Population Structure of Annona Crassiflora: an Endemic Plant Species of the Brazilian Cerrado
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Population structure of Annona crassiflora: an endemic plant species of the Brazilian Cerrado R. Gwinner1, T.A. Setotaw1, F.A. Rodrigues1, D.V.C. França2, F.A. da Silveira1, L.A.S. Pio1 and M. Pasqual1 1Laboratório de Cultura de Tecidos, Departamento de Agricultura, Universidade Federal de Lavras, Lavras, MG, Brasil 2Departamento de Agricultura, Universidade Federal de São Carlos, Araras, SP, Brasil Corresponding author: R. Gwinner E-mail: [email protected] Genet. Mol. Res. 15 (4): gmr15049137 Received September 2, 2016 Accepted November 16, 2016 Published December 23, 2016 DOI http://dx.doi.org/10.4238/gmr15049137 Copyright © 2016 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution ShareAlike (CC BY-SA) 4.0 License. ABSTRACT. Habitat fragmentation has numerous consequences, particularly to endemic species, and has a negative impact on the genetic diversity of neglected species, leading to genetic drift. Annona crassiflora Mart. is a species that is endemic to Brazil, and its incidence in the Cerrado biome has decreased. The identification and characterization of its remaining diversity is necessary for its conservation. Our aim was to study the population structure of A. crassiflora populations from different Cerrado regions in Minas Gerais State, Brazil (Corinto, Curvelo, Carmo da Mata, Boa Esperança, and Paraguaçu) using inter-simple sequence repeat (ISSR) markers and DNA content. Nuclear DNA content was estimated by flow cytometry using 10 individuals from each population. ISSR markers were used for genotyping accessions in order to study their genetic diversity and population structures. We found considerable genetic variation among Genetics and Molecular Research 15 (4): gmr15049137 R. Gwinner et al. 2 populations, with the highest variability observed in the Curvelo population. There was a significant positive correlation between DNA content and latitude (r = 0.46, P = 0. 0003). A Bayesian-based cluster analysis grouped the populations into three clusters, which followed their geographical origins. There was some level of genetic diversity and differentiation among the populations, suggesting the need for a conservation plan for this species. The ISSR markers and DNA content analysis were effective in studying the genetic diversity and population structure of A. crassiflora. Key words: Flow cytometry; Marolo; ISSR marker; Annona crassiflora INTRODUCTION Agricultural expansion and urbanization have resulted in the degradation of the Cerrado biome in Brazil (Brannstrom et al., 2008), which has had a direct impact on the population sizes of endemic species, and, therefore, constitutes a threat to Cerrado biodiversity. Despite the richness of its genetic resources (Mittermeier et al., 2005), the Cerrado has considerably decreased in area, and robust conservation measures are needed to avoid further biodiversity loss. Of the several plant species that are endemic to the Cerrado, Annona crassiflora Mart. is particularly important for its potential as a food source and its pesticidal and allelopathic properties (de Omena et al., 2007; Inoue et al., 2010; Roesler, 2011; Ribeiro et al., 2013). A. crassiflora is commonly known as marolo in Brazil, and is distributed from Goiás State to Minas Gerais State. Minas Gerais has considerable importance in the genetic diversity of A. crassiflora, because the species has expanded its range in this state. Using random amplified polymorphic DNA (RAPD) markers, Cota et al. (2011) reported high genetic diversity among A. crassiflora populations in the north of Minas Gerais. Using simple sequence repeat (SSR) markers, Collevatti et al. (2014) found high genetic variability in populations of this species in Goiás State, highlighting the negative impact of habitat fragmentation, which can result in a high fixation index due to mating amongst closely related individuals. These results highlight the need for the conservation and characterization of the species’ remaining diversity. In order to design an appropriate conservation strategy, it is necessary to study the species’ genetic diversity among different geographical regions. This can be conducted in several ways, including molecular marker techniques and quantification of the genomic DNA content. Inter-simple sequence repeats (ISSRs) are frequently used to study genetic diversity and population structures of different species, including endangered taxa such as Ammopiptanthus (Ge et al., 2005), montane plant species (Deshpande et al., 2001), and Citrullus lanatus landraces (Dje et al., 2010). This marker is particularly useful if there is insufficient information available on the species of interest, or if the study species has no specific markers, such as A. crassiflora. ISSR markers are multi-locus, species nonspecific, are amplified along the genome in a random manner, and are able to detect differences among accessions. We also analyzed A. crassiflora diversity using the DNA content, which is referred to as the C value (Bennett and Leitch, 1995) and indicates genome size. This value varies between species and between individuals of the same species (Schifino-Wittmann, 2001), is linked to species evolution, and can be correlated with various phenotypic and phenological traits (Bennett et al., 2000). Brazilian biomes are being continuously destabilized, so the existence of a large Genetics and Molecular Research 15 (4): gmr15049137 Population structure of Annona crassiflora 3 number of endemic species makes species characterization a difficult task. Studies that focus on the recovery and conservation of genetic resources are necessary for sustainable economic development. The nuclear DNA content of A. crassiflora has not been described. Understanding the genetic diversity and population structure of A. crassiflora is the first step in making recommendations for its conservation and sustainable use. The information obtained from molecular markers is more stable and not as affected by environmental factors as phenotypic information, and can help in developing a conservation strategy for this species. This study had the following objectives: 1) study the nuclear DNA content of A. crassiflora populations in different mesoregions of Minas Gerais State, and verify the feasibility of using flow cytometry as a tool for detecting genetic variability among isolated populations of A. crassiflora; and 2) study the population structure and genetic diversity of A. crassiflora populations in different mesoregions of Minas Gerais State using ISSR markers. MATERIAL AND METHODS Study area Sample collection was conducted in the municipalities of Boa Esperança, Carmo da Mata, Paraguaçu, Corinto, and Curvelo (Figure 1). For each analysis, independent samples were collected. Figure 1. Populations of Annona crassiflora in Corinto (yellow), Curvelo (light green), Carmo da Mata (red), Boa Esperança (blue), and Paraguaçu (green) in Minas Gerais State, Brazil. Genomic DNA content estimation To estimate the C value of A. crassiflora, 10 adult plants from each in situ population were identified and georeferenced with a global positioning system device (eTrex Vista® HCx, Garmin, USA). Leaf samples that were in good phytosanitary condition were collected from adult plants and kept in a low-temperature container under high moisture. The collected samples were analyzed within 24 h at Laboratório de Cultura de Tecidos, Departamento de Agricultura, Universidade Federal de Lavras. The samples’ DNA content was analyzed using flow cytometry according to the methodology described Genetics and Molecular Research 15 (4): gmr15049137 R. Gwinner et al. 4 by Magalhães et al. (2015), with some modifications. Tomato (Solanum lycopersicum L.) was used as an internal reference standard, the nuclear DNA content of which was 1.96 pg. The samples were kept under low temperature in the dark and analyzed using a flow cytometer (BD FACSCaliburTM, BD Biosciences) to obtain histograms. The 2C DNA content was estimated using the software WinMDI 2.8, and the estimated value was subjected to an analysis of variance (ANOVA) and a mean separation test. The relationship between DNA content and latitude was investigated using correlation analysis. All of the statistical analyses were performed using GENES (Cruz, 2013) and R (R Core Team, 2014). ISSR analysis Plant materials Fifty-five A. crassiflora accessions from five different locations (11 from Corinto, 10 from Curvelo, 10 from Carmo da Mata, 12 from Boa Esperança, and 12 from Paraguaçu) were included. A list of the collection sites is presented in Table 1. The leaf samples were collected in the specified regions from randomly selected adult plants, and transported to the Laboratory of Plant Biotechnology, Empresa de Pesquisa Agropecuária de Minas Gerais, Caldas, Minas Gerais. The leaves were washed and stored in a freezer at -80°C for at least 2 h, then lyophilized until dry. The lyophilized leaves were ground and stored until DNA extraction. Table 1. Characteristics of Annona crassiflora populations sampled in Minas Gerais State, Brazil. Location (County) Latitude (south) Longitude (west) Altitude (m) Number of samples Minas Gerais (Mesoregion) Corinto 18°24'02'' 44°27'44'' 674 11 Central Curvelo 18°49'10'' 44°29'19'' 724 10 Central Carmo da Mata 20°33'59'' 44°52'09'' 869 10 West Boa Esperança 21°04'59'' 45°41'53'' 814 12 South/Southeast Paraguaçu 21°33'03'' 45°45'29'' 846 12 South/Southeast DNA extraction DNA was extracted according to the method described by Nunes et al. (2011)