Development and characterization of microsatellite markers in <i>Campomanesia adamantium</i>, a native plant of the Cerrado ecoregions of South America

Crispim, Bruno do Amaral; Déo, Thamiris Gatti; Fernandes, Juliana dos Santos; Vasconcelos, Adrielle Ayumi de; Vieira, M. do C.; Carnevali, Thiago de Oliveira; Bajay, Miklos Maximiliano; Zucchi, Maria Imaculada; Barufatti, Alexéia

doi:10.1002/aps3.11287

Cited by 4 publications

(5 citation statements)

References 21 publications

(25 reference statements)

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“…Crispim et al [21] characterized a set of 41 specific microsatellites in C. adamantium, out of which, 10 were used in this study, and, as expected, their results were similar to those of our study. Thus, our results indicate that specific markers provide a more accurate assessment than others of aspects related to genetic variability, possibly because the transfer of microsatellites between species may produce an inaccurate representation of genetic diversity, ultimately causing misinterpretation of the actual situation of populations [40].…”

Section: Discussionsupporting

confidence: 90%

“…Studies with microsatellite markers in C. adamantium were conducted by Miranda et al [19] and Crispim et al [20] and both studies evaluated genetic diversity using markers derived from Eucalyptus sp., also a member of the Myrtaceae family. Recently, Crispim et al [21] characterized a set of microsatellites specific for C. adamantium, and their results were different from those mentioned regarding inbreeding in native populations of the species, thus indicating that the use of species-specific microsatellite sets can provide more accurate information on genetic variability. The lack of information about the genetic diversity of C. admantium using species-specific microsatellite sets as well as the relations of land use and land cover could have influenced the parameters of genetic diversity, once anthropic actions converted areas previously occupied by forest fragments into agricultural areas.…”

Section: Introductionmentioning

confidence: 87%

“…The leaves (200 mg) were macerated in liquid nitrogen and DNA was extracted using the protocol adapted from Doyle and Doyle [25], using an extraction buffer containing 3% CTAB (w/v), 25 mM EDTA, 100 mM Tris-HCl (pH 8.0), 2 M NaCl, 5% PVP (w/v), and 2% betamercaptoethanol (v/v). Then, 10 species-specific microsatellite marker loci (Table S1), developed by Crispim et al [21], were amplified.…”

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

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Genetic Diversity of Campomanesia adamantium and Its Correlation with Land Use and Land Cover

et al. 2021

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(1) Background: Campomanesia adamantium is an endemic species of the Cerrado and this biome has been under threat by its constant degradation. The genetic diversity of C. adamantium was characterized using species-specific microsatellites in two different time periods and correlations of these parameters of genetic diversity with the land use and land cover data. (2) Methods: We used 10 microsatellite loci to analyze C. adamantium from five populations, collected in 2011 and 2017. Maps of land use and land cover of the collection sites in both years were generated and subsequently correlated with genetic diversity. (3) Results: No significant loss of genetic diversity was observed in the analyzed period and a positive inbreeding coefficient was observed in all populations. AMOVA and STRUCTURE showed that there is no population structure between years and populations. Significant Pearson correlations were observed in 2017 between parameters of genetic diversity and land use and land cover, with a positive correlation between expected heterozygosity and secondary vegetation, and a negative correlation between inbreeding coefficient and exposed soil. (4) Conclusions: There was no decline in genetic diversity from 2011 to 2017. The high rates of the inbreeding coefficient could lead, for the species, in the long run, to an inbreeding depression as the Cerrado fragmentation might cause a population bottleneck.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 87%

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

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Genetic Diversity of Campomanesia adamantium and Its Correlation with Land Use and Land Cover

et al. 2021

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“…SSR markers are characterized by repeated sequences comprising mono-, di-, tri-, tetra-, penta- or hexa-nucleotide units that are characterized by tandem repeats (1-10 nucleotide motifs) that exhibit locus-specific codominance and high heterozygosity, are distributed throughout the genome, and are easier to detect than other molecular markers [ 6 ]. Microsatellite markers have been successfully used in the assessment of many plants, e.g., Vicia faba [ 7 , 8 ], Campomanesia adamantium [ 9 ], Populus deltoides [ 10 ], Olea europaea [ 11 ], and Cunninghamia lanceolata [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers

Zhang

Gao³

et al. 2021

BMC Plant Biol

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Vicia amoena is a high-nutritional quality forage similar to alfalfa. However, studies on the genetic background of V. amoena are scarce. In the present study, the genetic variation of 24 V. amoena populations was assessed with newly developed simple sequence repeat (SSR) markers. A total of 8799 SSRs were identified in the V. amoena genomic-enriched sequences, and the most abundant repeat number was four. A total of 569 sampled individuals were assayed to evaluate the genetic diversity of the V. amoena populations based on 21 polymorphic SSR primers. The polymorphism information content (PIC) ranged from 0.896 to 0.968, with an average of 0.931, which indicated that the markers were highly informative. Based on analysis of molecular variance, 88% of the variance occurred within populations, and the remaining 12% of the variance occurred among populations. The high degree of gene flow (Nm= 4.958) also showed slight differentiation among the V. amoena populations. The V. amoena populations were mainly clustered by steppe and mountain habitats based on principal coordinate analysis (PCoA) and STRUCTURE analysis. This indicated that the elevation and special habitat of geographical origins may be important factors affecting the clustered pattern of V. amoena populations. Neighbour-joining (NJ) analysis did not separate the populations well by geographical origin, which indicated that the genetic structure of V. amoena was complex and needs further study. Overall, our results showed that the newly developed SSR markers could benefit the V. amoena research community by providing genetic background information to help establish a foundation for breeding improvement and germplasm resource conservation.

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“…Both studies using microsatellite loci from Eucalyptus disclosed more alleles per locus than the number found here for C. phaea likely because the analyses of polymorphism were conducted in automatic sequencers using uorescence, which can be more accurate in detecting alleles. In another study with C. adamantium based on 36 polymorphic microsatellite loci speci cally developed for this species, the number of alleles varied from 2 to 14 per locus (mean 8.14), whereas mean values of H e and H o were 0.46 and 0.52, respectively, but based on a small sample (n=10) (Crispim et al 2019). In general, the overall levels of expected and observed heterozygosity were comparable among the Campomanesia species, mostly with higher H e than H o , but not by a large margin.…”

Section: Resultsmentioning

confidence: 99%

Genetic Diversity of Cambuci (Campomanesia Phaea) Revealed by Microsatellite Markers

Moreira

Bressan

Neto

et al. 2021

Preprint

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Campomanesia phaea (Myrtaceae), known as cambuci, is a native species from the Brazilian Atlantic Forest with great potential to be developed as a new fruit crop. Microsatellite markers were developed for cambuci to characterize the genetic diversity and to investigate the genetic structure of a group of accessions originally collected at the presumed center of diversity of the species. The work involved the collection of 145 accessions from five regional groups (Juquitiba, Paraibuna, Mogi das Cruzes, Ribeirão Pires, and Salesópolis) in São Paulo state, Brazil. Fourteen loci were identified in an enriched genomic library developed from one of these accessions. Six out of 14 loci revealed to be polymorphic, disclosing 26 alleles. Based on the allele frequencies, the calculated genetic parameters of the five groups indicated an average allele number per loci (A) of 3.83, with the expected heterozygosity (He) of 0.57 and the observed heterozygosity (Ho) of 0.54. The analysis of the genetic structure indicated that most of the genetic diversity is found within each population (HS = 0.57), whereas the genetic diversity among populations was low (GST = 0.19). The genetic diversity parameter of Nei was considered low for the cambuci analyzed populations, with no evidence of inbreeding. Based on Darwin analysis, we chose 18 accessions from the five regional populations to compose a core collection that includes most of the genetic diversity found in this study. Our findings may contribute to define better conservation strategies and genetic breeding approaches for this native species in Brazil.

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Development and characterization of microsatellite markers in Campomanesia adamantium, a native plant of the Cerrado ecoregions of South America

Cited by 4 publications

References 21 publications

Genetic Diversity of Campomanesia adamantium and Its Correlation with Land Use and Land Cover

Genetic Diversity of Campomanesia adamantium and Its Correlation with Land Use and Land Cover

Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers

Genetic Diversity of Cambuci (Campomanesia Phaea) Revealed by Microsatellite Markers

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