. 2017 Nov 7;17:194. doi: 10.1186/s12870-017-1143-y

Table 1.

Cd-regulated differentially expressed genes (DEGs) mapped to the metabolic pathways

BinName	FPKM		Cd1h/ck1h		Rice gene annotation
Transcript ID	ck1h	Cd1h	log2FC	q_value	Rice gene annotation
Jasmonate synthesis-degradation and signaling
Os06g11290.1^△	5.18	435.09	6.39	0.0019	12-oxophytodienoate reductase, *OsOPR1*
Os06g11210.1^#	58.99	717.03	3.60	0.0019	OsOPR5 [Q69TI0]
Os06g11240.1	14.15	339.14	4.58	0.0019	OPR
Os06g11200.1	0.15	2.40	3.98	0.0188	OPR
Os03g55800.1^∑	29.03	146.45	2.33	0.0019	allene oxide synthase, AOS1
Os03g12500.1^∑	2.23	13.52	2.60	0.0019	allene oxide synthase, AOS2
Os12g05440.1*	1.85	58.66	*4.98*	0.002	cytochrome P450, *CYP94C2b*
Os03g08310.1*	1.88	27.26	*3.86*	0.002	ZIM domain containing protein, *OsJAZ9*
Os03g28940.1^△	38.17	106.38	1.48	0.0019	ZIM domain containing protein
Os09g02710.1	0.63	4.20	2.73	0.0035	Arabidopsis loss of the timing of Et and JA biosynthesis 1
Abscisic acid synthesis-degradation and signaling
Os03g44380.1^△	0.53	5.75	3.43	0.0019	9-cis-epoxycarotenoid dioxygenase, *OsNCED3*
Os07g05940.1^△	0.59	99.97	7.41	0.0019	*OsNCED4*
Os12g42280.1^△	2.63	32.42	3.62	0.0019	OsNCED5
Os12g29400.1^△	5.88	14.09	1.26	0.0019	ABA-responsive protein [Q2QQY9]
Os04g44510.1	51.06	244.45	2.26	0.0019	ABA-responsive protein (GRAM domain)
Os04g44500.1	17.60	49.88	1.50	0.0019	ABA-responsive protein (GRAM domain)
Os10g04860.1	5.05	2.26	−1.16	0.0019	aldehyde oxidase
Os02g52780.2	0.71	14.01	4.30	0.0019	*OsbZIP23*
Ethylene signaling
Os07g48630.1^△	52.93	109.98	1.06	0.002	ethylene-insensitive 3
Os02g43790.1^△	41.57	265.23	2.67	0.002	ethylene-responsive transcription factor, OsBIERF3
Os03g09170.1^△	20.44	218.22	3.42	0.002	ERF
Os04g46220.1^Ⓜ	44.26	119.27	1.43	0.002	ERF
Os08g31580.1	102.51	268.56	1.39	0.002	ERF
Os01g54890.1	4.75	31.18	2.71	0.034	ERF2
Os01g58420.1	49.28	134.22	1.45	0.002	*OsERF3*
Os11g06770.2*	0.10	0.70	*2.75*	0.027	ERF110
Os02g43970.1*	2.93	7.61	*1.37*	0.002	ABA-responsive DREB gene, *ARAG1*
Os10g41330.2*	5.79	64.06	*3.47*	0.002	AP2 domain
Os06g10780.1*	2.17	6.55	*1.59*	0.002	AP2 domain
Os02g43940.1*	1.74	6.56	*1.92*	0.002	AP2 domain, OsDREB4–1
Os09g28440.1	0.59	47.37	6.32	0.002	AP2 domain, *OsEATB*
Os08g36920.1^#	0.76	70.32	6.53	0.002	AP2 domain
Os03g08460.1^Ⓜ	91.75	42.47	−1.11	0.002	AP2 domain
Os03g08490.1	215.27	81.73	−1.40	0.002	AP2 domain
Os03g08500.1	538.17	256.44	−1.07	0.002	AP2 domain
Os04g08740.3	68.92	31.96	−1.11	0.002	ethylene receptor, OsETR2 [Q7XX84]
Gibberellin synthesis-degradation
Os06g37300.2	0.22	0.01	−2.36	1.1290	ent-kaurene oxidase 4, OsKO4 [Q0DBF4]
Os03g63970.1*	18.68	0.00	*−1.12*	40.5099	gibberellin 20 oxidase 1
Os05g48700.1	2.84	0.01	1.34	1.1252	gibberellin 2-beta-dioxygenase
Metal binding, chelation and storage
Os04g57200.1^△	54.50	169.43	1.64	0.002	heavy metal transport/detoxification protein
Os04g57200.2	3.10	47.85	3.95	0.002	heavy metal transport/detoxification protein
Os04g17100.1^△	2.63	32.28	3.62	0.0063	heavy metal-associated domain protein, HMAD HMAD
Os04g17100.2	43.72	123.38	1.50	0.0019	heavy metal-associated domain protein, HMAD HMAD
Os03g05750.1^△	0.54	89.45	7.38	0.003	HMAD
Os03g05750.2	9.01	212.68	4.56	0.002	HMAD
Os02g37290.1^△	38.65	132.69	1.78	0.002	HMAD
Os02g37300.1^△	11.63	66.20	2.51	0.002	HMAD
Os02g37330.1^△	3.99	98.49	4.63	0.002	HMAD
Os04g39350.1^△	4.57	33.87	2.89	0.002	HMAD
Os04g39010.1	0.94	3.69	1.97	0.022	HMAD
Os02g37320.1	2.57	19.20	2.90	0.002	HMAD
Os02g37320.2	9.45	84.16	3.15	0.002	HMAD
Os01g48710.1	116.94	46.15	−1.34	0.002	HMAD
Os03g64340.1*	5.31	12.44	*1.23*	0.0050	HMAD
Divalent cations transporters
Os08g10630.1^△	19.33	6.55	−1.56	0.0019	ZRT/IRT-like protein, OsZIP4 [Q6ZJ91]
Os05g10940.1^Ⓜ	40.47	19.81	−1.03	0.0019	OsZIP7 [Q6L8F7]
Os05g39560.1	5.37	1.36	−1.98	0.0113	OsZIP5 [Q6L8G0]
Os05g39560.2	40.35	9.21	−2.13	0.002	OsZIP5 [Q6L8G0]
Os06g37010.1	5.56	2.13	−1.39	0.0050	OsZIP10 [Q5Z653]
Os05g39540.2*	97.22	25.45	*−1.93*	0.0019	OsZIP9 [Q0DHE3]
Os03g46470.1*	14.68	2.46	*−2.58*	0.0076	Iron-regulated transporter 1, *OsIRT1*
ABC transporters and pleiotropic drug resistance proteins
Os01g42380.1^#	1.35	5.99	2.15	0.0019	ABCG36/*OsPDR9* , pleiotropic drug resistance protein
Os01g42410.1^∑	3.66	21.96	2.59	0.0050	ABCG37/OsPDR8 [Q8GU89]
Os02g11760.1^△	0.34	2.90	3.10	0.0019	ABCG39/OsPDR7 [Q8GU88]
Os01g42370.1	0.28	0.91	1.68	0.0019	ABCG35/OsPDR11 [Q8GU92]
Os08g29570.1	0.32	8.42	4.72	0.0101	ABCG44/OsPDR17 [Q6YW62]
Os08g29570.2	4.95	18.57	1.91	0.002	ABCG44/OsPDR17 [Q6YW62]
Os01g61940.1*	10.43	25.90	*1.31*	0.0019	ABC transporter family protein
MATE family of citrate/H⁺ antiport transporters
Os08g43654.1*	1.05	2.52	*1.26*	0.026	MATE efflux family protein
Os12g03260.1*	1.50	4.33	*1.53*	0.047	MATE
Os04g48290.1	3.72	8.19	1.14	0.002	MATE
Os02g45380.1	1.23	8.37	2.76	0.002	MATE
other transporters
Os12g25200.1^Ⓜ	123.93	50.25	−1.30	0.002	chloride transporter
Os02g36414.1	162.32	70.28	−1.21	0.002	transporter family protein
Os04g37970.1	118.36	43.01	−1.46	0.002	transporter family protein
Os07g24230.1	1.26	0.38	−1.71	0.014	integral membrane transporter family protein
Os01g14520.1	131.86	45.76	−1.53	0.002	dicarboxylate /malic acid transport protein
Os09g31130.1	1.58	7.13	2.17	0.035	citrate transporter
Os10g30790.1^△	26.30	94.24	1.84	0.046	inorganic phosphate transporter, *OsPT8*
Os10g30790.3*	25.00	80.55	1.69	0.016	inorganic phosphate transporter, *OsPT8*
Mitochondrial electron transport
Os07g37730.1^△	0.15	9.07	5.96	0.0035	NADH-ubiquinone oxidoreductase
Os04g51150.1^△	14.41	35.47	1.30	0.0019	AOX1A, alternative oxidase
Os04g51160.1^Ⓜ	0.66	46.99	6.15	0.0019	AOX1B
Os10g39870.1	10.79	29.33	1.44	0.0019	Arabidopsis Transmembrane protein G1P-related 1
Os05g09550.1	1.37	4.81	1.81	0.0482	Der1-like family domain containing protein
Os02g37000.1*	6.37	16.29	*1.35*	0.0019	mitochondrial prohibitin complex protein 1
Heat-shock transcription factor (HSF) family
Os09g35790.1*	0.76	6.99	*3.20*	0.0168	OsHsfB2c [Q652B0]
Os09g35790.2*	9.03	26.10	*1.53*	0.0019	OsHsfB2c [Q652B0]
Os02g32590.1^△	1.21	7.07	2.55	0.0019	OsHsfA3 [Q6H6Q7]
Os02g32590.2	0.38	2.76	2.88	0.0218	OsHsfA3 [Q6H6Q7]
Os04g48030.1^△	3.05	14.05	2.20	0.0178	OsHsfB2a [Q7XRX3]
Os10g28340.1	0.62	12.76	4.36	0.0019	*OsHsfA2c*
Os10g28340.2	3.72	15.96	2.10	0.0135	*OsHsfA2c*
Os03g12370.3	0.40	4.95	3.65	0.0101	OsHsfA9 [Q10PR4]
Os08g43334.2	2.45	44.04	4.17	0.0019	OsHsfB2b [Q6Z9C8]
Os02g13800.1	15.01	50.05	1.74	0.0019	OsHsfC2a [Q6EUG4]
NAC domain transcription factor family
Os01g50360.1*	2.52	1.09	*−1.21*	0.026	NAC domain containing protein
Os11g03300.2	16.07	38.93	1.28	0.002	*OsNAC10*
Os01g60020.1^∑	5.77	25.25	2.13	0.002	*OsNAC4*
Os07g12340.1^Ⓜ	12.81	455.79	5.15	0.002	OsNAC3 [Q7EZT1]
Os03g60080.1^#	88.35	942.97	3.42	0.002	*SNAC1*
WRKY domain transcription factor family
Os02g08440.1^#	2.03	125.38	5.95	0.0019	WRKY71
Os02g08440.4	24.26	179.27	2.89	0.0019	WRKY71
Os05g27730.1^△	101.45	430.59	2.09	0.0019	*OsWRKY53*
Os01g61080.1^△	6.51	92.36	3.83	0.0019	*OsWRKY24*
Os01g09100.1^△	29.32	195.59	2.74	0.0019	OsWRKY10
Os05g50610.2	0.89	2.44	1.45	0.0317	WRKY8
Os08g13840.2	130.82	404.49	1.63	0.0019	WRKY25
Os05g09020.1	1.47	13.65	3.21	0.0019	WRKY67
Os05g09020.2	9.62	51.47	2.42	0.0019	WRKY67
Os11g29870.1	5.02	15.26	1.60	0.0019	WRKY72
Os09g25060.1	3.11	24.14	2.95	0.0019	*OsWRKY76*
Os01g60600.1*	0.42	1.68	*1.99*	0.0323	WRKY108

The Cuffdiff utility was used to evaluate the transcript differential expression between ck1h and Cd1h samples. The DEGs uniquely identified in our RNAseq samples are marked with stars. Rice genes with experimentally verified functions are presented in bold fonts. Rice gene annotation was also referred from UniProt (square brackets contain the accession number). The DEGs marked with pound signs were also upregulated by medium and low Cd stress in rice seedling roots in 3 previous reports [21, 27, 48]. The DEGs marked with sigma were also upregulated uniformly by the lowest Cd treatment [48] as well as in one of the two high-throughput transcriptome study [21, 27]. Those marked with triangle were regulated uniformly by Cd treatment in the two high-throughput studies, and those labeled M were detected only in the microarray analysis [21]