Abstract
In this study, we report the development and characterization of 15 new microsatellite markers for Stryphnodendron adstringens (Leguminosae) in order to support future analyses of genetic diversity in populations of this species. In screening with 48 individuals from three different populations of S. adstringens, we tested the amplification of 20 microsatellite loci, of which five are not useful for population genetic studies due to the lack of polymorphisms or amplification failures. For the final set of 15 loci, the number of alleles ranged from 2 to 15, with a total of 116 alleles. The expected heterozygosity ranged from 0.1219 to 0.8965, with an average of 0.6694 per locus. The combined probability of genetic identity (PI = 8.12 × 10−15) and paternity exclusion (Q = 0.99999) estimations showed that the loci may be useful to discriminate between individuals of S. adstringens. Initial cross-amplification tests were satisfactory in three species of the genus Stryphnodendron: S. rotundifolium, S. coriaceum and S. polyphyllum. This new set of markers will be a useful tool for population genetic studies, contributing to the knowledge about the evolutionary history of S. adstringens and, additionally, correlated species.
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References
Andrews S (2015) FastQC: a quality control tool for high throughput sequence data. Available online at http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Barbará T, Palma-Silva C, Paggi GM, Bered F, Fay MFC, Lexer C (2007) Cross-species transfer of nuclear microsatellite markers: potential and limitations. Mol Ecol. https://doi.org/10.1111/j.1365-294X.2007.03439.x
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btu170
Branco EA, Zimback L, Lima AB, Mori ES, Aoki H (2010) Estrutura Genética de populações de Stryphnodendron adstringens (Mart.), pp 31–37. Available online at https://smastr16.blob.core.windows.net/iflorestal/RIF/SerieRegistros/IFSR42/IFSR42.pdf
Creste S, Tulmann Neto A, Figueira A (2001) Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining. Plant Mol Biol Rep. https://doi.org/10.1007/BF02772828
Diniz VSS, Franceschinelli EV (2015) Estrutura populacional e brotamento de três espécies nativas do cerrado em diferentes regimes de queimadas. J Neotr Biol. https://doi.org/10.5216/rbn.v11i2.29488
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19(1):11
Glasenapp JS, Casali VWD, Barbosa PB et al (2014) Description of genetic diversity of natural populations of barbatimão Stryphnodendron adstringens (Mart.) Coville in conservation areas from Minas Gerais. Rev Arvore. https://doi.org/10.1590/S0100-67622014000100010
Goudet J (2002) FSTAT, a program to estimate and test gene diversities and fixation indices (Version 2.9.3.2). Available online at http://www.unil.ch/izea/softwares/fstat.html
Meglécz E, Pech N, Gilles A et al (2014) QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate. Mol Ecol Res. https://doi.org/10.1111/1755-0998.12271
Mendonça PC, Bertoni BW, Amui SF et al (2012) Genetic diversity of Stryphnodendron adstringens (Mart.) Coville determined by AFLP molecular markers. Biochem Syst Ecol. https://doi.org/10.1016/j.bse.2011.12.007
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individual. Genetics 89:583–590
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
Pellenz NL, Barbisan F, Azzolin VF, Marques LPS, Mastella MH, Teixeira CF, Ribeiro EE, da Cruz IBM (2019) Healing activity of Stryphnodendron adstringens (Mart.), a Brazilian tannin-rich species: a review of the literature and a case series. Wound Med. https://doi.org/10.1016/j.wndm.2019.100163
Pryszcz LP, Gabaldón T (2016) Redundans: an assembly pipeline for highly heterozygous genomes. Nucl Acids Res. https://doi.org/10.1093/nar/gkw294
Rizzini CT, Heringer EP (1966) Estudo sobre os sistemas subterrâneos difusos de plantas campestres. Anais da Acad Bras de Ciênc 38:85–112
Rousset F (2008) GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Res. https://doi.org/10.1111/j.1471-8286.2007.01931.x
Souza VC, Lima AG (2020) Stryphnodendron in Flora do Brasil 2020 em construção. Jardim Botânico do Rio de Janeiro. Available online at http://reflora.jbrj.gov.br/reflora/floradobrasil/FB23174
Souza-Moreira TM, Queiroz-Fernandes GM, Pietro RCLR (2018) Stryphnodendron species known as “Barbatimão”: a comprehensive report. Molecules. https://doi.org/10.3390/molecules23040910
Taheri S, Abdullah TL, Yusop MR et al (2018) Mining and development of novel SSR markers using Next Generation Sequencing (NGS) data in plants. Molecules. https://doi.org/10.3390/molecules23020399
R Core Team (2020) R: a language and environment for statistical computing R Foundation for Statistical Computing. Vienna, Austria. Available online at http://www.r-projectorg/
Unamba CIN, Nag A, Sharma RK (2015) Next generation sequencing technologies: the doorway to the unexplored genomics of non-model plants. Front Plant Sci. https://doi.org/10.3389/fpls.2015.01074
Wagner HW, Sefc KM (1999) IDENTITY 1.0. Centre for Applied Genetics, University of Agricultural Sciences, Vienna (version 4.0). Available online at http://www.uni-graz.at/~sefck
Weir BS (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Associates Inc., Sunderland
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370
Wright S (1951) The genetic structure of populations. Ann Eug 15:323–354
Zalapa JE, Cuevas H, Zhu H et al (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot. https://doi.org/10.3732/ajb.1100394
Zimin AV, Marçais G, Puiu D et al (2013) The MaSuRCA genome assembler. Bioinformatics. https://doi.org/10.1093/bioinformatics/btt476
Acknowledgements
This work was supported by a PRONEX project from: PRONEX—FAPEG/CNPq (CP 07/2012) and CNPq (447754/2014-9). A.R.G, L.O.B, and U.J.B.S were supported by a fellowship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). Works conducted by A.N.S.P., B.W.B, and M.P.C.T. have been continuously supported by productivity fellowships from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). 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 Fundação de Amparo à Pesquisa do Estado de Goiás (FAPEG), which we gratefully acknowledge.
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Gonçalves, A.R., Barateli, L.O., de Souza, U.J.B. et al. Development and characterization of microsatellite markers in Stryphnodendron adstringens (Leguminosae). Physiol Mol Biol Plants 26, 2095–2101 (2020). https://doi.org/10.1007/s12298-020-00876-1
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DOI: https://doi.org/10.1007/s12298-020-00876-1