田间条件下不同棉花品种叶片响应化学脱叶剂噻苯隆的转录组分析

doi:10.3724/SP.J.1006.2023.24261

Abstract

Abstract:

Thidiazuron (TDZ) is the main chemical agent for cotton defoliation, which plays a key role in realizing cotton mechanical harvesting. At present, there are few studies on the molecular regulation mechanism of TDZ induced cotton leaf abscission in the field environment. In this study, TDZ sensitive variety (Jifeng 914) and non-sensitive line (04-1685) were used as the experimental materials. Ethylene, cytokinin, and abscisic acid contents in leaves were determined. RNA-seq was used to analyze the changes of gene expression in leaves at 0, 1, 3, and 5 d after TDZ treatment. WGCNA (Weighted gene coexpression network analysis), GO and KEGG were used to analyze and screen gene coexpression modules and gene functions, respectively. The results showed that the ethylene, cytokinin, and abscisic acid contents of Jifeng 914 reached the highest level at 1 d after treatment, and the hormone contents of 04-1685 reached the highest level at 3 d after treatment. A total of 33,283 differentially expressed genes (DEGs) were screened by RNA-seq. Through WGCNA analysis, 2 and 3 modules highly related to hormone and samples were screened respectively. The genes in the modules mainly participate in abiotic stress response, circadian rhythm, and material metabolism. By analyzing the relative expression of plant hormone, stress response, and circadian rhythm related genes, the expression of hormone related genes in sensitive variety Jifeng 914 was higher, among which ethylene signal response genes were kept at a higher expression level within 5 days after treatment, abscisic acid signal response genes were kept at a higher expression level within 1 day after treatment, and cytokinin metabolism related genes expressed very low within 1 day after treatment and increased sharply at 3 d and 5 d after treatment. At 1 d and 3 d after treatment, heat shock protein genes (HSP70, HSP90, and ATJ3), calcium homeostasis regulating genes (CRT3, NCL), and circadian rhythm genes (LNK2, APRR9, CCA1) were significantly down regulated, while circadian rhythm genes (ARR8) were up regulated. Spraying TDZ in the field environment, while causing changes in hormone content, may damage the plant's circadian rhythm and reduce the stress ability to abiotic stress, and thus accelerating leaf senescence and abscission. This study provides more ideas for enriching the molecular regulation mechanism of TDZ induced leaf abscission.

Key words: upland cotton, thidiazuron, RNA-seq, plant hormone, abiotic stress, circadian rhythm

ZHU Ji-Jie, WANG Shi-Jie, ZHAO Hong-Xia, JIA Xiao-Yun, LI Miao, WANG Guo-Yin. Transcriptome analysis of different cotton varieties' leaves in response to chemical defoliant agent thidiazuron under field conditions[J].Acta Agronomica Sinica, 2023, 49(10): 2705-2716.

Figures/Tables 11

Table 1

Fig. 1

Table S1

Fig. 2

Table 2

Fig. 3

Fig. 4

Table 3

GO items enriched by genes in each module"

性状 Trait	模块 Module	GO号 GO ID	描述 Description	条目类型 Term type	基因数量 Gene number	校正P值P-adjust
激素 Hormone	棕色 Brown	GO:0003913	DNA光解酶活性 DNA photolyase activity	MF	5	0
		GO:0016703	氧化还原酶活性, 作用于结合分子氧的单个供体, 结合一个氧原子(内部单加氧酶或内部混合作用氧化酶) Oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases)	MF	6	0.002
		GO:0010277	叶绿素a加氧酶[总]活性 Chlorophyllide a oxygenase [overall] activity	MF	6	0.002
		GO:0005372	水跨膜转运子活性 Water transmembrane transporter activity	MF	6	0.003
		GO:0042044	液体转运 Fluid transport	BP	6	0
		GO:0006833	水分转运 Water transport	BP	6	0
		GO:0009628	响应非生物刺激 Response to abiotic stimulus	BP	31	0.007
		GO:0007623	昼夜节律 Circadian rhythm	BP	6	0.017
		GO:0048511	节律过程 Rhythmic process	BP	6	0.017
	品红 Magenta	GO:0042752	昼夜节律调控 Regulation of circadian rhythm	BP	4	0.001
	品红 Magenta	GO:0042753	昼夜节律正向调控 Positive regulation of circadian rhythm	BP	3	0.009
样品 Sample	棕色 Brown	GO:0005198	结构分子活性 Structural molecule activity	MF	59	0.013
		GO:0003735	核糖体结构组分 Structural constituent of ribosome	MF	53	0.020
		GO:0047334	二磷酸果糖-6-磷酸-1-磷酸转移酶活性Diphosphate-fructose-6-phosphate- 1-phosphotransferase activity	MF	4	0.043
		GO:0005840	核糖体 Ribosome	CC	55	0.011
		GO:0043228	无膜包裹的细胞器 Non-membrane-bounded organelle	CC	67	0.038
		GO:0043232	细胞内部无膜包裹的细胞器 Intracellular non-membrane-bounded organelle	CC	67	0.038
		GO:0006412	翻译 Translation	BP	49	0.044
	品红Magenta	GO:0003951	NAD⁺激酶活性 NAD⁺ kinase activity	MF	3	0.938
	粉色 Pink	GO:0042752	昼夜节律调控 Regulation of circadian rhythm	BP	4	0.008
	粉色 Pink	GO:0042753	昼夜节律正向调控 Positive regulation of circadian rhythm	BP	3	0.066

Table 3

Table 4

Table S2

Expression level of the genes in the modules"

基因 Genes	模体 Symbol	JF914-0d	JF914-1d	JF914-3d	JF914-5d	04-1685-0d	04-1685-1d	04-1685-3d	04-1685-5d
Ghir_A01G008930	-	17.0	20.2	12.3	7.5	20.8	19.8	16.7	8.8
Ghir_A01G010550	-	0.5	0.2	0.4	0.4	0.6	0.3	0.3	0.3
Ghir_A01G016940	-	8.3	8.7	6.4	4.3	8.1	7.7	7.6	4.0
Ghir_A02G005410	-	16.2	6.9	7.0	9.2	12.4	6.8	7.4	9.6
Ghir_A02G007670	ATCAO, CAO, CH1	20.5	13.2	8.2	28.4	23.3	13.8	6.4	24.9
Ghir_A02G009880	-	20.4	29.8	39.1	15.0	18.2	22.2	30.5	9.4
Ghir_A02G012150	ATSKP2;2,SKP2B	7.3	4.8	4.1	6.9	5.7	4.7	3.8	6.5
Ghir_A02G012620	AtCRT3,CRT3,EBS2,PSL1	269.8	121.8	123.9	95.2	204.6	88.7	188.8	66.5
Ghir_A02G013520	ARA-7,ARA7,atARA7,ATRAB-F2B,ATRAB5B,ATRABF2B,RAB-F2B,RABF2B	12.1	15.0	10.1	9.3	6.9	13.1	9.7	9.1
Ghir_A02G014320	AtRABA4a,RABA4a	2.5	2.2	3.6	2.1	2.5	2.0	4.5	1.7
Ghir_A02G017730	SUVR5	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_A02G019660	AtACER,ATCES1	2.0	2.8	2.1	1.5	2.3	2.2	2.3	1.5
Ghir_A03G001740	-	3.1	1.7	0.8	1.9	3.4	2.2	0.5	2.7
Ghir_A03G004650	-	16.7	18.3	12.7	7.4	18.4	16.1	17.3	8.1
Ghir_A03G008550	ENO1	6.6	9.8	5.3	3.8	6.0	8.0	6.5	3.2
Ghir_A03G011460	-	0.1	0.0	0.1	0.0	0.1	0.1	0.0	0.0
Ghir_A03G014410	GAPC-2,GAPC2	0.1	0.2	0.0	0.0	0.0	0.1	0.0	0.0
Ghir_A03G020480	-	4.3	6.9	5.2	4.2	5.8	6.9	5.4	3.1
Ghir_A04G005850	-	1.6	2.3	1.6	0.9	2.1	2.5	1.5	0.9
Ghir_A04G011920	AGAL1,AtAGAL1	8.7	12.5	11.1	3.0	6.5	9.9	6.2	5.0
Ghir_A04G012800	TUA2	9.0	10.2	20.2	3.2	7.1	9.4	22.0	4.8
Ghir_A05G006080	ALDH11A3	3.7	5.6	4.5	3.0	1.7	3.3	3.0	1.9
Ghir_A05G006290	ACD1,LLS1,PAO	32.3	16.4	5.8	25.9	31.4	19.5	5.4	22.3
Ghir_A05G006740	ABC1K1,ACDO1,AtACDO1,PGR6	9.9	7.6	2.6	6.6	10.3	8.5	2.0	6.0
Ghir_A05G007340	AGT,AGT1,SGAT	63.9	39.5	22.6	44.2	64.1	46.1	16.5	70.0
Ghir_A05G008440	BIC1	51.6	11.1	1.3	22.1	62.0	16.3	0.8	27.4
Ghir_A05G012590	APT5	1.4	4.9	2.4	2.3	1.1	2.3	3.2	1.8
Ghir_A05G019810	ATHAL3B,HAL3,HAL3B	2.0	1.7	1.7	1.8	2.1	1.6	1.3	1.8
Ghir_A05G021970	TUA2	2.5	3.3	2.7	1.6	2.4	3.1	4.0	1.3
Ghir_A05G027740	ATRABG3B,RAB7,RAB75,RABG3B	1.1	1.8	2.2	1.0	1.4	1.6	2.7	1.0
Ghir_A05G028660	LNK2	24.9	13.8	6.8	18.2	27.2	14.2	6.9	14.6
Ghir_A05G030390	UBC19	1.4	1.3	1.0	1.9	1.7	1.8	1.3	1.7
Ghir_A05G041300	ARR8,ATRR3,RR3	2.4	24.9	14.9	4.7	1.5	17.4	12.9	8.6
Ghir_A06G001750	COR27	2.3	11.4	6.0	4.6	1.5	11.3	5.5	4.7
Ghir_A06G004640	LACS9	3.1	2.2	0.9	2.7	3.1	2.1	0.8	2.0
Ghir_A06G005970	-	15.1	19.9	13.6	6.5	14.1	18.4	16.0	7.9
Ghir_A06G006470	ATRAB-F2A,ATRAB5A,ATRABF2A,RAB-F2A,RAB5A,RABF2A,RHA1	3.4	4.0	3.3	2.5	3.0	3.7	3.8	2.2
Ghir_A06G010230	-	5.5	6.4	6.8	3.8	5.3	6.0	6.8	3.3
Ghir_A06G012540	CRY3	10.8	3.8	2.2	8.7	12.5	4.8	1.6	10.6
Ghir_A06G016380	-	23.7	30.6	26.6	14.3	18.0	25.3	21.3	11.2
Ghir_A06G017580	CRY3	6.1	19.2	18.3	11.6	5.0	19.8	17.7	10.1
Ghir_A06G018020	AT-HSC70-1,AtHsp70-1,HSC70,HSC70-1,HSP70-1	251.1	101.9	51.0	145.5	276.6	94.0	82.0	149.5
Ghir_A06G020430	-	27.0	28.9	21.5	11.9	27.8	29.7	25.1	13.6
Ghir_A06G021400	RPL16A	5.1	5.4	5.0	3.3	4.4	5.8	5.5	5.1
Ghir_A06G022650	UVR3	18.4	14.3	7.2	15.6	21.0	15.2	6.1	16.8
Ghir_A07G002950	-	10.5	17.9	21.9	6.5	11.6	15.4	17.5	12.4
Ghir_A07G007580	ATDGK1,DGK1	3.4	2.9	3.6	3.1	4.0	3.0	4.5	2.5
Ghir_A07G007590	UGD3	1.4	2.9	2.0	1.1	3.2	2.6	2.2	0.3
Ghir_A07G012010	atENP1,ENP1	5.2	5.3	3.3	1.2	5.8	5.3	4.8	1.5
Ghir_A07G012630	TUB6	0.0	0.0	0.0	0.0	0.0	0.0	0.2	0.1
Ghir_A07G015600	GAE3	0.8	0.8	1.0	0.4	1.3	0.9	1.4	0.5
Ghir_A07G016260	PALE1,TH-2,TH2	2.2	2.6	3.3	2.6	2.8	2.2	4.2	2.0
Ghir_A07G017020	ATCHIP,CHIP	5.5	5.5	4.3	5.8	6.6	5.2	4.1	6.4
Ghir_A07G018990	GAUT9	2.0	2.9	1.7	0.9	2.1	2.8	1.9	0.8
Ghir_A07G023100	GAUT9	0.7	1.2	1.5	0.2	0.6	1.5	1.9	0.2
Ghir_A08G000130	-	3.3	3.2	3.1	3.8	2.7	3.6	2.5	4.0
Ghir_A08G001580	ACD1-LIKE,PTC52,TIC55-IV	15.8	10.0	6.2	18.3	19.1	9.0	9.4	19.0
Ghir_A08G003090	AtHsp90.2,ERD8,HSP81-2,HSP81.2,HSP90.2	369.6	136.9	30.6	116.6	326.4	122.5	58.2	131.7
Ghir_A08G005550	ARS27A,RS27A	9.3	10.7	7.8	5.6	12.1	10.0	10.5	5.1
Ghir_A08G009530	ARS27A,RS27A	3.2	3.5	3.2	1.8	2.4	3.2	3.3	1.3
Ghir_A08G011680	PGY2	36.1	39.6	28.7	16.5	37.4	41.4	37.4	17.8
Ghir_A08G014320	GAE3	1.1	1.7	1.8	1.0	1.3	1.9	1.8	1.2
Ghir_A08G017930	-	9.4	8.2	9.4	8.0	8.9	6.7	11.9	6.3
Ghir_A08G019290	ATGID1B,GID1B	2.0	6.7	4.2	3.5	1.7	3.3	4.3	2.8
Ghir_A08G021740	RPL18	0.0	0.0	0.0	0.0	0.1	0.0	0.1	0.1
Ghir_A08G022220	-	8.5	11.9	5.6	1.6	9.5	11.8	5.4	1.1
Ghir_A08G023180	-	11.8	10.4	4.9	15.1	9.7	13.1	3.1	9.5
Ghir_A08G023710	-	4.0	6.8	2.5	1.3	2.3	3.2	2.4	0.9
Ghir_A09G002690	-	7.9	9.1	7.6	4.7	10.1	8.9	10.6	4.8
Ghir_A09G006240	-	1.9	3.4	1.3	0.5	2.1	3.8	1.6	0.5
Ghir_A09G010800	-	6.7	7.6	6.1	4.0	6.4	7.8	7.4	4.7
Ghir_A09G014710	AHP5,AHP5	33.2	32.2	27.0	13.2	31.4	32.4	33.1	16.5
Ghir_A09G015860	RPL12C	2.9	3.0	3.2	2.5	3.3	2.7	3.5	2.2
Ghir_A09G015880	PIP2;2,PIP2B	27.8	3.6	1.3	9.6	23.3	3.3	0.4	5.8
Ghir_A09G016580	AT-HSC70-1,AtHsp70-1,HSC70,HSC70-1,HSP70-1	14.3	5.0	1.5	4.4	15.6	3.7	2.5	7.1
Ghir_A09G018290	EFO2,RUP2	9.1	2.9	0.2	4.1	8.8	4.8	0.3	3.3
Ghir_A09G018820	ATRBL3,RBL3	1.3	3.3	3.0	0.7	1.1	2.9	2.8	0.8
Ghir_A09G022090	BBX24,BBX24,STO	88.0	53.3	25.6	64.9	113.4	64.4	17.8	55.6
Ghir_A10G016320	-	0.3	0.4	0.2	0.4	0.5	0.5	0.3	0.3
Ghir_A10G018160	RPL10B	1.2	2.4	1.6	0.4	1.3	1.7	0.3	0.3
Ghir_A10G018930	-	8.9	38.9	24.6	17.5	11.7	40.0	29.3	25.2
Ghir_A10G020390	-	2.1	1.6	2.0	1.3	1.9	1.6	1.8	1.2
Ghir_A10G023690	ATHH2,PIP1;2,PIP1B,TMP-A	49.3	3.8	1.3	7.5	26.0	2.7	0.8	7.0
Ghir_A10G024010	ATHH2,PIP1;2,PIP1B,TMP-A	0.5	21.6	13.8	0.9	0.4	11.5	10.9	0.5
Ghir_A11G001650	APRR5,PRR5	8.0	6.1	3.6	7.5	9.6	5.9	2.3	6.9
Ghir_A11G003880	RGP,RGP3	14.5	18.6	24.4	12.7	24.7	16.9	36.9	10.0
Ghir_A11G003900	GAUT11	2.2	2.2	2.0	1.4	2.2	1.7	2.5	1.4
Ghir_A11G005950	-	10.6	14.2	11.2	7.7	12.5	12.2	14.9	9.2
Ghir_A11G006660	-	4.5	2.9	1.5	10.8	3.6	5.2	4.5	6.3
Ghir_A11G007090	-	9.4	11.4	7.9	4.9	8.0	11.5	7.3	5.0
Ghir_A11G010130	RRP41	8.9	9.3	7.5	4.3	6.7	7.9	6.1	3.6
Ghir_A11G010230	SPA1	4.3	2.5	1.4	3.6	4.2	2.9	1.7	3.7
Ghir_A11G010900	APRR9,PRR9,TL1	9.9	2.7	0.5	3.8	8.9	3.5	0.4	2.6
Ghir_A11G012240	ATMHX,ATMHX1,MHX,MHX1	16.7	20.7	12.9	7.6	16.2	17.9	14.7	6.7
Ghir_A11G013550	-	2.3	3.2	2.6	3.7	3.6	2.7	2.6	3.3
Ghir_A11G017790	AtPERK8,PERK8	2.9	4.0	2.3	2.1	2.4	3.8	2.9	1.8
Ghir_A11G017880	-	4.2	5.3	4.0	3.3	4.1	3.6	5.5	4.2
Ghir_A11G024630	RPS2	5.9	7.2	6.7	1.5	5.6	6.3	6.8	1.7
Ghir_A11G031350	AtNCL,NCL	7.0	1.5	0.5	1.9	6.2	2.4	0.5	1.6
Ghir_A11G035290	ABCI20,ATNAP9,NAP9	1.8	1.4	1.6	1.8	1.4	1.5	1.2	1.7
Ghir_A12G001470	LNK1	15.1	4.4	3.3	6.1	17.5	5.0	3.6	5.2
Ghir_A12G004550	-	0.4	0.2	0.2	0.2	0.3	0.5	0.3	0.4
Ghir_A12G008430	EMB3010,RPS6B	0.5	0.6	0.2	0.0	0.6	0.5	0.2	0.4
Ghir_A12G012130	SINAT3	1.3	1.3	1.2	1.3	1.4	1.0	0.9	1.4
Ghir_A12G012650	AtCCA1,CCA1	1.3	0.4	0.0	1.2	1.8	1.0	0.0	0.6
Ghir_A12G022310	-	4.7	12.9	7.3	6.2	6.0	10.0	6.4	3.8
Ghir_A12G022870	ACX1,ATACX1	0.0	0.0	0.0	0.0	0.2	0.0	0.0	0.0
Ghir_A12G025940	APRR5,PRR5	15.0	9.1	3.5	11.1	14.8	10.2	3.3	8.7
Ghir_A13G006290	-	0.5	3.9	0.8	0.3	0.7	2.3	1.9	0.4
Ghir_A13G006750	APRR5,PRR5	13.2	3.3	2.6	5.5	14.0	4.0	3.6	5.2
Ghir_A13G008670	SAC56	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_A13G009930	ATNADK2,NADK2	2.6	2.2	1.2	2.7	2.6	2.3	1.3	2.9
Ghir_A13G021180	ATNUDT19,ATNUDX19,NUDX19	12.8	9.2	5.8	13.2	13.4	9.2	7.2	13.9
Ghir_A13G023720	DDB2	3.5	2.8	2.0	4.5	4.5	2.6	1.7	6.7
Ghir_D01G007810	ATEHD1,EHD1	4.8	4.9	4.7	9.1	5.9	5.6	4.3	7.4
Ghir_D01G008810	AtHsp90.2,ERD8,HSP81-2,HSP81.2,HSP90.2	71.3	20.6	4.6	20.9	76.9	20.5	10.2	24.3
Ghir_D01G009340	-	23.4	24.0	16.7	10.7	26.1	24.2	21.8	11.6
Ghir_D01G010350	-	14.1	10.6	9.2	22.8	13.6	8.4	5.6	40.8
Ghir_D01G011590	-	4.0	2.5	3.1	3.3	4.0	2.7	2.9	3.8
Ghir_D01G015500	ATRPAC43,RPAC43	0.0	0.2	0.1	0.7	0.4	0.3	0.0	0.3
Ghir_D02G000260	VHA-E2	2.4	2.2	1.7	0.9	1.1	1.9	1.1	0.6
Ghir_D02G001270	VHA-E2	0.9	1.2	1.5	0.1	1.4	1.7	1.4	1.2
Ghir_D02G001290	VHA-E2	0.5	0.8	1.3	0.2	0.5	0.5	1.4	0.5
Ghir_D02G001350	VHA-E2	5.4	9.0	5.1	1.1	8.2	8.7	6.3	2.7
Ghir_D02G002390	GAE6	6.0	6.8	4.8	2.0	4.0	5.7	9.1	4.9
Ghir_D02G002560	AtACER,ATCES1	1.5	2.0	1.4	1.0	1.8	1.6	1.6	1.0
Ghir_D02G002620	DAYSLEEPER	0.8	1.2	1.0	0.2	1.4	1.0	1.2	0.6
Ghir_D02G007380	ADH,ADH1,ATADH,ATADH1	10.4	9.8	10.0	6.1	10.3	9.4	11.8	11.0
Ghir_D02G008120	ATCAO,CAO,CH1	16.6	10.0	7.4	19.3	18.3	12.0	5.8	18.1
Ghir_D02G008760	AtTIFY1,GATA25,TIFY1,ZIM	4.6	4.5	3.6	5.0	4.1	3.8	3.4	4.9
Ghir_D02G012890	AtSBH2,SBH2	138.7	326.3	31.0	22.9	90.9	200.7	17.2	6.9
Ghir_D02G012900	SBH1	4.0	4.7	4.2	2.9	4.6	4.5	5.5	3.1
Ghir_D02G021570	-	9.3	14.0	13.7	5.7	9.0	10.8	8.3	10.0
Ghir_D03G006610	SKP2A	9.9	5.0	3.9	7.2	7.5	4.8	3.2	6.1
Ghir_D03G007190	ARA-7,ARA7,atARA7,ATRAB-F2B,ATRAB5B,ATRABF2B,RAB-F2B,RABF2B	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D03G007840	-	0.7	1.0	0.4	0.7	0.5	0.9	0.9	0.5
Ghir_D03G008510	Nog1-1	12.4	12.9	8.4	5.9	13.6	12.4	11.2	5.9
Ghir_D03G010330	-	2.5	1.0	4.2	0.1	1.7	2.3	1.0	0.1
Ghir_D03G011050	ENO1	7.7	12.0	9.0	3.9	7.2	9.3	8.8	3.7
Ghir_D03G012330	GOX1	0.0	0.1	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D03G012450	-	2.8	7.3	9.5	0.1	1.1	13.0	12.0	10.4
Ghir_D03G017250	-	5.5	3.7	1.4	5.7	6.7	4.3	1.2	5.2
Ghir_D04G003680	AtSRT2,SRT2	6.1	4.9	0.8	4.5	8.1	6.5	0.6	4.5
Ghir_D04G006910	CYT1,EMB101,GMP1,SOZ1,VTC1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D04G008340	-	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D04G014000	AIRP2,AtAIRP2	2.0	1.3	1.3	2.3	1.4	1.6	1.0	1.8
Ghir_D04G014250	-	0.9	0.6	0.2	1.0	1.1	0.7	0.2	0.9
Ghir_D04G014510	-	3.0	3.0	4.4	2.4	3.2	3.0	3.9	1.9
Ghir_D04G015550	ATRMA1,RMA1	12.7	10.2	5.0	12.2	13.6	10.7	2.5	8.9
Ghir_D04G016690	LNK1	5.4	0.9	1.8	3.4	5.8	1.1	2.5	3.5
Ghir_D04G020270	PGM3	10.0	10.1	10.0	6.4	8.8	11.1	11.0	6.0
Ghir_D05G001960	ARRS1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D05G004490	SQD1	42.7	71.7	29.8	17.5	34.4	66.9	29.0	12.5
Ghir_D05G006370	ACD1,LLS1,PAO	1.7	0.7	0.2	1.8	0.9	0.5	0.1	1.4
Ghir_D05G016900	-	8.7	8.8	7.3	3.7	9.2	10.3	7.1	3.9
Ghir_D05G019180	ARF5,IAA24,MP,MP	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D05G021900	TUA2	9.8	13.4	11.7	3.6	8.6	13.5	14.9	2.6
Ghir_D05G027740	ATRABG3B,RAB7,RAB75,RABG3B	1.6	1.6	2.1	1.1	1.5	2.0	2.5	1.6
Ghir_D05G028650	-	11.8	13.8	15.5	8.9	18.5	17.8	18.2	9.4
Ghir_D05G029680	-	1.7	3.9	1.6	1.9	0.5	1.8	3.4	0.9
Ghir_D05G030330	UBC19	5.1	5.9	3.1	6.3	6.0	5.7	3.0	7.3
Ghir_D05G039710	-	2.3	3.4	2.9	2.4	3.1	2.6	2.9	2.0
Ghir_D06G003560	-	0.4	2.5	1.2	0.1	0.8	1.6	1.1	0.1
Ghir_D06G004700	LACS9	0.1	0.1	0.1	0.6	0.3	0.2	0.0	0.0
Ghir_D06G009240	HSP17.6II	1.0	1.1	2.2	3.2	1.2	1.1	1.3	2.4
Ghir_D06G011830	CRY3	11.2	3.7	1.9	7.6	12.6	4.5	1.7	9.1
Ghir_D06G012390	AtSBH2,SBH2	3.7	3.2	3.3	2.5	3.4	2.9	3.5	1.8
Ghir_D06G015060	AtRABA1c,RABA1c	8.1	8.8	12.8	7.7	10.2	7.9	15.1	6.8
Ghir_D06G016860	ADT1,AtADT1	1.6	2.8	2.6	2.1	1.4	2.7	2.2	1.8
Ghir_D06G017240	-	23.8	32.3	32.2	17.8	18.5	25.5	24.3	12.9
Ghir_D06G017430	-	9.1	8.7	5.7	8.7	8.4	6.5	3.2	13.0
Ghir_D06G018900	AT-HSC70-1,AtHsp70-1,HSC70,HSC70-1,HSP70-1	302.1	106.9	48.7	130.6	306.0	98.0	75.9	125.3
Ghir_D06G022590	ATNUDT15,ATNUDX15,NUDX15	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D07G006200	OLD5,QS,SUFE3	16.5	11.9	4.6	15.4	19.3	13.0	4.2	13.9
Ghir_D07G007590	ATDGK1,DGK1	2.9	2.6	3.0	2.5	2.9	2.2	4.0	2.3
Ghir_D07G011020	HSP17.6B	2.2	0.7	1.5	1.0	1.2	0.6	0.8	1.0
Ghir_D08G001600	ACD1-LIKE,PTC52,TIC55-IV	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D08G003190	AtHsp90.2,ERD8,HSP81-2,HSP81.2,HSP90.2	43.1	27.8	10.4	37.9	60.3	28.9	15.4	29.5
Ghir_D08G003210	AtHsp90.2,ERD8,HSP81-2,HSP81.2,HSP90.2	88.6	40.3	15.9	42.4	84.9	42.8	20.3	38.1
Ghir_D08G009200	L18aB,RPL18aB	0.5	0.2	0.3	0.0	0.0	0.3	0.1	0.1
Ghir_D08G012060	BIP,BIP2	23.3	5.4	4.9	17.4	23.2	4.0	8.7	17.9
Ghir_D08G015210	GAE3	1.3	1.4	1.2	0.5	1.3	1.5	1.7	0.9
Ghir_D08G017160	ATSYP22,ATVAM3,SGR3,SYP22,VAM3	6.3	5.5	5.2	5.2	5.3	5.6	6.1	3.9
Ghir_D08G022110	RPT2	60.6	25.3	15.1	25.8	49.5	30.0	13.2	25.8
Ghir_D08G022550	-	4.1	8.2	6.5	3.0	5.5	8.0	5.6	2.9
Ghir_D08G022910	-	2.5	3.2	2.0	0.6	1.9	2.5	2.1	0.7
Ghir_D08G024630	-	3.4	7.2	3.7	2.1	2.9	4.0	3.0	2.0
Ghir_D08G025270	DECR,SDRB	23.5	12.5	1.9	14.9	27.0	16.0	1.1	13.4
Ghir_D08G025770	HY5,TED 5	7.9	3.8	1.4	3.9	6.6	4.2	1.3	3.8
Ghir_D09G004530	TUB8	37.3	59.0	46.9	22.6	37.9	63.7	42.2	22.7
Ghir_D09G010540	-	6.1	7.0	5.9	4.2	7.3	6.7	6.8	4.1
Ghir_D09G010620	ATJ,ATJ3,J3	89.9	21.7	12.6	28.6	74.2	17.0	18.9	28.2
Ghir_D09G011610	ATNADK-1,NADK1	3.8	2.6	1.1	1.5	3.2	2.5	1.0	0.9
Ghir_D09G014410	-	4.6	5.8	3.8	0.4	3.6	6.8	4.5	0.5
Ghir_D09G015310	-	0.3	0.1	0.0	0.2	0.2	0.1	0.0	0.1
Ghir_D09G015320	PIP2;2,PIP2B	5.3	1.0	0.2	2.1	7.9	1.1	0.2	1.6
Ghir_D09G017780	EFO2,RUP2	8.4	3.5	0.5	4.3	9.9	5.5	0.2	3.5
Ghir_D09G022230	RPS24B	21.8	21.7	22.3	7.9	25.5	27.0	32.2	11.1
Ghir_D09G025630	-	0.2	1.3	1.6	0.6	1.0	1.1	1.8	0.7
Ghir_D10G001380	-	0.8	2.5	0.9	0.2	0.5	1.5	1.2	0.4
Ghir_D10G004090	-	1.6	2.1	2.2	1.7	1.9	2.0	2.5	1.7
Ghir_D10G008440	ATTSO2,TSO2	0.7	1.8	1.8	0.9	0.5	2.2	1.6	1.6
Ghir_D10G010460	-	1.8	2.0	1.9	1.5	2.5	1.9	2.2	1.4
Ghir_D10G019760	RPS26e	22.6	27.3	24.3	11.3	27.2	24.6	26.7	13.2
Ghir_D10G020440	ARR9,ATRR4	10.6	42.9	33.4	17.9	12.9	45.9	46.1	29.7
Ghir_D10G026150	ATHH2,PIP1;2,PIP1B,TMP-A	11.2	0.7	0.2	1.8	6.8	0.2	0.1	3.2
Ghir_D10G026160	ATHH2,PIP1;2,PIP1B,TMP-A	0.8	0.0	0.0	0.1	0.3	0.1	0.0	0.1
Ghir_D10G026170	ATHH2,PIP1;2,PIP1B,TMP-A	23.2	6.8	1.8	7.5	18.0	4.9	0.9	6.6
Ghir_D10G026440	-	0.9	34.4	22.7	4.7	0.2	18.4	24.5	2.0
Ghir_D11G002530	ATOXA1,OXA1,OXA1a,OXA1AT	0.5	0.0	0.1	0.0	0.3	0.6	0.1	0.3
Ghir_D11G004470	-	42.6	55.2	38.2	23.1	46.4	57.7	45.9	16.6
Ghir_D11G010190	SPA1	1.8	1.4	1.0	1.7	2.7	1.3	1.1	1.8
Ghir_D11G010820	APRR9,PRR9,TL1	6.8	1.8	0.4	4.7	7.2	3.2	0.6	3.2
Ghir_D11G010920	LHY,LHY,LHY1	0.5	0.1	0.0	0.6	0.5	0.4	0.0	0.5
Ghir_D11G013600	-	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D11G013840	AtcPT1,cPT1	1.1	1.9	1.5	1.2	0.5	1.9	1.5	1.2
Ghir_D11G016270	ATCOP1,COP1,DET340,EMB168,FUS1	7.8	7.7	5.0	7.5	9.6	8.4	4.3	5.2
Ghir_D11G019410	-	26.2	40.9	17.4	16.4	18.4	34.8	13.6	9.7
Ghir_D11G023570	-	0.3	1.3	1.6	0.1	1.1	1.3	1.5	0.9
Ghir_D11G024810	AtUGP1,UGP,UGP1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D11G027800	GSDA	22.3	23.7	18.0	10.3	19.9	22.5	21.4	12.1
Ghir_D11G029450	-	1.7	1.0	1.1	0.0	2.2	3.6	3.2	2.5
Ghir_D11G030550	-	2.0	1.2	2.2	1.2	1.2	2.3	1.1	0.9
Ghir_D11G032310	GAPCP-2	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ghir_D11G032690	ATSNF4,SNF4	3.6	9.4	4.5	2.6	3.3	7.1	6.2	2.2
Ghir_D11G035310	-	0.0	0.0	0.0	0.3	0.0	0.0	0.0	0.0
Ghir_D11G035370	RPL20	7.3	8.9	7.0	6.5	6.1	7.8	8.6	6.4
Ghir_D11G036090	AT-HSC70-1,AtHsp70-1,HSC70,HSC70-1,HSP70-1	45.7	22.9	20.7	43.9	46.8	18.8	29.2	54.0
Ghir_D11G036150	ABCI20,ATNAP9,NAP9	6.5	4.5	3.2	10.0	7.8	5.5	2.6	10.7
Ghir_D12G001500	LNK1	5.8	1.4	1.0	2.5	5.7	1.3	1.1	1.9
Ghir_D12G004770	DECR,SDRB	4.9	2.6	1.5	4.5	3.3	2.0	1.1	4.5
Ghir_D12G012900	LHY,LHY,LHY1	8.7	3.2	1.1	11.4	13.3	3.8	1.0	9.5
Ghir_D12G018990	-	10.3	11.5	10.7	6.7	11.2	13.2	13.3	7.2
Ghir_D12G023930	ATUGE1,UGE1	1.5	2.0	0.0	0.0	0.4	0.8	0.0	0.0
Ghir_D12G026480	ATSIG5,SIG5,SIGE	64.4	9.8	6.4	28.1	75.6	15.4	5.6	24.0
Ghir_D13G001020	AtSEC23C	1.9	1.4	1.6	2.2	2.2	2.0	1.4	2.0
Ghir_D13G005430	FLL2	0.0	0.0	0.3	0.1	0.1	0.1	0.0	0.1
Ghir_D13G006450	FLL2	1.6	1.7	1.9	0.9	1.5	1.7	1.7	1.0
Ghir_D13G010310	SAC56	13.8	12.2	12.6	7.5	13.8	11.1	18.5	7.3
Ghir_D13G017060	RGP5,RGP5	5.3	6.9	4.0	2.6	4.3	6.4	4.2	2.2
Ghir_D13G022040	ATNUDT19,ATNUDX19,NUDX19	12.4	7.9	5.4	13.3	14.6	7.7	6.0	14.0
Ghir_D13G024440	DDB2	2.7	2.7	1.4	3.9	3.1	2.6	1.4	4.0

Table S2

Table S3

Expression level of the hormone related genes"

基因Gene	JF914-0d	JF914-1d	JF914-3d	JF914-5d	04-1685-0d	04-1685-1d	04-1685-3d	04-1685-5d
Ghir_A05G018480	3.35	0.35	0.97	0.71	1.05	0.21	1.01	0.64
Ghir_D01G010310	0.36	1.00	9.87	9.04	0.38	0.65	9.54	8.21
Ghir_D05G018480	6.67	0.51	0.80	1.65	4.70	0.51	0.95	3.70
Ghir_A06G022780	0.90	12.83	0.10	0.05	0.49	13.31	1.13	0.06
Ghir_A05G004020	0.59	12.38	684.35	342.12	0.71	4.44	624.00	319.09
Ghir_A06G007640	0.06	24.90	47.09	7.50	0.13	6.82	59.38	3.16
Ghir_A07G001250	0.00	20.27	432.61	403.08	0.26	28.52	578.43	344.64
Ghir_D06G007800	0.06	23.61	30.62	4.46	0.04	5.32	72.94	3.22
Ghir_D06G009100	7.69	7.64	2.81	2.74	7.43	10.80	3.03	1.86
Ghir_D07G001260	0.06	42.18	923.40	796.81	0.42	8.75	892.12	607.89
Ghir_A12G023980	1.12	4.40	67.96	64.17	0.65	0.76	36.46	51.44
Ghir_D12G023960	51.54	74.85	1468.21	1527.31	14.41	12.06	1073.61	1389.37
Ghir_D02G013160	24.30	23.66	0.27	1.44	14.73	22.58	0.58	0.52
Ghir_D03G018940	20.59	14.36	0.27	1.12	31.30	18.19	0.37	0.87
Ghir_D11G011550	0.96	2.53	2.90	1.20	0.62	0.31	3.61	2.03
Ghir_D05G036790	4.96	4.08	26.36	28.09	4.57	2.65	20.39	51.20
Ghir_A11G004510	7.74	12.81	0.40	3.16	5.01	12.71	1.00	0.28
Ghir_D11G004410	13.00	32.39	0.72	4.99	7.73	27.73	0.92	0.56
Ghir_D13G007620	2.64	3.38	1.07	1.61	4.80	4.09	0.45	0.45
Ghir_A04G003200	202.97	177.83	125.29	146.35	174.05	168.09	106.68	86.76
Ghir_D05G036360	2.70	2.10	2.17	1.08	2.77	2.29	1.35	0.17
Ghir_A12G024510	0.47	2.63	3.41	0.25	1.06	0.62	16.73	1.52
Ghir_A03G010240	5.79	5.08	0.13	0.34	8.27	4.43	0.00	0.01
Ghir_D12G027950	81.66	69.07	0.58	2.42	72.95	64.66	1.08	0.23
Ghir_A09G020320	0.24	0.45	0.34	0.39	0.23	0.69	0.62	0.20
Ghir_A09G014150	4.65	4.19	0.51	2.46	6.22	4.45	1.13	0.45
Ghir_D09G013610	7.96	6.79	1.02	3.90	9.77	6.27	1.58	0.67
Ghir_A11G032930	5.25	4.98	0.57	0.71	6.21	6.44	0.46	0.21
Ghir_A05G003480	145.13	219.18	0.08	0.92	219.04	222.37	0.90	0.13
Ghir_A05G010280	148.27	68.77	42.13	52.75	158.04	84.90	53.31	30.03
Ghir_D05G010000	202.78	89.17	86.89	89.03	203.65	110.99	113.36	51.42
Ghir_A09G023900	1.26	2.81	24.07	20.89	0.94	1.41	24.59	34.80

Table S3

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基因 Gene	正向引物 Forward primer (5°-3°)	反向引物 Reverse primer (5°-3°)
GhHis3	TCAAGACTGATTTGCGTTTCCA	GCGCAAAGGTTGGTGTCTTC
Ghir_D07G009830	CAATCAGACAAGCCAACA	CTAAACCGACTTCTATGC
Ghir_D08G005270	CAAGGCTCGTCGTAAGGG	TTGGCATAGTTGACTTTGTTGA
Ghir_A01G018610	AAGTTCACCACCGTCAGA	CTCAAAGGACCATCAATC
Ghir_D08G001540	GGCTAACGCTGACCCTAC	ATCCTCCGTGACTCCAAG
Ghir_D07G008630	AGGGTTGGAATCTTGGTA	CCAGGTTTCGCTTGAATA
Ghir_D11G029010	ATCCAACAATAGGCAAGG	TCAAACTCCGACCACTCT
Ghir_A05G006740	GAACACTTGCCTCCTTCT	CTTAATAGCCTGTGGGTC
Ghir_A04G002920	CTCCTCTGGATTGGGTTTA	GGTTCCTTGGCAGTTGGT
Ghir_D08G020190	GCAACATCCTCCTTCACC	AAGCCCTCCAATACCAAT
Ghir_A06G003210	CAATAGCCAGGCAAGCGG	GGGCAATAGCAAACAGCA

样品 Sample	原始数据 Raw data (bp)	干净数据 Clean data (bp)	Q30 (%)	GC含量 GC content (%)	总比对率 Total mapped (%)	特异比对率 Uniquely mapped (%)
JF914-0d_1	7.52×10⁹	7.11×10⁹	93.78	45.01	92.83	84.09
JF914-0d_2	7.85×10⁹	7.57×10⁹	93.79	44.42	94.72	87.9
JF914-0d_3	7.46×10⁹	7.19×10⁹	93.55	44.45	95.47	88.46
JF914-1d_1	7.31×10⁹	7.11×10⁹	93.88	44.22	95.62	89.28
JF914-1d_2	7.92×10⁹	7.73×10⁹	93.79	44.19	95.68	89.6
JF914-1d_3	7.07×10⁹	6.88×10⁹	93.76	44.24	94.48	88.34
JF914-3d_1	6.97×10⁹	6.83×10⁹	93.87	43.87	94.42	88.06
JF914-3d_2	7.69×10⁹	7.50×10⁹	93.84	44.08	95.31	88.84
JF914-3d_3	6.96×10⁹	6.80×10⁹	93.47	43.83	95.18	88.84
JF914-5d_1	7.34×10⁹	7.16×10⁹	93.47	43.99	95.19	88.99
JF914-5d_2	7.03×10⁹	6.86×10⁹	93.89	44.12	95.4	89.32
JF914-5d_3	6.37×10⁹	6.24×10⁹	93.03	43.92	95.16	89.37
04-1685-0d_1	7.67×10⁹	7.40×10⁹	93.24	44.25	95.04	88.39
04-1685-0d_2	7.98×10⁹	7.60×10⁹	93.42	43.99	95.42	88.26
04-1685-0d_3	7.10×10⁹	6.82×10⁹	93.12	44.19	94.8	88.09
04-1685-1d_1	7.07×10⁹	6.85×10⁹	93.91	44.33	95.61	88.98
04-1685-1d_2	6.35×10⁹	6.21×10⁹	93.78	44.24	95.61	89.61
04-1685-1d_3	7.22×10⁹	7.05×10⁹	93.51	44.28	95.58	89.49
04-1685-3d_1	7.41×10⁹	7.23×10⁹	93.75	44.02	94.06	86.81
04-1685-3d_2	7.85×10⁹	7.67×10⁹	93.82	43.88	95.82	89.12
04-1685-3d_3	6.94×10⁹	6.79×10⁹	93.57	44.06	94.01	86.79
04-1685-5d_1	7.53×10⁹	7.35×10⁹	93.44	44.17	94.64	88.69
04-1685-5d_2	6.92×10⁹	6.74×10⁹	93.43	44.1	93.8	87.47
04-1685-5d_3	6.67×10⁹	6.49×10⁹	93.29	44.09	93.49	86.86

比较 Comparison	所有DEGs Total DEGs	上调 Up regulated	下调 Down regulated
JF914-0d vs JF914-1d	2151	1180	971
JF914-1d vs JF914-3d	20,189	8045	12,144
JF914-3d vs JF914-5d	5039	2476	2563
JF914-0d vs 04-1685-0d	644	269	375
JF914-1d vs 04-1685-1d	539	218	321
JF914-3d vs 04-1685-3d	339	133	206
JF914-5d vs 04-1685-5d	1971	740	1231
04-1685-0d vs 04-1685-1d	3355	1892	1463
04-1685-1d vs 04-1685-3d	22,461	9019	13,442
04-1685-3d vs 04-1685-5d	5790	2520	3270

性状 Trait	模块 Module	KEGG通路号 KEGG pathway ID	描述 Description	基因数量 Gene number	校正P值 P-adjust
激素 Hormone	棕色 Brown	map04712	昼夜节律-植物 Circadian rhythm-plant	13	3.02E-06
		map00760	烟酸和烟酰胺代谢 Nicotinate and nicotinamide metabolism	5	0.079
		map04141	内质网中的蛋白质加工 Protein processing in endoplasmic reticulum	18	0.162
		map04146	过氧化物酶体 Peroxisome	9	0.494
		map03060	蛋白质外排 Protein export	6	0.647
		map04120	泛素介导的蛋白水解 Ubiquitin mediated proteolysis	11	0.698
	品红 Magenta	map04075	植物激素信号转导 Plant hormone signal transduction	5	0.006
		map00230	嘌呤代谢 Purine metabolism	2	0.168
		map00400	苯丙氨酸、酪氨酸和色氨酸生物合成 Phenylalanine, tyrosine, and tryptophan biosynthesis	1	0.769
		map00240	嘧啶代谢 Pyrimidine metabolism	1	0.992
样品 Sample	棕色 Brown	map00010	糖酵解/糖异生 Glycolysis/Gluconeogenesis	18	0.062
		map03010	核糖体 Ribosome	38	0.088
		map00520	氨基糖和核苷酸唐代谢 Amino sugar and nucleotide sugar metabolism	17	0.170
		map04145	噬菌体 Phagosome	14	0.586
		map00030	戊糖磷酸途径 Pentose phosphate pathway	8	0.830
		map00600	鞘磷脂代谢 Sphingolipid metabolism	6	0.867
	品红 Magenta	map00730	硫胺素代谢 Thiamine metabolism	2	0.195
		map04144	内吞作用 Endocytosis	4	0.426
		map04145	吞噬体 Phagosome	3	0.527
	粉色 Pink	map04075	植物激素信号转导 Plant hormone signal transduction	5	0.420
	粉色 Pink	map00900	萜类主链生物合成 Terpenoid backbone biosynthesis	2	0.740

Transcriptome analysis of different cotton varieties' leaves in response to chemical defoliant agent thidiazuron under field conditions

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