盐胁迫下不同甘薯品种的转录组测序分析

doi:10.3724/SP.J.1006.2023.24143

Abstract

Abstract:

The objective of this study is to obtain the salt tolerant transcriptome sequence information of sweet potato, mine and identify the differentially expressed genes and their related metabolic pathways. Rongshu 819 (salt-tolerant variety) and Rongshu 910 (salt-sensitive variety) under salt treatment for 0, 3, and 6 days were conducted for the transcriptome by high-throughput sequencing. The results showed that a total of 157,252 Unigenes with an average length of 576 bp were obtained from the two varieties. The 83,264 Unigenes, accounting for 52.95% of the total Unigenes, were annotated in the 7 functional databases. NR annotation revealed that sweet potato Unigenes had the most homologous sequences in Ipomoea nil with a total of 43,620 accounting for 57.05%. The annotation of Unigenes in the KOG database is mainly concentrated in general functional prediction only (8752), signal transformation mechanisms (5067), and post translation modification, protein transformation, molecular chaperones (4471). The qRT-PCR indicated that, in Rongshu 819, the number of differentially expressed genes in 3 days and 6 days of salt treatment was 3752 and 807, respectively, which classified into 33 GO functional categories and 302 KEGG metabolic pathways. In Rongshu 910, the number of differentially expressed genes in 3 days and 6 days of salt treatment was 5554 and 7395, respectively, which classified into 50 GO functional categories and 329 KEGG metabolic pathways. The heat map was drawn based on the transcriptome data of partial differentially expressed genes. The result showed that 7 differentially expressed β-Glucosidase genes annotated into starch and sucrose metabolic pathway were up-regulated in salt-tolerant variety while down-regulated in salt-sensitive variety. Seven calmodulin-like genes annotated into Ca²⁺ signaling pathway were specifically expressed in two varieties, among which 2 were specifically up-regulated in salt-tolerant variety and 5 were specifically down-regulated in salt-sensitive variety. The expression heat map of differentially expressed transcription factors indicated that IbERF1 was only specifically expressed in salt-tolerant varieties, IbNAC3, IbNAC11, IbERF3, and IbERF4 were only specifically expressed in salt-sensitive varieties, while IbNAC29 was down-regulated in salt-tolerant varieties and up-regulated in salt-sensitive varieties. In conclusion, the number of Unigenes obtained from transcriptome of sweet potato under salt stress was large and the sequence information was rich. The differentially expressed genes and high abundance transcription factors may play an important role in sweet potato response to salt stress.

Key words: sweet potato, salt stress, transcriptome, high-throughput sequencing

ZHANG Xiao-Hong, PENG Qiong, YAN Zheng. Transcriptome sequencing analysis of different sweet potato varieties under salt stress[J].Acta Agronomica Sinica, 2023, 49(5): 1432-1444.

Figures/Tables 11

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项目 Item	单基因簇 Unigene	转录本 Transcript
序列总数 Total sequence number	157,252	211,688
所有序列长度之和 Total sequence length (bp)	90,649,057	160,878,660
平均长度 Average length (bp)	576	759
GC碱基的数量占比 Percent GC (%)	41.12	41.14
N50长度 N50 length (bp)	1064	1646
N90长度 N90 length (bp)	243	262

	注释数据库 Anno database							总计 Total
	COG	GO	KEGG	KOG	Pfam	Swissprot	NR	总计 Total
注释的Unigene数(条) Annotated number (Unigene)	20,446	32,635	44,445	42,285	38,863	53,196	76,583	83,264

差异分组 DEG set	差异表达基因数量 DEG number	上调数量 Number of the up-regulated DEGs	下调数量 Number of the down-regulated DEGs
R1-1_R1-2_R1-3_vs_R2-1_R2-2_R2-3	323	206	117
R1-1_R1-2_R1-3_vs_R3-1_R3-2_R3-3	3752	1926	1826
T1-1_T1-2_T1-3_vs_T2-1_T2-2_T2-3	5554	2122	3432
T1-1_T1-2_T1-3_vs_T3-1_T3-2_T3-3	7395	3353	4042
R1-1_R1-2_R1-3_vs_T1-1_T1-2_T1-3	9352	5129	4223
R2-1_R2-2_R2-3_vs_T2-1_T2-2_T2-3	7538	3338	4200
R3-1_R3-2_R3-3_vs_T3-1_T3-2_T3-3	9903	4709	5194

Transcriptome sequencing analysis of different sweet potato varieties under salt stress

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转录因子 Transcription factor	数量 Number
转录因子 Transcription factor	R1-1_R1-2_R1-3_vs_R2-1_R2-2_R2-3	R1-1_R1-2_R1-3_vs_R3-1_R3-2_R3-3	T1-1_T1-2_T1-3_vs_T2-1_ T2-2_T2-3	T1-1_T1-2_T1-3_vs_T3-1_ T3-2_T3-3
AP2/ERF	3	88	152	182
B3	5	63	114	131
bHLH	3	49	111	138
bZIP	3	39	51	76
C2C2	4	49	78	78
C2H2	6	75	96	126
C3H	14	97	128	166
GNAT	5	62	97	144
GRAS	6	32	73	92
HB	6	60	98	108
MYB	9	131	177	244
mTERF	12	55	79	99
NAC	12	69	117	133
SNF2	5	48	54	61
WRKY	8	38	113	149
其他 Other	65	675	1139	1376
总计 Total	166	1630	2677	3303

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[2]	TANG Wen-Qiang, ZHANG Wen-Long, ZHU Xiao-Qiao, DONG Bi-Zheng, LI Yong-Cheng, YANG Nan, ZHANG Yao, WANG Yun-Yue, HAN Guang-Yu. Effects of diverse mixture intercropping on the structure and function of bacterial communities in rice rhizosphere [J]. Acta Agronomica Sinica, 2023, 49(4): 1111-1121.
[3]	ZHANG Wen-Xuan, LIANG Xiao-Mei, DAI Cheng, WEN Jing, YI Bin, TU Jin-Xing, SHEN Jin-Xiong, FU Ting-Dong, MA Chao-Zhi. Genome editing of BnaMPK6 gene by CRISPR/Cas9 for loss of salt tolerance in Brassica napus L. [J]. Acta Agronomica Sinica, 2023, 49(2): 321-331.
[4]	XIAO Jian, WEI Xing-Xuan, YANG Shang-Dong, LU Wen, TAN Hong-Wei. Effects of intercropping with watermelons on cane yields, soil physicochemical properties and micro-ecology in rhizospheres of sugarcanes [J]. Acta Agronomica Sinica, 2023, 49(2): 526-538.
[5]	DING Hong, ZHANG Zhi-Meng, XU Yang, ZHANG Guan-Chu, GUO Qing, QIN Fei-Fei, DAI Liang-Xiang. Physiological and transcriptional regulation mechanisms of nitrogen alleviating drought stress in peanut [J]. Acta Agronomica Sinica, 2023, 49(1): 225-238.
[6]	WU Xu-Li, WU Zheng-Dan, WAN Chuan-Fang, DU Ye, GAO Yan, LI Ze-Xuan, WANG Zhi-Qian, TANG Dao-Bin, WANG Ji-Chun, ZHANG Kai. Functional identification of sucrose transporter protein IbSWEET15 in sweet potato [J]. Acta Agronomica Sinica, 2023, 49(1): 129-139.
[7]	ZHANG Tian-Yu, WANG Yue, LIU Ying, ZHOU Ting, YUE Cai-Peng, HUANG Jin-Yong, HUA Ying-Peng. Bioinformatics analysis and core member identification of proline metabolism gene family in Brassica napus L. [J]. Acta Agronomica Sinica, 2022, 48(8): 1977-1995.
[8]	XIE Li-Ming, JIANG Zhong-Yu, LIU Hong-Juan, HAN Jun-Jie, LIU Ben-Kui, WANG Xiao-Lu, SHI Chun-Yu. Suitable soil moisture promotes sugar supply and tuberization in sweet potato at root branching stage [J]. Acta Agronomica Sinica, 2022, 48(8): 2080-2087.
[9]	GUO Jia-Xin, LU Xiao-Yu, TAO Yi-Fan, GUO Hui-Juan, MIN Wei. Analysis of metabolites and pathways in cotton under salt and alkali stresses [J]. Acta Agronomica Sinica, 2022, 48(8): 2100-2114.
[10]	LI Pei-Ting, ZHAO Zhen-Li, HUANG Chao-Hua, HUANG Guo-Qiang, XU Liang-Nian, DENG Zu-Hu, ZHANG Yu, ZHAO Xin-Wang. Analysis of drought responsive regulatory network in sugarcane based on transcriptome and WGCNA [J]. Acta Agronomica Sinica, 2022, 48(7): 1583-1600.
[11]	YAN Jia-Qian, GU Yi-Biao, XUE Zhang-Yi, ZHOU Tian-Yang, GE Qian-Qian, ZHANG Hao, LIU Li-Jun, WANG Zhi-Qin, GU Jun-Fei, YANG Jian-Chang, ZHOU Zhen-Ling, XU Da-Yong. Different responses of rice cultivars to salt stress and the underlying mechanisms [J]. Acta Agronomica Sinica, 2022, 48(6): 1463-1475.
[12]	LEI Xin-Hui, WAN Chen-Xi, TAO Jin-Cai, LENG Jia-Jun, WU Yi-Xin, WANG Jia-Le, WANG Peng-Ke, YANG Qing-Hua, FENG Bai-Li, GAO Jin-Feng. Effects of soaking seeds with MT and EBR on germination and seedling growth in buckwheat under salt stress [J]. Acta Agronomica Sinica, 2022, 48(5): 1210-1221.
[13]	XIAO Jian, CHEN Si-Yu, SUN Yan, YANG Shang-Dong, TAN Hong-Wei. Characteristics of endophytic bacterial community structure in roots of sugarcane under different fertilizer applications [J]. Acta Agronomica Sinica, 2022, 48(5): 1222-1234.
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