Skip to main content

Advertisement

SpringerLink
Log in

Genetic variability and effective population size in Hymenaea stigonocarpa (Fabaceae) germplasm collection: tools for breeding programs and genetic conservation

  • Original Paper
  • Published:
Genetica Aims and scope Submit manuscript

Abstract

The conservation of plant genetic resources is essential for breeding programs. Regarding the native species of the Brazilian Cerrado biome, many studies have demonstrated their high potential for use in both medicines and foods. Hymenaea stigonocarpa, a tree with wide occurrence in the Cerrado, has economic importance, and due its extractive use, the establishment of a breeding program is relevant for sustainable use and conservation. Thus, the first germplasm collection of the species was installed at the Federal University of Goiás (UFG). To know the magnitude of genetic variability and how it was distributed in the collection, 353 individuals, distributed in 119 families from 24 subpopulations collected in the Cerrado biome, were genotyped using capillary electrophoresis. Nine pairs of microsatellite markers were genotyped. The UFG germplasm collection showed a high level of genetic diversity (mean \(\bar{H}e\) = 0.554) at the evaluated loci. By Analysis of Molecular Variance (AMOVA), a significant genetic structure was detected (θP = 0.152, p < 0.01), which was expected since the subpopulations that originated the germplasm collection were collected in geographically distant locations. In addition, the germplasm collection had a population effective size of 54.9 and presented an allelic representation of 79.89% compared to 32 natural subpopulations. These results demonstrate that the germplasm collection preserves a high genetic diversity of H. stigonocarpa with a population effective size considered sufficient for the conduction of a breeding program.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Ahuja MR, Jain SM (2017) Biodiversity and conservation of woody plants. Sustainable development and biodiversity. Springer. https://doi.org/10.1007/978-3-319-66426-2

  • Almeida GQ, Chaves LJ, Vieira MC, Ganga RMD (2019) Agronomic evaluation of a Hancornia speciosa Gomes germplasm collection from the Brazilian Cerrado. Crop Breeding and Appl Biotechnol. https://doi.org/10.1590/1984-70332019v19n1a02

  • Barcaccia G (2010) Molecular markers for characterizing and conserving crop plant germplasm. In: Jain SM, Brar DS (eds) Molecular techniques in crop improvement, 2rd edn. Springer, Cham. https://doi.org/10.1007/978-90-481-2967-6

    Chapter  Google Scholar 

  • Batista AG, Esteves EA, Dessimoni-Pinto NAV, Oliveira LG, Pires ST, Santana RC (2011) Chemical composition of Jatobá-do-Cerrado (Hymenaea stigonocarpa Mart.) flour and its effect on growth of rats. Alim Nutr, ISSN 0103-4235

  • Batista CM, Freitas MLM, de Moraes MA, Zanatto ACS, Santos PC, Zanata M, Moraes MLT, Sebbenn AM (2012) Estimativas de parâmetros genéticos e a variabilidade em procedências e progênies de Handroanthus vellosoi. Pesquisa Florestal Brasileira, Colombo 32(71):269–276. https://doi.org/10.4336/2012.pfb.32.71.269

    Article  Google Scholar 

  • Braga RS, Pinto RB, Chaves LJ, Diniz-Filho JAF, Soares TN, Collevatti RG, Telles MPC (2019) Hierarchical genetic and spatial structure among varieties and populations of Hymenaea stigonocarpa (Fabaceae) in Brazilian savannah. Tree Genet Genomes. ISSN: 1614–2950

  • Bretting PK, Duvick DN (1997) Dynamic conservation of plant genetic resources. Adv Agron 61:1–51. https://doi.org/10.1016/s0065-2113(08)60661-6

    Article  Google Scholar 

  • Buonamici A, Cavers S, Vendramin GG (2008) Microsatellite loci isolated from the tropical tree Hymenaea courbaril L (Fabaceae). Mol Ecol Res. https://doi.org/10.1111/j.1755-0998.2008.02140.x

    Article  Google Scholar 

  • Carvalho PER (2006) Espécies Arbóreas Brasileiras v2. Embrapa Informação Tecnológica, Brasília

    Google Scholar 

  • Carvalho PER (2007) Jatobá-do-cerrado—Hymenaea stigonocarpa. Embrapa Florestas, Colombo

    Google Scholar 

  • Chaves LJ, Vencovsky R, Silva RSM, Telles MPC, Zucchi MI, Coelho ASG (2011) Estimating inbreeding depression in natural plant populations using quantitative and molecular data. Conserv Genet 12(2):569–576. https://doi.org/10.1007/s10592-010-0164-y

    Article  Google Scholar 

  • Ciampi AY, Azevedo VCR, Gaiotto FA, Ramos ACS, Lovato MB (2008) Isolation and characterization of microsatellite loci for Hymenaea courbaril and transferability to Hymenaea stigonocarpa, two tropical timber species. Mol Ecol Res. https://doi.org/10.1111/j.1755-0998.2008.02159.x

    Article  Google Scholar 

  • Coelho ASG (2000) BOOD: Avaliação de dendrogramas baseados em estimativas de distâncias/similaridades genéticas através do procedimento de bootstrap (software). Laboratório de Genética Vegetal, ICB-UFG, Goiânia

    Google Scholar 

  • Collevatti RG, Telles MPC, Nabout JC, Chaves LJ, Soares TN (2013) Demographic history and the low genetic diversity in Dipteryx alata (Fabaceae) from Brazilian Neotropical savannas. Heredity (Edinb) 111:97–105. https://doi.org/10.1038/hdy.2013.23

    Article  CAS  Google Scholar 

  • de Vries A, Ripley BD (2016) Ggdendro: Create Dendrograms and Tree Diagrams Using ‘ggplot2′ R package version 01–20. https://CRAN.R-project.org/package=ggdendro

  • Dias BFS (2008) Conservação da biodiversidade no bioma Cerrado: histórico dos impactos antrópicos no bioma Cerrado. In: Faleiro FG, Farias-Neto AL (eds) Savanas: desafios e estratégias para o equilíbrio entre sociedade, agronegócio e recursos naturais. Embrapa Cerrados, Planaltina, pp 303–333

    Google Scholar 

  • Doyle JJ, Doyle JL (1987) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Durigan G (2003) Bases e diretrizes para a restauração da vegetação de Cerrado. In: Kageyama PY, Oliveira RE, Moraes LFO, Engel VE, Gandara FB (eds) Restauração ecológica de sistemas naturais. FEPAP, Botucatu, pp 187–204

    Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction sites. Genetics 131:479–491

    CAS  PubMed  PubMed Central  Google Scholar 

  • Feres JM, Guidugli MC, Mestriner MA, Sebbenn AM, Ciampi AY, Alzate-Marin AL (2009) Microsatellite diversity and effective population size in a germplasm bank of Hymenaea courbaril var. stilbocarpa (Leguminosae), an endangered tropical tree: recommendations for conservation. Genet Resour Crop Evol 6:797–807. https://doi.org/10.1007/s10722-008-9402-2

    Article  CAS  Google Scholar 

  • Fiori GML, Fachin AL, Correa VSC, Bertoni BW, Giuliatti S, Amui SF, França SC, Pereira MAS (2013) Antimicrobial activity and rates of tannins in Stryphnodendron adstringens Mart. accessions collected in the Brazilian cerrado. Am J Plant Sci 4:2193–2198. https://doi.org/10.4236/ajps.2013.411272

    Article  CAS  Google Scholar 

  • Forzza RC, Baumgratz JFA, Bicudo CEM et al (2012) New Brazilian floristic list highlights conservation challenges. Bioscience 62:39–45. https://doi.org/10.1525/bio.2012.62.1.8

    Article  Google Scholar 

  • Frankel OH, Brown AHD, Burdon JJ (1995) Conservation of plant biodiversity. Cambridge University Press, Cambridge

    Google Scholar 

  • Ganga RMD, Chaves LJ, Naves RV (2009) Parâmetros genéticos em progênies de Hancornia speciosa Gomes do Cerrado. Scientia Forestalis 37(84):395–404

    Google Scholar 

  • Gibbs PE, Oliveira PE, Bianchi MB (1999) Postzygotic control of selfing in Hymenaea stigonocarpa (Leguminosae—Caesalpinioideae), a bat-pollinated tree of the Brazilian cerrados. The University of Chica. Int J Plant Sci 160:72–78

    Article  Google Scholar 

  • Gonela A, Sebbenn AM, Soriani HH, Mestriner MA, Martinez CA, Alzate-Marin AL (2013) Genetic diversity and mating system of Copaifera langsdorffii (Leguminosae/Caesalpinioideae). Genet Mol Res 12(1):569–580. https://doi.org/10.4238/2013

    Article  CAS  PubMed  Google Scholar 

  • Goudet J (2002) FSTAT, a program to estimate and test gene diversities and fixation indices (Version 2.9.3.2). http://www.unil.ch/izea/softwares/fstat.html

  • Guimarães RA, Miranda KMC, Mota EES, Chaves LJ, Telles MPC, Soares TN (2019) Assessing genetic diversity and population structure in a Dipteryx alata germplasm collection utilizing microsatellite markers. Crop Breeding Appl Biotechnol 19:329–336. https://doi.org/10.1590/1984-70332019v19n3a45

    Article  Google Scholar 

  • Hartl DL, Clark AG (2010) Princípios de genética de populações, 4th edn. Editora Artmed, Porto Alegre

    Google Scholar 

  • IBPGR (1991) Elsevier’s dictionary of plant genetic resources. Elsevier Science Publishers, Amsterdam, p 187

    Google Scholar 

  • Jamieson IG, Allendorf FW (2012) How does the 50/500 rule apply to MVPs. Trends Ecol Evol. https://doi.org/10.1016/j.tree.2012.07.001

    Article  PubMed  Google Scholar 

  • Jombart T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405. https://doi.org/10.1093/bioinformatics/btn129

    Article  CAS  PubMed  Google Scholar 

  • Killeen TJ, García EE, Beck SG (1993) Guía de Arboles de Bolivia. IOP Publishing Usaid. http://pdf.usaid.gov/pdf_docs/pnaca189.pdf Accessed 20 March 2018

  • Langenheim JH, Lee YT (1974) Reinstatement of the genus Hymenaea (Leguminosae: Caesalpinioideae) in Africa. Brittonia 26:3–21

    Article  Google Scholar 

  • Lee YT, Langenheim JH (1975) Systematics of the genus Hymenaea L. (Leguminosae—Caesalpinioideae) Detarieae. University of California Press, Berkley

    Google Scholar 

  • Lorenzi H (1992) Árvores Brasileiras: manual de identificação e cultivo de plantas arbóreas nativas do Brasil. Instituto Plantarum, Nova Odessa

    Google Scholar 

  • Lughadha EN, Govaerts R, Belyaeva I et al (2016) Counting counts: revised estimates of numbers of accepted species of flowering plants, seed plants, vascular plants and land plants with a review of other recent estimates. Phytotaxa 272:82–88. https://doi.org/10.11646/phytotaxa.272.1.5

    Article  Google Scholar 

  • Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27(2):209–220

    CAS  PubMed  Google Scholar 

  • Maranhão CA, Pinheiro IO, Santana ALBD, Oliveira LS, Nascimento MS, Bieber LW (2013) Antitermitic and antioxidant activities of heartwood extracts and main flavonoids of Hymenaea stigonocarpa Mart. Int Biodeterior Biodegrad. https://doi.org/10.1016/j.ibiod.2013.01.005

    Article  Google Scholar 

  • Moraes MLT, Sebbenn AM (2011) Pollen dispersal between isolated trees in the Brazilian savannah: a case study of the Neotropical tree Hymenaea stigonocarpa. Biotropica 43:192–199. https://doi.org/10.1111/j.1744-7429.2010.00679.x

    Article  Google Scholar 

  • Moura NF, Chaves LJ, Naves RV, Aguiar AV, Sobierajski GR (2013) Variabilidade entre procedências e progênies de Pequizero (Caryocar brasiliense Camb.). Scientia Forestalis 41(97):103–112

  • Olifiers N, Cerqueira R (2006) Fragmentação de habitat: efeitos históricos e ecológicos. In: Rocha CFD, Bergallo HG, Sluys MV, Alves MAS (eds) Biologia da conservação: Essências. RiMa, São Carlos, pp 261–275

    Google Scholar 

  • Orsi PR, Bonamin F, Severi JA, Santos RC, Vilegas W, Hirumalima CA, Stasi LCD (2012) Hymenaea stigonocarpa Mart. ex Hayne: a Brazilian medicinal plant with gastric and duodenal anti-ulcer and antidiarrheal effects in experimental rodent models. J Ethnopharmacol. https://doi.org/10.1016/j.jep.2012.06.001

    Article  Google Scholar 

  • Paetkau D, Calvert W, Stirling I, Strobeck C (1995) Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol. https://doi.org/10.1111/j.1365-294X.1995.tb00227.x

    Article  PubMed  Google Scholar 

  • R Core Team (2018) R: A language and environment for statistical computing R Foundation for Statistical Computing. Vienna, Austria. http://www.r-projectorg/

  • Rohlf FJ (2000) Numerical taxonomy and multivariate analysis system version 2.1.1. IOP Publishing Exetersoftware. https://www.exetersoftware.com/downloads/ntsysguide21.pdf. Accessed 05 April 2018

  • Sano SM, da Fonseca CEL (2003) Taxa de sobrevivência e frutificação de espécies nativas do cerrado. Embrapa Cerrados, Planaltina. Available at https://ainfo.cnptia.embrapa.br/digital/bitstream/CPAC-2009/25076/1/bolpd_83.pdf. Accessed 12 January 2018

  • Sebbenn AM (2003) Tamanho amostral para conservação ex situ de espécies arbóreas com sistema misto de reprodução. Revista do Instituto Florestal 15:147–162

    Google Scholar 

  • Silva MR, Silva MS, Martins KA, Borges S (2001) Utilização tecnológica dos frutos de jatobá-do-cerrado e de jatobá-da-mata na elaboração de biscoitos fontes de fibra alimentar e isentos de açúcares. Ciência e Tecnologia de Alimentos, vol 21. IOP Publishing, Bristol, pp 176–182. http://www.scielo.br/pdf/cta/v21n2/7463.pdf. Accessed 12 January 2018

  • Singh J, Dhall RK (2011) Molecular characterization of biodiversity in molecular vegetables—a review. Agric Rev 32:193–201

    Google Scholar 

  • Souza CD, Felfili JM (2006) Uso de plantas medicinais na região de Alto Paraíso de Goiás, GO, Brasil. Acta Bot Bras. https://doi.org/10.1590/S0102-33062006000100013

    Article  Google Scholar 

  • Souza HAV, Collevatti RG, Lima-Ribeiro MS, Lemos-Filho JP, Lovato MB (2017) A large historical refugium explains spatial patterns of genetic diversity in a Neotropical savannah tree species. Ann Bot 119:239–252. https://doi.org/10.1093/aob/mcw096

    Article  CAS  PubMed  Google Scholar 

  • Ulloa CU, Acevedo-Rodríguez P, Beck S et al (2017) An integrated assessment of the vascular plant species of the Americas. Science. https://doi.org/10.1126/science.aao0398

    Article  PubMed  Google Scholar 

  • Valois AC, Nass LL, Goes M (2001) Conservação ex situ de recursos genéticos vegetais. In: Nass LL, Valois ACC, Melo IS, Valadares-Inglis MC (eds) Recursos Genéticos & Melhoramento—Plantas. Fundação de Apoio à Pesquisa Agropecuária de Mato Grosso—Fundação MT, Rondonópolis, pp 423–441

    Google Scholar 

  • van Jaarsveld AS, Freitag S, Chown SL, Muller C, Koch S, Hull H, Bellamy C, Kruger M, Endrody-Younga S, Mansell MW (1998) Biodiversity assessment and conservation strategies. Science 27(279):2106–2108

    Article  Google Scholar 

  • van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538. https://doi.org/10.1111/j.1471-8286.2004.00684.x

    Article  CAS  Google Scholar 

  • Vencovsky R, Nass LL, Cordeiro CMT, Ferreira MAJF (2007) Amostragem em recursos genéticos vegetais. In: Nass LL (ed) Recursos genéticos vegetais. Embrapa Recursos Genéticos e Biotecnologia, Brasília, pp 231–280

    Google Scholar 

  • Wagner HW, Sefc KM (1999) IDENTITY 1.0. Centre for Applied Genetics, University of Agricultural Sciences, Vienna (version 4.0). http://www.uni-graz.at/~sefck

  • Walter BMT, Cavalcanti TB, Bianchetti LB, Valls JFM (2005) Coleta de germoplasma vegetal: relevância e conceitos básicos. In: Walter BMTE, Cavalcanti TB (eds) Fundamentos para a coleta de germoplasma vegetal. Embrapa Recursos Genéticos e Biotecnologia, Brasília, pp 28–55

    Google Scholar 

  • Weir BS (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Associates Inc., Sunderland

    Google Scholar 

  • Yokomizo GKI, Maia MCC, Trindade CF (2017) Morphological dissimilarity among mangabeira tree populations from Amapá and Paraíba, Brazil. Rev. Caatinga 30(2):521–529. https://doi.org/10.1590/1983-21252017v30n228rc

    Article  Google Scholar 

  • Zimmerman MJO, Teixeira MG (1996) Bancos de Germoplasma. In: Araujo RS, Rava CA, Stone LF, Zimmermam MJO (eds) Cultura do feijoeiro comum no Brasil. Potafos, Piracicaba, pp 65–66

    Google Scholar 

Download references

Acknowledgements

This work was supported by several grants and fellowships to the research network PRONEX ‘‘Núcleo de Excelência em Genética e Conservação de Espécies do Cerrado” (Pronex—Fapeg/CNPq (CP 07/2012) and Universal CNPq (447754/2014-9). Work by A.R.G was supported by a fellowship from CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior). Work by M.P.C.T. and L.J.C. has been continuously supported by productivity fellowships from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico). Our current research in Genetics and Genomics is developed in the context of National Institutes for Science and Technology (INCT) in Ecology, Evolution and Biodiversity Conservation, supported by MCTIC/CNPq (proc. 465610/2014-5) and FAPEG (Fundação de Amparo à Pesquisa do estado de Goiás). This paper is dedicated to Professor Roland Vencovsky (1936–2016), who has contributed so much to research in biometrics, genetics and plant breeding, and has left us his knowledge as a legacy and source of inspiration.

Author information

Authors and Affiliations

  1. Programa de pós-graduação em Genética e Melhoramento de Plantas (PGMP), Escola de Agronomia, Universidade Federal de Goiás, Campus II, Goiânia, GO, Brazil

    Ariany Rosa Gonçalves

  2. Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II, PO Box 131, Goiânia, GO, 74001-970, Brazil

    Ariany Rosa Gonçalves & Mariana Pires de Campos Telles

  3. Escola de Agronomia, Universidade Federal de Goiás, Avenida Esperança, Goiânia, GO, 74690-900, Brazil

    Lázaro José Chaves

  4. Escola de Ciências Agrárias e Biológicas, Pontifícia Universidade Católica de Goiás, Goiânia, GO, 74605-010, Brazil

    Mariana Pires de Campos Telles

Authors
  1. Ariany Rosa Gonçalves
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lázaro José Chaves
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mariana Pires de Campos Telles
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mariana Pires de Campos Telles.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 46 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gonçalves, A.R., Chaves, L.J. & de Campos Telles, M.P. Genetic variability and effective population size in Hymenaea stigonocarpa (Fabaceae) germplasm collection: tools for breeding programs and genetic conservation. Genetica 147, 359–368 (2019). https://doi.org/10.1007/s10709-019-00076-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10709-019-00076-0

Keywords

Search

Navigation