小麦响应干旱胁迫环状RNA的鉴定

doi:10.3864/j.issn.0578-1752.2022.23.002

Abstract

Abstract:

【Objective】 Drought is one of the foremost abiotic stress limiting global wheat production. Exploring the molecular mechanism of wheat response to drought stress have great significance in wheat molecular breeding. Circular RNAs (circRNAs) have been proved to play an important role in the process of plants tolerance to environmental stresses. Therefore, identifying circRNAs involved in drought stress response will help to construct a regulatory network of wheat drought tolerance, and lay a foundation for analyzing the drought resistance mechanism in wheat. 【Method】 In this study, two wheat varieties (Zhoumai13 and Jimai38) with significant differences in drought resistance were used and circRNA-seq was performed on their root samples under well-watered and drought conditions. Differentially expressed circRNAs related to drought stress response were screened based on the identified circRNAs and their microRNAs (miRNAs) targets were predicted. Further, potential circRNA-miRNA-mRNA regulatory modules related to wheat drought stress response were constructed according to the expression patterns of miRNAs and their target genes under drought stress..【Result】 A total of 1 409 wheat circRNAs were identified, most of which (68.91%) were exonic circRNAs. Only 133 circRNAs were simultaneously identified in both varieties. A total of 239 differentially expressed circRNAs were identified under drought stress, of which 138 circRNAs were specifically differentially expressed in the drought-resistant variety Zhoumai 13 (ZM13), and 19 circRNAs were differentially expressed simultaneously in both varieties. Besides, 34 targeted miRNAs and 1 408 miRNA target genes were predicted. Based on the expression patterns of these differentially expressed circRNAs, targeted miRNAs, and miRNA target genes, five potential circRNA-miRNA-mRNA regulatory modules centered on tae-miR9664-3p, tae-miR1122b-3p, tae-miR9662a-3p, tae-miR6197-5p and tae-miR1120c-5p in response to drought stress were screened..【Conclusion】 Wheat circRNAs have obvious specificity in different cultivars and different expression patterns among different drought-tolerant wheat cultivars. A total of 239 wheat circRNAs and 5 potential circRNA-miRNA-mRNA regulatory modules in response to drought stress were identified in the present study.

Key words: wheat, circular RNAs, drought stress, microRNAs

LI Ning,LIU Kun,LIU TongTong,SHI YuGang,WANG ShuGuang,YANG JinWen,SUN DaiZhen. Identification of Wheat Circular RNAs Responsive to Drought Stress[J].Scientia Agricultura Sinica, 2022, 55(23): 4583-4599.

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Table 9

circRNA-miRNA-mRNA regulatory modules"

模块编号 Module number	差异表达circRNA Differentially expressed circRNAs	差异表达的靶向miRNA Differentially expressed target miRNAs	差异表达的miRNA靶基因 Target genes of differentially expressed miRNA	靶基因功能注释 Target gene functional annotation
1	chr1B:642165761\|642197014 chr4D:65120787\|65147651	tae-miR9664-3p	TraesCS5B02G405300	过氧化物酶Peroxidase
			TraesCS5A02G141700	乙烯反应转录因子 Ethylene-responsive transcription factor
			TraesCS5D02G084300	细胞色素P450 Cytochrome P450
			TraesCS3D02G225900	细胞色素P450 Cytochrome P450
			TraesCS3B02G256400	细胞色素P450 Cytochrome P450
			TraesCS3A02G224900	钙依赖性蛋白激酶Calcium-dependent protein kinase
			TraesCS3B02G254500	钙依赖性蛋白激酶Calcium-dependent protein kinase
			TraesCS3D02G228700	钙依赖性蛋白激酶Calcium-dependent protein kinase
			TraesCS4B02G365000	ABC转运体A家族成员 ABC transporter A family member
			TraesCSU02G138200	ABC转运体A家族成员 ABC transporter A family member
2	chr1B:642165761\|642197014 chr1B:477404890\|477416633	tae-miR1122b-3p	TraesCS1A02G272100	丝氨酸/苏氨酸蛋白激酶Serine/threonine-protein kinase
			TraesCS7B02G481100	E3 泛素蛋白连接酶E3 ubiquitin-protein ligase
			TraesCS7B02G165100	E3 泛素蛋白连接酶E3 ubiquitin-protein ligase
			TraesCS6D02G330500	谷氨酸受体Glutamate receptor
			TraesCS6B02G281000	乙烯反应转录因子 Ethylene-responsive transcription factor
			TraesCS7D02G416700	胆碱单加氧酶Choline monooxygenase
			TraesCS1B02G138100	生长素反应蛋白Auxin-responsive protein
			TraesCS2D02G404800	水通道蛋白Aquaporin
			TraesCS3D02G258200	ABC转运体B家族成员 ABC transporter B family member
3	chr5D:543694782\|543696753	tae-miR9662a-3p	TraesCS7A02G218600	锌指蛋白Zinc finger protein
			TraesCS7D02G220300	锌指蛋白Zinc finger protein
			TraesCS7B02G125500	锌指蛋白Zinc finger protein
			TraesCS5B02G526300	富含半胱氨酸的受体蛋白激酶 Cysteine-rich receptor-like protein kinase
4	chr2B:32870327\|32874189	tae-miR6197-5p	TraesCS4A02G193600	WRKY转录因子WRKY transcription factor
			TraesCS1D02G276100	转录因子TGAL5 Transcription factor TGAL5
			TraesCS4D02G056900	转录因子bHLH25 Transcription factor bHLH25
			TraesCS4D02G273600	丝氨酸/苏氨酸蛋白激酶Serine/threonine-protein kinase
5	chr3B:778404617\|778442815 chr6D:454657953\|454748495	tae-miR1120c-5p	TraesCS4A02G119400	普遍胁迫蛋白Universal stress protein
			TraesCS4B02G275000	丝氨酸/苏氨酸蛋白激酶Serine/threonine-protein kinase
			TraesCS4D02G273600	丝氨酸/苏氨酸蛋白激酶Serine/threonine-protein kinase
			TraesCS3A02G045200	富含半胱氨酸的受体蛋白激酶 Cysteine-rich receptor-like protein kinase
			TraesCS7B02G298200	肉桂酰辅酶A还原酶Cinnamoyl-CoA reductase
			TraesCS7D02G391800	肉桂酰辅酶A还原酶Cinnamoyl-CoA reductase

Table 9

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circRNA ID	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)
chr4A:135615436\|135616027	GAAGTGGGGGTGCGTCTC	CCCAGTCCCTTTCTTCCTCG
chr2A:391871653\|391873055	GGTCGACCCGGAGATGAAAA	GACCACCAAAGGGATCTGGG
chr3B:734912137\|734913464	ATTCCTTCAAGCCCCCGAAG	GAGGAGAGGCATGAACCGAG
chr6D:68976712\|68979761	TTTGCTCTTCCTTGCGTTGC	TGTTCAGATCAAGACGGCCC
chr6D:68978282\|68979761	AGGACAGAGGTGCAATGCTT	TCCTCCTCGTAGTCCAAGCA
chr3B:774401803\|774404734	ATCCCTTCAAGCCCCCAAAG	AGGACGAATTGCCTCACCAG
chr3D:456098361\|456098885	CTCGGACAACCCCAAGATCC	TGAGGTGAAGAGGCGACATG
chr7D:45482308\|45483763	GGCTCTGATGGTGTGCTTCT	CAGTGCATGTTCCTCCTCAGT
chr3B:438537516\|438537814	TGCTTTGCCTGTCCACTTCT	TGTGGAAATGCGGTTACAAGC
GAPDH	ACATTAAGGGTGGTGCCAAG	TGGTCATCAAACCCTCAACA

样本ID^a Sample ID	Clean read数量 No. of clean reads	Clean data总碱基数 No. of bases in clean data	Q30 (%)	对比率 Percentage of mapped reads (%)
JM38-CK-1	118952370	17735106554	93.08	99.68
JM38-CK-2	116572800	17380371520	93.19	99.47
JM38-CK-3	120557430	17933660922	93.60	99.61
JM38-T-1	97797440	14495476172	94.01	98.74
JM38-T-2	115322786	17223097988	94.79	99.55
JM38-T-3	101091222	15052976916	93.24	99.47
ZM13-CK-1	109456900	16361760332	95.37	99.79
ZM13-CK-2	158882218	23410171332	94.23	99.32
ZM13-CK-3	129129306	19198145718	93.53	99.40
ZM13-T-1	120213128	17925334142	93.34	99.52
ZM13-T-2	106276928	15847825216	93.01	99.59
ZM13-T-3	119369138	17788551356	93.18	99.65

GO类别 GO category	GO名称 GO name	GO ID	宿主基因数量 No. of host genes
生物过程 Biological process	代谢过程Metabolic process	GO:0008152	5
	细胞过程Cellular process	GO:0009987	3
	生物调节Biological regulation	GO:0065007	2
细胞组分 Cellular component	细胞外区域Extracellular region	GO:0005576	2
	膜Membrane	GO:0016020	2
	膜组分Membrane part	GO:0044425	2
分子功能 Molecular function	结合Binding	GO:0005488	2
分子功能 Molecular function	催化活性Catalytic activity	GO:0003824	2

KEGG通路名称 Name of the KEGG pathway	KEGG编号 KEGG number	宿主基因数量 No. of host genes	通路名称 Name of the KEGG pathway	KEGG编号 KEGG number	宿主基因数量 No. of host genes
植物-病原菌互作 Plant-pathogen interaction	ko04626	9	内吞作用 Endocytosis	ko04144	6
真核生物中的核糖体生物发生Ribosome biogenesis in eukaryotes	ko03008	4	植物激素信号转导 Plant hormone signal transduction	ko04075	4
苯丙烷生物合成 Phenylpropanoid biosynthesis	ko00940	4	过氧化物酶体 Peroxisome	ko04146	4
剪切体 Spliceosome	ko03040	3	氧化磷酸化 Oxidative phosphorylation	ko00190	2
mRNA监测途径 mRNA surveillance pathway	ko03015	2	RNA转运 RNA transport	ko03013	2
甘油磷脂代谢 Glycerolipid metabolism	ko00561	2	鞘糖脂生物合成 Glycosphingolipid biosynthesis	ko00604	2

KEGG通路名称 Name of the KEGG pathway	KEGG编号 KEGG number	宿主基因数量 No. of host genes	通路名称 Name of the KEGG pathway	KEGG编号 KEGG number	宿主基因数量 No. of host genes
植物-病原菌互作 Plant-pathogen interaction	ko04626	5	内吞作用 Endocytosis	ko04144	4
RNA转运RNA transport	ko03013	2	过氧化物酶体Peroxisome	ko04146	2
氧化磷酸化 Oxidative phosphorylation	ko00190	2	mRNA监测途径 mRNA surveillance pathway	ko03015	2
剪切体Spliceosome	ko03040	2

Identification of Wheat Circular RNAs Responsive to Drought Stress

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KEGG通路名称 Name of the KEGG pathway	KEGG编号 KEGG number	宿主基因 Host genes	差异表达circRNA Differentially expressed circRNAs
剪切体Spliceosome	ko03040	TraesCS4D02G214100	chr4D:367041574\|367041924
真核生物中的核糖体生物发生Ribosome biogenesis in eukaryotes	ko03008	TraesCS2B02G435400	chr2B:625556656\|625557509
植物激素信号转导Plant hormone signal transduction	ko04075	TraesCS4A02G446600	chr4A:714100537\|714100686
苯丙烷生物合成Phenylpropanoid biosynthesis	ko00940	TraesCS2B02G613900	chr2B:793034311\|793034526
过氧化物酶体Peroxisome	ko04146	TraesCS6D02G174600	chr6D:164766767\|164767073
甘油磷脂代谢Glycerolipid metabolism	ko00561	TraesCS5A02G157700	chr5A:337941529\|337942323
氨基糖和核苷酸糖代谢Amino sugar and nucleotide sugar metabolism	ko00520	TraesCS1A02G353400	chr1A:536974543\|536974758

差异表达circRNA Differentially expressed circRNAs	宿主基因 Host genes	水稻同源基因 Homologous genes in rice	同源基因功能 Homologous gene function
chr2A:52664278\|52664553	TraesCS2A02G099900	OsEIL2 （LOC_Os07g48630）	耐盐Tolerant to salt stress^[30]
chr1D:299577794\|299577982	TraesCS1D02G214200	OsNRT1.1B（LOC_Os10g40600）	耐低氮Tolerant to low nitrogen stress^[31]
chr3A:638334965\|638335214	TraesCS3A02G390200	OsPUB15（LOC_Os08g01900）	耐盐Tolerant to salt stress^[32]
chr3D:394765145\|394765294	TraesCS3D02G285400	OsTT1 （LOC_Os03g26970）	耐高温Tolerant to high temperature stress^[33]
chr4B:606908755\|606908957	TraesCS4B02G317200	OsPht1;2（LOC_Os03g05640）	耐低钾Tolerance to low potassium stress ^[34]
chr4D:41728977\|41729938	TraesCS4D02G066700	OsHOS1（LOC_Os03g52700）	耐冷Tolerant to cold stress^[35]
chr5B:17981442\|17981743	TraesCS5B02G018700	OsASTOL1（LOC_Os12g42980）	耐砷Tolerant to arsenic stress^[36]
chr6A:608632503\|608632694	TraesCS6A02G396400	OsPP1a（LOC_Os03g16110）	耐盐Tolerant to salt stress^[37]
chr7A:222784992\|222785194	TraesCS7A02G245100	OsSAP11（LOC_Os08g39450）	耐盐和耐旱Tolerant to salt and drought stress^[38]
chr7A:222784992\|222785194	TraesCS7A02G245100	OsSAP1（LOC_Os09g31200）	耐盐和耐旱Tolerant to salt and drought stress^[39]

circRNA ID	靶向miRNA <BOLD>T</BOLD>arget miRNAs
chr2B:56775826\|56778058	tae-miR9778
chr7A:735704463\|735710613	tae-miR9673-5p; tae-miR9661-5p
chr1B:642165761\|642197014	tae-miR9664-3p; tae-miR1133; tae-miR1122b-3p
chr5D:543694782\|543696753	tae-miR9662a-3p
chr1B:518799941\|518803372	tae-miR1137a
chr1B:477404890\|477416633	tae-miR1137a; tae-miR1133; tae-miR1122b-3p
chr5B:528574134\|528588868	tae-miR1135; tae-miR1133; tae-miR1127a; tae-miR1122a; tae-miR9668-5p; tae-miR1127b-3p
chr2B:32870327\|32874189	tae-miR1121; tae-miR6197-5p;tae-miR9653a-3p
chr5A:482358772\|482427161	tae-miR1117; tae-miR1125
chr7B:68317992\|68345006	tae-miR1117
chr3B:778404617\|778442815	tae-miR1117; tae-miR1133; tae-miR1131; tae-miR1127a; tae-miR1120c-5p
chr2B:787486469\|787538256	tae-miR5384-3p
chr3A:7907994\|7923795	tae-miR1117; tae-miR5049-3p
chr2A:771191685\|771242152	tae-miR1117; tae-miR7757-5p; tae-miR1131
chr6D:454657953\|454748495	tae-miR1121; tae-miR5175-5p; tae-miR1118; tae-miR1130b-3p; tae-miR1120c-5p
chr7B:1308928\|1352258	tae-miR1122c-3p; tae-miR1133; tae-miR1127a; tae-miR1122a; tae-miR1127b-3p
chr4A:668278340\|668323672	tae-miR1131; tae-miR9673-5p
chr2B:16815429\|16856732	tae-miR1117; tae-miR1139; tae-miR1118; tae-miR408
chr4D:65120787\|65147651	tae-miR1117; tae-miR9664-3p; tae-miR7757-5p; tae-miR1127a; tae-miR1122a
chr6D:469968655\|469986922	tae-miR7757-5p; tae-miR1133
chr3B:54538153\|54591607	tae-miR5384-3p; tae-miR9659-3p
chr6B:265924545\|265976740	tae-miR9674a-5p
chr7D:615903829\|615904057	tae-miR1122c-3p; tae-miR1130b-3p; tae-miR1120b-3p
chr1A:589450964\|589476548	tae-miR1121; tae-miR1122c-3p; tae-miR1133; tae-miR171b; tae-miR1130a; tae-miR1130b-3p; tae-miR1120b-3p

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