BACKGROUND
one of the largest ex situ germplasm collections in the world is comprised of rice accessions   <cit> .
its two cultivated asian subspecies, indica and japonica, have constituted one of the pillars of human diet for thousands of years.
in brazil, rice production and consumption is comparable to that of some asian countries, and japonica rice accounts for 40% of the total rice production, a value above the 20% average observed in other parts of the world  <cit> .
embrapa keeps a germplasm bank of landraces collected all around the country within a 25-year period.
most of these landraces have been collected in villages and isolated rural areas, where cultivated rice has been grown since its introduction in brazil, centuries ago  <cit> .
they may represent an extraordinary source of genes that control traits of economic importance, such as drought tolerance and resistance to plant pathogens.
the great majority of these rice accessions have not been characterized by any means yet.
technical information is limited to field observation, farmer testimony and descriptive data of the collection site.
it is, therefore, an ideal material for genetic characterization based on molecular technology.
molecular data would provide a basis for better management and conservation of the collection and could be used as reference for its enhanced use in breeding programs.
of particular interest is the understanding of the genetic structure of the collection and its potential exploitation for cultivar improvement.
molecular marker technology has proved to be an efficient tool for plant genetic resource characterization, conservation, and management.
among all different classes of molecular markers available for evaluating genetic diversity, microsatellites or simple sequence repeats   <cit>  are well known for their potentially high information content and versatility as molecular tools  <cit> .
thousands of microsatellite markers have been developed for rice research so far, having their chromosomal location and polymorphism levels determined  <cit> .
they have been extensively used in various fields such as genetic mapping of economically important traits  <cit> , and assessments of the level and structure of genetic diversity in cultivars of interest  <cit> .
the use of fluorescently labeled microsatellite marker panels greatly increases the capacity of semiautomated genotyping of a large number of accessions, allowing for a faster and highly informative characterization of genetic resources.
fluorescently-based semiautomated genotyping was first reported for the analysis of restriction fragments  <cit> , and was later adapted for microsatellite analysis  <cit> .
in rice genetics, the use of  <dig> fluorescently labeled markers in four panels for the analysis of rice genetic diversity has been described  <cit> , as well as the development of multiplex panels aiming genetic assessments with a complete coverage of the rice genome  <cit> .
in both studies, however, pcr's were performed individually for each marker and the pcr products mixed before electrophoresis.
we believe that one could greatly increase the amount of collected information and decrease labor if pcr of multiple loci is done in a single assay prior to electrophoresis.
in this study, fluorescently labeled microsatellite marker panels for semiautomated genotyping were designed and tested on a large number of rice landraces collected and deposited in the embrapa rice gene bank.
only one pcr per sample was used to amplify alleles at multiple microsatellite loci composing each specific multiplex panel.
the obtained data were used to estimate the efficiency of the combined multiplex panels in molecular characterization and cultivar identification.
it also allowed for the estimation of genetic diversity parameters, germplasm organization, and for the establishment of a database of allelic frequencies for japonica rice landraces collected in brazil.
RESULTS
genetic background of the rice accessions
initially, it was necessary to verify if the accessions of rice collected in different parts of brazil belonged to the same genetic background , as indicated by previous information on each of the accessions.
any genetic parameter estimated with the three multiplex marker panels tested in this study could be affected otherwise.
therefore, pairwise genetic distances among  <dig> accessions were estimated and neighbor-joining analysis suggested that the rice accessions could actually be classified into two main clusters, corresponding to materials with a possible indica and japonica genetic backgrounds .
however, the great majority of the accessions  belonged to the major cluster, where no indica accessions were included.
in order to identify possible accessions which still might have been erroneously identified as japonica, a bootstrap analysis of the collected data sets for all possible indica samples was performed, so that the relative probabilities of inclusion for these samples in the japonica or indica gene pools would be obtained  <cit> .
these calculations were performed using the whichrun software v. <dig> .
the allelic frequencies previously estimated for japonica and indica cultivars  <cit>  were taken as references and used as baseline input data for the comparisons.
the results showed that all  <dig> samples of the minor cluster  would be more probably described as possessing an indica background, with a minimum probability which was at least  <dig> orders of magnitude higher than the probability of inclusion of these samples in the japonica group.
therefore, a total of  <dig> accessions of the original collection of  <dig> rice varieties were classified as japonica rice.
in the group of  <dig> japonica accessions,  <dig> upland rice landraces have been collected in the brazilian territory.
it should be clarified that subspecies identification was not the purpose of this study.
the definition of the indica cluster and its elimination from some of the further analyses  had the main objective of avoiding contamination of accessions possessing a probable indica genetic background, what could interfere with the multiplex panel analysis.
diversity analysis and multiplex panel efficiency in molecular characterization
the level of polymorphism among the  <dig> japonica accessions detected by the three multiplex panels was estimated by calculating the number of different alleles for each locus, the observed heterozygosity , gene diversity , and pic values .
the three panels of  <dig> ssr markers produced a total of  <dig> alleles for all loci, ranging from  <dig> alleles for markers rm <dig> and rm <dig> to  <dig> alleles for marker og <dig>  with an average number of  <dig>  gene diversity  values averaged  <dig> , ranging from a low of  <dig>  for rm <dig> to a high of  <dig>  to og <dig>  pic values averaged  <dig> .
the database of allelic frequencies shows that rare alleles  comprised  <dig> % of all alleles, while intermediate  and abundant alleles  comprised  <dig> % and  <dig> % of all detected alleles, respectively.
the matching probability or the probability of identical genotypes was estimated for all combined loci as  <dig>  × 10- <dig> .
finally, the combined power of exclusion of the  <dig> loci in the three multiplex panels was estimated as being greater than  <dig> % .
genetic structure of the germplasm collection
the model-based program structure was used to infer population structure that might be present in this sample of  <dig> landraces  collected in brazil.
estimated likelihood values for a given k in five independent runs were consistent, and increased as the values of k increased, a behavior which is expected when factors such as inbreeding and departures from hardy-weinberg equilibrium are present  <cit> .
these factors could lead to an overestimation of the number of populations k. in order to overcome the difficulty in interpreting which the real value of k would be, another ad hoc quantity  was used.
it was developed and tested under different simulation routines where real population structure was present  <cit> .
Δk showed to be a good predictor of the uppermost hierarchical level present in a sample, although problems such as its inability in detecting the absence of structure  are present.
in this study, the highest value of Δk for the  <dig> accessions was for k =  <dig>  with values for other k's being close to zero .
other information provided by structure, namely the value of α and its behavior, and patterns in the assignment of individuals to different groups led us to choose k =  <dig> for the remaining analyses .
however, other values of k due to the presence of subgroups inside the major groups are possible.
most of the accessions were clearly assigned to a single population following the analysis with k =  <dig> – those which presented more than 70% of their inferred ancestry to a single group – with  <dig> accessions  identified as admixed.
as expected, when those accessions presenting an indica genetic background were excluded from the analysis, the  <dig> japonica landraces presented a most probable number of clusters of k =  <dig>
the amova based on the collection of  <dig> accessions shows that  <dig> % of the variation was caused by differences among groups, with the remaining  <dig> % being caused by differences within groups.
pairwise fst estimates among groups ranged from  <dig>  to  <dig> , showing that groups  <dig> and  <dig> are those more differentiated from each other .
overall fst  value was  <dig> , indicating a considerable degree of differentiation among the three groups.
overall fis and fit values were  <dig>  and  <dig> , respectively, reflecting the effect of inbreeding for a self-pollinating species such as rice.
all values are significantly greater than zero .
pairwise rst estimates among groups ranged from  <dig>  to  <dig> , in agreement with fst values regarding greater differences among groups  <dig> and  <dig>
a comparison of the levels of polymorphism in the three defined groups shows how genetic diversity is organized and divided among the inferred populations .
when only the two groups comprised of japonica accessions , with no evidence of an indica genetic background are compared, group  <dig>  constituted mostly by accessions from northeastern brazil, is the one with higher levels of gd and pic .
however, group  <dig>  with a much smaller number of accessions, but comprised of those with a probable indica genetic background, embodies the highest levels of polymorphism .
discussion
efficiency of three microsatellite multiplex panels for the genetic characterization of rice germplasm
limitations on morphological characterization, including difficulties concerning the definition and validation of neutral traits, experimental costs, evaluation time and genotype × environment interaction are widely discussed in germplasm characterization studies  <cit> .
the molecular characterization based on panels of microsatellite markers allowed for an in depth look at the genetic information and organization of the germplasm collection evaluated.
the three multiplex panels are the first of a series of panels currently being tested in our laboratory for coverage of all rice chromosomes.
when compared with previous reports by blair and colleagues  <cit> , who also used multiplex panels for the genotyping of rice cultivars, and by ni and colleagues  <cit> , who used  <dig> ssr markers for the evaluation of diversity in rice subspecies, the present study detected a higher average allele number.
garris and colleagues  <cit>  also detected a smaller average allele number than the results presented here for a sample of  <dig> rice accessions representing the geographic range of o. sativa.
such differences in average allele number are probably due to the much smaller number of ssr loci analyzed in this report in comparison to the cited works.
since most loci described here are highly polymorphic regarding the number of different alleles, that is reflected as a higher average allele number for a smaller number of loci.
on the other hand, the average pic value in this study was similar to those reported for o. sativa  <cit> , and for japonica rice accessions  <cit> .
in addition, in comparison with the first two reports, if only japonica accessions are considered, our data indicates that values estimated for  <dig> japonica landraces collected in brazil are much higher.
diversity values such as pic and gd, which account for a more reliable estimate of the value of the ssr markers used, are therefore quite similar to those in previous reports and even higher when only japonica accessions are compared.
when looking at the analyzed plant material used in the cited studies, one can realize a possible cause for the considerable levels of genetic diversity detected in the present work: never before such a high number of japonica accessions of a single country alone had been genotyped and analyzed altogether in multiplex panel studies.
blair and colleagues' work  <cit>  included  <dig> japonica accessions; ni and colleagues  <cit> studied  <dig> japonica accessions, while garris and colleagues  <cit>  analyzed a total of  <dig> japonica accessions.
microsatellite markers have been used for identification purposes in plants, animals and humans  <cit> .
the power of a set of ssr markers for identification of individuals can be measured using different parameters.
the matching probability of identical genotypes, also known as the probability of identity , when combined for all loci, represents the likelihood of the presence of two individuals with the same genotype in a population.
in other words, it is an estimate of the number of individuals which would have to be analyzed in order to find the same dna pattern of a randomly selected individual.
the combined estimate of  <dig>  × 10- <dig> demonstrates that the probability of finding two accessions of japonica rice with the same ssr pattern is almost null when the panels of microsatellite markers discussed here are used.
the power of exclusion of the loci composing the three ssr panels is an estimate of the probability of exclusion of a non-parent from a paternity or maternity survey.
the combined power of exclusion for the multiplex panels was greater than  <dig> %, indicating their ability for parentage determination in rice.
the approach clearly indicates that the use of fluorescently labeled panels of microsatellite markers in semiautomated fashion can greatly contribute to the understanding and management of germplasm collections.
the advances in molecular characterization, especially in the possibility of high throughput genotyping of whole collections with a great number of markers distributed throughout the genome open up new opportunities for germplasm characterization.
this goal will be achieved if a set of panels based on just one pcr reaction can be developed for the species, such as the three panels described here.
upland germplasm diversity and patterns of genetic differentiation
genetic structure studies have been performed and reported for the two rice cultivated species o. sativa and o. glaberrima  <cit> , but this is the first to focus on traditional landraces collected in brazil, where rice stands as a major staple food.
the plant material used in this study was composed primarily of traditional upland rice cultivars collected in brazil and kept at the rice germplasm collection of embrapa.
these accessions have been collected within a 25-year period in different geographical regions of the country, and only a few have been previously characterized by morphological parameters.
the analyzed samples provide a picture of a few hundred years of rice cultivation in the brazilian territory, where the first introductions of cultivated rice are documented far back to the 16th and 17th centuries  <cit> .
it is believed that the first introduced rice varieties were "red rice" samples from venice, italy, brought from portugal by immigrants from the azores islands to the northern provinces which now comprises the state of maranhão.
as they disseminated among local farmers, these varieties were given the popular names of "venice rice", "red rice" or "country rice".
from there, rice cultivation made its way from the north to the southern and mid-western regions of the country.
production, primarily focusing on japonica "red rice" varieties, was later replaced by "white rice" indica cultivars.
there is strong evidence that the cluster of  <dig> accessions would probably have an indica genetic background based on both genetic distance and bootstrap analysis.
that represents about 11% of the sample of  <dig> accessions which was referred by preliminary description as composed of japonica varieties.
bayesian model-based analysis confirmed the presence of a well defined group containing indica accessions.
since there was practically no previous knowledge about the history of the studied germplasm regarding origin, development and introduction in brazil, the fact that a considerable number of traditional upland rice landraces were mixed with indica cultivars is quite intriguing.
it is possible that some of these indica varieties have been cultivated in lowland production regimes , which differs from the traditional production system of irrigated rice by capitalizing on high watersheds on riverine regions and does not use artificial irrigation.
further investigations would be necessary to more consistently confirm this relationship.
in general, when the different methods applied for clustering and structure analyses were compared – genetic distance and clustering analysis, amova and a bayesian model-based approach – similar patterns of groupings of accessions could be noticed.
the distribution of the  <dig> accessions which shared at least 70% ancestry to one of the three inferred groups is summarized on table  <dig>  group  <dig> consists of  <dig> accessions, which are colored green on the dendrogram  and corresponds to a first subcluster of the major japonica cluster previously mentioned.
these accessions are distributed among all six different origins of collection delimited for the purpose of this analysis , but with a higher prevalence of accessions from the mid-western region of brazil .
the second subcluster is represented by group  <dig>  with  <dig> accessions, colored blue on the dendrogram, consisting predominantly of accessions collected in northeastern brazil , where rice varieties were first introduced in the country.
finally, group  <dig> includes  <dig> accessions plus the control indica cultivars irga  <dig> and irga  <dig> cl, corresponding to the minor cluster detected by genetic distance-based neighbor-joining dendrogram construction.
most of them were obtained via exchange of germplasm material with foreign institutions, and are named "international accessions" on table  <dig>  accessions belonging to group  <dig> are colored red on the dendrogram.
accessions identified as admixed are colored black and are equally distributed among different clusters of the dendrogram.
a search for landrace names provided at the time of the collection trips which might reflect a relation with the oldest rice varieties introduced in brazil was performed.
we found  <dig> accessions with popular names which might be historically meaningful – those referring to the term "red", as well as those known to be the names of traditional and old rice varieties  <cit> .
interestingly, 71% of these possessed a higher ancestry coefficient with group  <dig>  in this group, 51% of all  <dig> accessions were collected in two neighboring states – maranhao and piaui, the region where rice production in brazil first took place  <cit> .
on the other hand, group  <dig> is comprised mostly of accessions collected in the mid-western region of the country .
inclusion in any of the groups was significantly correlated with accession origin .
historically, upland rice production migrated from maranhao in the north to the southeastern region and then to the states of goias and mato grosso, both in the mid-west  <cit> .
even though we might still be far from a view of the whole scenario, this seems to be an indication of the differentiations which took place on upland rice gene pools as its cultivation in brazil developed throughout the centuries.
significant estimates of stratification among the three inferred groups were found, and the strong effects of an autogamous breeding system were detected by wright's statistics coefficients, as well as slatkin's coefficient of stratification.
values are consistent with those previously reported  <cit> , where fst estimates were  <dig>  between tropical and temperate japonica, and  <dig>  between indica and tropical japonica.
however, when looking at how diversity is partitioned among groups via amova, we noticed that most of the diversity was attributed to differences within groups , rather than among the three inferred groups.
a greater partitioning of diversity among, rather than within groups, would be expected for an autogamous species in the absence of human-mediated gene flow.
nevertheless, when compared to a study of maize inbred lines, where  <dig> % of the variation was caused by differences among groups  <cit> , our data present comparable values.
Δk, an ad hoc quantity related to the second order change of the log probability of data with respect to the number of clusters inferred by the structure program, proved an useful method for identifying a more probably true value of k when there was no previous model or a pre-defined number of groups to rely on.
its rational is to detect the break in slope in the distribution of the log probability values which occurs at the true k. in this study, since we expected most of the accessions to belong to the japonica subspecies – in addition to the fact that the geographical origins of accessions extended over  <dig> states in the brazilian territory – defining a probable number of subgroups prior to an analysis such as the construction of a dendrogram seemed impossible.
our data shows that genetic distance base clustering as well as model-based grouping methods provided consistent results regarding the distribution of accessions among distinct groups .
CONCLUSIONS
the data gathered here demonstrates the feasibility of genotyping extensive germplasm collections at marker loci in rice genome using panels of microsatellite markers, each of them multiplexed with a single pcr assay prior to electrophoresis.
the accuracy of allele sizing and speed of genotyping would allow the characterization of large collections in short periods of time.
the development of algorithms for extracting information from the dataset using straightforward molecular genetic data can possibly expedite improvements in management and use of the germplasm by breeding programs, as well as in the identification, protection and assessments of genetic relationship of rice germplasm.
the use of a model-based approach for genetic structure analysis provided important inputs on the knowledge about upland rice germplasm differentiations which happened in brazil in the last few centuries, since its introduction in the country.

 one of the largest ex situ germplasm collections in the world is comprised of rice accessions. its two cultivated asian subspecies, indica and japonica, have constituted one of the pillars of human diet for thousands of years. in brazil, rice production and consumption is comparable to that of some asian countries, and japonica rice accounts for 40% of the total rice production, a value above the 20% average observed in other parts of the world. embrapa keeps a germplasm bank of landraces collected all around the country within a 25-year period. most of these landraces have been collected in villages and isolated rural areas, where cultivated rice has been grown since its introduction in brazil, centuries ago. they may represent an extraordinary source of genes that control traits of economic importance, such as drought tolerance and resistance to plant pathogens. the great majority of these rice accessions have not been characterized by any means yet. technical information is limited to field observation, farmer testimony and descriptive data of the collection site. it is, therefore, an ideal material for genetic characterization based on molecular technology. molecular data would provide a basis for better management and conservation of the collection and could be used as reference for its enhanced use in breeding programs. of particular interest is the understanding of the genetic structure of the collection and its potential exploitation for cultivar improvement. molecular marker technology has proved to be an efficient tool for plant genetic resource characterization, conservation, and management. among all different classes of molecular markers available for evaluating genetic diversity, microsatellites or simple sequence repeats are well known for their potentially high information content and versatility as molecular tools. thousands of microsatellite markers have been developed for rice research so far, having their chromosomal location and polymorphism levels determined. they have been extensively used in various fields such as genetic mapping of economically important traits, and assessments of the level and structure of genetic diversity in cultivars of interest. the use of fluorescently labeled microsatellite marker panels greatly increases the capacity of semiautomated genotyping of a large number of accessions, allowing for a faster and highly informative characterization of genetic resources. fluorescently-based semiautomated genotyping was first reported for the analysis of restriction fragments, and was later adapted for microsatellite analysis. in rice genetics, the use of fluorescently labeled markers in four panels for the analysis of rice genetic diversity has been described, as well as the development of multiplex panels aiming genetic assessments with a complete coverage of the rice genome. in both studies, however, pcr's were performed individually for each marker and the pcr products mixed before electrophoresis. we believe that one could greatly increase the amount of collected information and decrease labor if pcr of multiple loci is done in a single assay prior to electrophoresis. in this study, fluorescently labeled microsatellite marker panels for semiautomated genotyping were designed and tested on a large number of rice landraces collected and deposited in the embrapa rice gene bank. only one pcr per sample was used to amplify alleles at multiple microsatellite loci composing each specific multiplex panel. the obtained data were used to estimate the efficiency of the combined multiplex panels in molecular characterization and cultivar identification. it also allowed for the estimation of genetic diversity parameters, germplasm organization, and for the establishment of a database of allelic frequencies for japonica rice landraces collected in brazil.  genetic background of the rice accessions initially, it was necessary to verify if the accessions of rice collected in different parts of brazil belonged to the same genetic background, as indicated by previous information on each of the accessions. any genetic parameter estimated with the three multiplex marker panels tested in this study could be affected otherwise. therefore, pairwise genetic distances among accessions were estimated and neighbor-joining analysis suggested that the rice accessions could actually be classified into two main clusters, corresponding to materials with a possible indica and japonica genetic backgrounds. however, the great majority of the accessions belonged to the major cluster, where no indica accessions were included. in order to identify possible accessions which still might have been erroneously identified as japonica, a bootstrap analysis of the collected data sets for all possible indica samples was performed, so that the relative probabilities of inclusion for these samples in the japonica or indica gene pools would be obtained. these calculations were performed using the whichrun software v.. the allelic frequencies previously estimated for japonica and indica cultivars were taken as references and used as baseline input data for the comparisons. the results showed that all samples of the minor cluster would be more probably described as possessing an indica background, with a minimum probability which was at least orders of magnitude higher than the probability of inclusion of these samples in the japonica group. therefore, a total of accessions of the original collection of rice varieties were classified as japonica rice. in the group of japonica accessions, upland rice landraces have been collected in the brazilian territory. it should be clarified that subspecies identification was not the purpose of this study. the definition of the indica cluster and its elimination from some of the further analyses had the main objective of avoiding contamination of accessions possessing a probable indica genetic background, what could interfere with the multiplex panel analysis. diversity analysis and multiplex panel efficiency in molecular characterization the level of polymorphism among the japonica accessions detected by the three multiplex panels was estimated by calculating the number of different alleles for each locus, the observed heterozygosity, gene diversity, and pic values. the three panels of ssr markers produced a total of alleles for all loci, ranging from alleles for markers rm and rm to alleles for marker og with an average number of gene diversity values averaged, ranging from a low of for rm to a high of to og pic values averaged. the database of allelic frequencies shows that rare alleles comprised % of all alleles, while intermediate and abundant alleles comprised % and % of all detected alleles, respectively. the matching probability or the probability of identical genotypes was estimated for all combined loci as × 10-. finally, the combined power of exclusion of the loci in the three multiplex panels was estimated as being greater than %. genetic structure of the germplasm collection the model-based program structure was used to infer population structure that might be present in this sample of landraces collected in brazil. estimated likelihood values for a given k in five independent runs were consistent, and increased as the values of k increased, a behavior which is expected when factors such as inbreeding and departures from hardy-weinberg equilibrium are present. these factors could lead to an overestimation of the number of populations k. in order to overcome the difficulty in interpreting which the real value of k would be, another ad hoc quantity was used. it was developed and tested under different simulation routines where real population structure was present. Δk showed to be a good predictor of the uppermost hierarchical level present in a sample, although problems such as its inability in detecting the absence of structure are present. in this study, the highest value of Δk for the accessions was for k = with values for other k's being close to zero. other information provided by structure, namely the value of α and its behavior, and patterns in the assignment of individuals to different groups led us to choose k = for the remaining analyses. however, other values of k due to the presence of subgroups inside the major groups are possible. most of the accessions were clearly assigned to a single population following the analysis with k = – those which presented more than 70% of their inferred ancestry to a single group – with accessions identified as admixed. as expected, when those accessions presenting an indica genetic background were excluded from the analysis, the japonica landraces presented a most probable number of clusters of k = the amova based on the collection of accessions shows that % of the variation was caused by differences among groups, with the remaining % being caused by differences within groups. pairwise fst estimates among groups ranged from to, showing that groups and are those more differentiated from each other. overall fst value was, indicating a considerable degree of differentiation among the three groups. overall fis and fit values were and, respectively, reflecting the effect of inbreeding for a self-pollinating species such as rice. all values are significantly greater than zero. pairwise rst estimates among groups ranged from to, in agreement with fst values regarding greater differences among groups and a comparison of the levels of polymorphism in the three defined groups shows how genetic diversity is organized and divided among the inferred populations. when only the two groups comprised of japonica accessions, with no evidence of an indica genetic background are compared, group constituted mostly by accessions from northeastern brazil, is the one with higher levels of gd and pic. however, group with a much smaller number of accessions, but comprised of those with a probable indica genetic background, embodies the highest levels of polymorphism. discussion efficiency of three microsatellite multiplex panels for the genetic characterization of rice germplasm limitations on morphological characterization, including difficulties concerning the definition and validation of neutral traits, experimental costs, evaluation time and genotype × environment interaction are widely discussed in germplasm characterization studies. the molecular characterization based on panels of microsatellite markers allowed for an in depth look at the genetic information and organization of the germplasm collection evaluated. the three multiplex panels are the first of a series of panels currently being tested in our laboratory for coverage of all rice chromosomes. when compared with previous reports by blair and colleagues, who also used multiplex panels for the genotyping of rice cultivars, and by ni and colleagues, who used ssr markers for the evaluation of diversity in rice subspecies, the present study detected a higher average allele number. garris and colleagues also detected a smaller average allele number than the results presented here for a sample of rice accessions representing the geographic range of o. sativa. such differences in average allele number are probably due to the much smaller number of ssr loci analyzed in this report in comparison to the cited works. since most loci described here are highly polymorphic regarding the number of different alleles, that is reflected as a higher average allele number for a smaller number of loci. on the other hand, the average pic value in this study was similar to those reported for o. sativa, and for japonica rice accessions. in addition, in comparison with the first two reports, if only japonica accessions are considered, our data indicates that values estimated for japonica landraces collected in brazil are much higher. diversity values such as pic and gd, which account for a more reliable estimate of the value of the ssr markers used, are therefore quite similar to those in previous reports and even higher when only japonica accessions are compared. when looking at the analyzed plant material used in the cited studies, one can realize a possible cause for the considerable levels of genetic diversity detected in the present work: never before such a high number of japonica accessions of a single country alone had been genotyped and analyzed altogether in multiplex panel studies. blair and colleagues' work included japonica accessions; ni and colleagues studied japonica accessions, while garris and colleagues analyzed a total of japonica accessions. microsatellite markers have been used for identification purposes in plants, animals and humans. the power of a set of ssr markers for identification of individuals can be measured using different parameters. the matching probability of identical genotypes, also known as the probability of identity, when combined for all loci, represents the likelihood of the presence of two individuals with the same genotype in a population. in other words, it is an estimate of the number of individuals which would have to be analyzed in order to find the same dna pattern of a randomly selected individual. the combined estimate of × 10- demonstrates that the probability of finding two accessions of japonica rice with the same ssr pattern is almost null when the panels of microsatellite markers discussed here are used. the power of exclusion of the loci composing the three ssr panels is an estimate of the probability of exclusion of a non-parent from a paternity or maternity survey. the combined power of exclusion for the multiplex panels was greater than %, indicating their ability for parentage determination in rice. the approach clearly indicates that the use of fluorescently labeled panels of microsatellite markers in semiautomated fashion can greatly contribute to the understanding and management of germplasm collections. the advances in molecular characterization, especially in the possibility of high throughput genotyping of whole collections with a great number of markers distributed throughout the genome open up new opportunities for germplasm characterization. this goal will be achieved if a set of panels based on just one pcr reaction can be developed for the species, such as the three panels described here. upland germplasm diversity and patterns of genetic differentiation genetic structure studies have been performed and reported for the two rice cultivated species o. sativa and o. glaberrima, but this is the first to focus on traditional landraces collected in brazil, where rice stands as a major staple food. the plant material used in this study was composed primarily of traditional upland rice cultivars collected in brazil and kept at the rice germplasm collection of embrapa. these accessions have been collected within a 25-year period in different geographical regions of the country, and only a few have been previously characterized by morphological parameters. the analyzed samples provide a picture of a few hundred years of rice cultivation in the brazilian territory, where the first introductions of cultivated rice are documented far back to the 16th and 17th centuries. it is believed that the first introduced rice varieties were "red rice" samples from venice, italy, brought from portugal by immigrants from the azores islands to the northern provinces which now comprises the state of maranhão. as they disseminated among local farmers, these varieties were given the popular names of "venice rice", "red rice" or "country rice". from there, rice cultivation made its way from the north to the southern and mid-western regions of the country. production, primarily focusing on japonica "red rice" varieties, was later replaced by "white rice" indica cultivars. there is strong evidence that the cluster of accessions would probably have an indica genetic background based on both genetic distance and bootstrap analysis. that represents about 11% of the sample of accessions which was referred by preliminary description as composed of japonica varieties. bayesian model-based analysis confirmed the presence of a well defined group containing indica accessions. since there was practically no previous knowledge about the history of the studied germplasm regarding origin, development and introduction in brazil, the fact that a considerable number of traditional upland rice landraces were mixed with indica cultivars is quite intriguing. it is possible that some of these indica varieties have been cultivated in lowland production regimes, which differs from the traditional production system of irrigated rice by capitalizing on high watersheds on riverine regions and does not use artificial irrigation. further investigations would be necessary to more consistently confirm this relationship. in general, when the different methods applied for clustering and structure analyses were compared – genetic distance and clustering analysis, amova and a bayesian model-based approach – similar patterns of groupings of accessions could be noticed. the distribution of the accessions which shared at least 70% ancestry to one of the three inferred groups is summarized on table group consists of accessions, which are colored green on the dendrogram and corresponds to a first subcluster of the major japonica cluster previously mentioned. these accessions are distributed among all six different origins of collection delimited for the purpose of this analysis, but with a higher prevalence of accessions from the mid-western region of brazil. the second subcluster is represented by group with accessions, colored blue on the dendrogram, consisting predominantly of accessions collected in northeastern brazil, where rice varieties were first introduced in the country. finally, group includes accessions plus the control indica cultivars irga and irga cl, corresponding to the minor cluster detected by genetic distance-based neighbor-joining dendrogram construction. most of them were obtained via exchange of germplasm material with foreign institutions, and are named "international accessions" on table accessions belonging to group are colored red on the dendrogram. accessions identified as admixed are colored black and are equally distributed among different clusters of the dendrogram. a search for landrace names provided at the time of the collection trips which might reflect a relation with the oldest rice varieties introduced in brazil was performed. we found accessions with popular names which might be historically meaningful – those referring to the term "red", as well as those known to be the names of traditional and old rice varieties. interestingly, 71% of these possessed a higher ancestry coefficient with group in this group, 51% of all accessions were collected in two neighboring states – maranhao and piaui, the region where rice production in brazil first took place. on the other hand, group is comprised mostly of accessions collected in the mid-western region of the country. inclusion in any of the groups was significantly correlated with accession origin. historically, upland rice production migrated from maranhao in the north to the southeastern region and then to the states of goias and mato grosso, both in the mid-west. even though we might still be far from a view of the whole scenario, this seems to be an indication of the differentiations which took place on upland rice gene pools as its cultivation in brazil developed throughout the centuries. significant estimates of stratification among the three inferred groups were found, and the strong effects of an autogamous breeding system were detected by wright's statistics coefficients, as well as slatkin's coefficient of stratification. values are consistent with those previously reported, where fst estimates were between tropical and temperate japonica, and between indica and tropical japonica. however, when looking at how diversity is partitioned among groups via amova, we noticed that most of the diversity was attributed to differences within groups, rather than among the three inferred groups. a greater partitioning of diversity among, rather than within groups, would be expected for an autogamous species in the absence of human-mediated gene flow. nevertheless, when compared to a study of maize inbred lines, where % of the variation was caused by differences among groups, our data present comparable values. Δk, an ad hoc quantity related to the second order change of the log probability of data with respect to the number of clusters inferred by the structure program, proved an useful method for identifying a more probably true value of k when there was no previous model or a pre-defined number of groups to rely on. its rational is to detect the break in slope in the distribution of the log probability values which occurs at the true k. in this study, since we expected most of the accessions to belong to the japonica subspecies – in addition to the fact that the geographical origins of accessions extended over states in the brazilian territory – defining a probable number of subgroups prior to an analysis such as the construction of a dendrogram seemed impossible. our data shows that genetic distance base clustering as well as model-based grouping methods provided consistent results regarding the distribution of accessions among distinct groups.  the data gathered here demonstrates the feasibility of genotyping extensive germplasm collections at marker loci in rice genome using panels of microsatellite markers, each of them multiplexed with a single pcr assay prior to electrophoresis. the accuracy of allele sizing and speed of genotyping would allow the characterization of large collections in short periods of time. the development of algorithms for extracting information from the dataset using straightforward molecular genetic data can possibly expedite improvements in management and use of the germplasm by breeding programs, as well as in the identification, protection and assessments of genetic relationship of rice germplasm. the use of a model-based approach for genetic structure analysis provided important inputs on the knowledge about upland rice germplasm differentiations which happened in brazil in the last few centuries, since its introduction in the country. 
a sample of accessions of traditional upland rice landraces collected in brazil in the last years was genotyped, a database of allelic frequencies was established, estimates of genetic parameters were performed and analysis of genetic structure of the collection was developed. genetic structure analysis of the collection using a bayesian approach detected three possible major clusters, with an overall fst value of. gene diversity values averaged, and pic values averaged. this study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of loci of the rice genome, based on single pcr reactions of each panel. the three multiplex panels described here represent a powerful tool for rice genetic analysis, offering a rapid and efficient option for rice germplasm characterization. important inputs on the knowledge about upland rice germplasm differentiations which happened in brazil in the last few centuries were also achieved and are discussed. it contributes to the advancement of research on large scale characterization and management of germplasm banks, as well as identification, protection and assessments of genetic relationship of rice germplasm. a few samples presented a genetic background of indica rice. the data gathered demonstrates the feasibility of genotyping extensive germplasm collections using panels of multiplexed microsatellite markers.
 this study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of loci of the rice genome, based on single pcr reactions of each panel. a sample of accessions of traditional upland rice landraces collected in brazil in the last years was genotyped, a database of allelic frequencies was established, estimates of genetic parameters were performed and analysis of genetic structure of the collection was developed.  the three panels yielded a combined matching probability of × 10- polymorphism information content of, and a combined power of exclusion greater than %. a few samples presented a genetic background of indica rice. the ssr loci produced a total of alleles. gene diversity values averaged, and pic values averaged. genetic structure analysis of the collection using a bayesian approach detected three possible major clusters, with an overall fst value of. important inputs on the knowledge about upland rice germplasm differentiations which happened in brazil in the last few centuries were also achieved and are discussed.  the three multiplex panels described here represent a powerful tool for rice genetic analysis, offering a rapid and efficient option for rice germplasm characterization. the data gathered demonstrates the feasibility of genotyping extensive germplasm collections using panels of multiplexed microsatellite markers. it contributes to the advancement of research on large scale characterization and management of germplasm banks, as well as identification, protection and assessments of genetic relationship of rice germplasm. 