Abstract
Key message
Transcriptome of Prunus persica revealed several and specific differences in gene expression when subjected to flooding, which provides valuable information for identifying mechanisms involved in the response under stressful conditions.
Abstract
Soil flooding stress in fruit trees affects growth, vegetative and reproductive development, which is reflected in low productivity, poor fruit quality, and premature decay of trees. Using Illumina Hiseq2500 we performed transcriptome analysis of leaves from ‘Capdeboscq’ (P. persica) rootstocks, which are sensitive to hypoxia. Transcriptomes from control and flood-stressed plants (48 h) were compared, using P. persica as reference genome. The flooding conditions changed the transcription profile in ‘Capdeboscq’, and the RNA-seq analysis showed 2971 differentially expressed genes (DEGs), of which 1559 were up-regulated and 1412 were down-regulated. The functional scoring of DEGs was carried out by means of the software MapMan and through the identification of over-represented GOs referring to three ontological classes: biological processes, cell components and molecular function. The major up-regulated processes were those related to the secondary metabolism of lipids, sugars, and tetrapyrrole molecules whereas, for the down-regulated processes, the luminous reactions, photorespiration, metabolism of nitrate and cell wall have stood out. The transcriptome profiling of peach trees supports the development of specific molecular markers for the complete elucidation of molecular mechanisms involved in the response of P. persica under flooding, and this is essential to aid breeding programs in the selection of more tolerant genotypes.
Similar content being viewed by others
References
Al-Shahrour F, Arbiza L, Dopazo H, Huerta-Cepas J, Mínguez P, Montaner D, Dopazo J (2007) From genes to functional classes in the study of biological systems. BMC Bioinform 8:1–17. doi:10.1186/1471-2105-8-114
Arismendi MJ, Almada R, Pimentel P, Bastias A, Salvatierra A, Rojas P, Hinrichsen P, Pinto M, Genova AD, Travisany D, Maass A, Sagredo B (2015) Transcriptome sequencing of Prunus sp. rootstocks roots to identify candidate genes involved in the response to root hypoxia. Tree Genet Genomes 11: 1–16. doi:10.1007/s11295-015-0838-1
Bailey-Serres J, Voesenek LA (2008) Flooding stress: acclimations and genetic diversity. Annu Rev Plant Biol 59:313–339. doi:10.1146/annurev.arplant.59.032607.092752
Bianchi VJ, Sansavini S, Fachinello JC (2005) Microsatellite markers for identification of Prunus spp. Rootstocks. Sci Agric 61:303–306
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 1:170–177
Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Jones DC, Campbell T (2013) RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. PLoS One 8:e82634. doi:10.1371/journal.pone.0082634
Ferner E, Rennenberg H, Kreuzwieser J (2012) Effect of flooding on C metabolism of flood-tolerant (Quercus robur) and non-tolerant (Fagus sylvatica) tree species. Tree Physiol 32:135–145. doi:10.1093/treephys/tps009
Goff L, Trapnell C, Kelley D (2012) CummeRbund: analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data. R package version 2.6.1
Herrera A (2013) Responses to flooding of plant water relations and leaf gas exchange in tropical tolerant trees of a black-water wetland. Front Plant Sci 4:1–12. doi:10.3389/fpls.2013.00106
IBGE Database (2016) http://www.sidra.ibge.gov.br/bda/agric/default.asp?z=t&o=11&i=P. Accessed 23 May 2016
Isaakadis A, Sotiropoulos T, Almaliotis D, Therios I, Stylianidis D (2004) Response to severe water stress of the almond (Prunus amygdalus) ‘Ferragnès’ grafted on eight rootstocks. J Crop Hortic Sci 32:355–362. doi:10.1080/01140671.2004.9514316
Kreuzwieser J, Rennenberg H (2014) Molecular and physiological responses of trees to waterlogging stress. Plant Cell Environ 10:2245–2259. doi:10.1111/pce.12310
Lang GA (2000) Precocious, dwarfing, and productive—how will new cherry rootstocks impact the sweet cherry industry? Hortic Technol 10(4):719–725
LeProvost G, Sulmon C, Frigerio JM, Bodénès C, Kremer A, Plomion C (2012) Role of waterlogging-responsive genes in shaping interspecific differentiation between two sympatric oak species. Tree Physiol 32:119–134. doi:10.1093/treephys/tpr123
Loreti E, Veen HV, Perata P (2016) Plant responses to flooding stress. Curr Opin Plant Biol 33:64–71. 10.1016/j.pbi.2016.06.005
Ma X, Xin Z, Wang Z, Yang Q, Guo S, Guo X, Cao L, Lin T (2015) Identification and comparative analysis of differentially expressed miRNAs in leaves of two wheat (Triticum aestivum L.) genotypes during dehydration stress. BMC Plant Biol 21:1–15. doi:10.1186/s12870-015-0413-9
Martinazzo EG, Perboni AT, Oliveira PV, Bianchi VJ, Bacarin MA (2013) Atividade fotossintética em plantas de ameixeira submetidas ao déficit hídrico e ao alagamento. Ciênc Rural 43:35–41
Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) AP2/ERF family transcription factors in plant abiotic stress responses. Biochim Biophys Acta 1819:86–96. doi:10.1016/j.bbagrm.2011.08.004
Niyogi KK (2000) Safety valves for photosynthesis. Plant Biol 3:455–460
Park W, Scheffler BE, Bauer PJ, Campbell BT (2012) Genome-wide identification of differentially expressed genes under water deficit stress in upland cotton (Gossypium hirsutum L.). BMC Plant Biol 12:1–12. doi:10.1186/1471-2229-12-90
Pervaiz T, Sun X, Zhang Y, Tao R, Zhang J, Fang J (2015) Association between chloroplast and mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium). BMC Plant Biol 15:1–10. doi:10.1186/s12870-014-0402-4
Pfaffl MW, Horgan GW, Dempfle L (2002) Relative expression algoritmo tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30:1–10
Pimentel P, Alamada RD, Salvatierra A, Toro G, Arismendi MJ, Pinto MT, Sagredo B, Pinto M (2014) Physiological and morphological responses of Prunus species with different degree of tolerance to long-term root hypoxia. Sci Hortic 180:14–23
Rabello AR, Guimarães CM, Rangel PHN, Silva FR, Seixas D (2008) Identification of drought-responsive genes in roots of upland rice (Oryza sativa L). BMC Genomics 9:1–13. doi:10.1186/1471-2164-9-485
Rodamilans B, León DS, Mühlberger L, Candresse T, Neumuller M, Oliveros GJA (2014) Analysis of Prunus domestica undergoing hypersensitive response to plum pox virus infection. PLoS One 9(6): e100477. doi:10.1371/journal.pone.0100477
Socquet-Juglard D, Kamber T, Pothier JIF, Christen D, Gessler C, Duffy B, Patocchi A (2013) Comparative RNA-Seq analysis of early-infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. Pruni. PLoS One 8(1): e54196. doi:10.1371/journal.pone.0054196
Supek F, Bošnjak M, Škunca N, Šmuc T (2011) REVIGO sumarizes and visualizes long lists of gene ontology terms. PLoS One 6(7):e21800. doi:10.1371/journal.pone.0021800
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-SEq. Bioinformatics 25:1105–1111. doi:10.1093/bioinformatics/btp120
Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, Van Baren MJ, Salzberg SL, Wold B, Pachter L (2010) Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nat Biotechnol 28(5):511–515. doi:10.1038/nbt0.1621
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7(3):562–578. doi:10.1038/nprot.2012.016
Usadel B, Poree F, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environ 32:1211–1229. doi:10.1111/j.1365-3040.2009.01978.x
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genetics 10:57–63. doi:10.1038/nrg2484
Webster AD (2001) Rootstocks for temperate fruit crops: current uses, future potential and alternative strategies. Acta Hortic 557:25–34. doi:10.17660/ActaHortic.2001.557.1
Xiong H, Li P, Duan J, Zhao Y, Guo X, Li Y, Zhang H, Ali J, Li Z (2014) Overexpression of OsMYB48-1, a novel MYB-related transcription factor, enhances drought and salinity tolerance in rice. PLoS One 9(3):e92913. doi:10.1371/journal.pone.0092913
Yang S-Y, Hao D, Song Z-Z, Yang G-Z, Wang L, Su Y-H (2015) RNA-Seq analysis of differentially expressed genes in rice under varied nitrogen supplies. Gene 555:305–317. doi:10.1016/j.gene.2014.11.021
Zhang X, Yao D, Wang Q, Xu W, Wei Q (2013a) mRNA-seq analysis of the Gossypium arboretum transcriptome reveals tissue selective signaling in response to water stress during seedling stage. PLoS One 8(1):e54762. doi:10.1371/journal.pone.0054762
Zhang Z, Huang S, Wang J, Zhang X, Villena FPM, McMillan L, Wang W (2013b) GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment. Bioinformatics 29:i291–i299. doi:10.1093/bioinformatics/btt216
Zhu Y, Li Y, Xin D, Chen W, Shao X, Wang Y, Guo W (2015) RNA-Seq-based transcriptome analysis of dormant flower buds of Chinese cherry (Prunus pseudocerasus). Gene 555:362–376. 10.1016/j.gene.2014.11.032
Acknowledgements
The authors are thankful to the Brazilian Research Council (CNPq), Coordination of Support to Superior Education (CAPES) and Rio Grande do Sul State Agency for Support to Research (FAPERGS) for grants and fellowships.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Communicated by I. Porth.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Klumb, E.K., Arge, L.W.P., do Amaral, M.N. et al. Transcriptome profiling of Prunus persica plants under flooding. Trees 31, 1127–1135 (2017). https://doi.org/10.1007/s00468-017-1532-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00468-017-1532-8