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Genetic effect in leaf and xylem transcriptome variations among Eucalyptus urophylla x grandis hybrids in field conditions Cover

Genetic effect in leaf and xylem transcriptome variations among Eucalyptus urophylla x grandis hybrids in field conditions

Open Access
|Jun 2018

References

  1. 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]
  2. 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.x
  3. 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/btq281289451920562416
  4. 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/.1069516
  5. 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/s12870-014-0256-9418975725260963
  6. 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.1331325684249
  7. 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.2003.68.40315338642
  8. 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/bti61016081474
  9. 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.x20055957
  10. 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
  11. Falconer DS, Mackay Longman TFC (1996) Introduction to Quantitative Genet­ics, 4th ed. Harlow, UK: Pearson United Kingdom, 480p, ISBN 9780582243026
  12. 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.2005.08.01016154229
  13. 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.2008.06.001258307118597885
  14. Gilmour AR, Gogel BJ, Cullis BR, Welham SJ, Thompson R (2006) ASReml, User Guide. Release 2.0. VSN International Ltd: Hemel Hempstead, UK
  15. 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-r86
  16. 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/gkr944
  17. 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/srep18662
  18. 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.13277
  19. 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.2008.0080
  20. 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-050213-035715
  21. 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)02310-1
  22. 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.103.03796052080415299141
  23. 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.104.039198144959715687266
  24. 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_11
  25. 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.110034022268221
  26. 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/btp515278175119706745
  27. 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.0113091423904525412179
  28. 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-x
  29. 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/b978-0-12-385531-2.00002-5
  30. 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_2
  31. 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
  32. 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.2013.00066361269723554602
  33. 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.17.1.200
  34. 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/gks042337888222287627
  35. 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 10.1186/1471-2164-11-681305359121122097
  36. 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 10.1038/13308
  37. 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.1933.0009
  38. 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]
  39. 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/gkv007440251025605792
  40. 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/btp616279681819910308
  41. 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 10.1186/1471-2164-14-201361833623521840
  42. 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 10.1137/1.9780898719017
  43. 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.1303925250741
  44. 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 10.1186/1471-2229-13-221387810924358981
  45. 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.0101104407273124967893
  46. 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.2014.00619422406125426129
  47. 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
  48. 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 10.1186/1471-2164-12-538324802822047139
  49. 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.1307725353719
  50. Yandell BS (1997) Practical Data Analysis for Designed Experiments. London, UK: Chapman & Hall, 440p, ISBN 9780412063411 10.1007/978-1-4899-3035-4
  51. 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 10.1186/1471-2164-15-13402805524405759
  52. 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.0078644389419224454679
DOI: https://doi.org/10.2478/sg-2018-0008 | Journal eISSN: 2509-8934 | Journal ISSN: 0037-5349
Language: English
Page range: 57 - 65
Published on: Jun 28, 2018
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2018 Alexandre Vaillant, Astrid Honvault, Stéphanie Bocs, Maryline Summo, Garel Makouanzi, Philippe Vigneron, Jean-Marc Bouvet, published by Johann Heinrich von Thünen Institute
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.