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Cited by 42Plant Molecular Biology ResearchPlant Parasitism and ResistancePlant nutrient uptake and metabolism

Temporal patterns of gene expression associated with tuberous root formation and development in sweetpotato (Ipomoea batatas)

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Wang, Zhangying, Fang, Boping, Chen, Xinliang, Liao, Minghuan, Chen, Jingyi, Zhang, Xiongjian, Huang, Lifei, Luo, Zhongxia +2 more·2015·BMC Plant Biology
DOI 10.1186/s12870-015-0567-5PMC PMC4502468
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Abstract

BACKGROUND: The tuberous root of sweetpotato is undisputedly an important organ from agronomic and biological perspectives. Little is known regarding the regulatory networks programming tuberous root formation and development. RESULTS: Here, as a first step toward understanding these networks, we analyzed and characterized the genome-wide transcriptional profiling and dynamics of sweetpotato root in seven distinct developmental stages using a customized microarray containing 39,724 genes. Analysis of these genes identified temporal programs of gene expression, including hundreds of transcription factor (TF) genes. We found that most genes active in roots were shared across all developmental stages, although significant quantitative changes in gene abundance were observed for 5,368 (including 435 TFs) genes. Clustering analysis of these differentially expressed genes pointed out six distinct expression patterns during root development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that genes involved in different processes were enriched at specific stages of root development. In contrast with the large number of shared expressed genes in root development, each stage or period of root development has only a small number of specific genes. In total, 712 (including 27 TFs) and 1,840 (including 115 TFs) genes were identified as root-stage and root-period specific, respectively at the level of microarray. Several of the specific TF genes are known regulators of root development, including DA1-related protein, SHORT-ROOT and BEL1-like. The remaining TFs with unknown roles would also play critical regulatory roles during sweetpotato tuberous root formation and development. CONCLUSIONS: The results generated in this study provided spatiotemporal patterns of root gene expression in support of future efforts for understanding the underlying molecular mechanism that control sweetpotato yield and quality.

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  • Previous RNA-Seq data have revealed that three homeobox genes are notably upregulated during the formation and thickening of storage roots.

    “Previous RNA-Seq data have revealed that three homeobox genes are notably upregulated during the formation and thickening of storage roots [37].”

    From RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.) (2019) · cites this paper as [37]

    The Results sections on specific and shared genes identify homeodomain or homeobox-related genes during sweetpotato root development, including genes associated with later stages and an increasing expression cluster (page not provided). They do not establish that exactly three homeobox genes were notably upregulated during formation and thickening. The Methods section on hybridization and data extraction identifies the expression experiment as a microarray, not RNA-Seq. (LLM, conf=0.86)

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References 53 · Cited by 42

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  1. [2]Wang Z Fang B Chen J Zhang X Luo Z Huang L De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas) BMC Genomics 2010 11 726 10.1186/1471-2164-11-726 21182800 PMC3016421 · DOI · Paper page
  2. [3]Kokubu T. Thermatological studies on the relationship between the structure of tuberous root and its starch accumulating function in sweet potato varieties. Bull Fac Agric Kogoshima Univ. 1973;23:1–126.
  3. [4]Togari Y. A study in the tuberous-root formation of sweetpotatoes. Bull Natl Agric Exp Sta. 1950;68:1–96.
  4. [6]Eguchi T, Kitano M, Eguchi H. Growth of sweetpotato tuber as affected by the ambient humidity. Biotronics. 1998;27: 93–96.
  5. [7]Hill J Douglas D David P Mortley D Trotman A Bonsi C Biomass accumulation in hydroponically grown sweetpotato in a controlled environment: a preliminary study Acta Hortic 1996 440 25 30 11541575
  6. [8]Kano Y, Ming ZJ. Effects of soil temperature on the thickening growth and the quality of sweetpotato during the latter part of their growth. Environ Control Biol. 2000;38:113–120.
  7. [9]Loretan PA, Bonsi CK, Mortley DG, Wheeler RM, Mackowiak CL, Hill WA, et al. Effects of several environmental factors on sweetpotato growth. Advances in Space Research. 1994;14:277–280. 11540193
  8. [10]Mortley D Hill J Loretan P Bonsi C Hill W Hileman D Elevated carbon dioxide influences yield and photosynthetic responses of hydroponically-grown [correction of glown] sweetpotato Acta Hortic 1996 440 31 36 11541577
  9. [11]Pardales JR, Ban˜ oc DM, Yamauchi A, Iijima M, Kono Y. Root system development of cassava and sweetpotato during early growth stage as affected by high root zone temperature. Plant Production Sci. 1999;2:247–251.
  10. [12]Van Heerden PD Laurie R Effects of prolonged restriction in water supply on photosynthesis, shoot development and storage root yield in sweet potato Physiol Plant 2008 134 99 109 10.1111/j.1399-3054.2008.01111.x 18494734 · DOI
  11. [13]Sugiyama T, Suye S, Hashizume T. Massspectrometric determination of cytokinins in young sweet-potato plants using deuterium-labeled standards. Agric Biol Chem. 1983;47:315–318.
  12. [14]Matsuo T, Mitsuzono H, Okada R, Itoo S. Variations in the levels of major free cytokinins and free abscisic acid during tuber development of sweetpotato. J Plant Growth Regul. 1988;7:249–258.
  13. [15]Nakatani M Komeichi M Changes in endogenous indole acetic acid level during development of roots in sweet potato Japan J Crop Sci 1992 61 683 684 10.1626/jcs.61.683 · DOI
  14. [18]Gan LJ, Zeng XC, Zhou X. Possible involvement of jasmonates in the morphogenesis of underground storage organs in plants. Chinese Bulletin of Botany. 2001;18:546–553.
  15. [20]Tanaka M Takahata Y Nakatani M Analysis of genes developmentally regulated during storage root formation of sweet potato J Plant Physiol 2005 162 91 102 10.1016/j.jplph.2004.06.003 15700424 · DOI
  16. [21]Tanaka M Kato N Nakayama H Nakatani M Takahata Y Expression of class I knotted1-like homeobox genes in the storage roots of sweetpotato (Ipomoea batatas) J Plant Physiol 2008 165 1726 1735 10.1016/j.jplph.2007.11.009 18242774 · DOI · Paper page
  17. [24]Ku AT Huang YS Wang YS Ma D Yeh KW IbMADS1 (Ipomoea batatas MADS-box 1 gene) is involved in tuberous root initiation in sweet potato (Ipomoea batatas) Ann Bot 2008 102 57 67 10.1093/aob/mcn067 18463111 PMC2712425 · DOI · Paper page
  18. [25]Xie F Burklew CE Yang Y Liu M Xiao P Zhang B De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome Planta 2012 236 101 113 10.1007/s00425-012-1591-4 22270559 · DOI
  19. [29]Pertea G Huang X Liang F Antonescu V Sultana R Karamycheva S TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets Bioinformatics 2003 19 651 652 10.1093/bioinformatics/btg034 12651724 · DOI
  20. [30]Yang J An D Zhang P Expression profiling of cassava storage roots reveals an active process of glycolysis/gluconeogenesis J Integr Plant Biol 2011 53 193 211 10.1111/j.1744-7909.2010.01018.x 21205184 · DOI · Paper page
  21. [31]Peng Y Ma W Chen L Yang L Li S Zhao H Control of root meristem Size by DA1-RELATED PROTEIN2 in Arabidopsis Plant Physiol 2013 161 1542 1556 10.1104/pp.112.210237 23296689 PMC3585615 · DOI
  22. [32]Helariutta Y Fukaki H Wysocka-Diller J Nakajima K Jung J Sena G The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling Cell 2000 101 555 567 10.1016/S0092-8674(00)80865-X 10850497 · DOI
  23. [33]Qin YM Hu CY Pang Y Kastaniotis AJ Hiltunen JK Zhu YX Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis Plant Cell 2007 19 3692 3704 10.1105/tpc.107.054437 17993622 PMC2174872 · DOI
  24. [34]Devaiah BN Karthikeyan AS Raghothama KG WRKY75 transcription factor is a modulator of phosphate acquisition and root development in Arabidopsis Plant Physiol 2007 143 1789 1801 10.1104/pp.106.093971 17322336 PMC1851818 · DOI
  25. [35]Zhao L Hao D Chen L Lu Q Zhang Y Li Y Roles for a soybean RAV-like orthologue in shoot regeneration and photoperiodicity inferred from transgenic plants J Exp Bot 2012 63 3257 3270 10.1093/jxb/ers056 22389516 · DOI
  26. [36]Okushima Y Fukaki H Onoda M Theologis A Tasaka M ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis Plant Cell 2007 19 118 130 10.1105/tpc.106.047761 17259263 PMC1820965 · DOI
  27. [37]Wang JW Wang LJ Mao YB Cai WJ Xue HW Chen XY Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis Plant Cell 2005 17 2204 2216 10.1105/tpc.105.033076 16006581 PMC1182483 · DOI
  28. [38]Sun CW Huang YC Chang HY CIA2 coordinately up-regulates protein import and synthesis in leaf chloroplasts Plant Physiol 2009 150 879 888 10.1104/pp.109.137240 19386807 PMC2689949 · DOI
  29. [39]Wang L Xu Y Zhang C Ma Q Joo SH Kim SK OsLIC, a Novel CCCH-Type Zinc Finger Protein with Transcription Activation, Mediates Rice Architecture via Brassinosteroids Signaling PLoS One 2008 3 e3521 10.1371/journal.pone.0003521 18953406 PMC2567845 · DOI
  30. [41]Yin WB Reinke AW Szilagyi M Emri T Chiang YM Keating AE bZIP transcription factors affecting secondary metabolism, sexual development and stress responses in Aspergillus nidulans Microbiology 2013 159 77 88 10.1099/mic.0.063370-0 23154967 PMC3542729 · DOI
  31. [42]Banerjee AK Chatterjee M Yu Y Suh SG Miller WA Hannapel DJ Dynamics of a mobile RNA of potato involved in a long-distance signaling pathway Plant Cell 2006 18 3443 3457 10.1105/tpc.106.042473 17189340 PMC1785412 · DOI
  32. [43]Lin T Sharma P Gonzalez DH Viola IL Hannapel DJ The impact of the long-distance transport of a BEL1-like messenger RNA on development Plant Physiol 2013 161 760 772 10.1104/pp.112.209429 23221774 PMC3561017 · DOI
  33. [44]Le BH Cheng C Bui AQ Wagmaister JA Henry KF Pelletier J Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors Proc Natl Acad Sci U S A 2010 107 8063 8070 10.1073/pnas.1003530107 20385809 PMC2889569 · DOI
  34. [45]Zrenner R Salanoubat M Willmitzer L Sonnewald U Evidence of the crucial role of sucrose synthase for sink strength using transgenic potato plants (Solanum tuberosum L.) Plant J 1995 7 97 107 10.1046/j.1365-313X.1995.07010097.x 7894514 · DOI
  35. [46]Prat S Frommer WB Hofgen R Keil M Kossmann J Koster-Topfer M Gene expression during tuber development in potato plants FEBS Lett 1990 268 334 338 10.1016/0014-5793(90)81281-R 2200713 · DOI
  36. [47]Gou JY Wang LJ Chen SP Hu WL Chen XY Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis Cell Res 2007 17 422 434 17387330
  37. [48]Hutchings D Rawsthorne S Emes MJ Fatty acid synthesis and the oxidative pentose phosphate pathway in developing embryos of oilseed rape (Brassica napus L.) J Exp Bot 2005 56 577 585 10.1093/jxb/eri046 15611146 · DOI
  38. [49]Hills MJ Control of storage-product synthesis in seeds Curr Opin Plant Biol 2004 7 302 308 10.1016/j.pbi.2004.03.003 15134751 · DOI
  39. [50]Zhang Y, Fang B. Descriptors and data standard for sweetpotato [Ipomoea batatas (L.) Lam.]. China Agricultural Press. Beijing, 2006: p.83.
  40. [51]Wang Z Li J Luo Z Huang L Chen X Fang B Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas) BMC Plant Biol 2011 11 139 10.1186/1471-2229-11-139 22011271 PMC3206431 · DOI
  41. [52]Conesa A Gotz S Garcia-Gomez JM Terol J Talon M Robles M Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Bioinformatics 2005 21 3674 3676 10.1093/bioinformatics/bti610 16081474 · DOI
  42. [53]Laux T Wurschum T Breuninger H Genetic regulation of embryonic pattern formation Plant Cell 2004 16 Suppl S190 202 10.1105/tpc.016014 15100395 PMC2643395 · DOI
  43. [54]Seo JS Joo J Kim MJ Kim YK Nahm BH Song SI OsbHLH148, a basic helix-loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice Plant J 2011 65 907 921 10.1111/j.1365-313X.2010.04477.x 21332845 · DOI
  44. [55]Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci U S A 1998 95 14863 14868 10.1073/pnas.95.25.14863 9843981 PMC24541 · DOI · Paper page

Authors
Wang, Z., Fang, B., Chen, X., Liao, M., Chen, J., Zhang, X., Huang, L., Luo, Z., Yao, Z., & Li, Y.
Affiliations
Guangdong Academy of Agricultural Sciences (CN)
Corresponding author
Fang, Boping
ORCID
Venue
BMC Plant Biology
Publisher
Springer Science and Business Media LLC
Published
2015-07-16
Volume
15
Issue
1
Pages
180-180
ISSN
1471-2229 (ISSN-L)
DOI
10.1186/s12870-015-0567-5
PMC
PMC4502468
OpenAlex
W1508958840
Cited by
42
References
53
Citations by year
2026: 1 · 2025: 3 · 2024: 8 · 2023: 5 · 2022: 3 · 2021: 4 · 2020: 4 · 2019: 5 · 2018: 3 · 2017: 3 · 2016: 3
FWCI
3.63
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Plant Biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Pearl River Science and Technology Nova of Guangzhou (2012J2200067)
  • earmarked fund for Modern Agro-industry Technology Research System (nycytx-16-B-5)
  • National Natural Science Foundation of China (31000737)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Parasitism and Resistance
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant nutrient uptake and metabolism
Keywords
Ipomoea batatas, root development, temporal gene expression, transcription factors, differentially expressed genes, SHORT-ROOT, gene regulatory networks
MeSH terms
Gene Expression Regulation, Plant, Gene Expression Regulation, Developmental, Plant Roots, Oligonucleotide Array Sequence Analysis, Ipomoea batatas, Transcriptome

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