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Publishing Language: Chinese

Analysis of Conserved Genes in Adventitious Root Formation Based on Cross Species Transcriptomes

LuLu XIE, Fu LI, SiYuan ZHANG, JianChang GAO( )
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding, Beijing 100081
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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.

Keywords

adventitious root formationadventitious root inductioncross species transcriptomeconserved genes analysismonocotyledondicotyledon

References

[1]
BELLINI C, PACURAR D I, PERRONE I. Adventitious roots and lateral roots: Similarities and differences. Annual Review of Plant Biology, 2014, 65: 639-666.
Crossref Google Scholar
[2]
VERSTRAETEN I, SCHOTTE S, GEELEN D. Hypocotyl adventitious root organogenesis differs from lateral root development. Frontiers in Plant Science, 2014, 5: 495.
Crossref Google Scholar
[3]
STEFFENS B, RASMUSSEN A. The physiology of adventitious roots. Plant Physiology, 2016, 170(2): 603-617.
Crossref Google Scholar
[4]
BLAKESLEY D, WESTON G D, HALL J F. The role of endogenous auxin in root initiation. Plant Growth Regulation, 1991, 10(4): 341-353.
Crossref Google Scholar
[5]
DE KLERK G J, VAN DER KRIEKEN W, DE JONG J C. Review the formation of adventitious roots: New concepts, new possibilities. In Vitro Cellular & Developmental Biology-Plant, 1999, 35(3): 189-199.
Crossref Google Scholar
[6]
AHKAMI A, SCHOLZ U, STEUERNAGEL B, STRICKERT M, HAENSCH K T, DRUEGE U, REINHARDT D, NOURI E, VON WIRÉN N, FRANKEN P, HAJIREZAEI M R. Comprehensive transcriptome analysis unravels the existence of crucial genes regulating primary metabolism during adventitious root formation in Petunia hybrida. PLoS ONE, 2014, 9(6): e100997.
Crossref Google Scholar
[7]
VILLACORTA-MARTÍN C, SÁNCHEZ-GARCÍA A B, VILLANOVA J, CANO A, VAN DE RHEE M, DE HAAN J, ACOSTA M, PASSARINHO P, PÉREZ-PÉREZ J M. Gene expression profiling during adventitious root formation in carnation stem cuttings. BMC Genomics, 2015, 16: 789.
Crossref Google Scholar
[8]
XU X W, CHEN M Y, JI J, XU Q, QI X H, CHEN X H. Comparative RNA-seq based transcriptome profiling of waterlogging response in cucumber hypocotyls reveals novel insights into the de novo adventitious root primordia initiation. BMC Plant Biology, 2017, 17(1): 129.
Crossref Google Scholar
[9]
ZHANG Y, XIAO Z A, ZHAN C, LIU M F, XIA W X, WANG N. Comprehensive analysis of dynamic gene expression and investigation of the roles of hydrogen peroxide during adventitious rooting in poplar. BMC Plant Biology, 2019, 19(1): 99.
Crossref Google Scholar
[10]
LARSKAYA I, GORSHKOV O, MOKSHINA N, TROFIMOVA O, MIKSHINA P, KLEPIKOVA A, GOGOLEVA N, GORSHKOVA T. Stimulation of adventitious root formation by the oligosaccharin OSRG at the transcriptome level. Plant Signaling & Behavior, 2020, 15(1): 1703503.
Crossref Google Scholar
[11]
CHEN K M, GUO B, YU C M, CHEN P, CHEN J K, GAO G, WANG X F, ZHU A G. Comparative transcriptome analysis provides new insights into the molecular regulatory mechanism of adventitious root formation in ramie (Boehmeria nivea L.). Plants, 2021, 10(1): 160.
Crossref Google Scholar
[12]
LUO J, NVSVROT T, WANG N. Comparative transcriptomic analysis uncovers conserved pathways involved in adventitious root formation in poplar. Physiology and Molecular Biology of Plants, 2021, 27(9): 1903-1918.
Crossref Google Scholar
[13]
DA COSTA C T, DE ALMEIDA M R, RUEDELL C M, SCHWAMBACH J, MARASCHIN F S, FETT-NETO A G. When stress and development go hand in hand: Main hormonal controls of adventitious rooting in cuttings. Frontiers in Plant Science, 2013, 4: 133.
Crossref Google Scholar
[14]
JING T T, ARDIANSYAH R, XU Q J, XING Q, MÜLLER-XING R. Reprogramming of cell fate during root regeneration by transcriptional and epigenetic networks. Frontiers in Plant Science, 2020, 11: 317.
Crossref Google Scholar
[15]
LAKEHAL A, BELLINI C. Control of adventitious root formation: Insights into synergistic and antagonistic hormonal interactions. Physiologia Plantarum, 2019, 165(1): 90-100.
Crossref Google Scholar
[16]
VIDOZ M L, LORETI E, MENSUALI A, ALPI A, PERATA P. Hormonal interplay during adventitious root formation in flooded tomato plants. The Plant Journal, 2010, 63(4): 551-562.
Crossref Google Scholar
[17]
GUTIERREZ L, MONGELARD G, FLOKOVÁ K, PĂCURAR D I, NOVÁK O, STASWICK P, KOWALCZYK M, PĂCURAR M, DEMAILLY H, GEISS G, BELLINI C. Auxin controls Arabidopsis adventitious root initiation by regulating jasmonic acid homeostasis. The Plant Cell, 2012, 24(6): 2515-2527.
Crossref Google Scholar
[18]
RASMUSSEN A, MASON M G, DE CUYPER C, BREWER P B, HEROLD S, AGUSTI J, GEELEN D, GREB T, GOORMACHTIG S, BEECKMAN T, BEVERIDGE C A. Strigolactones suppress adventitious rooting in Arabidopsis and pea. Plant Physiology, 2012, 158(4): 1976-1987.
Crossref Google Scholar
[19]
STEFFENS B, WANG J X, SAUTER M. Interactions between ethylene, gibberellin and abscisic acid regulate emergence and growth rate of adventitious roots in deepwater rice. Planta, 2006, 223(3): 604-612.
Crossref Google Scholar
[20]
PATEL R K, JAIN M. NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE, 2012, 7(2): e30619.
Crossref Google Scholar
[21]
KIM D, LANGMEAD B, SALZBERG S L. HISAT: A fast spliced aligner with low memory requirements. Nature Methods, 2015, 12(4): 357-360.
Crossref Google Scholar
[22]
TRAPNELL C, ROBERTS A, GOFF L, PERTEA G, KIM D, KELLEY D R, PIMENTEL H, SALZBERG S L, RINN J L, PACHTER L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 2012, 7(3): 562-578.
Crossref Google Scholar
[23]
LOVE M I, HUBER W, ANDERS S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 2014, 15(12): 550.
Crossref Google Scholar
[24]
ALTSCHUL S F, GISH W, MILLER W, MYERS E W, LIPMAN D J. Basic local alignment search tool. Journal of Molecular Biology, 1990, 215(3): 403-410.
Crossref Google Scholar
[25]
ASHBURNER M, BALL C A, BLAKE J A, BOTSTEIN D, BUTLER H, CHERRY J M, DAVIS A P, DOLINSKI K, DWIGHT S S, EPPIG J T, HARRIS M A, HILL D P, ISSEL-TARVER L, KASARSKIS A, LEWIS S, MATESE J C, RICHARDSON J E, RINGWALD M, RUBIN G M, SHERLOCK G. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics, 2000, 25(1): 25-29.
Crossref Google Scholar
[26]
KOLDE R. pheatmap: Pretty Heatmaps. R package version1.0.12. 2019.
[27]
LIVAK K J, SCHMITTGEN T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C(T)) Method. Methods, 2001, 25(4): 402-408.
Crossref Google Scholar
[28]
RASMUSSEN A, HOSSEINI S A, HAJIREZAEI M R, DRUEGE U, GEELEN D. Adventitious rooting declines with the vegetative to reproductive switch and involves a changed auxin homeostasis. Journal of Experimental Botany, 2015, 66(5): 1437-1452.
Crossref Google Scholar
[29]
KROUK G, TILLARD P, GOJON A. Regulation of the high-affinity NO3- uptake system by NRT1.1-mediated NO3- demand signaling in Arabidopsis. Plant Physiology, 2006, 142(3): 1075-1086.
Crossref Google Scholar
[30]
MOTTE H, VANNESTE S, BEECKMAN T. Molecular and environmental regulation of root development. Annual Review of Plant Biology, 2019, 70: 465-488.
Crossref Google Scholar
[31]
YANG M M, WANG Y X, CHEN C, XIN X, DAI S S, MENG C, MA N N. Transcription factor WRKY75 maintains auxin homeostasis to promote tomato defense against Pseudomonas syringae. Plant Physiology, 2024, 195(2): 1053-1068.
Crossref Google Scholar
[32]
DE VEYLDER L, BEECKMAN T, INZÉ D. The ins and outs of the plant cell cycle. Nature Reviews Molecular Cell Biology, 2007, 8: 655-665.
Crossref Google Scholar
[33]
LUKOWITZ W, MAYER U, JÜRGENS G. Cytokinesis in the Arabidopsis embryo involves the syntaxin-related KNOLLE gene product. Cell, 1996, 84(1): 61-71.
Crossref Google Scholar
[34]
NISHIHAMA R, SOYANO T, ISHIKAWA M, ARAKI S, TANAKA H, ASADA T, IRIE K, ITO M, TERADA M, BANNO H, YAMAZAKI Y, MACHIDA Y. Expansion of the cell plate in plant cytokinesis requires a kinesin-like protein/MAPKKK complex. Cell, 2002, 109(1): 87-99.
Crossref Google Scholar
[35]
JEZ J M, BOWMAN M E, DIXON R A, NOEL J P. Structure and mechanism of the evolutionarily unique plant enzyme Chalcone isomerase. Nature Structural Biology, 2000, 7(9): 786-791.
Crossref Google Scholar
[36]
MARJAMAA K, KUKKOLA E M, FAGERSTEDT K V. The role of xylem class III peroxidases in lignification. Journal of Experimental Botany, 2009, 60(2): 367-376.
Crossref Google Scholar
[37]
CORREA L R, STEIN R J, FETT-NETO A G. Adventitious rooting of detached Arabidopsis thaliana leaves. Biologia Plantarum, 2012, 56(1): 25-30.
Crossref Google Scholar
[38]
ZHU Y N, SHI D Q, RUAN M B, ZHANG L L, MENG Z H, LIU J, YANG W C. Transcriptome analysis reveals crosstalk of responsive genes to multiple abiotic stresses in cotton (Gossypium hirsutum L.). PLoS ONE, 2013, 8(11): e80218.
Crossref Google Scholar
[39]
LIAO P, HEMMERLIN A, BACH T J, CHYE M L. The potential of the mevalonate pathway for enhanced isoprenoid production. Biotechnology Advances, 2016, 34(5): 697-713.
Crossref Google Scholar
[40]
CAPUTI L, LIM E K, BOWLES D J. Discovery of new biocatalysts for the glycosylation of terpenoid scaffolds. Chemistry, 2008, 14(22): 6656-6662.
Crossref Google Scholar
Scientia Agricultura Sinica
Volume 58 Issue 6,
March 2025
Pages 1195-1209
DOI: 10.3864/j.issn.0578-1752.2025.06.011

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Cite this article:
XIE L, LI F, ZHANG S, et al. Analysis of Conserved Genes in Adventitious Root Formation Based on Cross Species Transcriptomes. Scientia Agricultura Sinica, 2025, 58(6): 1195-1209. https://doi.org/10.3864/j.issn.0578-1752.2025.06.011

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Received: 17 August 2024
Accepted: 07 November 2024
Published: 16 March 2025
© 2025 The Journal of Scientia Agricultura Sinica