No CrossRef data available.
Article contents
Genetic characterisation of Annona crassiflora as basis for conservation and breeding
Published online by Cambridge University Press: 09 October 2024
Abstract
Annona crassiflora is a fruit-bearing tree species native to the Cerrado that has ecological and economic potential, mainly due to the production of attractive and useful fruits for a number of species, including humans. To provide a basis for its conservation and breeding, the objective was to assess the diversity and genetic structure of natural populations of the species using inter-simple sequence repeat (ISSR) molecular markers. Eight populations were analysed in the state of Minas Gerais, Brazil, with 24 individuals randomly sampled in each population, reaching a total of 192 trees. Ten ISSR primers were used, resulting in high genetic diversity for the combined data (H* = 0.35 and I* = 0.52). However, a wide range of representative values was observed in the individual assessment of populations, with JAN, GM and MC standing out for their low genetic diversity, resulting in H* of 0.19, 0.23 and 0.24 and I* of 0.28, 0.34 and 0.35, respectively. An analysis of molecular variance showed greater variation within populations, indicating gene flow (Nm), but genetic differentiation between populations was moderate. Bayesian analysis, although resulting in four genetic groups, revealed the presence of a majority group for the GM and JAN populations. We propose measures to maintain these populations, such as raising awareness of local extractivism and planting genetically divergent seedlings. Furthermore, we recommend including of all populations in conservation and breeding programmes, aiming to cover the maximum genetic variation for the species.
- Type
- Research Article
- Information
- Copyright
- Copyright © The Author(s), 2024. Published by Cambridge University Press on behalf of National Institute of Agricultural Botany
References
Aguilar, LG, López, AMS, Aceituno, CB, Ávila, JAC, Guerreiro, JAL and Quesada, RA (2016) DNA source selection for downstream applications based on DNA quality indicators analysis. Biopreservation and Biobanking 14, 264–270.CrossRefGoogle Scholar
Alvares, CA, Stape, JL, Sentelhas, PC, Gonçalves, JLM and Sparovek, G (2013) Köppen's climate classification map for Brazil. Meteorologische Zeitschrift 22, 711–728.CrossRefGoogle Scholar
Arruda, HS, Botrel, DA, Fernandes, RVB and Almeida, MEF (2016) Development and sensory evaluation of products containing the Brazilian savannah fruits araticum (Annona crassiflora Mart.) and cagaita (Eugenia dysenterica Mart.). Brazilian Journal of Food Technology 19, 1–7.CrossRefGoogle Scholar
Auguie, B and Antonov, A (2017) Miscellaneous functions for ‘Grid’ graphics. R package version 2.3. Available at https://cran.r-project.org/web/packages/gridExtra/gridExtra (accessed 14 January 2022).Google Scholar
Cavalcante, TRM, Naves, RV, Franceschinelli, EV and Silva, RP (2009) Polinização e formação de frutos em araticum. Bragantia 68, 13–21.CrossRefGoogle Scholar
Cohen, KO, Sano, SM, Silva, JCS and Melo, JT (2010) Avaliação das características físicas e físico-químicas dos frutos de araticum procedentes de Cabeceiras, GO. Embrapa Cerrados, Planaltina, Distrito Federal. 17 p.Google Scholar
Cruz, CD (2016) Genes software – extended and integrated with the R, Matlab and Selegen. Acta Scientiarum Agronomy 38, 547–552.CrossRefGoogle Scholar
Earl, DA and Vonholdt, BM (2012) Structure Harvester: a website and program for visualizing structure output and implementing the Evanno method. Conservation Genetics Resources 4, 359–361.CrossRefGoogle Scholar
Ellegren, H and Galtier, N (2016) Determinants of genetic diversity. Nature Reviews Genetics 17, 422–433.CrossRefGoogle ScholarPubMed
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software Structure: a simulation study. Molecular Ecology 14, 2611–2620.CrossRefGoogle ScholarPubMed
Excoffier, L and Lischer, HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10, 564–567.CrossRefGoogle ScholarPubMed
Excoffier, L, Smouse, PE and Quattro, JM (1992) Analysis of molecular variance inferred from metric distance among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479–449.CrossRefGoogle ScholarPubMed
Falush, D, Stephens, M and Pritchard, J (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 7, 574–578.CrossRefGoogle ScholarPubMed
Filippos, A (2016) Conservation and monitoring of tree genetic resources in temperate forests. Current Forestry Reports 2, 119–129.Google Scholar
Galili, T, Benjamini, Y, Simpson, G, Jefferis, G, Gallota, M, Renaudie, J, Hornik, K, Ligges, U, Spiess, AN, Horvath, S, Langfelder, P, Loo, MVD, Vries, A, Gu, Z, Cath, G, Ma, J, Krzysiek, G, Hummel, M, Clark, C, Graybuck, L, Jdetribol, J, Ho, B, Perreault, S, Hennig, C, Bradley, D, Huang, H and Schupp, P (2020) Extending ‘dendrogram’ functionality in R. R package version 1.13.4, 2020. Available at https://cran.r-project.org/web/packages/dendextend/dendextend (accessed 14 January 2022).Google Scholar
Gwinner, R, Setotaw, TA, Rodrigues, FA, França, DVC, Silveira, FA, Pio, LAS and Pasqual, M (2016) Population structure of Annona crassiflora: an endemic plant species of the Brazilian Cerrado. Genetics and Molecular Research 15, 1–13.CrossRefGoogle ScholarPubMed
Inoue, MH, Santana, DC, Vilhena, KSS, Souza Filho, APS, Guilhon, GMSP, Possamai, ACS, Silva, LE and Dallacort, R (2010) Avaliação do potencial alelopático de substâncias isoladas em sementes de araticum (Annona crassiflora). Planta Daninha 28, 735–741.CrossRefGoogle Scholar
Kassambara, A (2020) ‘ggplot2’ based publication ready plots. R package version 0.4.0, 2020. Available at https://cran.r-project.org/web/packages/ggpubr/ggpubr. (accessed 14 January 2022).Google Scholar
Kassambara, A and Mundt, F (2017) Factoextra: extract and visualize the results of multivariate data analyses. R package version 1.0.5, 2017. Available at https://CRAN.R-project.org/package=factoextra (accessed 14 January 2022).Google Scholar
Kiill, LHP and Costa, JG (2003) Biologia floral e sistema de reprodução de Annona squamosa L. (Annonaceae) na região de Petrolina-PE. Ciência Rural 33, 851–856.CrossRefGoogle Scholar
Lewontin, RC (1972) The apportionment of human diversity. Evolutionary Biology 6, 381–398.Google Scholar
Maechler, M, Rousseeuw, P, Struyf, A, Hubert, M, Hornik, K, Studer, M, Roudier, P, Gonzalez, J, Kozlowski, K, Schubert, R, Murphy, K (2019) ‘Finding groups in Data’: cluster analysis extended Rousseeuw et al. R package version 2.1.0, 2019. Available at https://cran.r-project.org/web/packages/cluster/cluster (accessed 14 January 2022).Google Scholar
Mantel, N (1967) The detection of disease clustering and a generalized regression approach. Cancer Research 27, 209–220.Google Scholar
Ministério do Meio Ambiente – MMA (2022) O bioma Cerrado. Available at https://antigo.mma.gov.br/biomas/cerrado.html (accessed 14 January 2022).Google Scholar
Mojena, R (1977) Hierarchical grouping methods and stopping rules: an evaluation. The Computer Journal 20, 359–363.CrossRefGoogle Scholar
Moog, RJ and Bond, JM (2003) A cheap, reliable and rapid method of extracting high-quality DNA from plants. Molecular Ecology Notes 3, 666–668.CrossRefGoogle Scholar
Nei, M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583–590.CrossRefGoogle ScholarPubMed
Oksanen, J, Blanchet, FG, Friendly, M, Kindt, R, Legendre, P, Mcglinn, D, Minchin, PR, O'hara, RB, Simpson, GL, Solymos, P, Stevens, MHH, Szoecs, E and Wagner, E (2018) Vegan: community ecology package. R package version 2.4-5, 2018. Available at https://CRAN.R-project.org/package=vegan (accessed 14 January 2022).Google Scholar
Pereira, JCM, Lemes, RCGG, Castro, JDB, Peixoto, JC, Safadi, GMVV and Oliveira, MF (2022) Valoração do Araticum (Annona crassiflora Mart.). Research, Society and Development 17, 1–15.Google Scholar
Pimenta, AC, Amano, E and Zuffellato-Riba, KC (2017) Estaquia e anatomia caulinar de Annona crassiflora Mart. Caderno de Ciências Agrárias 9, 1–7.Google Scholar
R Core Team (2016) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.Google Scholar
Sá, GH, Lima, FCD, Viana, JPG, Lopes, ACA, Carvalho, LCB, Valente, SES and Lima, PSC (2022) Genetic diversity and structure of an active germplasm collection of Annona squamosa L. Ecological Genetics and Genomics 25, 1–8.CrossRefGoogle Scholar
Samaradiwakara, SHMRNP, Samarasinghe, WLG, Shantha, PGS, Jayarathna, KGCN, Dehigaspitiya, P and Ubeysekera, NM (2020) Genetic diversity assessment of selected Annona muricata L. germplasm in Sri Lanka. Asian Journal of Agricultural and Horticultural Research 7, 1–13.CrossRefGoogle Scholar
Santo-Silva, EE, Almeida, WR, Tabarelli, M and Peres, CA (2016) Habitat fragmentation and the future structure of tree assemblages in a fragmented Atlantic Forest landscape. Plant Ecology 217, 1129–1140.CrossRefGoogle Scholar
Santos, IG and Oliveira, MS (2020) Fatores que alteram o equilíbrio de Hardy-Weinberg. In Oliveira, MS and Cruz, CD (eds), Genética de Populações com o Aplicativo GPOP. Curitiba, PR: Brazil Publishing, pp. 97–141.Google Scholar
Shannon, CE and Weaver, WA (1949) Mathematical Model of Communication. Urbana: University of Illinois Press.Google Scholar
Silva Júnior, AL, Cabral, RLR, Sartori, L, Souza, LC, Miranda, FD, Caldeira, MVW, Moreira, SO and Godinho, TO (2020) Evaluation of diversity and genetic structure as strategies for conservation of natural populations of Dalbergia nigra (vell.) Allemão ex Benth. Cerne 26, 435–443.CrossRefGoogle Scholar
Souza, JLC, Souza, ERB, Naves, RV, Guimarães, RN and Melo, APC (2020) Propagação de araticum por estaquia. Agrossistemas 12, 223–236.CrossRefGoogle Scholar
Strassburg, BBN, Brooks, T, Feltran-Barbieri, R, Iribarrem, A, Crouzeilles, R, Loyola, R, Latawiec, AE, Oliveira Filho, FJB, Scaramuzza, CAM, Scarano, FR, Soares Filho, B and Balmford, A (2017) Moment of truth for the Cerrado hotspot. Nature Ecology & Evolution 1, 1–3.CrossRefGoogle ScholarPubMed
Tatikonda, L, Wani, SP, Kannan, S, Beerelli, N, Sreedevi, TK, Hoisington, DA, Devi, P and Varshney, RK (2009) AFLP-based molecular characterization of an elite germplasm collection of Jatropha curcas L. biofuel plant. Plant Science 176, 505–513.CrossRefGoogle ScholarPubMed
Trackmaker (2022) GPS TrackMaker Version 13.9.608. Geo Studio Technology. Available at https://www.trackmaker.com/main/pt/licenca-gps-software-gratis (accessed 9 September 2022).Google Scholar
Turchetto-Zolet, AC, Turchetto, C, Zanella, AM and Passaia, G (2017) Marcadores Moleculares na Era genômica: Metodologias e Aplicações. Sociedade Brasileira de Genética, Ribeirão Preto.Google Scholar
Vieira, AAR, Souza, AC, Silva Júnior, AL, Alves, BQ, Miranda, FD, Moreira, SO and Caldeira, MVW (2022) Diversity and genetic structure of Astronium concinnum Schott ex Spreng. in conservation units. Plant Genetic Resources: Characterization and Utilization 19, 530–537.CrossRefGoogle Scholar
Wilke, CO (2019) Streamlined plot theme and plot annotations for ‘ggplot2’. R package version 1.0.0, 2019. Available at https://cran.r-project.org/web/packages/cowplot/cowplot (accessed 14 January 2022).Google Scholar
Wright, S (1951) The genetical structure of populations. Annals of Eugenic 15, 323–354.CrossRefGoogle ScholarPubMed
Wright, S (1978) Evolution and the Genetics of Populations: Variability within and among Natural Populations. Chicago, IL, USA: University of Chicago press.Google Scholar
Yeh, FC and Boyle, TJB (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belgian Journal of Botany 129, 156–157.Google Scholar