Transcriptome profiling and phytohormone responses of Arabidopsis roots to different ambient temperatures

Figures & data

Figure 1. Volcano plot. The number of differentially expressed genes of wide-type roots at 17°C vs 22°C(A) and 22°C vs 27°C (B). Red means up-regulated genes, green means down-regulated genes, and blue means no significant genes.

Table 1. GO and KEGG classification of low temperature-regulated transcripts.

	Category	Up-regulated transcripts			Down-regulated transcripts
		ID	Description	p value	ID	Description	p value
GO	Biological process	GO:0005976	Polysaccharide metabolic process	5.57E−15	GO:0009751	Response to salicylic acid	1.90E−06
		GO:0044042	Glucan metabolic process	1.39E−11	GO:0009753	Response to jasmonic acid	4.29E−06
		GO:0010411	Xyloglucan metabolic process	1.25E−10	GO:0071215	Cellular response to abscisic acid stimulus	1.09E−06
		GO:0006096	Glycolytic process	8.14E−09	GO:0009738	Abscisic acid-activated signaling pathway	1.64E−05
		GO:0051186	Cofactor metabolic process	2.79E−09	GO:0009620	Response to fungus	2.21E−07
		GO:0006757	ATP generation from ADP	8.14E−09	GO:0050832	Defense response to fungus	0.0000558
		GO:1903825	Organic acid transmembrane transport	1.98E−05	GO:0009617	Response to bacterium	0.000171
		GO:1905039	Carboxylic acid transmembrane transport	1.98E−05	GO:0009648	Photoperiodism	0.0000639
		GO:0098656	Anion transmembrane transport	4.07E−05	GO:0048573	Photoperiodism, flowering	0.0000198
		GO:0071555	Cell wall organization	3.10E−28	GO:0009408	Response to heat	2.08E−05
		GO:0071669	Plant-type cell wall organization or biogenesis	5.42E−13	GO:0008037	Cell recognition	4.86E−05
		GO:0010383	Cell wall polysaccharide metabolic process	4.80E−09	GO:0071229	Cellular response to acid chemical	4.34E−09
	Molecular function	GO:0016758	Transferase activity	1.57E−10	GO:0004620	Phospholipase activity	3.03E−07
		GO:0004553	Hydrolase activity	2.48E−08	GO:0004722	Protein serine/threonine phosphatase activity	3.30E−05
		GO:0016705	Oxidoreductase activity	2.63E−06	GO:0004871	Signal transducer activity	5.78E−06
		GO:0016829	Lyase activity	5.43E−06	GO:0004872	Receptor activity	3.92E−05
		GO:0008509	Anion transmembrane transporter activity	2.33E−05	GO:0060089	Molecular transducer activity	3.92E−05
		GO:0005342	Organic acid transmembrane transporter activity	1.92E−05	GO:0043531	ADP binding	0.0002
		GO:0046943	Carboxylic acid transmembrane transporter activity	1.92E−05	GO:0005347	ATP transmembrane transporter activity	0.000253
KEGG	Pathway	ath0120	Carbon metabolism	3.44E−10	ath04144	Endocytosis	4.07E−07
		ath00010	Glycolysis/Gluconeogenesis	5.82E−09	ath04626	Plant-pathogen interaction	2.74E−05
		ath01230	Biosynthesis of amino acids	1.84E−06	ath04016	MAPK signaling pathway	0.0004386

Table 2. GO and KEGG classification of high temperature-regulated transcripts.

	Category	Up-regulated transcripts			Down-regulated transcripts
		ID	Description	p value	ID	Description	p value
GO	Biological process	GO:0019758	Glycosinolate biosynthetic process	1.67E−07	GO:0048511	Rhythmic process	1.42E−08
		GO:0019761	Glucosinolate biosynthetic process	1.67E−07	GO:0042787	Protein ubiquitination	8.80E−08
		GO:1901659	Glycosyl compound biosynthetic process	8.49E−05	GO:0010498	Proteasomal protein catabolic process	2.29E−07
		GO:0019748	Secondary metabolic process	9.60E−05	GO:000762	Circadian rhythm	5.40E−07
		GO:0006820	Anion transport	9.77E−06	GO:0016054	Organic acid catabolic process	6.93E−07
		GO:0015849	Organic acid transport	1.69E−05	GO:0046395	Carboxylic acid catabolic process	6.93E−07
		GO:0046942	Carboxylic acid transport	1.69E−05	GO:0006914	Autophagy	2.86E−06
		GO:0006091	Generation of precursor metabolites and energy	1.39E−06	GO:1901565	Organonitrogen compound catabolic process	1.18E−06
		GO:0009851	Auxin biosynthetic process	0.0002684	GO:0090693	Plant organ senescence	4.26E−06
		GO:0009734	Auxin-activated signaling pathway	0.000454	GO:0006979	Response to oxidative stress	4.97E−06
		GO:0015743	Malate transport	0.000749	GO:0012501	Programmed cell death	5.70E−06
	Molecular function	GO:0019904	Protein domain specific binding	5.96E−13	GO:0061630	Ubiquitin protein ligase activity	3.39E−05
		GO:0005342	Organic acid transmembrane transporter activity	4.10E−05	GO:0061659	Ubiquitin-like protein ligase activity	3.39E−05
		GO:0008509	Anion transmembrane transporter activity	0.000139	GO:0005543	Phospholipid binding	0.000151
KEGG	Pathway	ath00195	Photosynthesis	4.02E−10	ath00280	Valine, leucine and isoleucine degradation	9.64E−09
		ath00966	Glucosinolate biosynthesis	9.57E−05	ath04141	Protein processing in endoplasmic reticulum	2.31E−05
		ath04712	Circadian rhythm	0.032353	ath04075	Plant hormone signal transduction	0.003093

Table 3. Identification of hormone-related genes elevated ambient temperature.

ID	Gene name	27vs22	Category
AT2G28305	LOG1	↓	Cytokinin riboside 5′-monophosphate phosphoribohydrolase
AT5G06300	LOG7	↓	Cytokinin riboside 5′-monophosphate phosphoribohydrolase LOG7
AT1G67110	CYP735A2	↓	Cytokinin hydroxylase
AT4G29740	CKX4	↑	Cytokinin dehydrogenase 4
AT5G21482	CKX7	↑	Cytokinin dehydrogenase 7
AT5G35750	AHK2	↓	Histidine kinase 2
AT1G19050	ARR7	↓	response regulator 7
AT4G16110	ARR2	↓	response regulator 2
AT3G16857	ARR1	↓	Two-component response regulator ARR1
AT1G10470	ARR4	↓	Two-component response regulator ARR4
AT2G25180	ARR12	↓	Two-component response regulator ARR12
AT1G80340	GA3OX2	↑	Gibberellin 3-beta-dioxygenase 2
AT1G78440	GA2OX1	↑	Gibberellin 2-beta-dioxygenase 1
AT1G47990	GA2OX4	↑	Gibberellin 2-beta-dioxygenase 4
AT5G17490	RGL3	↓	DELLA protein RGL3
AT2G01570	RGA	↓	DELLA protein RGA
AT4G39400	BRI1	↓	Protein BRASSINOSTEROID INSENSITIVE 1
AT4G00710	BSK3	↓	BR-signaling kinase 3

Figure 2. (A, B) Relative expression of 18 genes presented by qRT-PCR (left side) and RNA-seq (right side).

Figure 3. Phenotypes of mutant response to different ambient temperatures. (A) Seedlings were grown on vertical MS plates at 22°C, and 27°C for 7 days. Bar = 5 mm. (B) Relative ratios of root lengths in mutants grown under the same conditions. (n = 25–50; P < 0.001, based on t-test).