Skip to main content

Advertisement

Log in

Genetic diversity and population structure of a drought-tolerant species of Eucalyptus, using microsatellite markers

  • Original Article
  • Published:
Journal of Plant Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

Given the impact of climate change on the availability of water resources, it becomes necessary the use of plant species well suited to planting on dryland sites. Eucalyptus cladocalyx, a native tree of South Australia, is capable of growing under relatively dry environments and saline soils. Two hundred twenty simple sequence repeat (microsatellites) markers, from a consensus linkage map of Eucalyptus, were selected to examine genetic diversity and population structure in a collection of E. cladocalyx introduced to southern Atacama Desert, Chile. A total of 130 microsatellites were successfully amplified, some of which are associated with quantitative traits of interest in Eucalyptus. Genetic analysis revealed a total of 457 alleles, ranging from 2 to 8 alleles per locus. A moderate level of genetic diversity (He = 0.492) and differentiation (FST = 0.086) was found among the populations. Mount Remarkable and Marble Range showed the highest and lowest level of genetic diversity, respectively. The Bayesian clustering analysis revealed three homogeneous genetic groups confirming that the individuals of E. cladocalyx from natural forest are highly and significantly structured. These results provide a novel information for the development of breeding strategies in E. cladocalyx by using marker-assisted selection in regions with low rainfall patterns.

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

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others

Abbreviations

AR:

Allelic richness

FST:

Genetic differentiation

MCMC:

Markov chain Monte Carlo

QTL:

Quantitative trait loci

SSR:

Simple sequence repeat

References

  • Arriagada O, Mora F, Dellarossa JC, Ferreira MF, Cervigni GD, Schuster I (2012) Bayesian mapping of quantitative trait loci (QTL) controlling soybean cyst nematode resistant. Euphytica 186:907–917

    Article  Google Scholar 

  • Ballesta P, Mora F, Contreras-Soto R, Ruiz E, Perret S (2015a) Analysis of the genetic diversity of Eucalyptus cladocalyx (sugar gum) using ISSR markers. Acta Sci Agron 37:133–140

    Article  Google Scholar 

  • Ballesta P, Mora F, Ruiz E, Contreras-Soto R (2015b) Marker-trait associations for survival, growth, and flowering components in Eucalyptus cladocalyx under arid conditions. Biol Plant 59(2):389–393

    Article  CAS  Google Scholar 

  • Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Mol Ecol 11:155–165

    Article  PubMed  Google Scholar 

  • Brondani RPV, Brondani C, Tarchini R, Grattapaglia D (1998) Development, characterization and mapping of microsatellite markers in Eucalyptus grandis and E. urophylla. Theor Appl Genet 97:816–827

    Article  CAS  Google Scholar 

  • Brondani RPV, Williams ER, 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  PubMed Central  Google Scholar 

  • Brooker MIH (2000) A new classification of the genus Eucalyptus L’Her. (Myrtaceae). Aust Syst Bot 13:79–148

    Article  Google Scholar 

  • Bush D, Thumma B (2013) Characterising a Eucalyptus cladocalyx breeding population using SNP markers. Tree Genet Genomes 9:741–752

    Article  Google Scholar 

  • Bush D, Jackson T, Driscoll J, Harwood C (2009) Australian low rainfall tree improvement group: metadata from measures of hardwood tree improvement trials in southern Australia. Rural Industries Research and Development Corporation. https://rirdc.infoservices.com.au/downloads/09-078. Accessed 30 Sept 2015

  • Bush D, Mc Carthy K, Meder R (2011) Genetic variation of natural durability traits in Eucalyptus cladocalyx (sugar gum). Ann For Sci 68:1057–1066

    Article  Google Scholar 

  • Bush D, Kain D, Kanowski P, Matheson C (2015) Genetic parameter estimates informed by a marker-based pedigree: a case study with Eucalyptus cladocalyx in southern Australia. Tree Genet Genomes 11:1–16

    Article  Google Scholar 

  • Cané-Retamales C, Mora F, Vargas-Reeve F, Perret S, Contreras-Soto R (2011) Bayesian threshold analysis of breeding values, genetic correlation and heritability of flowering intensity in Eucalyptus cladocalyx under arid conditions. Euphytica 178:177–183

    Article  Google Scholar 

  • Cappa EP, El-Kassaby YA, Garcia MN, Acuña C, Borralho NMG, Grattapaglia D, Marcucci-Poltri SN (2013) Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus. PLoS ONE 8:e81267

    Article  PubMed  PubMed Central  Google Scholar 

  • Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631

    Article  CAS  PubMed  Google Scholar 

  • Clarke B, McLeod I, Vercoe T (2009) Trees for farm forestry: 22 promising species. Rural Industries Research and Development Corporation. https://rirdc.infoservices.com.au/downloads/09-015.pdf. Accessed 21 Sept 2015

  • Contreras-Soto R, Ballesta P, Ruiz E, Mora F (2015) Identification of ISSR markers linked to flowering traits in a representative sample of Eucalyptus cladocalyx. J For Res. doi:10.1007/s11676-015-0149-2

    Google Scholar 

  • da Silva MN (2010) Extraction of genomic DNA from leaf tissues of mature native species of the cerrado. Rev Árvore 34:973–978

    Article  Google Scholar 

  • da Silva TA, Cantagalli LB, Saavedra J, Lopes AD, Mangolin CA, da Silva MDFP, Scapim CA (2015) Population structure and genetic diversity of Brazilian popcorn germplasm inferred by microsatellite markers. Electron J Biotechnol 18:181–187

    Article  Google Scholar 

  • De Lange WJ, Veldtman R, Allsopp MH (2013) Valuation of pollinator forage services provided by Eucalyptus cladocalyx. J Environ Manag 125:12–18

    Article  Google Scholar 

  • Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc B 39:1–38

    Google Scholar 

  • Dutkowski GW, Potts BM (2012) Genetic variation in the susceptibility of Eucalyptus globulus to drought damage. Tree Genet Genomes 8:757–773

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Feng S, Fu Q (2013) Expansion of global drylands under a warming climate. Atmos Chem Phys 13:14637–14665

    Article  Google Scholar 

  • Flint-Garcia SA, Thornsberry JM, Iv B (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

    Article  CAS  PubMed  Google Scholar 

  • Freeman JS, Whittock SP, Potts MB, Vaillancourt RE (2009) QTL influencing growth and wood properties in Eucalyptus globulus. Tree Genet Genomes 5:713–722

    Article  Google Scholar 

  • Gleadow RM, Woodrow IE (2002) Defense chemistry of Eucalyptus cladocalyx seedlings is affected by water supply. Tree Physiol 22:939–945

    Article  CAS  PubMed  Google Scholar 

  • Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from http://www.unil.ch/izea/softwares/fstat.html

  • Grattapaglia D, Kirst M (2008) Eucalyptus applied genomics: from gene sequences to breeding tools. New Phytol 179:911–929

    Article  CAS  PubMed  Google Scholar 

  • Grattapaglia D, Vaillancourt RE, Shepherd M, Thumma BR, Foley W, Külheim C, Potts MB, Myburg AA (2012) Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus. Tree Genet Genomes 8:463–508

    Article  Google Scholar 

  • Hartings H, Berardo N, Mazzinelli GF, Valoti P, Verderio A, Motto M (2008) Assessment of genetic diversity and relationships among maize (Zea mays L.) Italian landraces by morphological traits and AFLP profiling. Theor Appl Genet 117:831–842

    Article  CAS  PubMed  Google Scholar 

  • Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59:1633–1638

    Article  CAS  PubMed  Google Scholar 

  • Heidelberger P, Welch PD (1983) Simulation run length control in the presence of an initial transient. Oper Res 31(6):1109–1144

    Article  Google Scholar 

  • Jones ME, Shepherd M, Henry R, Delves A (2008) Pollen flow in Eucalyptus grandis determined by paternity analysis using microsatellite markers. Tree Genet Genomes 4:37–47

    Article  Google Scholar 

  • Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellites markers: an overview of the recent progress in plants. Euphytica 177:309–334

    Article  CAS  Google Scholar 

  • Kirst M, Cordeiro CM, Rezende GDSP, Grattapaglia D (2005) Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations. J Hered 96:161–166

    Article  CAS  PubMed  Google Scholar 

  • Marcucci-Poltri SN, Zelener N, Traverso JR, Gelid P, Hopp HE (2003) Selection of a seed orchard of Eucalyptus dunnii based on genetic diversity criteria calculated using molecular markers. Tree Physiol 23:625–632

    Article  CAS  PubMed  Google Scholar 

  • Marques C, Brondani RPV, Grattapaglia D, Sederoff R (2002) Conservation of microsatellite loci and QTL for vegetative propagation in Eucalyptus tereticornis, E. globulus, E. grandis and E. urophylla. Theor Appl Genet 105:474–478

    Article  CAS  PubMed  Google Scholar 

  • Marshall TC, Slate JBKE, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655

    Article  CAS  PubMed  Google Scholar 

  • McDonald MW, Rawlings M, Butcher PA, Bell JC (2003) Regional divergence and inbreeding in Eucalyptus cladocalyx (Myrtaceae). Aust J Bot 51:393–403

    Article  Google Scholar 

  • Meirmans PG (2006) Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution 60:2399–2402

    Article  PubMed  Google Scholar 

  • Meirmans PG, Hedrick PW (2011) Assessing population structure: F ST and related measures. Mol Ecol Resour 11:5–18

    Article  PubMed  Google Scholar 

  • Missiaggia AA, Piacezzi AL, Grattapaglia D (2005) Genetic mapping of Eef1, a major effect QTL for early flowering in Eucalyptus grandis. Tree Genet Genomes 1:79–84

    Article  Google Scholar 

  • Mora F, Serra N (2014) Bayesian estimation of genetic parameters for growth, stem straightness, and survival in Eucalyptus globulus on an Andean Foothill site. Tree Genet Genomes 10:711–719

    Article  Google Scholar 

  • Mora F, Gleadow R, Perret S, Scapim CA (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 

  • Mora F, Castillo D, Lado B, Matus I, Poland J, Belzile F, del Pozo A (2015) Genome-wide association mapping of agronomic traits and carbon isotope discrimination in a worldwide germplasm collection of spring wheat using SNP markers. Mol Breeding 35:1–12

    Article  CAS  Google Scholar 

  • Moura JCMS, Araújo P, dos Santos Brito M, Souza UR, Viana JOF, Mazzafera P (2012) Validation of reference genes from Eucalyptus spp. under different stress conditions. BMC Res Notes 5:634

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Myburg AA, Grattapaglia D, Tuskan GA et al (2014) The genome of Eucalyptus grandis. Nature 510:356–362

    CAS  PubMed  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nevill PG, Reed A, Bossinger G, Vaillancourt RE, Larcombe M, Ades PK (2008) Cross-species amplification of Eucalyptus microsatellite loci. Mol Ecol Resour 8:1277–1280

    Article  CAS  PubMed  Google Scholar 

  • O’Reilly PT, Canino MF, Bailey KM, Bentzen P (2004) Inverse relationship between FST and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure. Mol Ecol 13:1799–1814

    Article  PubMed  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Raymond CA (2002) Genetics of Eucalyptus wood properties. Ann For Sci 59:525–531

    Article  Google Scholar 

  • Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225

    Article  PubMed  Google Scholar 

  • Rousset F (2008) Genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Article  PubMed  Google Scholar 

  • Saavedra J, Silva TA, Mora F, Scapim CA (2013) Bayesian analysis of genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR). Chil J Agric Res 73:99–107

    Article  Google Scholar 

  • Sumathi M, Ramasamy Y (2014) Microsatellite resources of Eucalyptus: current status and future perspectives. Bot Stud 55:73

    Article  PubMed  PubMed Central  Google Scholar 

  • Vargas-Reeve F, Mora F, Perret S, Scapim CA (2013) Heritability of stem straightness and genetic correlations in Eucalyptus cladocalyx in the semi-arid region of Chile. Crop Breed Appl Biotechol 13:107–112

    Article  Google Scholar 

  • Woodrow IE, Slocum DJ, Gleadow RM (2002) Influence of water stress on cyanogenic capacity in Eucalyptus cladocalyx. Funct Plant Biol 29:103–110

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank Mr. Augusto Gomes for providing the samples of E. cladocalyx. Osvin Arriagada thanks CONICYT for a doctoral fellowship (CONICYT-PCHA/Doctorado Nacional/año 2013-folio 21130812).

Funding

This study was funded by FONDECYT (Grant Number 1130306).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Freddy Mora.

Ethics declarations

Conflict of interest

Freddy Mora, Osvin Arriagada, Paulina Ballesta, and Eduardo Ruiz declare that they have no conflict of interest.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 34 kb)

Supplementary material 2 (DOCX 21 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mora, F., Arriagada, O., Ballesta, P. et al. Genetic diversity and population structure of a drought-tolerant species of Eucalyptus, using microsatellite markers . J. Plant Biochem. Biotechnol. 26, 274–281 (2017). https://doi.org/10.1007/s13562-016-0389-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13562-016-0389-z

Keywords

Navigation