatase 1
KO00010	PGSC0003DMG400030624	AT4G37840	己糖激酶 Hexokinase
KO00010	PGSC0003DMG400018084	AT3G47800	醛糖-1-表异构酶 Aldose-1-epimerase
KO00010	PGSC0003DMG403001316	AT5G15140	非细胞自主蛋白途径2 Non-cell-autonomous protein pathway 2
KO00010	PGSC0003DMG400012308	AT5G57330	醛糖1-表异构酶 Aldose 1-epimerase
KEGG通路ID KEGG ID	基因ID Gene ID	对应拟南芥基因ID Gene in A. thaliana	基因功能 Gene function
KO00010	PGSC0003DMG400004800	AT4G17260	L-乳酸脱氢酶B L-lactate dehydrogenase B
KO00562	PGSC0003DMG400022715	AT2G26870	磷酸酯酶家族蛋白 Phosphoesterase family protein
KO00562	PGSC0003DMG401000287	AT4G26260	肌醇加氧酶 Myo-inositol oxygenase
KO00562	PGSC0003DMG400004872	AT1G14520	肌醇加氧酶 Myo-inositol oxygenase
KO00562	PGSC0003DMG400030038	AT1G09870	多肌醇多磷酸磷酸酶1 Multiple inositol polyphosphate phosphatase 1
KO00562	PGSC0003DMG401023603	AT3G02870	肌醇单磷酸酶1 Inositol monophosphatase 1
KO04075	PGSC0003DMG400019274	AT5G54510	吲哚-3-乙酸酰胺合成酶GH3.6 Indole-3-acetic acid-amido synthetase GH3.6
KO04075	PGSC0003DMG400005108	AT3G19690	致病相关蛋白1 pathogenesis-related protein 1-like
KO04075	PGSC0003DMG400005112	AT4G33720	碱性PR-1蛋白 Basic PR-1 protein
KO04075	PGSC0003DMG400021210	AT5G45110	NIM1 1
KO04075	PGSC0003DMG400020139	AT5G43700	生长素诱导蛋白22B Auxin-induced protein 22B
KO04075	PGSC0003DMG400005116	AT2G14580	PR1蛋白 PR1 protein
KO04075	PGSC0003DMG400017231	AT3G23240	转录因子TSRF1 Transcription factor TSRF1
KO04075	PGSC0003DMG400005110	AT3G19690	PR1蛋白 PR1 protein
KO04075	PGSC0003DMG400021676	AT4G03400	吲哚-3-乙酸酰胺合成酶GH3.5 Indole-3-acetic acid-amido synthetase GH3.5
KO04075	PGSC0003DMG400025856	AT2G14960	生长素和乙烯响应性GH3 Auxin and ethylene responsive GH3
KO04075	PGSC0003DMG400023921	AT2G14610	细胞质小热休克蛋白I类 Cytoplasmic small heat shock protein class I
KO04075	PGSC0003DMG400026261	AT5G47220	ATERF-2/ATERF2/ERF2
KO04075	PGSC0003DMG400024978	AT2G14960	吲哚-3-乙酸酰胺合成酶GH3.3 Indole-3-acetic acid-amido synthetase GH3.3
KO04075	PGSC0003DMG400013765	AT4G32280	ATP结合蛋白 ATP binding protein

Table 4

Fig. 5

Fig. 6

Fig. 7

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基因 Gene	正向引物 Forward primer (5'-3')	反向引物 Reverse primer (5'-3')
Actin	AGGAGCATCCTGTCCTCCTAA	CACCATCACCAGAGTCCAACA
PGSC0003DMG400001333	CTCAATTGCACCTACTAAGCAC	GTGATATTCTTGCATGCAGAGG
PGSC0003DMG400005108	GTTGTGTTCTTGGTTTTAGGCT	GTGGCATATTCATGGGCATAAG
PGSC0003DMG400005112	TCGAATTCTTGTCAACCTGGTA	CCTGGTGGATCATAATTGCAAG
PGSC0003DMG400005116	CACAATGAAGCTCGTAGACAAG	CACATACTCTACCTGCTTGACA
PGSC0003DMG400017231	CACGAATTCCAAGAAAAGCAGT	CCCCAAATCTTCAAACACAACT
PGSC0003DMG400023921	CAACAAATGTGCTAGTGGGAAA	TGTTTCCTGAAGGAGCATAGTT
PGSC0003DMG400002176	GCAGTCAAGTCAAGAAATATCTACC	TGAACACGTACAAGTAAGTGGA
PGSC0003DMG400004977	GATTGATGATGTGAAGAGTGCC	TGTCATAATGAAGGCCTTGAGT
PGSC0003DMG400011012	AATTTTTGTGTGTGGAGGGATG	TATTCATTTGAGAGTAGCCGCA
PGSC0003DMG400016722	AACTAACAGGAACCACACTG	GTTGTGTCCCATTTTAGGGA
PGSC0003DMG400020253	GCTGGAAGGTTCATGAAAGATG	GGAATGGATATTCTCAATGGCG
PGSC0003DMG400024232	GAGCAGGATTTAGCCGTTTTAG	AGGTGCAATTACTCCGTAGAAA
PGSC0003DMG400006270	ATGCAATTGCTGGTGCTTATAG	AGCCTGATAGCAAGTAACAGTT
PGSC0003DMG400030038	ATGAAGTTTAGGGGTGACTCAG	TACACAAACTTCCCGTATGTGA
PGSC0003DMG400030624	TGCTGAAAGTTCATATCCTGGT	GAAGTGTCTTGATGCATAGCAG
PGSC0003DMG403001316	GATGCTGTGAATCACCCAAATT	GATGGTGAACGTATACAACACG
PGSC0003DMG401000287	CTTCATTTGACTGGCCTCATTC	TCATCAAAAGCACAACCAAGAG
PGSC0003DMG401023603	TTAACTGATGAACCGACTTGGA	CAATTGTGAGACCAATCGAGAC
PGSC0003DMG400013765	TAAGTGCCAGAAGATTGGTCAT	TACATCTCTTGCTCCTCAATCG
PGSC0003DMG400019274	CTGGGCTTTATAGGTATCGTGT	ATATGAAGTTGAATTGAGGCGC
PGSC0003DMG400020139	AGCAACAAAAGACCTTCATCAC	CATGCTCACTTTAACGTAGCTC
PGSC0003DMG400026261	GGATTTGAATTCGAGACGTCTG	TCGTTGTAGAAATCATCGCAAC

样品ID Sample ID	总reads数 Total reads	总碱基数 Total bases (G)	GC含量 GC content (%)	Q20 (%)	Q30 (%)	比对率 Mapped reads (%)
AtC_0h	132,318,050	19.85	44.33	99.93	96.45	82.13
AtA_2h	149,098,932	22.36	44.33	99.95	96.58	89.28
AtA_6h	157,099,124	23.56	44.50	99.94	96.40	84.40
AtA_12h	137,418,600	20.61	44.67	99.94	96.42	91.26
AtA_24h	146,797,368	22.02	45.67	99.95	96.59	91.93
AtM_2h	137,686,150	20.65	46.83	99.95	96.76	94.64
AtM_6h	147,166,226	22.07	45.67	99.91	96.45	79.18
AtM_12h	132,018,290	19.80	44.17	99.91	96.20	78.02
AtM_24h	143,830,794	21.57	44.83	99.94	96.43	87.10
QsC_0h	137,904,066	20.69	44.67	99.90	96.41	82.46
QsA_2h	133,480,780	20.02	45.67	99.93	96.68	92.56
QsA_6h	143,833,564	21.58	45.00	99.94	96.47	92.32
QsA_12h	150,781,586	22.62	44.67	99.93	96.41	84.35
QsA_24h	134,038,164	20.11	44.17	99.92	96.42	75.56
QsM_2h	145,819,266	21.87	44.83	99.92	96.43	81.50
QsM_6h	136,496,172	20.47	44.33	99.92	96.30	89.37
QsM_12h	130,599,502	19.59	44.50	99.93	96.40	85.07
QsM_24h	150,207,156	22.53	44.33	99.94	96.42	90.72

处理 Treatment	比较组合 Comparison	差异基因数 Number of DEGs	上调差异基因数 Up-regulated DEGs	下调差异基因数 Down-regulated DEGs
对照Control	A vs. Q_0h	1030	515	515
干旱Drought	A vs. Q_2h	568	384	184
	A vs. Q_6h	994	560	434
	A vs. Q_12h	519	321	198
	A vs. Q_24h	1251	471	780
DNA去甲基化 Demethylation	A vs. Q_2h	1603	1033	570
	A vs. Q_6h	1142	501	641
	A vs. Q_12h	1153	576	577
	A vs. Q_24h	981	465	516

Key genes mining of DNA methylation involved in regulating drought stress response in potato

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