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1.  Population genetic relationships between Casearia sylvestris (Salicaceae) varieties occurring sympatrically and allopatrically in different ecosystems in south-east Brazil 
Annals of Botany  2010;106(4):627-636.
Background and Aims
Species delimitation can be problematic, and recently diverged taxa are sometimes viewed as the extremes of a species' continuum in response to environmental conditions. Using population genetic approaches, this study assessed the relationship between two Casearia sylvestris (Salicaceae) varieties, which occur sympatrically and allopatrically in the landscape of south-east Brazil, where intermediate types are also found.
Methods
In total, 376 individuals from nine populations in four different ecosystems were sampled, and nine microsatellite markers were used to assess the relative effects of the ecosystems and varieties on the distribution of genetic diversity among populations of this species.
Key Results
As a by-product of this study, several PCR products with more than two alleles were observed. The possibility that extra bands represent non-specific amplification or PCR artefacts was discarded by sequencing a sample of these bands. We suggest that (partial) genome duplication in C. sylvestris most probably explains this phenomenon, which may be a key factor in the differentiation of the two taxa, as it was markedly more frequent in one of the varieties. AMOVA indicated that approx. 22 % of the total genetic diversity was found between the two varieties. Bayesian analysis identified varieties and ecosystems as evolutionary units, rather than the individual populations sampled.
Conclusions
The results are in agreement with field observations and support the recognition of two varieties, as well as documenting the occurrence of hybridization between them.
doi:10.1093/aob/mcq151
PMCID: PMC2944974  PMID: 20699231
Atlantic Forest; Casearia sylvestris; Cerrado; ecotones; hybrid zone; microsatellites; population genetic structure; SSR, sympatry
2.  Phylogenetic relationships in genus Arachis based on ITS and 5.8S rDNA sequences 
BMC Plant Biology  2010;10:255.
Background
The genus Arachis comprises 80 species and it is subdivided into nine taxonomic sections (Arachis, Caulorrhizae, Erectoides, Extranervosae, Heteranthae, Procumbentes, Rhizomatosae, Trierectoides, and Triseminatae). This genus is naturally confined to South America and most of its species are native to Brazil. In order to provide a better understanding of the evolution of the genus, we reconstructed the phylogeny of 45 species using the variation observed on nucleotide sequences in internal transcribed spacer regions (ITS1 and ITS2) and 5.8 S of nuclear ribosomal DNA.
Results
Intraspecific variation was detected, but in general it was not enough to place accessions of the same species in different clades. Our data support the view that Arachis is a monophyletic group and suggested Heteranthae as the most primitive section of genus Arachis. The results confirmed the circumscriptions of some sections (Caulorrhizae, Extranervosae), but raised questions about others. Sections Erectoides, Trierectoides and Procumbentes were not well defined, while sections Arachis and Rhizomatosae seem to include species that could be moved to different sections. The division of section Arachis into A and B genome species was also observed in the phylogenetic tree and these two groups of species may not have a monophyletic origin. The 2n = 2x = 18 species of section Arachis (A. praecox, A. palustris and A. decora) were all placed in the same clade, indicating they are closely related to each other, and their genomes are more related to B genome than to the A genome. Data also allowed insights on the origin of tetraploid A. glabrata, suggesting rhizome appeared twice within the genus and raising questions about the placement of that species in section Rhizomatosae.
Conclusion
The main clades established in this study in general agreed with many other studies that have used other types of evidences and sets of species, being some of them included in our study and some not. Thus, the relationships established can be a useful framework for future systematic reviews of genus Arachis and for the selection of species to pre-breeding programs.
doi:10.1186/1471-2229-10-255
PMCID: PMC3095334  PMID: 21092103
3.  Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers 
Genetics and Molecular Biology  2010;33(1):109-118.
Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.
doi:10.1590/S1415-47572010005000001
PMCID: PMC3036074  PMID: 21637613
Arachis; genetic diversity; germplasm; microsatellites; molecular markers
4.  A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome 
BMC Plant Biology  2009;9:40.
Background
Arachis hypogaea (peanut) is an important crop worldwide, being mostly used for edible oil production, direct consumption and animal feed. Cultivated peanut is an allotetraploid species with two different genome components, A and B. Genetic linkage maps can greatly assist molecular breeding and genomic studies. However, the development of linkage maps for A. hypogaea is difficult because it has very low levels of polymorphism. This can be overcome by the utilization of wild species of Arachis, which present the A- and B-genomes in the diploid state, and show high levels of genetic variability.
Results
In this work, we constructed a B-genome linkage map, which will complement the previously published map for the A-genome of Arachis, and produced an entire framework for the tetraploid genome. This map is based on an F2 population of 93 individuals obtained from the cross between the diploid A. ipaënsis (K30076) and the closely related A. magna (K30097), the former species being the most probable B genome donor to cultivated peanut. In spite of being classified as different species, the parents showed high crossability and relatively low polymorphism (22.3%), compared to other interspecific crosses. The map has 10 linkage groups, with 149 loci spanning a total map distance of 1,294 cM. The microsatellite markers utilized, developed for other Arachis species, showed high transferability (81.7%). Segregation distortion was 21.5%. This B-genome map was compared to the A-genome map using 51 common markers, revealing a high degree of synteny between both genomes.
Conclusion
The development of genetic maps for Arachis diploid wild species with A- and B-genomes effectively provides a genetic map for the tetraploid cultivated peanut in two separate diploid components and is a significant advance towards the construction of a transferable reference map for Arachis. Additionally, we were able to identify affinities of some Arachis linkage groups with Medicago truncatula, which will allow the transfer of information from the nearly-complete genome sequences of this model legume to the peanut crop.
doi:10.1186/1471-2229-9-40
PMCID: PMC2674605  PMID: 19351409
5.  Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea) 
BMC Plant Biology  2007;7:9.
Background
The genus Arachis includes Arachis hypogaea (cultivated peanut) and wild species that are used in peanut breeding or as forage. Molecular markers have been employed in several studies of this genus, but microsatellite markers have only been used in few investigations. Microsatellites are very informative and are useful to assess genetic variability, analyze mating systems and in genetic mapping. The objectives of this study were to develop A. hypogaea microsatellite loci and to evaluate the transferability of these markers to other Arachis species.
Results
Thirteen loci were isolated and characterized using 16 accessions of A. hypogaea. The level of variation found in A. hypogaea using microsatellites was higher than with other markers. Cross-transferability of the markers was also high. Sequencing of the fragments amplified using the primer pair Ah11 from 17 wild Arachis species showed that almost all wild species had similar repeated sequence to the one observed in A. hypogaea. Sequence data suggested that there is no correlation between taxonomic relationship of a wild species to A. hypogaea and the number of repeats found in its microsatellite loci.
Conclusion
These results show that microsatellite primer pairs from A. hypogaea have multiple uses. A higher level of variation among A. hypogaea accessions can be detected using microsatellite markers in comparison to other markers, such as RFLP, RAPD and AFLP. The microsatellite primers of A. hypogaea showed a very high rate of transferability to other species of the genus. These primer pairs provide important tools to evaluate the genetic variability and to assess the mating system in Arachis species.
doi:10.1186/1471-2229-7-9
PMCID: PMC1829157  PMID: 17326826

Results 1-5 (5)