Skip to main content
SpringerLink
Log in

Application of High-Throughput Sequencing Technologies in Native Forest Tree Species in Argentina: Implications for Breeding

  • Chapter
  • First Online:
Low Intensity Breeding of Native Forest Trees in Argentina

  • 324 Accesses

Abstract

High-throughput sequencing (HTS) technologies became a powerful approach to generate genomic resources in non-model tree species and to assist breeding programs. These technologies are being used in native forest trees of Argentina and this chapter summarizes the state-of-the-art knowledge. A brief description of the HTS technologies is followed by general applications of HTS on forest trees for genomic resources development and massive genotyping. Genomic strategies to accelerate tree breeding includes genome-wide association studies and genomic selection. HTS technologies were applied to Argentina’s native tree species for transcriptome and genome sequencing of Nothofagus species and transcriptome sequencing of Prosopis alba and Cedrela balansae. Ongoing HTS projects include the transcriptome sequencing of Austrocedrus chilensis, Handroanthus impetiginosus and Cordia trichotoma; the genome sequencing of Austrocedrus chilensis and the transcriptome sequencing of Nothofagus alpina and N. obliqua under drought stress conditions. Current and future genetic studies on native forest tree species and implications for breeding are discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Strategy A: (TITLE-ABS-KEY (“next-generation sequencing” OR “massive sequencing” OR “high-throughput sequencing”) AND TITLE-ABS-KEY (“forest tree” OR “tree species” OR “native tree”)). Strategy B: (TITLE-ABS-KEY (“transcriptome” OR “genome” AND sequencing) AND TITLE-ABS-KEY (“forest tree” OR “tree species” OR “native tree”)). Search date: 04-04-2019.

References

  • Adams J (2008) DNA sequencing technologies. Nature Education 1:1931

    Google Scholar 

  • Aguirre N, Filippi C, Zaina G, Rivas J, Acuña C, Villalba P et al (2019) Optimizing ddRADseq in non-model species: a case study in Eucalyptus dunnii. Agronomy 9:484

    Article  CAS  Google Scholar 

  • Alvarez M, Mosquera T, Blair M (2014) The use of association genetics approaches in plant breeding. In: Janick J (ed) Plant breeding reviews, vol 38. Wiley, Hoboken, pp 17–68

    Google Scholar 

  • Andrews K, Good J, Miller M, Luikart G, Hohenlohe P (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet 17:81–92

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aranzana M, Kim S, Zhao K, Bakker E, Horton M et al (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1:e60

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Azpilicueta M, Caron H, Bodénès C, Gallo L (2004) SSR markers for analyzing South American Nothofagus species. Silvae Genet 53:240–243

    Article  Google Scholar 

  • Azpilicueta M, Soliani C, Gallo L, van Zonneveld M, Thomas E, Moreno C, Marchelli P (2013) Definición de zonas genéticas en cuatro especies de Nothofagus de los bosques andino- patagónicos IV Congreso Forestal Argentino y Latinoamericano. Iguazú, 23–27 September

    Google Scholar 

  • Azpilicueta M, El Mujtar V, Gallo L (2016) Searching for molecular insight on hybridization in Nothofagus spp. forests at Lagunas de Epulauquen, Argentina. Bosque 37:591–601

    Article  Google Scholar 

  • Badenes M, Fernández I, Ríos G, Rubio-Cabetas M (2016) Application of genomic technologies to the breeding of trees. Front Genet 7:198

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Baird N, Etter P, Atwood T, Currey M, Shiver A, Lewis Z et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Barros V, Boninsegna J, Camilloni I, Chidiak M, Magrín G, Rusticucci M (2015) Climate change in Argentina: trends, projections, impacts and adaptation. Wiley Interdiscip Rev Clim Change 6:151–169

    Article  Google Scholar 

  • Bartholomé J, Van Heerwaarden J, Isik F, Boury C, Vidal M, Plomion C, Bouffier L (2016) Performance of genomic prediction within and across generations in maritime pine. BMC genomics 17:604

    Article  PubMed  PubMed Central  Google Scholar 

  • Beilsmith K, Thoen M, Brachi B, Gloss A, Khan H, Bergelson J (2019) Genome-wide associations studies on the phyllosphere microbiome: embracing complexity in host-microbe interactions. Plant J. 97:164–181

    Article  CAS  PubMed  Google Scholar 

  • Bernardo R (2008) Molecular markers and selection for complex traits in plants: Learning from the last 20 years. Crop Sci 48:1649–1664

    Article  Google Scholar 

  • Bessega C, Pometti C, Miller J, Watts R, Saidman B, Vilardi J (2013) New microsatellite loci for Prosopis alba and P. chilensis (Fabaceae). Appl Plant Sci 1:1200324

    Article  Google Scholar 

  • Birol I, Raymond A, Jackman S, Pleasance S, Coope R, Taylor G et al (2013) Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btt178

  • Blott S, Kim J, Moisio S, Schmidt-Kuntzel A, Cornet A et al (2003) Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics 163:253–266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33(Suppl):228–237

    Article  CAS  PubMed  Google Scholar 

  • Brachi B, Morris G, Borevitz J (2011) Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol 12:232

    Article  PubMed  PubMed Central  Google Scholar 

  • Brousseau L, Tinaut A, Duret C, Lang T, Garnier-Gere P, Scotti I (2014) High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species. BMC Genomics 15:238

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Budde K, Heuertz M, Hernández-Serrano A, Pausas J, Vendramin G, Verdú M, González-Martínez S (2014) In situ genetic association for serotiny, a fire-related trait, in Mediterranean maritime pine (Pinus pinaster Aiton). New Phytol 201:230–241

    Article  CAS  PubMed  Google Scholar 

  • Canales J, Bautista R, Label P, Gómez Maldonado J, Lesur I, Fernández Pozo N et al (2014) De novo assembly of maritime pine transcriptome: Implications for forest breeding and biotechnology. Plant Biotechnol J 12:286–299

    Article  CAS  PubMed  Google Scholar 

  • Cappa E, Marco de Lima B, da Silva-Junior O, Garcia C, Mansfield S, Grattapaglia D (2019) Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP. Plant Sci 84:9–15

    Article  CAS  Google Scholar 

  • Catchen J, Hohenlohe P, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140

    Article  PubMed  PubMed Central  Google Scholar 

  • Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 11:113–116

    Article  CAS  Google Scholar 

  • Chhetri H, Macaya-Sanz D, Kainer D, Biswal A, Evans L, Chen J et al (2019) Multi-trait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits. New Phytol 223:293–309

    Article  CAS  PubMed  Google Scholar 

  • Chinwalla A, Cook L, Delehaunty K, Fewell G, Fulton L, Fulton R et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562

    Article  PubMed  CAS  Google Scholar 

  • Collevatti R, Novaes E, Silva-Junior O, Vieira L, Lima-Ribeiro M, Grattapaglia D (2019) A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree. Heredity 123:117–137

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A et al (2016) A survey of best practices for RNA-seq data analysis. Genome Biol 17:13

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Davey J, Hohenlohe P, Etter P, Boone J, Catchen J, Blaxter L (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet. 12:499–510

    Article  CAS  PubMed  Google Scholar 

  • De Pristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498

    Article  CAS  Google Scholar 

  • De Villemereuil P, Gaggiotti O, Mouterde M, Till-Bottraud I (2016) Common garden experiments in the genomic era: new perspectives and opportunities. Heredity 116:249–254

    Article  PubMed  Google Scholar 

  • Du Q, Lu W, Quan M, Xiao L, Song F, Li P, Zhou D, Xie J, Wang L, Zhang D (2018) Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects. Front Plant Sci 9:1912

    Article  PubMed  PubMed Central  Google Scholar 

  • Eckert A, Wegrzyn J, Liechty J, Lee J, Cumbie W, Davis J et al (2013) The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae). Genetics 195:1353–1372

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • El Mujtar V, Gallo L, Lang T, Garnier-Géré P (2014) Development of genomic resources for Nothofagus species using next-generation sequencing data. Mol Ecol Resour 14:1281–1295

    Article  PubMed  CAS  Google Scholar 

  • El Mujtar V, Guichoux E, Boury C, Pilliet M, Delcamp A, Salin F, Garnier Géré P (2015) Validating the use of a genotyping by sequencing approach for population genomic studies in non-model species. 3ème Colloque de Génomique Environnementale, “Le vivant à l’ère des nouvelles technologies de séquençage des génomes”. 26–28 Octubre, Montpellier.

    Google Scholar 

  • El Mujtar V, López M, Amalfi S, Pomponio F, Marcucci Poltri S, Torales S (2017b) Characterization and transferability of transcriptomic microsatellite markers for Nothofagus species. N Z J Bot 55:347–356

    Article  Google Scholar 

  • El Mujtar V, Aparicio A, Sola G, Gallo L (2017a) Pattern of natural introgression in a Nothofagus hybrid zone from South American temperate forests. Tree Genet Genomes 13:49

    Article  Google Scholar 

  • Elshire R, Glaubitz J, Sun Q, Poland J, Kawamoto K, Buckler E, Mitchell S (2011) A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS One 6:e19379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Estravis-Barcala M, Mattera M, Soliani C, Bellora N, Opgenoorth L, Heer K, Arana M (2019) Molecular bases of responses to abiotic stress in tres. J Exp Bot. https://doi.org/10.1093/jxb/erz532

  • Ettori L, Siqueira A, Sato A, Campos O (1996) Variabilidade genética em populações de Ipê-roxo – Tabebuia heptaphylla (Vell.) Tol. – para conservação ex situ. Revista do Instituto Florestal 8:61–70

    Google Scholar 

  • Fasanella M, Suarez M, Hasbún R, Premoli A (2019) Genomic markers as indicators of potential drought adaptation in Nothofagus dombeyi. Topwood Conference, Bariloche, 12–15 March

    Google Scholar 

  • Feuillet C, Leach J, Rogers J, Schnable P, Eversole K (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16:77–88

    Article  CAS  PubMed  Google Scholar 

  • Geraldes A, Difazio S, Slavov G, Ranjan P, Muchero W, Hannemann J et al (2013) A 34K SNP genotyping array for Populus trichocarpa: Design application to the study of natural populations and transferability to other Populus species. Mol Ecol Res 13:306–323

    Article  CAS  Google Scholar 

  • Grattapaglia D, Resende M (2011) Genomic selection in forest tree breeding. Tree Genet Genomes 7:241–255

    Article  Google Scholar 

  • Grattapaglia D, Silva-Junior O, Resende R, Cappa E, Müller B, Tan B et al (2018) Quantitative genetics and genomics converge to accelerate forest tree breeding. Front Plant Sci 9:1693

    Article  PubMed  PubMed Central  Google Scholar 

  • Greene C, Tan J, Ung M, Moore J, Cheng C (2014) Big data bioinformatics. J Cell Physiol 229:1896–1900

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goodwin S, McPherson J, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351

    Article  CAS  PubMed  Google Scholar 

  • Hasbún R, González J, Iturra C, Fuentes G, Alarcón D, Ruiz E (2016) Using genome-wide SNP discovery and genotyping to reveal the main source of population differentiation in Nothofagus dombeyi (Mirb.) Oerst. in Chile. Int J Genomics. Article ID 3654093. https://doi.org/10.1155/2016/3654093

  • Heather J, Chain B (2016) The sequence of sequencers: The history of sequencing DNA. Genomics 107:1–8

    Article  CAS  PubMed  Google Scholar 

  • IPCC (2014) Cambio climático. Quinto Informe de Evaluación del Grupo Intergubernamental de Expertos sobre el Cambio Climático [Equipo principal de redacción, RK Pachauri y LA Meyer (eds.)]. Ginebra, Suiza, 157 págs

    Google Scholar 

  • Kageyama P, Gandara F (1998) Consecuencias de la fragmentación sobre poblaciones de especies arbóreas, Camará – Centro de Apoio às Sociedades Sustentáveis. Serie técnica IPEF 12:65–70

    Google Scholar 

  • Karan M, Evans D, Reilly D, Schulte K, Wright C, Innes D et al (2012) Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity. Mol Ecol Res 12:344–353

    Article  CAS  Google Scholar 

  • Kchouk M, Gibrat J, Elloumi M (2017) Generations of sequencing technologies: from first to next generation. Biol Med (Aligarh) 9:3

    Article  CAS  Google Scholar 

  • Klein L, Spoljaric M, Torales S (2019) Identificación de genotipos estables en 19 familias de Prosopis alba usando marcadores de microsatélites y parámetros de productividad. Quebracho 27:26–36

    Google Scholar 

  • Krishnan N, Pattnaik S, Jain P, Gaur P, Choudhary R, Vaidyanathan S et al (2012) A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. BMC Genomics 13:464

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lesur I, Le Provost G, Bento P, Da Silva C, Leplé J-C, Murat F et al (2015) The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics 16:112

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol. Article ID 251364. https://doi.org/10.1155/2012/251364

  • Liu F, Hong Z, Yang Z, Zhang N, Liu X, Xu D (2019) De novo transcriptome analysis of Dalbergia odorifera T. Chen (Fabaceae) and transferability of SSR markers developed from the transcriptome. Forests 10:98

    Article  Google Scholar 

  • Logacheva M, Kasianov A, Vinogradov D, Samigullin T, Gelfand M, Makeev V, Penin A (2011) De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics 12:30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • López de Heredia U, Vázquez-Poletti J (2016) RNA-seq analysis in forest tree species: bioinformatic problems and solutions. Tree Genet Genomes 12:30

    Article  Google Scholar 

  • Mahony CR, MacLachlan IR, Lind BM, Yoder JB, Wang T, Aitken SN (2019) Evaluating genomic data for management of local adaptation in a changing climate: a lodgepole pine case study. https://doi.org/10.1101/568725

  • Marchelli P, Caron H, Azpilicueta M, Gallo L (2008) A new set of highly polymorphic nuclear microsatellite markers for Nothofagus nervosa and related South American species. Silvae Genet 57:82–85

    Article  Google Scholar 

  • Marchelli P, Thomas E, Azpilicueta M, van Zonneveld M, Gallo L (2017) Integrating genetics and suitability modelling to bolster climate change adaptation planning in Patagonian Nothofagus forests. Tree Genet Genom 13:119

    Article  Google Scholar 

  • Matias E, Ferreira A, Nascimento Silva M, Alencar Carvalho V, Melo Coutinho H, Martins da Costa J (2015) The genus Cordia: botanists, ethno, chemical and pharmacological aspects. Revista Brasileira de Farmacognosia 25:542–552

    Article  CAS  Google Scholar 

  • Martins S (2012) Restauração ecológica de ecossistemas degradados. Visçosa, Brasil. UFV 293 p

    Google Scholar 

  • Menezes J, Machado F, Lemos T, Silveira E, Filho R, Pessoa O (2004) Sesquiterpenes and a Phenylpropanoid from Cordia trichotoma. Z Naturforsch 59:19–22

    Article  Google Scholar 

  • Meuwissen T, Hayes B, Goddard M (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Minamikawa M, Takada N, Terakami S, Saito T, Onogi A, Kajiya-Kanegae H et al (2018) Genome-wide association study and genomic prediction using parental and breeding populations of Japanese pear (Pyrus pyrifolia Nakai). Sci Rep 8:2045–2322

    Article  CAS  Google Scholar 

  • Mottura M, Finkeldey R, Verga A, Gailing O (2005) Development and characterization of microsatellite markers for Prosopis chilensis and Prosopis flexuosa and cross-species amplification. Mol Ecol Not 5:487–489

    Article  CAS  Google Scholar 

  • Naidoo S, Slippers B, Plett J, Coles D, Oates C (2019) The road to resistance in forest trees. Front Plant Sci 10:273

    Article  PubMed  PubMed Central  Google Scholar 

  • Neale D, Williams C (1991) Restriction-Fragment-Length-Polymorphism mapping in conifers and applications to forest genetics and tree improvement. Can J Forest Res Revue Can Rech Forest 21:545–554

    Article  CAS  Google Scholar 

  • Neale D (2007) Genomics to tree breeding and forest health. Curr Opin Genet Dev 17:539–544

    Article  CAS  PubMed  Google Scholar 

  • Neale D, Wheeler N (2019) The conifers: genomes, variation and evolution. Springer; Edición: 1st ed

    Google Scholar 

  • Neto G, de Morais R (2003) Recursos medicinais de espécies do cerrado de Mato Grosso: um estudo bibliográfico. Acta Botânica Brasileira 17:561–584

    Article  Google Scholar 

  • Nordborg M, Tavare S (2002) Linkage disequilibrium: What history has to tell us. Trends Genet 18:83–90

    Article  CAS  PubMed  Google Scholar 

  • Oza M, Kulkarni Y (2017) Traditional uses, phytochemistry and pharmacology of the medicinal species of the genus Cordia (Boraginaceae). J Pharm Pharmacol 69:755–789

    Article  CAS  PubMed  Google Scholar 

  • Parchman T, Geist K, Grahnen J, Benkman C, Buerkle C (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Parchman T, Jahner J, Uckele K, Galland L, Eckert A (2018) RADseq approaches and applications for forest tree genetics. Tree Genet Genomes 14:39

    Article  Google Scholar 

  • Parent G, Raherison E, Sena J, MacKay J (2015) Forest Tree Genomics: Review of Progress. Adv Bot Res 74:39–92

    Article  CAS  Google Scholar 

  • Pastorino M, Gallo L (2002) Quaternary evolutionary history of Austrocedrus chilensis, a cypress native to the Andean-Patagonian Forest. J Biogeogr 29:1167–1178

    Article  Google Scholar 

  • Pastorino M, El Mujtar V, Azpilicueta M, Aparicio A, Marchelli P, Mondino V et al (2016) Subprograma Nothofagus. Domesticación y Mejoramiento de Especies Forestales. INTA-UCAR 6:161–188

    Google Scholar 

  • Pavy N, Gagnon F, Rigault P, Blais S, Deschenes A, Boyle B et al (2013) Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners. Mol Ecol Res 13:324–336

    Article  CAS  Google Scholar 

  • Pellicer J, Hidalgo O, Dodsworth S, Leitch I (2018) Genome size diversity and its impact on the evolution of land plants. Genes 9:88

    Article  PubMed Central  CAS  Google Scholar 

  • Peterson B, Weber J, Kay E, Fisher H, Hoekstra H (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pfeiffer F, Gröber C, Blank M, Händler K, Beyer M, Schultze J, Mayer G (2018) Systematic evaluation of error rates and causes in short samples in next-generation sequencing. Sci Rep 8:10950

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pomponio M, Torales S, Gallo L, Pastorino M, Marchelli P, Cervera M, Marcucci Poltri S (2013) DNA Sequence Variation of Drought-Response candidate genes in Austrocedrus chilensis. Electron J Biotechnol 16(2)

    Google Scholar 

  • Pomponio M, Marcucci Poltri S, López Lauenstein D, Torales S (2014) Identification of single nucleotide polymorphisms (SNPs) at candidate genes involved in abiotic stress in two Prosopis species and hybrids. For Syst 23:490–493

    Google Scholar 

  • Pomponio M, Acuña C, Pentreath V, López Lauenstein D, Marcucci Poltri S, Torales S (2015) Characterization of functional SSR markers in Prosopis alba and their transferability across Prosopis species. For Syst 24:2

    Google Scholar 

  • Pomponio M, Fornés L, Marcucci S, Torales S (2019) Desarrollo del transcriptoma foliar y marcadores microsatélites del Lapacho Rosado (Handroanthus impetiginosus). XVIII Reunión GEMFO 2019 (Bella Vista, Corrientes, Argentina) Trabajos Técnicos.

    Google Scholar 

  • Reuter J, Spacek D, Snyder M (2015) High-Throughput Sequencing Technologies. Mol Cell 58:586–597

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516–1517

    Article  CAS  PubMed  Google Scholar 

  • Roberts RJ, Carneiro MO, Schatz MC (2013) The advantages of SMRT sequencing. Genome Biol 14:405

    Article  PubMed  PubMed Central  Google Scholar 

  • Sabatier Y, Azpilicueta M, Marchelli P, González Peñalba M, Lozano L, García L et al (2011) Distribución natural de Nothofagus alpina y Nothofagus obliqua (nothofagaceae) en Argentina, dos especies de primera importancia forestal de los bosques templados norpatagónicos. Bol Soc Argent Bot 46:131–138

    Google Scholar 

  • Sanger F, Nicklen S, Coulson A (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Secretaría de Ambiente y Desarrollo Sustentable – Dirección de Bosques (2007) Informe sobre desforestación en Argentina

    Google Scholar 

  • Sewell M, Neale D (2000) Mapping quantitative traits in forest trees. Molecular biology of woody plants. For Sci 64:407–423

    CAS  Google Scholar 

  • Stephens Z, Lee S, Faghri F, Campbell R, Zhai C, Efron M et al (2015) Big data: astronomical or genomical. PLoS Biol 13:e1002195

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Silva A, Ribeiro de Paiva S, Figueiredo M, Coelho Kaplan M (2012) Biological activity of naphthoquinones from Bignoniaceae species. Revista Fitos 7:4

    Google Scholar 

  • Sola G, El Mujtar V, Gallo L, Vendramin G, Marchelli P (2020) Staying close: short local dispersal distances on a managed forest of two Patagonian Nothofagus spp. Forestry 93(5):652–661

    Google Scholar 

  • Soliani C, Sebastiani F, Marchelli P, Gallo L, Vendramin G (2010) Development of novel genomic microsatellite markers in the southern beech Nothofagus pumilio (Poepp. Et Endl.) Krasser. Mol Ecol Res 10:404–408

    Google Scholar 

  • Soliani C, Azpilicueta M, Arana M, Marchelli P (2020) Clinal variation along precipitation gradients in Patagonian temperate forests: unravelling demographic and selection signatures in three Nothofagus spp. Ann For Sci 77:4

    Article  Google Scholar 

  • Strauss S, Lande R, Namkoong G (1992) Limitations of molecular-marker-aided selection in forest tree breeding. Can J For Res 22:1050–1061

    Article  CAS  Google Scholar 

  • Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, Jomchai N, Tragoonrung S (2010) The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Res 17:11–22

    Article  CAS  PubMed  Google Scholar 

  • Thistlethwaite F, Ratcliffe B, Klápště J, Porth I, Chen C, Stoehr M, El-Kassaby Y (2019) Genomic selection of juvenile height across a single-generational gap in Douglas-fir. Heredity 122:848

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thornsberry J, Goodman M, Doebley J, Kresovich S, Nielsen D, Buckler E (2001) Dwarf polymorphisms associate with variation in flowering time. Nat Genet 28:286–289

    Article  CAS  PubMed  Google Scholar 

  • Torales S, Rivarola M, Pomponio M, Fernández P, Acuña C, Marchelli P et al (2012) Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. alpina): assembly, annotation and molecular marker discovery. BMC Genomics 13:291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Torales S, Rivarola M, Pomponio M, Gonzalez S, Acuña C, Fernández P et al (2013) De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba. BMC Genomics 14:705

    Article  PubMed  PubMed Central  Google Scholar 

  • Torales S, Rivarola M, Gonzalez S, Inza M, Pomponio M, Fernández P et al (2018) De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina. PLoS One 13:e0203768

    Article  PubMed  PubMed Central  Google Scholar 

  • Toro M, Varona L (2010) A note on mate allocation for dominance handling in genomic selection. Genet Sel Evol 42:33

    Article  PubMed  PubMed Central  Google Scholar 

  • Torre S, Tattini M, Brunetti C, Fineschi S, Fini A, Ferrini F, Sebastiani F (2014) RNA-Seq analysis of Quercus pubescens leaves: de novo transcriptome assembly, annotation and functional markers development. PLoS One 9:e112487

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tuskan G, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. and Gray). Science 313:1596–1604

    Article  CAS  PubMed  Google Scholar 

  • Tyson J, O’Neil N, Jain M, Olsen H, Hieter P, Snutch T (2018) MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome. Genome Res 28:266–274

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ueno S, Le Provost G, Léger V, Klopp NC, Frigerio J et al (2010) Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics 11:650

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Varela S, Gyenge J, Fernández ME, Schlichter T (2010) Seedling drought stress susceptibility in two deciduous Nothofagus species of NW Patagonia. Trees 24:443–453

    Article  Google Scholar 

  • Venter J (2001) The sequence of the human genome. Science 291:1304–1351

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Yang Q, Wang Z (2015) The evolution of nanopore sequencing. Front Genetics 5:449

    Article  CAS  Google Scholar 

  • Wang Y, Chen X, Wang J, Xun H, Sun J, Tang F (2016) Comparative analysis of the terpenoid biosynthesis pathway in Azadirachta indica and Melia azedarach by RNA-seq. SpringerPlus 5:819

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Williams C, Neale D (1992) Conifer wood quality and marker-aided selection – a case-study. Can J Forest Res Revue Can Rech Forest 22:1009–1017

    Article  Google Scholar 

  • Zhu C, Gore M, Buckler E, Yu J (2008) Status and prospects of association maping in plants. Plant Genome 1:5–20

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Instituto de Recursos Biológicos (IRB), Centro de Investigaciones de Recursos Naturales (CIRN), INTA. Hurlingham, Buenos Aires, Argentina

    Susana L. Torales, Florencia Pomponio, María Virginia Inza & Micaela López

  2. Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB) INTA-CONICET, Bariloche, Argentina

    Verónica El Mujtar, Carolina Soliani & Verónica Arana

  3. Instituto de Agrobiotecnología y Biología Molecular (IABiMO) INTA-CONICET, Buenos Aires, Argentina

    Susana Marcucci-Poltri, Pamela Villalba, Martín García, Natalia C. Aguirre, Máximo Rivarola, Cintia Acuña, Sergio González & Sabrina Amalfi

  4. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) CONICET–UNCo, San Carlos de Bariloche, Argentina

    Maximiliano Estravis-Barcala & Nicolás Bellora

  5. INTA EEA Saénz Peña, Saénz Peña, Argentina

    Lorena Klein

  6. Universidad Nacional de la Patagonia San Juan Bosco, Comodoro Rivadavia, Argentina

    Vivien Pentreath

  7. INRAE, Paris, France

    Pauline Garnier-Géré

Authors
  1. Susana L. Torales
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Verónica El Mujtar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Susana Marcucci-Poltri
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Florencia Pomponio
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Carolina Soliani
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Pamela Villalba
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Maximiliano Estravis-Barcala
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Lorena Klein
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Martín García
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Vivien Pentreath
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. María Virginia Inza
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Natalia C. Aguirre
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Máximo Rivarola
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Cintia Acuña
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Sergio González
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Sabrina Amalfi
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Micaela López
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Pauline Garnier-Géré
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Nicolás Bellora
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Verónica Arana
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Susana L. Torales .

Editor information

Editors and Affiliations

  1. Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB) INTA-CONICET, National Agricultural Technology Institute - National Scientific and Technical Research Council, Bariloche, Rio Negro, Argentina

    Mario J. Pastorino

  2. Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB) INTA-CONICET, National Agricultural Technology Institute - National Scientific and Technical Research Council, Bariloche, Rio Negro, Argentina

    Paula Marchelli

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Torales, S.L. et al. (2021). Application of High-Throughput Sequencing Technologies in Native Forest Tree Species in Argentina: Implications for Breeding. In: Pastorino, M.J., Marchelli, P. (eds) Low Intensity Breeding of Native Forest Trees in Argentina. Springer, Cham. https://doi.org/10.1007/978-3-030-56462-9_17

Download citation

Publish with us

Policies and ethics

Search

Navigation