[show abstract][hide abstract] ABSTRACT: Microsatellite (SSR) markers were developed for the following tropical forage species, using accessions available from the plant genetic resources (PGR) collections held by EMBRAPA (Brazilian Agricultural Research Corporation): Brachiaria brizantha, B. humidicola, Panicum maximum, Paspalum spp., Stylosanthes capitata, S. guianensis, S. macrocephala, Calopogonium mucunoides and Centrosema spp. The markers were used to analyze population struc-ture and genetic diversity, evolution and origin of the genetic variability in the center of origin, mating systems and genetic resources in EMBRAPA’s germplasm bank. The results shed light on the amount of genetic variation within and between populations, revealed the need in some cases for further plant collection to adequately represent the spe-cies in PGR collections, allowed us to assemble core collections (subsets of the total collections) that should contain most of the available diversity and (in the case of the legumes) showed the need to avoid unwanted outcrossing when regenerating conserved material. The data will allow plant breeders to better select accessions for hybrid production, discriminate between genotypes and use marker-assisted selection in breeding programs. Our results will also underpin the construction of genetic maps, mapping of genes of agronomic interest and numerous other studies on genetic varia-bility, population structure, gene flow and reproductive systems for the tropical forage species studied in this work.
[show abstract][hide abstract] ABSTRACT: BACKGROUND: Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct identification of germplasms and quantification of their variability are necessary for the proper development of conservation and breeding programs. Evaluation of microsatellite markers in different species of Paspalum conserved in a germplasm bank allowed assessment of the genetic differences among them and assisted in their proper botanical classification. RESULTS: Seventeen new polymorphic microsatellites were developed for Paspalum atratum Swallen and Paspalum notatum Flugge, twelve of which were transferred to 35 Paspalum species and used to evaluate their variability. Variable degrees of polymorphism were observed within the species. Based on distance-based methods and a Bayesian clustering approach, the accessions were divided into three main species groups, two of which corresponded to the previously described Plicatula and Notata Paspalum groups. In more accurate analyses of P. notatum accessions, the genetic variation that was evaluated used thirty simple sequence repeat (SSR) loci and revealed seven distinct genetic groups and a correspondence of these groups to the three botanical varieties of the species (P. notatum var. notatum, P. notatum var. saurae and P. notatum var. latiflorum). CONCLUSIONS: The molecular genetic approach employed in this study was able to distinguish many of the different taxa examined, except for species that belong to the Plicatula group, which has historically been recognized as a highly complex group. Our molecular genetic approach represents a valuable tool for species identification in the initial assessment of germplasm as well as for characterization, conservation and successful species hybridization.
[show abstract][hide abstract] ABSTRACT: The aim of this study was to construct and characterize an SSR-enriched genomic library for Passiflora alata, a fruit species native to the Brazil-ian plateau and the eastern Amazon region. There is potential to improve this crop, as the fruit is attractive because of its pleasant aroma and fla-vour characteristics. Of 862 sequences, 391 (45%) were found to have SSRs. We identified 412 microsatellites: 69% were classified as perfect, 23% imperfect, 5% interrupted and 3% were compound microsatellites. The main types of repeat sequences were dinucleotide (62.5%) and trinu-cleotide (23%) repeats. It was possible to design 312 primer pairs, and 229 of them were synthesized and tested. The amplicons were electro-phoresed using denaturing and non-denaturing gels to screen for diver-gence between two phenotypically distinct parents of a mapping population of P. alata. Length and conformation polymorphisms within repeat sequences amounted to 35% and 28%, respectively. The impor-tance of the development of SSR markers for sweet passion fruit and the effectiveness of the SSCP approach to increase the available number of polymorphic SSRs are discussed.
[show abstract][hide abstract] ABSTRACT: Kielmeyera coriacea is one of the most char- acteristic entities of the Cerrado, a savanna vegetation of Central Brazil and it is a morphologically highly variable polyploid species. In the revision of the genus, an earlier variety was elevated to a related species. However, this proposal has not been accepted by the scientific community and the problematic taxonomic circumscription of the group raises doubts about various scientific studies on plants identified as K. coriacea. In the present study, we investigated the subject by a population genetics approach using eight microsatellite markers in an attempt to under- stand better the relationships between the proposed species. Like morphological and anatomical observations, molecu- lar studies of highly polymorphic markers showed a great similarity between K. coriacea and K. grandiflora. However, this tool could effectively screen the boundaries of the species complex and, in addition, detect an introgres- sive hybridization process.
Plant Systematics and Evolution 01/2013; 299:731-741. · 1.31 Impact Factor
[show abstract][hide abstract] ABSTRACT: Stylosanthes species are important forage legumes in tropical and subtropical areas. S. macrocephala and S. capitata germplasm collections that consist of 134 and 192 accessions, respectively, are maintained at the Brazilian Agricultural Research Corporation Cerrados (Embrapa-Cerrados). Polymorphic microsatellite markers were used to assess genetic diversity and population structure with the aim to assemble a core collection. The mean values of H(O) and H(E) for S. macrocephala were 0.08 and 0.36, respectively, whereas the means for S. capitata were 0.48 and 0.50, respectively. Roger's genetic distance varied from 0 to 0.83 for S. macrocephala and from 0 to 0.85 for S. capitata. Analysis with STRUCTURE software distinguished five groups among the S. macrocephala accessions and four groups among those of S. capitata. Nei's genetic diversity was 27% in S. macrocephala and 11% in S. capitata. Core collections were assembled for both species. For S. macrocephala, all of the allelic diversity was represented by 23 accessions, whereas only 13 accessions were necessary to represent all allelic diversity for S. capitata. The data presented herein evidence the population structure present in the Embrapa-Cerrados germplasm collections of S. macrocephala and S. capitata, which may be useful for breeding programs and germplasm conservation.
Genetics and Molecular Biology 12/2012; 35(4):847-61. · 0.74 Impact Factor
[show abstract][hide abstract] ABSTRACT: • Premise of the study: We developed and characterized nuclear microsatellite markers for Anadenanthera colubrina, a tropical tree species widely distributed in South America. • Methods and Results: Leaf samples of mature A. colubrina trees, popularly called "angico," were collected from an area that is greatly impacted by agricultural practices in the region of Ribeirão Preto in São Paulo State in southeastern Brazil. Twenty simple sequence repeat (SSR) markers were developed, 14 of which had polymorphic loci. A total of 96 alleles were detected with an average of 6.86 alleles per polymorphic locus. The expected heterozygosity, calculated at polymorphic loci, ranged from 0.18 to 0.83. Finally, we demonstrated that 18 loci were cross-amplified in A. peregrina. • Conclusions: A total of 14 polymorphic markers suggest a high potential for genetic diversity, gene flow, and mating system analyses in A. colubrina.
American Journal of Botany 03/2012; 99(4):e154-6. · 2.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: Acrocomia aculeata is a perennial, fruit-producing palm tree, native to tropical forests. Its fruits have spurred interest because of their significant potential for use in the cosmetic industry and as feedstock for biofuel. In the present study, the genetic structure and mating system in Acrocomia aculeata were analyzed, using eight nuclear micro-satellite loci and samples from São Paulo and Minas Gerais states, Brazil. By means of Bayesian analysis, these populations were clustered into two or three groups. A high multilocus outcrossing rate suggests that outcrosses were predominant, although a certain degree of biparental inbreeding also occurred. Thus, although monoecious and self-compatible, there is every indication that A. aculeata bears a mixed reproductive system, with a predominance of outcrossing. Given the genetic structure revealed hereby, future conservation strategies and germplasm collecting should be focussed on sampling and preserving individuals from different clusters.
Genetics and Molecular Biology 01/2012; 35(1):119-21. · 0.74 Impact Factor
[show abstract][hide abstract] ABSTRACT: A new set of microsatellite or simple sequence repeat (SSR) markers for garlic, an important medicinal spice, was developed to aid studies of genetic diversity and to define efficient strategies for germplasm conservation.
Using a (CT)(8)- and (GT)(8)-enriched library, a total of 16 SSR loci were developed and optimized in garlic. Ten loci were found to be polymorphic after screening 75 accessions. The parameters used to characterize the loci were observed and expected heterozygosity, number of alleles, Shannon Index, and polymorphism information content (PIC). A total of 44 alleles were identified, with an average of 4.4 alleles per loci. The vast majority of loci were moderate to highly informative according to PIC and the Shannon Index.
The new SSR markers have the potential to be informative tools for genetic diversity, allele mining, mapping and associative studies, and in the management and conservation of garlic collections.
American Journal of Botany 12/2011; 99(1):e17-9. · 2.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: • Premise of the study: This study was designed to develop and characterize a preliminary set of nuclear microsatellite markers for Aspidosperma polyneuron, an endangered tropical tree species. • Methods and Results: Leaf samples were collected from a group of mature A. polyneuron trees in a large area along the Pardo and Mogi-Guaçu river basins in São Paulo State in the southeastern region of Brazil. Twenty-five simple sequence repeat (SSR) markers were developed and 16 of 30 samples had polymorphic loci. The number of alleles per locus ranged from two to 17 (average = 7.06). A high diversity (H(e) = 0.65) and parentage exclusion probability for the first (0.9995) and second (0.9999) parents were measured. • Conclusions: These 16 polymorphic markers suggest a high potential for genetic diversity, gene flow, and mating system analyses in A. polyneuron.
American Journal of Botany 11/2011; 98(11):e300-2. · 2.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: Hebanthe eriantha (Amaranthaceae) is extensively collected and used in folk medicine. Microsatellite markers were developed and characterized to investigate the genetic structure and diversity of germplasm collections of this species.
Eleven highly polymorphic microsatellite markers were developed. The number of alleles observed for each locus ranged from two to eight. The observed and expected heterozygosities ranged from 0.000 to 0.808 and 0.455 to 0.851, respectively.
These results show the utility of microsatellite loci for studies of population genetics in H. eriantha, which are important for the future conservation and cultivation of this medicinal species.
American Journal of Botany 10/2011; 98(10):e282-3. · 2.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: Germplasm molecular and phenotypic characterization is instrumental to its utilization and to genetic variability incorporation into rice breeding programmes. The diversity within 192 Japanese rice accessions was analysed for 22 agro-morphological traits and 24 single sequence repeat markers. A total of 181 alleles were detected, 38 of which were exclusive. The number of alleles/marker ranged from 2 to 16, with an average of 7.54 alleles/locus and the He value ranged from 0.01 to 0.82, with an average of 0.46. The accessions showed diversity at molecular and phenotypic level and few showed also good agronomic performance. Tocher's method applied on a total-dissimilarity matrix was used to determine cluster formation of 13 diversity groups. Most of the accessions (81%) were clustered within a group, whereas eight accessions (Kyuushuu, Eika Ine, Ishiwari Mochi, Col/Fukui/1965, Ookuma Nishiki, Suzume Shirazu, Iwate Ryoon and Toga) did not cluster with other accessions.
[show abstract][hide abstract] ABSTRACT: Dioscorea alata L. is one of the most widely distributed species of the genus in the humid and semihumid tropics and is associated with traditional agriculture. Only a few microsatellite markers have been developed so far for this and other Dioscorea species.
We isolated 14 codominant polymorphic microsatellite markers using a microsatellite-enriched genomic library technique. Ten microsatellite loci were selected, and 80 D. alata accessions from different regions in Brazil were evaluated with nine polymorphic loci. The polymorphism information content (PIC) varied from 0.39 to 0.78 and the power discrimination (PD) ranged from 0.15 to 0.91. Six of the markers showed transferability for the species D. bulbifera, D. cayenensis-D. rotundata, and D. trifida.
The SSR markers obtained are an important tool for further studies aiming to characterize the genetic diversity in D. alata and other Dioscorea spp. accessions.
American Journal of Botany 06/2011; 98(6):e144-6. · 2.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: Microsatellite primers were developed for Aulonemia aristulata, an endangered species of economic interest, to further describe its genetic variability and population structure. We also tested cross-amplification in 18 other bamboo species.
Using an enrichment genomic library, 13 microsatellite loci were isolated and characterized in A. aristulata. Seven of these loci were polymorphic. Twelve markers were cross-amplified in at least ten of the tested bamboo species.
These markers will be useful for studies on the genetic diversity and structure of A. aristulata, which are important for future conservation, management and breeding programs of this species.
American Journal of Botany 04/2011; 98(4):e90-2. · 2.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: PREMISE OF STUDY: Microsatellite primers were developed for castor bean (Ricinus communis L.) to investigate genetic diversity and population structure, and to provide support to germplasm management. METHODS AND RESULTS: Eleven microsatellite loci were isolated using an enrichment cloning protocol and used to characterize castor bean germplasm from the collection at the Instituto Agronômico de Campinas (IAC). In a survey of 76 castor bean accessions, the investigated loci displayed polymorphism ranging from two to five alleles. CONCLUSIONS: The information derived from microsatellite markers led to significant gains in conserved allelic richness and provides support to the implementation of several molecular breeding strategies for castor bean.
American Journal of Botany 04/2011; 98(4):e87-9. · 2.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.
Genetics and Molecular Biology 01/2011; 34(1):88-102. · 0.74 Impact Factor
[show abstract][hide abstract] ABSTRACT: 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.
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.
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.
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.
Annals of Botany 10/2010; 106(4):627-36. · 3.45 Impact Factor
[show abstract][hide abstract] ABSTRACT: Coconut palms of the Tall group were introduced to Brazil from the Cape Verde Islands in 1553. The present study sought to evaluate the genetic diversity among and within Brazilian Tall coconut populations. Samples were collected of 195 trees from 10 populations. Genetic diversity was accessed by investigating 13 simple sequence repeats (SSR) loci. This provided a total of 68 alleles, ranging from 2 to 13 alleles per locus, with an average of 5.23. The mean values of gene diversity (H(e) ) and observed heterozygosity (H(o) ) were 0.459 and 0.443, respectively. The genetic differentiation among populations was estimated at θ^P=0.1600and the estimated apparent outcrossing rate was t(a) = 0.92. Estimates of genetic distances between the populations varied from 0.034 to 0.390. Genetic distance and the corresponding clustering analysis indicate the formation of two groups. The first consists of the Baía Formosa, Georgino Avelino, and São José do Mipibu populations and the second consists of the Japoatã, Pacatuba, and Praia do Forte populations. The correlation matrix between genetic and geographic distances was positive and significant at a 1% probability. Taken together, our results suggest a spatial structuring of the genetic variability among the populations. Geographically closer populations exhibited greater similarities.
Genetics and Molecular Biology 10/2010; 33(4):696-702. · 0.74 Impact Factor
[show abstract][hide abstract] ABSTRACT: • Premise of the study: We developed a new set of microsatellite markers for the black mangrove Avicennia germinans, to provide new informative tools for further studies of the mating system, interspecific hybridization, and population genetics. • Methods and Results: We used the microsatellite-enriched library approach to isolate and characterize 25 new primer pairs. Sixteen of them are polymorphic, showing a variable degree of variation in A. germinans, while nine were monomorphic in the samples examined. Eight exhibited private alleles in A. schaueriana. • Conclusions: These results indicate that these new microsatellite markers will be useful molecular tools for further studies of A. germinans and A. schaueriana population genetics, mating systems, and hybridization.
American Journal of Botany 09/2010; 97(9):e79-81. · 2.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: • Premise of the study: Microsatellite markers were developed, optimized, and characterized for Arrabidaea chica (Humb. & Bonpl.) Verl. (Bignoniaceae), a Neotropical liana extensively used in folk medicine. The aim of this study was to develop molecular tools to investigate the genetic structure and diversity of natural populations and germplasm collections of this species. • Methods and Results: Eight highly polymorphic microsatellite markers revealed a multibanded pattern, suggesting that the species is polyploid. The total number of bands per locus ranged from 9 to 17, revealing high levels of polymorphism. • Conclusions: The high level of polymorphism detected with these markers indicates their utility in devising conservation strategies and rational exploitation of A. chica.
American Journal of Botany 07/2010; 97(7):e63-4. · 2.59 Impact Factor