1. bookVolume 67 (2018): Edition 1 (February 2018)
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Genetic effect in leaf and xylem transcriptome variations among Eucalyptus urophylla x grandis hybrids in field conditions

Publié en ligne: 28 Jun 2018
Volume & Edition: Volume 67 (2018) - Edition 1 (February 2018)
Pages: 57 - 65
Détails du magazine
Première parution
22 Feb 2016
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To assess the genetic and environmental components of gene-expression variation among trees we used RNA-seq technology and Eucalyptus urophylla x grandis hybrid clones tested in field conditions. Leaf and xylem transcriptomes of three 20 month old clones differing in terms of growth, repeated in two blocks, were investigated. Transcriptomes were very similar between ramets. The number of expressed genes was significantly (P<0.05) higher in leaf (25,665±634) than in xylem (23,637±1,241). A pairwise clone comparisons approach showed that 4.5 to 14 % of the genes were diffe­rentially expressed (false discovery rate [FDR]<0.05) in leaf and 7.1 to 16 % in xylem. An assessment of among clone variance components revealed significant results in leaf and xylem in 3431 (248) genes (at FDR<0.2) and 160 (3) (at FDR<0.05), respectively. These two complementary approa­ches displayed correlated results. A focus on the phenylpro­panoid, cellulose and xylan pathways revealed a large majo­rity of low expressed genes and a few highly expressed ones, with RPKM values ranging from nearly 0 to 600 in leaf and 10,000 in xylem. Out of the 115 genes of these pathways, 45 showed differential expression for at least one pair of geno­type, five of which displaying also clone variance compo­nents. These preliminary results are promising in evaluating whether gene expression can serve as possible ‘intermediate phenotypes’ that could improve the accuracy of selection of grossly observable traits.


Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Cambridge: Babraham Institute Bioinformatics [online]. To be found at <http://www.bioinformatics.babraham.ac.uk/projects/fastqc> [quoted 18 June 2016] Search in Google Scholar

Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Roy Statist Soc Ser B (Method­ological) 57(1):289-300 10.1111/j.2517-6161.1995.tb02031.xSearch in Google Scholar

Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A, Galaxy Team (2010) Manipulation of FASTQ data with Galaxy. Bioinformatics 26(14):1783-1785. https://doi.org/10.1093/bioinformatics/btq281 10.1093/bioinformatics/btq281289451920562416Ouvrir le DOISearch in Google Scholar

Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcrip­tional regulation in budding yeast. Science 296(5568):752-755. https://doi.org/10.1126/science.1069516 10.1126/.1069516Ouvrir le DOISearch in Google Scholar

Camargo EL, Nascimento LC, Soler M, Salazar MM, Lepikson-Neto J, Marques WL, Alves A, Teixeira PJ, Mieczkowski P, Carazzolle MF, Martinez Y, Deckmann AC, Rodrigues JC, Grima-Pettenati J, Pereira GA (2014) Contrasting nitrogen fer­tilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus. BMC Plant Biol 14:256 https://doi.org/10.1186/s12870-014-0256-9 10.1186/s12870-014-0256-9418975725260963Ouvrir le DOISearch in Google Scholar

Carocha V, Soler M, Hefer C, Cassan-Wang H, Fevereiro P, Myburg AA, Paiva JA, Grima-Pettenati J (2015) Genome-wide analysis of the lignin toolbox of Eu­calyptus grandis. New Phytol 206(4):1297-1313. https://doi.org/10.1111/nph.13313 10.1111/nph.1331325684249Ouvrir le DOISearch in Google Scholar

Cheung VG, Jen KY, Weber T, Morley M, Devlin JL, et al. (2003) Genetics of quan­titative variation in human gene expression. Cold Spring Harbor Symp Quant Biol 68:403-407. https://doi.org/10.1101/sqb.2003.68.403 10.1101/sqb.2003.68.40315338642Ouvrir le DOISearch in Google Scholar

Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2go: a universal tool for annotation, visualization and analysis in functional ge­nomics research. Bioinformatics 21(18):3674-3676. https://doi.org/10.1093/bioinformatics/bti610 10.1093/bioinformatics/bti61016081474Ouvrir le DOISearch in Google Scholar

Druka A, Potokina E, Luo Z, Jiang N, Chen X, Kearsey M, Waugh R (2010) Expres­sion quantitative trait loci analysis in plants. Plant Biotechnol J 8(1):10-27. https://doi.org/10.1111/j.1467-7652.2009.00460.x 10.1111/j.1467-7652.2009.00460.x20055957Ouvrir le DOISearch in Google Scholar

Evtuguin DV, Pascoal Neto C (2007) Recent advances in eucalyptus wood chem­istry: Structural features through the prism of technological response. In: 3th International Colloquium on Eucalyptus Pulp. Belo Horizonte, Brasil Search in Google Scholar

Falconer DS, Mackay Longman TFC (1996) Introduction to Quantitative Genet­ics, 4th ed. Harlow, UK: Pearson United Kingdom, 480p, ISBN 9780582243026 Search in Google Scholar

Gibson G, Weir B (2005) The quantitative genetics of transcription. Trends Genet 21(11): 616-623. https://doi.org/10.1016/j.tig.2005.08.010 10.1016/j.tig.2005.08.01016154229Ouvrir le DOISearch in Google Scholar

Gilad Y, Rifkin SA, Pritchard JK (2008) Revealing the architecture of gene regula­tion: the promise of eQTL studies. Trends Genet 24(8):408-415. https://doi.org/10.1016/j.tig.2008.06.001 10.1016/j.tig.2008.06.001258307118597885Search in Google Scholar

Gilmour AR, Gogel BJ, Cullis BR, Welham SJ, Thompson R (2006) ASReml, User Guide. Release 2.0. VSN International Ltd: Hemel Hempstead, UK Search in Google Scholar

Goecks J, Nekrutenko A, Taylor J, Galaxy Team (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent compu­tational research in the life sciences. Genome Biol 11(8):R86. https://doi.org/10.1186/gb-2010-11-8-r86 10.1186/gb-2010-11-8-r86Search in Google Scholar

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012) Phytozome: a comparative plat­form for green plant genomics. Nucleic Acids Res 40(D1): D1178-D1186 https://doi.org/10.1093/nar/gkr944 10.1093/nar/gkr944Search in Google Scholar

Harikrishnan SL, Pucholt P, Berlin S (2015) Sequence and gene expression evolu­tion of paralogous genes in willows. Sci Rep 5:18662. https://doi.org/10.1038/srep18662 10.1038/srep18662Ouvrir le DOISearch in Google Scholar

Hefer CA, Mizrachi E, Myburg AA, Douglas CJ, Mansfield SD (2015) Comparative interrogation of the developing xylem transcriptomes of two wood-form­ing species: populus trichocarpa and Eucalyptus grandis. New Phytol 206(4):1391-1405. https://doi.org/10.1111/nph.13277 10.1111/nph.13277Ouvrir le DOISearch in Google Scholar

Hegarty MJ, Barker GLA, Brennan AC, Edwards KJ, Abbott RJ, Hiscock SJ (2008) Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio. Philos Trans R Soc B 363(1506):3055-3069. https://doi.org/10.1098/rstb.2008.0080 10.1098/rstb.2008.0080Ouvrir le DOISearch in Google Scholar

Huang X, Han B (2014) Natural variations and genome-wide association studies in crop plants. Annu Rev Plant Biol 65:531-551. https://doi.org/10.1146/annurev-arplant-050213-035715 10.1146/annurev-arplant-050213-035715Ouvrir le DOISearch in Google Scholar

Jansen RC, Nap JP (2001) Genetical genomics: the added value from segrega­tion. Trends Genet 17(7):388-391. https://doi.org/10.1016/s0168-9525(01)02310-1 10.1016/s0168-9525(01)02310-1Ouvrir le DOISearch in Google Scholar

Kirst M, Myburg AA, De León JPG, Kirst ME, Scott J, Sederoff RR (2004) Coordi­nated Genetic Regulation of Growth and Lignin Revealed by Quantitative Trait Locus Analysis of cDNA Microarray Data in an Interspecific Backcross of Eucalyptus. Plant Physiol 135(4):2368-2378. https://doi.org/10.1104/pp.103.037960 10.1104/pp.103.03796052080415299141Ouvrir le DOISearch in Google Scholar

Kirst M, Basten CJ, Myburg AA, Zeng ZB, Sederoff RR (2005) Genetic Architecture of Transcript-Level Variation in Differentiating Xylem of a Eucalyptus Hybrid. Genetics 169(4):2295-2303 . https://doi.org/10.1534/genetics.104.039198 10.1534/genetics.104.039198144959715687266Ouvrir le DOISearch in Google Scholar

Kirst M, Yu Q (2007) Genetical genomics: successes and prospects in plants. In: Varshney RK, Tuberosa R (ed) Genomics-Assisted Crop Improvement. Vol 1: Genomics Approaches and Platforms. Dordrecht, Netherlands: Springer, pp 245-265, ISBN 9781402062940. https://doi.org/10.1007/978-1-4020-6295-7_11 10.1007/978-1-4020-6295-7_11Search in Google Scholar

Kvam VM, Liu P, Si Y (2012) A comparison of statistical methods for detecting dif­ferentially expressed genes from RNA-seq data. Am J Bot 99(2):248-256. https://doi.org/10.3732/ajb.1100340 10.3732/ajb.110034022268221Ouvrir le DOISearch in Google Scholar

Lê Cao, K-A., González I. and Déjean S. (2009) integrOmics: an R package to un­ravel relationships between two omics data sets. Bioinformatics 25(21):2855-2856. NOTE: the package ‘integrOmics’ has been renamed to ‘mixOmics’ . https://doi.org/10.1093/bioinformatics/btp515 10.1093/bioinformatics/btp515278175119706745Ouvrir le DOISearch in Google Scholar

Liu Y, Jiang Y, Lan J, Zou Y, Gao J (2014) Comparative Transcriptomic Analysis of the Response to Cold Acclimation in Eucalyptus dunnii. PLoS One 9(11):e113091. https://doi.org/10.1371/journal.pone.0113091 10.1371/journal.pone.0113091423904525412179Search in Google Scholar

López de Heredia U, Vázquez-Poletti JL (2016) RNA-seq analysis in forest tree species: bioinformatic problems and solutions. Tree Genet. Genomes 12(2):30. https://doi.org/10.1007/s11295-016-0995-x 10.1007/s11295-016-0995-xOuvrir le DOISearch in Google Scholar

Lorenz AJ, Chao S, Asoro FG, Heffner EL, Hayashi T, Iwata H, Smith KP, Sorrells MK, Jannink JL (2011) Genomic selection in plant breeding: knowledge and prospects. Adv Agron 110:77-123. https://doi.org/10.1016/b978-0-12-385531-2.00002-5 10.1016/b978-0-12-385531-2.00002-5Ouvrir le DOISearch in Google Scholar

Lukens L, Downs G (2012) Bioinformatics Techniques for Understanding and An­alyzing Tree Gene Expression Data. In: Schnell RJ, Priyadarshan PM (eds) Ge­nomics of Tree Crops. Heidelberg, Germany: Springer, pp17-38. https://doi.org/10.1007/978-1-4614-0920-5_2 10.1007/978-1-4614-0920-5_2Ouvrir le DOISearch in Google Scholar

Makouanzi GC, (2015) Composantes de la variance phénotypique et de l’interac­tion GxE de la croissance et des traits écophysiologiques de l’Eucalyptus urophylla x Eucalyptus grandis. Dissertation. University of Marien Gouabi Search in Google Scholar

Martin LB, Fei Z, Giovannoni JJ, Rose JK (2013) Catalyzing plant science research with RNA-seq. Front Plant Sci 4:1-10. https://doi.org/10.3389/fpls.2013.00066 10.3389/fpls.2013.00066361269723554602Ouvrir le DOISearch in Google Scholar

Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17(1):10-12. https://doi.org/10.14806/ej.17.1.200 10.14806/ej.17.1.200Search in Google Scholar

McCarthy DJ, Chen Y, Smyth GK (2012) Differential expression analysis of multi­factor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 40(10):4288-4297. https://doi.org/10.1093/nar/gks042 10.1093/nar/gks042337888222287627Search in Google Scholar

Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA (2010) De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illu­mina mRNA-Seq. BMC Genomics 11:681. https://doi.org/10.1186/1471-2164-11-681 10.1186/1471-2164-11-681305359121122097Ouvrir le DOISearch in Google Scholar

Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jen­kins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Külheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tib­bits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Jou­bert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar D, Schmutz J (2014) The genome of Eucalyptus gran­dis. Nature 510(7505):356-362. https://doi.org/10.1038/nature13308 10.1038/13308Ouvrir le DOISearch in Google Scholar

Neyman J, Pearson ES (1933) On the Problem of the Most Efficient Tests of Statis­tical Hypotheses. Philos Trans R Soc, A 231(1933):289-337. https://doi.org/10.1098/rsta.1933.0009 10.1098/rsta.1933.0009Ouvrir le DOISearch in Google Scholar

R Development Core Team (2014) R: A language and environment for statistical computing [online]. Vienna, Austria: R Foundation for Statistical Computing, to be found at <http://www.R-project.org/> [quoted 12 January 2016] Search in Google Scholar

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43(7):e47. https://doi.org/10.1093/nar/gkv007 10.1093/nar/gkv007440251025605792Ouvrir le DOISearch in Google Scholar

Robinson MD, McCarthy DJ, Smyth GK (2010) EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinfor­matics 26(1):139-140. https://doi.org/10.1093/bioinformatics/btp616 10.1093/bioinformatics/btp616279681819910308Ouvrir le DOISearch in Google Scholar

Salazar MM, Nascimento LC, Camargo EL, Goncalves DC, Neto JL, Marques WL, Teixeira PJ, Mieczkowski P, Mondego JM, Carazzolle MF, Deckmann AC, Pereira GA (2013) Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species. BMC Genomics 14:201-214. https://doi.org/10.1186/1471-2164-14-201 10.1186/1471-2164-14-201361833623521840Ouvrir le DOISearch in Google Scholar

Shorack GR, Wellner JA (2009) Empirical processes with applications to statistics. Philadelphia, USA: Society for Industrial & Applied Mathematics, 956p. https://doi.org/10.1137/1.9780898719017 10.1137/1.9780898719017Ouvrir le DOISearch in Google Scholar

Soler M, Camargo ELO, Carocha V, Cassan-Wang H, San Clemente H, Savelli B, Hefer CA, Paiva JA, Myburg AA, Grima-Pettenati J (2015) The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function. New Phytol 206(4):1364-1377. https://doi.org/10.1111/nph.13039 10.1111/nph.1303925250741Ouvrir le DOISearch in Google Scholar

Song G, Guo Z, Liu Z, Cheng Q, Qu X, Chen R, Jiang D, Liu C, Wang W, Sun Y, Zhang L, Zhu Y, Yang D (2013) Global RNA sequencing reveals that geno­type-dependent allele-specific expression contributes to differential ex­pression in rice F1 hybrids. BMC Plant Biol 13:221. https://doi.org/10.1186/1471-2229-13-221 10.1186/1471-2229-13-221387810924358981Ouvrir le DOISearch in Google Scholar

Thavamanikumar S, Southerton S, Thumma B (2014) RNA-Seq using two popu­lations reveals genes and alleles controlling wood traits and growth in Eu­calyptus nitens. PLoS ONE 9(6):e101104. https://doi.org/10.1371/journal.pone.010110410.1371/journal.pone.0101104407273124967893Search in Google Scholar

Vélez-Bermúdez IC, Schmidt W (2014). The conundrum of discordant protein and mRNA expression. Are plants special? Front Plant Sci 5:619. https://doi.org/10.3389/fpls.2014.00619 10.3389/fpls.2014.00619422406125426129Ouvrir le DOISearch in Google Scholar

Vigneron P, Bouvet J-M (2001) Eucalyptus. In: Charrier A, Jacquot M, Hamon S, Nicolas D (eds) Tropical plant breeding. Montpellier: CIRAD-Science Publish­ers, pp 223-245, ISBN: 978-2-87614-426-2 Search in Google Scholar

Villar E, Klopp C, Noirot C, Novaes E, Kirst M, Plomion C, Gion JM (2011) RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyp­tus. BMC Genomics 12:538. https://doi.org/10.1186/1471-2164-12-538 10.1186/1471-2164-12-538324802822047139Ouvrir le DOISearch in Google Scholar

Vining KJ, Romanel E, Jones RC, Klocko A, Alves-Ferreira M, Hefer CA, Amarasing­he V, Dharmawardhana P, Naithani S, Ranik M, Wesley-Smith J, Solomon L, Jaiswal P, Myburg AA, Strauss SH (2015) The floral transcriptome of Eucalyp­tus grandis. New Phytol 206(4):1406-1422. https://doi.org/10.1111/nph.13077 10.1111/nph.1307725353719Ouvrir le DOISearch in Google Scholar

Yandell BS (1997) Practical Data Analysis for Designed Experiments. London, UK: Chapman & Hall, 440p, ISBN 9780412063411 10.1007/978-1-4899-3035-4Search in Google Scholar

Yang S, Liu Y, Jiang N, Chen J, Leach L, Luo Z, Wang M (2014) Genome-wide eQTLs and heritability for gene expression traits in unrelated individuals. BMC Genomics 15:13. https://doi.org/10.1186/1471-2164-15-13 10.1186/1471-2164-15-13402805524405759Ouvrir le DOISearch in Google Scholar

Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X (2014) Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One 9(1):e78644 . https://doi.org/10.1371/journal.pone.007864410.1371/journal.pone.0078644389419224454679Search in Google Scholar

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