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Tree Genetics & Genomes

, 11:11 | Cite as

Transcriptome sequencing of Prunus sp. rootstocks roots to identify candidate genes involved in the response to root hypoxia

  • María José Arismendi
  • Rubén Almada
  • Paula Pimentel
  • Adriana Bastias
  • Ariel Salvatierra
  • Pamela Rojas
  • Patricio Hinrichsen
  • Manuel Pinto
  • Alex Di Genova
  • Dante Travisany
  • Alejandro Maass
  • Boris Sagredo
Original Paper

Abstract

Root hypoxia in fruit trees affects growth, vegetative development, and reproductive development, which is reflected in low productivity, poor fruit quality, and premature decay of trees. Using Illumina Hiseq2000, we performed transcriptome analysis of roots from two different rootstocks, ‘Mariana 2624’ and ‘Mazzard F12/1,’ which are tolerant and sensitive to hypoxia, respectively. Transcriptomes from control and hypoxia-stressed plants (6, 24, and 72 h) were compared, using Prunus persica (L.) as reference genome. Hypoxic conditions altered the transcription in both genotypes. There were a high number of common differentially expressed genes (DEG) between the two genotypes for each sampling time, but also exclusive DEG for each genotype, with a few DEG that presented opposite modes of regulations during the hypoxia treatment. An important group of DEGs exclusively upregulated in the tolerant genotype are associated to enzymes of posttranslational protein modifications, such as leucine-rich repeat (LRR), kinases and ubiquitin-protein ligases, regulation of transcription, and process of oxide reduction. Singular enrichment analysis of gene ontology (GO), detected at least 115 GOs involved in the response to root hypoxia in the sensitive and/or tolerant genotypes. At least 25 GOs were identified as part of the baseline differences between the genotypes, most GO were disturbed in the sensitive genotype. The contribution from the baseline gene expression to the differential response between the Prunus genotypes is evidence that the resistant genotype is already “prepared” for a hypoxia event. An example are GO BP:0042221 of response to chemical stimulus; BP:0006979 of response to oxidative stress; MF:0016209 of antioxidant activity; MF:0016684 of oxidoreductase activity, acting on peroxide as acceptor; and MF:0004601 of peroxidase activity, which were disturbed only in the sensitive genotype, but not in the tolerant.

Keywords

Hypoxia Prunus qRT-PCR RNA-Seq Rootstock Transcriptome sequencing 

Notes

Acknowledgments

This work was funded by grants from FONDECYT (No. 1121117) and CEAF_R08I1001. We acknowledge the CONICYT scholarships “Doctorado en Chile 2008 (21080351)” and “Apoyo para la Realización de Tesis Doctoral 2010 (24100126),” both to MJ. This paper is part of MJ Arismendi doctoral degree dissertation from the Universidad de La Frontera, Temuco, Chile. R.A. and P.P. were supported by grants from CONICYT (Project No. 79095006). Rootstock plants were kindly provided by Agromillora Sur, S.A.

Data archiving statement

RNA-Seq time series data for Prunus avium cv F12 and Prunus cerasifera × Prunus munsoniana cv. Mariana 2624 can be downloaded from NCBI BioProjects PRJNA215068 and PRJNA215360, respectively.

Supplementary material

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • María José Arismendi
    • 1
    • 2
  • Rubén Almada
    • 2
    • 4
  • Paula Pimentel
    • 2
    • 4
  • Adriana Bastias
    • 2
    • 4
  • Ariel Salvatierra
    • 2
    • 4
  • Pamela Rojas
    • 2
    • 4
  • Patricio Hinrichsen
    • 2
    • 3
  • Manuel Pinto
    • 2
    • 3
  • Alex Di Genova
    • 5
  • Dante Travisany
    • 5
  • Alejandro Maass
    • 5
  • Boris Sagredo
    • 2
    • 4
  1. 1.Programa Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Facultad de Ciencias Agropecuarias y ForestalesUniversidad de La FronteraTemucoChile
  2. 2.Centro de Estudios Avanzados en Fruticultura (CEAF)RengoChile
  3. 3.Instituto de Investigaciones Agropecuarias CRI La PlatinaLa PintanaChile
  4. 4.Instituto de Investigaciones Agropecuarias CRI RayentuéRengoChile
  5. 5.Mathomics, Centro de Regulación del Genoma (Fondap 15090007) & Centro de Modelamiento MatemáticoUniversidad de ChileSantiagoChile

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