基于跨物种转录组解析影响不定根发生的保守基因

doi:10.3864/j.issn.0578-1752.2025.06.011

摘要/Abstract

摘要：

【目的】不定根（adventitious root）有利于扩大根系和增强抗逆性，其诱导发生已广泛应用于作物的无性繁殖技术中。通过比较不同物种不定根发生的差异表达基因，分析其中的跨物种保守基因，为全面了解不定根发生的调控机制提供候选基因。【方法】基于公共数据库中矮牵牛、康乃馨、黄瓜、欧美杨、荞麦的不定根发生转录组，采用HISAT和Cufflinks转录组分析流程计算基因转录本丰度，使用DESeq2统计和筛选差异表达基因。将同源比对获得的每个物种差异表达基因（拟南芥最似同源基因），通过集合分析获得处于交集中的基因，进行AmiGO功能注释和富集分析。并使用qPCR对5个物种以外作物的不定根发生相关表达模式进行检验。【结果】共获得保守上调基因15个，参与胁迫响应、细胞分裂、过氧化物、甲羟戊酸等调控路径。下调的保守基因和路径则主要参与离子和化合物稳态调节功能。上调的保守基因随不定根发育进程呈现出两类表达模式（Ⅰ和Ⅱ），NRT3.1和WRKY75在诱导24 h之前，即不定根原基产生时达到峰值（Ⅰ类），而CYCB2;4和KNOLLE表达量在诱导后48—96 h，即不定根凸出表皮时逐渐升高并维持到伸长期（Ⅱ类）。在番茄、西瓜、玉米的不定根诱导发生过程中检验保守基因的表达水平，在试验的双子叶植物类作物番茄、西瓜中，保守基因的表达模式一致，在试验的单子叶类作物玉米中，序列相似性高的WRKY75、CYCB2;4、KNOLLE具有相似的表达模式，序列相似性低的NRT3.1则不同。【结论】在不同物种、不同组织、不同诱导条件下，不定根诱导发生都有赖于胁迫响应和细胞分裂等保守路径和基因的功能发挥。保守上调基因NRT3.1、WRKY75、CYCB2;4、KNOLLE可作为不定根发生的候选基因，在一些双子叶物种中进行深入分析。

关键词: 不定根发生, 不定根诱导, 跨物种转录组, 保守基因分析, 单子叶植物, 双子叶植物

Abstract:

【Objective】 Adventitious root helps expanding root system and enhancing resistance, and its induction is widely used in asexual propagation of crops. Comparisons of the differentially expressed genes associated with adventitious root formation in different species, and analyze the conserved genes among them, so as to provide candidate genes for the comprehensive understanding of the regulatory mechanism of adventitious root formation. 【Method】 Based on the transcriptomes of adventitious root formation of Petunia hybrida, Dianthus caryophyllus, Cucumis sativus, Populus euramericana, and Fagopyrum esculentum that downloaded from the public database, we obtained transcript abundance via HISAT2 and Cufflinks pipeline, and counted and screened the differentially expressed genes by DESeq2. The homologs most similar to Arabidopsis and differentially expressed genes in each species were obtained by homologous alignment. The genes in the intersection set were obtained by set analysis, and their functional annotation and enrichment analysis were carried out in AmiGO. And qPCR was used to examine the expression patterns related to adventitious root development in crops other than these five species.【Result】 A total number of 15 conserved up-regulated genes were obtained from five species, which were mainly participate in stress response, cell division, peroxidase and mevalonate synthesis pathways. The conserved down-regulated genes and pathways mainly participate in the regulation of ion and chemical homeostasis. With the development of adventitious roots, two types (ⅠandⅡ) of expression patterns of up-regulated genes were seen. NRT3.1 and WRKY75 peaked at the early induction stage of 24 hours (typeⅠ), at the period of the adventitious root primordium formation. While the expression levels of CYCB2;4 and KNOLLE increased gradually in the later induction stage of 48-96 hours and extending to the elongation stage (typeⅡ), at the period of the adventitious root protruding beyond the periderm. Consistent patterns of the expression levels of conserved genes during the induction of adventitious roots were identified in tomatoes and watermelons, which belong to dicotyledon. While in monocotyledon like maizes, genes with higher similarity, such as WRKY75, CYCB2;4, and KNOLLE, performed similar patteren, except for NRT3.1. 【Conclusion】 Regardless of various species, tissues, and treatments, the adventitious root formation relies on the conserved pathways and genes involved in stress response and cell division. The conserved up-regulated genes NRT3.1, WRKY75, CYCB2;4, KNOLLE can be used as candidate genes for adventitious root formation for in-depth analysis in many dicotyledonous species.

Key words: adventitious root formation, adventitious root induction, cross species transcriptome, conserved genes analysis, monocotyledon, dicotyledon

谢露露, 李福, 张思远, 高建昌. 基于跨物种转录组解析影响不定根发生的保守基因[J]. 中国农业科学, 2025, 58(6): 1195-1209.

XIE LuLu, LI Fu, ZHANG SiYuan, GAO JianChang. Analysis of Conserved Genes in Adventitious Root Formation Based on Cross Species Transcriptomes[J]. Scientia Agricultura Sinica, 2025, 58(6): 1195-1209.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2025.06.011

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图/表 8

表1

图1

表2

表3

5个物种的差异表达基因集和显著富集GO条目"

物种 <BOLD>S</BOLD>pecies	分析样本 Analysis samples	上调 Up- regulated	下调 Down- regulated	上调基因显著富集GO条目 Significant GO enrichment items of up-regulated gene set	下调基因显著富集GO条目 Significant GO enrichment items of down-regulated gene set
矮牵牛 P. hybrida	72 h vs. 0 h	1757	2777	响应无机物，转录负调控，响应水缺乏，免疫应答，细胞周期 Response to inorganic substance (GO:0010035), Negative regulation of transcription, DNA- templated (GO:0045892), Response to water deprivation (GO:0009414), Immune response (GO:0006955), Cell cycle (GO:0007049)	光合作用，响应光照，碳水化合物合成，多糖代谢 Photosynthesis (GO:0015979), Response to light stimulus (GO:0009416), Carbohydrate biosynthetic process (GO:0016051), Polysaccharide metabolic process (GO:0005976)
康乃馨 D. caryophyllus	54 h vs. 0 h	2638	2679	响应光照，响应温度，光合作用，响应无机物 Response to light stimulus (GO:0009416), Response to temperature stimulus (GO:0009266), Photosynthesis (GO:0015979), Response to inorganic substance (GO:0010035)	响应光照，响应温度，响应创伤，响应脱落酸 Response to light stimulus (GO:0009416), Response to temperature stimulus (GO:0009266), Response to wounding (GO:0009611), Response to abscisic acid (GO:0009737)
黄瓜 C. sativus	48 h vs 0 h	862	632	响应缺氧，激素介导的信号途径，响应乙烯，响应创伤，响应脱落酸 Response to hypoxia (GO:0001666), Hormone- mediated signaling pathway (GO:0009755), Response to ethylene (GO:0009723), Response to wounding (GO:0009611), Response to abscisic acid (GO:0009737)	响应光照，响应温度，光合作用，响应无机物 Response to light stimulus (GO:0009416), Response to temperature stimulus (GO:0009266), Photosynthesis (GO:0015979), Response to inorganic substance (GO:0010035)
欧美杨 P. euramericana	48 h vs 0 h	2539	2527	羧酸代谢，小分子生物合成，响应无机物，响应缺氧，有机环状化合物合成 Carboxylic acid metabolic process (GO:0019752), Small molecule biosynthetic process (GO:0044283), Response to inorganic substance (GO:0010035), Response to hypoxia (GO:0001666), Organic cyclic compound biosynthetic process (GO:1901362)	激素介导的信号途径，细胞壁重组和合成，响应几丁质，响应脱落酸，蛋白质磷酸化 Hormone-mediated signaling pathway (GO:0009755), Cell wall organization or biogenesis (GO:0071554), Response to chitin (GO:0010200), Response to abscisic acid (GO:0009737), Protein phosphorylation (GO:0006468)
荞麦 F. esculentum	24 h vs. 0 h	3882	4826	细胞周期，细胞分裂，有机环状化合物合成，植物器官发育，结构形态发生 Cell cycle (GO:0007049), Cell division (GO: 0051301), Organic cyclic compound biosynthetic process (GO:1901362), Plant organ development (GO:0099402), Anatomical structure morphogenesis (GO:00096532)	光合作用，响应温度，响应光照，响应无机物 Photosynthesis (GO:0015979), Response to temperature stimulus (GO:0009266), Response to light stimulus (GO:0009416), Response to inorganic substance (GO:0010035)

表3

图2

表4

保守基因和路径"

5个物种共有上调基因 Conserved up-regulated genes of five species
拟南芥同源 Arabidopsis homolog	功能注释 Function annotation		矮牵牛 P. hybrida		康乃馨 D. caryophyllus		黄瓜 C. sativus	欧美杨 P. euramericana			荞麦 F. esculentum
AT1G08560.1 KNOLLE	突触融合蛋白类蛋白（膜定位） Syntaxin-related protein (membrane-located)		GO_drpoolB-CL8212Contig1		Dca493		Csa4M192200	Potri.019G030800			tr_5628
AT1G22380.1 UGT85A3	UDP-糖基转移酶 UDP-glycosyltransferase		SG_SGN-U210923, cn7701		Dca32668		Csa3M889760, Csa5M196570	Potri.016G020900, Potri.016G105400			tr_22583
AT1G72210.1 bHLH96	bHLH类转录因子（核定位） Transcription factor bHLH (nucleus-located)		GO_dr004P0004L09_F_ab1		Dca27554, Dca62583		Csa1M570740	Potri.005G071100, Potri.007G097600			tr_19165
AT1G76310.1 CYCB2;4	细胞周期蛋白 Cyclin		GO_dr001P0020K12_F_ab1		Dca10052, Dca44193		Csa4M658580	Potri.002G010000, Potri.009G165800			tr_227
AT1G76490.1 HMGR1	3-羟基-3-甲基戊二酰辅酶A还原酶（内质网膜定位） 3-hydroxy-3-methylglutaryl-coenzyme A reductase (ER-membrane located)		GO_drpoolB-CL1908Contig1, GO_drs31P0005E08_R_ab1, SG_SGN-U211455, cn6794		Dca47843		Csa7M029390	Potri.009G169900, Potri.011G145000			tr_20039, tr_14441
AT2G38870.1 PI	蛋白酶抑制子（细胞质定位） Protease inhibito (cytosol-located)		cn6384, cn6635		Dca48286, Dca9747		Csa3M142910, Csa5M285030, Csa5M027950	Potri.006G212000, Potri.016G078800, Potri.016G079100, Potri.T083400			tr_7136, tr_17033, tr_17679, tr_17678, tr_2447, tr_1043
AT3G20150.1 KIN12F	驱动蛋白样蛋白（微管定位） Kinesin-like protein (microtubule-located)		cn8687		Dca24841, Dca42277		Csa3M062600	Potri.001G360200			tr_8600
AT3G26040.1 AT	HXXXD型乙酰转移酶 HXXXD-type acyl-transferase family protein		GO_dr001P0012O21_F_ab1, GO_dr001P0019J23_F_ab1, GO_dr004P0003P05_F_ab1		Dca38473, Dca41006		Csa4M016450, Csa1M044900, Csa6M088700	Potri.008G180400, Potri.010G056300			tr_990
AT4G02340.1 HL	水解酶（过氧化物酶体定位） Hydrolase (peroxisome-located)		GO_dr001P0013L07_F_ab1		Dca30845, Dca38840, Dca42844, Dca46629, Dca49014, Dca55594		Csa4M001920	Potri.002G202700, Potri.013G134900, Potri.T121600, Potri.T121700			tr_15751, tr_26600
AT5G05340.1 PER	过氧化物酶（外泌） Peroxidase (secreted)		GO_drpoolB-CL2451Contig1, GO_drpoolB-CL7003Contig1, cn2976, cn8344, cn983, cn984		Dca21353, Dca21355, Dca3360, Dca46385, Dca5472		Csa7M049140, Csa6M213910, Csa6M013940	Potri.010G236900, Potri.013G083600, Potri.013G154400, Potri.014G143200, Potri.016G132700, Potri.T163200			tr_5055, tr_5053, tr_5612, tr_8218, tr_22676, tr_11166, tr_27995, tr_4319, tr_18916
AT5G13080.1 WRKY75	WRKY类转录因子（核定位） Probable WRKY transcription factor (nucleus-located)		IP_PHBS002E19u		Dca5929		Csa4M012390	Potri.001G058800, Potri.001G328000, Potri.003G169100, Potri.012G101000, Potri.015G099200, Potri.T043800			tr_16853
AT5G24090.1 CHIT	酸性内切酶（外泌） Acidic endochitinase (secreted)		GO_dr004P0005E08_F_ab1, cn3802		Dca5263, Dca5267		Csa5M139730	Potri.012G033900, Potri.015G024000, Potri.015G024200			tr_20433, tr_26990
AT5G47770.1 FPPS	FPP合成酶（线粒体定位） Farnesyl pyrophosphate synthase (mitochondrion-located)		GO_drpoolB-CL465Contig1		Dca41147, Dca46147		Csa6M017060	Potri.006G003400			tr_19042, tr_16531, tr_24570
AT5G50200.3 NRT3.1	高亲和力硝酸盐转运蛋白（膜定位） High-affinity nitrate transporter (membrane-located)		GO_drpoolB-CL2981Contig1		Dca23627		Csa1M047430	Potri.015G085000, Potri.015G085100			tr_15294
AT5G66230.1 CHI	查尔酮-类黄酮易异构酶 Chalcone-flavonone isomerase		GO_drpoolB-CL5208Contig1		Dca39417, Dca61062		Csa3M002810	Potri.005G114100, Potri.007G057800			tr_20373
5个物种和任意4个物种共有上调基因的GO富集条目 Conserved up-regulated GO enrichment items of five and any four species
路径名称 Pathway name				路径编号 Pathway No.			富集倍数 Fold enrichment			校正P值 Adjusted P value
甲羟戊酸途径Isopentenyl diphosphate biosynthetic process, mevalonate				GO:0019287			>100			0.02
细胞分裂Cell division				GO:0051301			6.62			0.03
响应外部刺激Response to external stimulus				GO:0009605			3.14			0.01
响应化学物质Response to chemical				GO:0042221			2.45			0.03
响应胁迫Response to stress				GO:0006950			2.34			0.01
响应刺激Response to stimulus				GO:0050896			1.97			0.00
5个物种共有下调基因 Conserved down-regulated genes of five species
拟南芥同源Arabidopsis homolog	功能注释 Function annotation		矮牵牛 P. hybrida		康乃馨 D. caryophyllus		黄瓜 C. sativus	欧美杨 P. euramericana			荞麦 F. esculentum
AT1G47670.1 AATL	赖氨酸组氨酸转运蛋白（膜定位） Lysine histidine transporter-like (Membrane-located)		GO_drpoolB-CL6245Contig1		Dca60793		Csa4M638420	Potri.014G036500			tr_13835, tr_21660
AT2G38090.1 HLP	类同源异型域蛋白（核定位） Homeodomain-like superfamily protein (Nucleus-located)		GO_drpoolB-CL6570Contig1, GO_drpoolB-CL6754Contig1, GO_drs13P0026H12_F_ab1		Dca186		Csa3M732480	Potri.001G248800			tr_19808
5个物种和任意4个物种共有下调基因的GO富集条目 Conserved down-regulated GO enrichment items of five and any four species
路径名称 Pathway name		路径编号 Pathway No.				富集倍数 Fold enrichment			校正P值 Adjusted P value
金属离子稳态Metal ion homeostasis		GO:0055065				12.09			0.01
阳离子稳态Cation homeostasis		GO:0055080				9.90			0.02
无机离子稳态Inorganic ion homeostasis		GO:0098771				9.43			0.03
化学稳态Chemical homeostasis		GO:0048878				7.22			0.05

表4

图3

图4

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物种 Species	组织 Tissue	培养体系 Cultivation system	时间点 Time point	数据编号 Accession No.	来源 Source
矮牵牛 P. hybrida	茎基 Stem base	基质扦插 Substrate cuttage	2 h, 6 h, 72 h, 192 h	GSE57752	[6]
康乃馨 D. caryophyllus	茎基 Stem base	水培扦插 Hydroponic cuttage	6 h, 24 h, 54 h	PRJEB9778	[7]
黄瓜 C. sativus	下胚轴 Hypocotyl	水淹 Water-logging	48 h	PRJNA328916	[8]
欧美杨 P. euramericana	茎基 Stem base	培养基扦插 Medium cuttage	2 d, 4 d, 6 d, 8 d	PRJNA516245	[9]
荞麦 F. esculentum	下胚轴外植体 Hypocotyl explants	含IAA培养基 Medium with IAA	6 h, 24 h	PRJNA595876	[10]

基因 Gene	基因序列号 Gene ID	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)
SlNRT3.1	Solyc03g112100.2.1	TTAGTACTCGTGCTATTTTCGTGGC	GACGATTTGTATGGCACCGTTGC
SlWRKY75	Solyc05g015850.2.1	GTCTCATCACGATGGATATGTTTCAT	CCTTGTTTGAAAAGCATATCTTGGTT
SlCYCB2;4	Solyc04g082430.2.1	CATCGTCCAATCACAAGGAAGTTAG	CACAATTGACCAATCTTCTGCATCT
SlKNOLLE	Solyc06g053760.2.1	CAATTCAGGAGCATGGTAGGGG	GGGGATAATGACTACCAGGATGAG
SlUFC1	Solyc04g076890.2.1	ACAGCGGCTGAAGGAAGAATAC	ATCTGGGGCAATTCTTTGCC
ClNRT3.1	ClG42_03g0031100.10	GGGATTCTCTCATGGAAATGTCCAT	TCCACTCAAACTTTTGAACCGTCTT
ClWRKY75	ClG42_07g0155600.10	GTTTTACACAGCCACCACCCG	CTTCTTCTCCAACCCATCTACTCC
ClCYCB2;4	ClG42_11g0205100.10	CCACCGACCCACTTCCAGAC	GAAGCGCAATACCCAGATCGT
ClKNOLLE	ClG42_04g0056600.10	GGCAGCCATGAAAGATCTCG	GATCGTATTACGAAGCGATTTGAG
ClRPB3	ClG42_11g0111300.10	CCGGGAACTCCGAGATGATTAC	GCAAGCATCACAGTCGCGAG
ZmNRT3.1	Zm00001eb007610_T001	TAAAAGACATCACCGAGTACTTCCAC	GAGTCGTTCTCCCTTCGTTGTCC
ZmWRKY75	Zm00001eb353670_T001	TTCGCGTTCCAGACGCG	AGGAGTTGATTAGTGCAAGACTGGA
ZmCYCB2;4	Zm00001eb429190_T001	GCTCACGGACATCAAGAACCTCG	CATATTCTGTTGCTGCAAGCGGG
ZmKNOLLE	Zm00001eb056410_T001	CTTCATGAGCTACGTCGACCTGAAG	GGAGGGCGTCCACCTGGC
ZmEIF5A	Zm00001eb148180_T001	GCATCACCATGAAGAACTCACATCT	ATCAGCTGGGATGCAGCCTGTA