An efficient and rapid DNA minipreparation procedure suitable for PCR/SSR and RAPD analyses in tropical forest tree species

Alzate-Marin, Ana Lília; Guidugli, Marcela Corbo; Soriani, Hilda Hildebrand; Martínez, Carlos A.; Mestriner, Moacyr Antonio

doi:10.1590/s1516-89132009000500020

Cited by 32 publications

(25 citation statements)

References 12 publications

(11 reference statements)

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“…Genomic DNA was extracted from leaves of each sample using a modified CTAB protocol as described in Alzate-Marin et al (2009). Amplification protocols for nine microsatellite loci can be found in Guidugli et al (2009).…”

Section: Methodsmentioning

confidence: 99%

Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat

et al. 2016

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Here, we explore the mating pattern and genetic structure of a tropical tree species, Cariniana estrellensis, in a small population in which progeny arrays (n = 399), all adults (n = 28) and all seedlings (n = 39) were genotyped at nine highly informative microsatellite loci. From progeny arrays we were able to identify the source tree for at least 78% of pollination events. The gene immigration rates, mainly attributable to pollen, were high, varying from 23.5 to 53%. Although gene dispersal over long distance was observed, the effective gene dispersal distances within the small population were relatively short, with mean pollination distances varying from 69.9 to 146.9 m, and seed dispersal distances occurring up to a mean of 119.6 m. Mating system analyses showed that C. estrellensis is an allogamous species (t m = 0.999), with both biparental inbreeding (t m − t s = − 0.016) and selfing rates (s = 0.001) that are not significantly different from zero. Even though the population is small, the presence of private alleles in both seedlings and progeny arrays and the elevated rates of gene immigration indicate that the C. estrellensis population is not genetically isolated. However, genetic diversity expressed by allelic richness was significantly lower in postfragmentation life stages. Although there was a loss of genetic diversity, indicating susceptibility of C. estrellensis to habitat fragmentation, no evidence of inbreeding or spatial genetic structure was observed across generations. Overall, C. estrellensis showed some resilience to negative genetic effects of habitat fragmentation, but conservation strategies are needed to preserve the remaining genetic diversity of this population.

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Section: Methodsmentioning

confidence: 99%

Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat

et al. 2016

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“…Protocols described by Billotte et al (1999) were used for construction of a (GA) n and (CA) n microsatellite-enriched library. Total genomic DNA was extracted from an individual of M. nigra according to Alzate-Marin et al (2009) and was digested with RsaI restriction enzyme. The fragments were then linked to adapters (Rsa21 5ꞌ-CTCTTGCTTACGCGTGGACTA-3ꞌ and Rsa25 5ꞌ-TAGTCCACGCGTAAGCAAGAGCACA-3ꞌ), amplified by polymerase chain reaction (PCR) and purified by Quiaquick PCR purification kit (Qiagen).…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity of Metrodorea nigra (Rutaceae) from a small forest remnant in Brazil assessed with microsatellite markers

Guidugli¹,

Ferreira-Ramos²,

Sousa³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Metrodorea nigra (Rutaceae) is an endemic Brazilian tree of great ecological importance, frequently found in the submontane regions of ombrophilous dense and semideciduous forests. This tree is useful for reforesting degraded areas and the wood can be employed in construction. We developed 12 microsatellite markers from a genomic library enriched for GA/CA repeats, for this species. Polymorphisms were assessed in 40 trees of a highly fragmented population found in Cravinhos, State of São Paulo, in southeastern Brazil. Among the 12 loci, 8 were polymorphic and only one had fixed alleles in this population. The number of alleles per locus and expected heterozygosity ranged from 2 to 11 and from 0.190 to 0.889, respectively. These results revealed mod- Microsatellite markers for Metrodorea nigra erate levels of genetic variation in M. nigra population when compared to other tropical species. Additionally, transferability of the 12 primers was tested in seven other Brazilian Rutaceae tree species (endemics: M. stipularis, Galipea jasminiflora, Esenbeckia leiocarpa and non-endemics: E. febrifuga, E. grandiflora, Balfourodendron riedelianum, Zanthoxylum riedelianum). Transferability ranged among species, but at least 8 loci (~67%) amplified in M. stipularis, demonstrating a high potential for transferring microsatellite markers between species of the same genus in the Rutaceae family.

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“…The previously lyophilized young leaves were subjected to DNA extraction, using approximately 1 g fresh leaves for each sample, based on the method described by Doyle and Doyle (1990), modified by Alzate-Marin et al (2009). DNA was quantified using the Nanodrop 2000c spectrophotometer (Thermo Scientific, USA).…”

Section: Dna Extraction and Issr-pcr Amplificationmentioning

confidence: 99%

Genetic diversity of native populations of Croton tetradenius Baill. using ISSR markers

Almeida-Pereira¹,

Silva²,

Alves³

et al. 2017

Genet. Mol. Res.

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ABSTRACT. Brazil has about 300 Croton species in different types of vegetation. Croton tetradenius Baill., which is endemic to the Northeast region and predominant in the Caatinga vegetation, stands out among the several species of this genus. Considering the importance of knowing the genetic variability of a species, the objective of this study was to analyze the genetic diversity of the genotypes of natural populations of C. tetradenius in the State of Sergipe, using ISSR molecular markers. Forty individuals were sampled in four natural populations of the State of Sergipe, Brazil. Thirteen primers were used for DNA amplification using ISSR-PCR, totaling 77 amplified fragments, of which 94.8% were polymorphic. Results of the cluster analysis obtained by the Jaccard's similarity index, using the UPGMA method, resulted in the formation of six distinct clusters. Analysis of molecular variance (AMOVA), used to estimate the genetic variability among populations, revealed significant genetic variance (P < 0.01) between and within the 2 C.S. Almeida-Pereira et al.Genetics and Molecular Research 16 (2): gmr16029602 studied populations, and most of the genetic diversity was found (87%) within populations. According to the Jaccard's similarity index, none of the studied plants was genetically identical. CTE210 and CTE305 presented high similarity index (0.76), while CTE105 presented low similarity index (<0.16) with all related individuals. ISSR markers were efficient and allowed the formation of a molecular profile, and had sufficient polymorphism to estimate the genetic variability between the accessions of the studied populations.

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An efficient and rapid DNA minipreparation procedure suitable for PCR/SSR and RAPD analyses in tropical forest tree species

Abstract: ABSTRACT

Cited by 32 publications

References 12 publications

Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat

Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat

Genetic diversity of Metrodorea nigra (Rutaceae) from a small forest remnant in Brazil assessed with microsatellite markers

Genetic diversity of native populations of Croton tetradenius Baill. using ISSR markers

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