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Quantitative trait locus (QTL) analysis of growth and vegetative propagation traits in Eucalyptus nitens full-sib families

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Abstract

Tree growth and vegetative propagation are complex but important traits under selection in many tree improvement programmes. To understand the genetic control of these traits, we conducted a quantitative trait locus (QTL) study in three full-sib families of Eucalyptus nitens growing at two different sites. One family growing at Ridgley, Tasmania had 300 progeny and two clonally replicated families growing at Mt. Gambier, South Australia had 327 and 210 progeny. Tree growth was measured over several years at both sites and percentages of roots produced by either stem cuttings or tissue culture were assessed in the two Mt. Gambier families. Linkage analysis of growth traits revealed several QTLs for later year traits but few for early year traits, reflecting temporal differences in the heritabilities of these traits. Two growth QTL positions, one on LG8 and another on LG11 were common between the Ridgley and Mt. Gambier families. Four QTLs were observed for each of the two vegetative propagation methods. Two QTLs for vegetative propagation on LG7 and LG11 were validated in the second family at Mt. Gambier. These results suggest that growth and vegetative propagation traits are controlled by several small effect loci. The QTLs identified in this study are useful starting points for identifying candidate genes using the Eucalyptus grandis genome sequence.

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References

  • Beavis WD (1998) QTL analysis: power, precision, and accuracy. In: Patterson HA (ed) Molecular dissection of complex traits. CRC, Boca Raton, pp 145–162

    Google Scholar 

  • Brondani R, Williams E, Brondani C, Grattapaglia D (2006) A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus. BMC Plant Biol 6:20

    Article  PubMed  Google Scholar 

  • Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Villeda HS, Sofia da Silva H, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD (2009) The Genetic Architecture of Maize Flowering Time. Science 325:714–718

    Article  CAS  PubMed  Google Scholar 

  • Bundock P, Potts B, Vaillancourt R (2008) Detection and stability of quantitative trait loci (QTL) in Eucalyptus globulus. Tree Genet Genom 4:85–95

    Article  Google Scholar 

  • Butcher PA, Southerton SG (2007) MAS in forestry species. Marker-assisted selection (MAS) in crops, livestock, forestry and fish: current status and the way forward. FAO, Rome, pp 283–305

    Google Scholar 

  • Byrne M, Murrell JC, Allen B, Moran GF (1995) An integrated genetic linkage map for eucalypts using RFLP, RAPD and isozyme markers. Theor Appl Genet 91:869–875

    Article  CAS  Google Scholar 

  • Byrne M, Parrish TL, Moran GF (1998) Nuclear RFLP diversity in Eucalyptus nitens. Heredity 81:225–233

    Article  CAS  Google Scholar 

  • Darvasi A, Soller M (1997) A simple method to calculate resolving power and confidence interval of QTL map location. Behav Genet 27:125–132

    Article  CAS  PubMed  Google Scholar 

  • de Little DW, Tibbits WN, Rasmussen GF, Ravenwood I (1992) Genetic improvement strategy for APPM Eucalypt tree farms in Tasmania. Mass Production Technology for Genetically Improved Fast Growing Forest Tree species ACTES proceedings. AFOCEL, France, Bordeaux, pp 177-188

  • Eckert AJ, Bower AD, Wegrzyn JL, Pande B, Jermstad KD, Krutovsky KV, St. Clair JB, Neale DB (2009) Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics 182:1289–1302

    Article  CAS  PubMed  Google Scholar 

  • El-Lithy ME, Bentsink L, Hanhart CJ, Ruys GJ, Rovito D, Broekhof JLM, van der Poel HJA, van Eijk MJT, Vreugdenhil D, Koornneef M (2006) New Arabidopsis Recombinant Inbred Line Populations Genotyped Using SNPWave and Their Use for Mapping Flowering-Time Quantitative Trait Loci. Genetics 172:1867–1876

    Article  CAS  PubMed  Google Scholar 

  • England N, Borralho N (1995) Heritability of rooting success in Eucalyptus globulus stem cuttings. In: Eds BM, Potts NMGB, Reid JB, Cromer RN, Tibbits WN, Raymond CA (ed) Eucalypt plantations: improving fibre yield and quality. Proceedings CRC-IUFRO Conference, Hobart, Tasmania, Australia, 19–24 Feb 1995 (CRC for Temperate Hardwood Forestry). pp 237–238

  • Falconer DS, Mackay TFC (eds) (1996) Introduction to Quantitative Genetics, 4th edn. Longman Scientific and Technical, New York

    Google Scholar 

  • Freeman J, Whittock S, Potts B, Vaillancourt R (2009) QTL influencing growth and wood properties in Eucalyptus globulus. Tree Genet Genom 5:713–722

    Article  Google Scholar 

  • Gilmour AR, Gogel BJ, Cullis BR, Thompson R (2006) ASReml User Guide Release 2.0. VSN International Ltd, Hemel Hempstead, HP1 1ES, UK

  • Gonzalez-Martinez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB (2007) Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175:399–409

    Article  PubMed  Google Scholar 

  • Grattapaglia D, Bradshaw HD Jr (1994) Nuclear DNA content of commercially important Eucalyptus species and hybrids. Can J For Res/Rev Can Rech For 24:1074–1078

    Article  Google Scholar 

  • Grattapaglia D, Bertolucci FL, Sederoff RR (1995) Genetic mapping of QTLs controlling vegetative propagation in Eucalyptus grandis and E. urophylla using a pseudo-testcross strategy and RAPD markers. Theor Appl Genet 90:933–947

    Article  CAS  Google Scholar 

  • Grattapaglia D, Bertolucci FLG, Penchel R, Sederoff RR (1996) Genetic mapping of quantitative trait loci controlling growth and wood quality traits in Eucalyptus grandis using a maternal half-sib family and RAPD markers. Genetics 144:1205–1214

    CAS  PubMed  Google Scholar 

  • Grattapaglia D, Plomion C, Kirst M, Sederoff RR (2009) Genomics of growth traits in forest trees. Curr Opin Plant Biol 12:148–156

    Article  CAS  PubMed  Google Scholar 

  • Hamilton MG, Potts BM (2008) Review of Eucalyptus nitens genetic parameters. NZ J For Sci 38:102–119

    Google Scholar 

  • Hetherington S, Orme RK (1989) Seedling variation in root formation of Eucalyptus globulus cuttings. Comb Proc Int Plant Propag Soc 39:56–60

    Google Scholar 

  • Hsu C-Y, Liu Y, Luthe DS, Yuceer C (2006) Poplar FT2 shortens the juvenile phase and promotes seasonal flowering. Plant Cell 18(8):1846–1861

    Article  CAS  PubMed  Google Scholar 

  • Izawa T, Takahashi Y, Yano M (2003) Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr Opin Plant Biol 6:113–120

    Article  CAS  PubMed  Google Scholar 

  • Marques CM, Vasquez-Kool J, Carocha VJ, Ferreira JG, O’Malley DM, Liu BH, Sederoff R (1999) Genetic dissection of vegetative propagation traits in Eucalyptus tereticornis and E. globulus. Theor Appl Genet 99:936–946

    Article  Google Scholar 

  • Marques MC, Brondani BR, Grattapaglia GD, Sederoff SR (2002) Conservation and synteny of SSR loci and QTLs for vegetative propagation in four Eucalyptus species. TAG Theor Appl Genet 105:474–478

    Article  CAS  Google Scholar 

  • Marques C, Carocha V, Pereira de Sá A, Oliveira M, Pires A, Sederoff R, Borralho N (2005) Verification of QTL linked markers for propagation traits in Eucalyptus. Tree Genet Genom 1:103–108

    Article  Google Scholar 

  • Mora F, Gleadow R, Perret S, Scapim C (2009) Genetic variation for early flowering, survival and growth in sugar gum (Eucalyptus cladocalyx F. Muell) in southern Atacama Desert. Euphytica 169:335–344

    Article  Google Scholar 

  • Seaton G, Haley CS, Knott SA, Kearsey M, Visscher PM (2002) QTL Express: mapping quantitative trait loci in simple and complex pedigrees. Bioinformatics 18:339–340

    Article  CAS  PubMed  Google Scholar 

  • Southerton SG, Strauss SH, Olive MR, Harcourt RL, Decroocq V, Zhu XM, Llewellyn DJ, Peacock WJ, Dennis ES (1998) Eucalyptus has a functional equivalent of the Arabidopsis floral meristem identity gene LEAFY. Plant Mol Biol 37:897–910

    Article  CAS  PubMed  Google Scholar 

  • Stackpole D, Vaillancourt R, de Aguigar M, Potts B (2009) Age trends in genetic parameters for growth and wood density in Eucalyptus globulus. Tree Genet Genom. doi:10.1007/s11295-009-0239-4

    Google Scholar 

  • Thamarus KA, Groom K, Murrell J, Byrne M, Moran GF (2002) A genetic linkage map for Eucalyptus globulas with candidate loci for wood, fibre, and floral traits. Theor Appl Genet 104:379–387

    Article  CAS  PubMed  Google Scholar 

  • Thumma BR, Nolan MR, Evans R, Moran GF (2005) Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics 171:1257–1265

    Article  CAS  PubMed  Google Scholar 

  • Thumma BR, Matheson BA, Zhang D, Meeske C, Meder R, Downes GM, Southerton SG (2009) Identification of a Cis-acting regulatory polymorphism in a Eucalypt COBRA-like gene affecting cellulose content. Genetics 183:1153–1164

    Article  CAS  PubMed  Google Scholar 

  • Thumma B, Southerton S, Bell J, Owen J, Henery M, Moran G (2010) Quantitative trait locus (QTL) analysis of wood quality traits in Eucalyptus nitens. Tree Genet Genom 6:305–317. doi:310.1007/s11295-11009-10250-11299

    Article  Google Scholar 

  • Van Ooijen JW (2006) JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V., Wageningen

    Google Scholar 

  • Van Ooijen JW (2009) MapQTL® 6, Software for the mapping of quantitative trait loci in experimental populations of diploid species. Kyazma BV, Wageningen

    Google Scholar 

  • Verhaegen D, Plomion C, Gion JM, Poitel M, Costa P, Kremer A (1997) Quantitative trait dissection analysis in Eucalyptus using RAPD markers: 1. Detection of QTL in interspecific hybrid progeny, stability of QTL expression across different ages. Theor Appl Genet 95:597–608

    Article  Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  CAS  PubMed  Google Scholar 

  • Weedon MN, Lettre G, Freathy RM, Lindgren CM, Voight BF, Perry JRB, Elliott KS, Hackett R, Guiducci C, Shields B, Zeggini E, Lango H, Lyssenko V, Timpson NJ, Burtt NP, Rayner NW, Saxena R, Ardlie K, Tobias JH, Ness AR, Ring SM, Palmer CNA, Morris AD, Peltonen L, Salomaa V, Smith GD, Groop LC, Hattersley AT, McCarthy MI, Hirschhorn JN, Frayling TM (2007) A common variant of HMGA2 is associated with adult and childhood height in the general population. Nat Genet 39:1245–1250

    Article  CAS  PubMed  Google Scholar 

  • Whiteman PH, Dean CA, Doran JC, Cameron JN (1992) Genetic parameters and selection strategies for Eucalyptus nitens (Dean and Maiden) in Victoria. Silvae Genet 41:77–81

    Google Scholar 

  • Wiltshire RJE, Reid JB, Potts BM (1998) Genetic Control of reproductive and vegetative phase change in the Eucalyptus risdonii-E. tenuiramis complex. Aust J Bot 46:45–63

    Article  Google Scholar 

  • Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci USA 90:10972–10976

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank Jan Murrell and Kylie Groom for their help in generating molecular marker data used in this study and John Owen for planting the stem cuttings and ortets at the Mt. Gambier field site. We are grateful to Tim Hingston, Helen Jones and Gillian Rasmussen (Gunn's Ltd.) for providing the vegetative propagation trait data used in this study. For analysing the ELF genes, we have used Eucalyptus DB provided by DOE Joint Genome Institute and Eucalyptus Genome Network, EUCAGEN.

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Authors and Affiliations

  1. CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia

    Bala R. Thumma, Brian S. Baltunis, John C. Bell & Simon G. Southerton

  2. EH Graham Centre for Agricultural Innovation, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia

    Livinus C. Emebiri

  3. School of Biology, Australian National University, Canberra, ACT, 2601, Australia

    Gavin F. Moran

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  1. Bala R. Thumma
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  2. Brian S. Baltunis
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  5. Gavin F. Moran
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  6. Simon G. Southerton
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Correspondence to Bala R. Thumma.

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Communicated by: D. Grattapaglia

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Fig. S1

Comparison of growth and wood quality QTLs in Eucalyptus nitens Ridgley family. WQ-wood quality, GR-growth (PDF 30 kb)

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Thumma, B.R., Baltunis, B.S., Bell, J.C. et al. Quantitative trait locus (QTL) analysis of growth and vegetative propagation traits in Eucalyptus nitens full-sib families. Tree Genetics & Genomes 6, 877–889 (2010). https://doi.org/10.1007/s11295-010-0298-6

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