Low Diversity and High Genetic Structure for Platonia insignis Mart., an Endangered Fruit Tree Species

Platonia insignis is a fruit tree native to Brazil of increasing economic importance, with its pulp trading among the highest market values. This study aimed to evaluate the structure and genomic diversity of P. insignis (bacurizeiro) accessions from six locations in the Brazilian States of Roraima, Amazonas, Pará (Amazon biome), and Maranhão (Cerrado biome). A total of 2031 SNP markers were obtained using genotyping-by-sequencing (GBS), from which 625 outlier SNPs were identified. High genetic structure was observed, with most of the genetic variability (59%) concentrated among locations, mainly between biomes (Amazon and Cerrado). A positive and significant correlation (r = 0.85; p < 0.005) was detected between genetic and geographic distances, indicating isolation by distance. The highest genetic diversity was observed for the location in the Cerrado biome (HE = 0.1746; HO = 0.2078). The locations in the Amazon biome showed low genetic diversity indexes with significant levels of inbreeding. The advance of urban areas, events of burning, and expansion of agricultural activities are most probably the main factors for the genetic diversity reduction of P. insignis. Approaches to functional analysis showed that most of the outlier loci found may be related to genes involved in cellular and metabolic processes.

Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns

The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.

Natural Populations of Astrocaryum aculeatum Meyer in Amazonia: Genetic Diversity and Conservation

Astrocaryum aculeatum, a palm tree incipiently domesticated from upland ecosystems in the Brazilian Amazon, is especially adapted to anthropized areas. The pulp of the fruit, obtained by extractivism, is consumed fresh by the Amazonian population. The objective of the study is to evaluate the diversity and genetic structure of the natural populations of A. aculeatum, exploited by extractive farmers in Amazonas, Brazil, seeking to suggest conservation and management strategies for this species. A total of 218 plants were sampled in 15 populations in 14 municipalities in the state of Amazonas, evaluated by 12 microsatellite loci. A total of 101 alleles were observed. The means of the observed heterozygosities (H_O = 0.6390) were higher than expected (H_E = 0.557), with high levels of heterozygotes in the populations. The fixation index in the loci and populations was negative. The F_ST (0.07) and AMOVA showed moderate population structure. Bayesian analysis indicated the grouping k = 4 as the most adequate. There is a high genetic diversity in populations, with a moderate genetic structure due to possible historical events, which could be related to the process of subpopulation formation, possibly presenting three historical moments: before and after the beginning of deforestation and today. The conservation and management policies of this species must be carried out at a watershed level.

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes

The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, due to overexploitation, conservation strategies are required to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (F_ST = 0.77), especially between E. edulis and E. precatoria (F_ST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.

Maize dispersal patterns associated with different types of endosperm and migration of indigenous groups in lowland South America

BACKGROUND AND AIMS

The lowlands of South America appear to be remarkably important in the evolutionary history of maize, due to new evidence that suggests that maize dispersed from Mexico and arrived in this region in a state of partial domestication. This study aimed to identify dispersal patterns of maize genetic diversity in this part of the continent.

METHODS

A total of 170 maize accessions were characterized with 4398 single nucleotide polymorphisms (SNPs) and analysed to determine if maize dispersal was associated with types of endosperm and indigenous language families.

KEY RESULTS

Four genetic groups were identified in the discriminant analysis of principal components and five groups in the cluster analysis (neighbour-joining method). The groups were structured according to the predominance of endosperm types (popcorn, floury, flint/semi-flint). Spatial principal component analysis of genetic variation suggests different dispersal patterns for each endosperm type and can be associated with hypotheses of expansions of different indigenous groups.

CONCLUSIONS

From a possible origin in Southwestern Amazonia, different maize dispersal routes emerged: (1) towards Northern Amazonia, which continued towards the Caatinga and south-eastern Atlantic Forest (Floury); (2) towards Southern Brazil, passing through the Cerrado and Southern Atlantic Forest reaching the Pampa region (Floury); and (3) along the Atlantic Coast, following Tupi movements originating from two separate expansions: one (Tupinamba) from north to south, and the other (Guarani) in the opposite direction, from south to north (flint, floury and popcorn).

Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties

Knowledge about genetic diversity is essential to promote effective use and conservation of crops, because it enables farmers to adapt their crops to specific needs and is the raw material for breeding. Manioc (Manihot esculenta ssp. esculenta) is one of the world's major food crops and has the potential to help achieve food security in the context of on-going climate changes. We evaluated single nucleotide polymorphisms in traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We assessed genome-wide diversity and identified selective signatures contrasting varieties from different biomes with samples of manioc's wild ancestor M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses that might have been important for the crop's domestication and diversification resulting from cultivation in different environments. Additionally, high neutral genetic diversity within groups of varieties from different biomes and low genetic divergence among biomes reflect the complexity of manioc's evolutionary dynamics under traditional cultivation. Our results exemplify how smallholder practices contribute to conserve manioc's genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.

Genetic Structure in Populations of Euterpe precatoria Mart. in the Brazilian Amazon

Euterpe precatoria is a palm tree belonging to the Arecaceae family, occurring in Western and Central Brazilian Amazonia. Its fruit, which is very appreciated in the Amazon region, produces pulp that is consumed in fresh form. Its production is carried out almost exclusively by extractive farmers. In order to establish adequate strategies to sustain this genetic resource, we need knowledge about the diversity and genetic structure in natural populations. This study aimed to evaluate the influence of geographic distance on genetic structure in the main extractive populations of E. precatoria in the Brazilian Amazon. Leaves from 377 plants were collected in 19 populations located in 16 municipalities in the State of Amazonas and three in the State of Rondônia. Twelve microsatellite loci were used to genotype the plants. The diversity and genetic structure among populations were estimated. The average number of alleles per locus was 5.97. The observed heterozygosity means (HO) were higher than expected (HE) at the population level (HO = 0.72, HE = 0.66) and fixation index (f = -0.100) was negative. The FST value (0.1820) and the AMOVA results (Φ = 0.1796) showed population structure. The populations were clustered into three groups (K = 3) in the Bayesian analysis. The Discriminant Analysis of Principal Components (DAPC) confirmed eight clusters, with the populations close to those identified by the Bayesian analysis. The geographic differentiation was confirmed by the groupings obtained in the Structure analysis and the DACP function. Information related to phenotypic, genetic and environmental characterization of populations is important to guide conservation and management strategies and the formulation of public species management policies in Amazonia.

A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia

Amazonia is a major world centre of plant domestication, but the genetics of domestication remains unclear for most Amazonian crops. Manioc (Manihot esculenta) is the most important staple food crop that originated in this region. Although manioc is relatively well-studied, little is known about the diversification of bitter and sweet landraces and how they were dispersed across Amazonia. We evaluated single nucleotide polymorphisms (SNPs) in wild and cultivated manioc to identify outlier SNPs putatively under selection and to assess the neutral genetic structure of landraces to make inferences about the evolution of the crop in Amazonia. Some outlier SNPs were in putative manioc genes possibly related to plant architecture, transcriptional regulation and responses to stress. The neutral SNPs revealed contrasting genetic structuring for bitter and sweet landraces. The outlier SNPs may be signatures of the genomic changes resulting from domestication, while the neutral genetic structure suggests independent dispersals for sweet and bitter manioc, possibly related to the earlier domestication and diversification of the former. Our results highlight the role of ancient peoples and current smallholders in the management and conservation of manioc genetic diversity, including putative genes and specific genetic resources with adaptive potential in the context of climate change.

Paternity analysis, pollen flow, and spatial genetic structure of a natural population of Euterpe precatoria in the Brazilian Amazon

Euterpe precatoria, known as açaí do Amazonas, is a regionally important palm of the Amazon rainforest for the fruit production through extractive agriculture. Little information is available with regard to genetic diversity, gene flow, and spatial genetic structure (SGS) of açaí populations, which are essential for the use, management, and conservation of genetic resources of the species. This research aimed to assess the genetic diversity, inbreeding level, SGS, and gene flow in four ontogenetic stages of a natural E. precatoria population in the Brazilian Amazon, based on 18 microsatellite loci. The study was carried out in a natural population dispersed in an area of about 10 ha. Leaf tissues of 248 plants were mapped and sampled and classified into four ontogenetic stages: reproductive (59), immature (70), young (60), and seedling (59). Genetic diversity indices were high for all ontogenetic stages. The fixation index (F) for all ontogenetic stages was not significantly different from zero, indicating the absence of inbreeding. A significant SGS was found for all ontogenetic stages (68-110 m), indicating seed dispersal over short distances. Paternity analysis detected pollen immigration of 39.1%, a selfing rate of 4.2%, and a mean pollen dispersal distance within the population of 531 m. The results indicate substantial allele input in the population via pollen immigration, contributing to the maintenance of the genetic diversity of the population. However, within a population, the renewal with new progenies selected from seed plants spaced at least 110 m apart is important to avoid collecting seeds from related plants.

Highly structured genetic diversity of Bixa orellana var. urucurana, the wild ancestor of annatto, in Brazilian Amazonia

Annatto (Bixa orellana L.) is a tropical American crop, commercially valuable due to its application in the food and cosmetics industries as a natural dye. The wild ancestor of cultivated annatto is B. orellana var. urucurana. Although never cultivated, this variety occurs in open forests and anthropogenic landscapes, and is always associated with riparian environments. In this study, we evaluated the genetic diversity and structure of B. orellana var. urucurana populations in Brazilian Amazonia using 16 microsatellite loci. We used Ecological Niche Modeling (ENM) to characterize the potential geographical range of this variety in northern South America. We analyzed 170 samples from 10 municipalities in the states of Rondônia, Pará and Roraima. A total of 194 alleles was observed, with an average of 12.1 alleles per locus. Higher levels of expected (H_E) than observed (H_O) heterozygosities were found for all populations. Bayesian analysis, Neighbor-Joining dendrograms and PCAs suggest the existence of three strongly structured groups of populations. A strong and positive correlation between genetic and geographic distances was found, suggesting that genetic differentiation might be caused by geographic isolation. From species distribution modelling, we detected that South Rondônia, Madre di Dios River basin, Llanos de Mojos, Llanos de Orinoco and eastern Ecuador are highly suitable areas for wild annatto to occur, providing additional targets for future exploration and conservation. Climatic adaptation analyses revealed strong differentiation among populations, suggesting that precipitation plays a key role in wild annatto’s current and potential distribution patterns.

Genetic diversity among air yam (Dioscorea bulbifera) varieties based on single sequence repeat markers

Dioscorea is the largest genus in the Dioscoreaceae family, and includes a number of economically important species including the air yam, D. bulbifera L. This study aimed to develop new single sequence repeat primers and characterize the genetic diversity of local varieties that originated in several municipalities of Brazil. We developed an enriched genomic library for D. bulbifera resulting in seven primers, six of which were polymorphic, and added four polymorphic loci developed for other Dioscorea species. This resulted in 10 polymorphic primers to evaluate 42 air yam accessions. Thirty-three alleles (bands) were found, with an average of 3.3 alleles per locus. The discrimination power ranged from 0.113 to 0.834, with an average of 0.595. Both principal coordinate and cluster analyses (using the Jaccard Index) failed to clearly separate the accessions according to their origins. However, the 13 accessions from Conceição dos Ouros, Minas Gerais State were clustered above zero on the principal coordinate 2 axis, and were also clustered into one subgroup in the cluster analysis. Accessions from Ubatuba, São Paulo State were clustered below zero on the same principal coordinate 2 axis, except for one accession, although they were scattered in several subgroups in the cluster analysis. Therefore, we found little spatial structure in the accessions, although those from Conceição dos Ouros and Ubatuba exhibited some spatial structure, and that there is a considerable level of genetic diversity in D. bulbifera maintained by traditional farmers in Brazil.

Spatial genetic structure, genetic diversity and pollen dispersal in a harvested population of Astrocaryum aculeatum in the Brazilian Amazon

Background

Astrocaryum aculeatum is a palm tree species native to the tropical regions of South America, exploited commercially by local farmers for the pulp extracted from its fruits. The objective of this research was to compare the genetic diversity between adult plants and seedlings from open-pollinated seeds, quantify the pollen flow and dispersal, the spatial genetic structure, and the effective size of a population that has been continuously harvested for its fruits. The study was carried out in a natural population of A. aculeatum distributed over approximately 8 ha in the State of Amazonas (Brazil), separated by 400 m from the closest neighboring population. In total, 112 potential pollen donors, 12 mother plants and 120 offspring were mapped and genotyped.

Results

Genetic diversity was high for parents and the offspring. The fixation indexes for adults (F = -0.035) and offspring (F = -0.060) were negative and not significant. A significant spatial genetic structure was detected for the adult plants (up to the distance of 45 m) indicating short-distance seed dispersal. Paternity analysis detected 9.2 % of pollen immigration and the average distance of pollination within the population was 81 m. The average effective pollination neighborhood area between plants was 1.51 ha.

Conclusions

Our results indicate that substantial introduction of new alleles has occurred in the population through pollen immigration, contributing to the maintenance of genetic diversity. Conservation efforts aimed at maintaining the gene pool of the current population or establishing new populations should utilize offspring from mother plants selected to be spaced by at least 50 m to prevent collecting seeds from relatives.

Genetic variability within and among populations of an invasive, exotic orchid

Despite the fact that invasive species are of great evolutionary interest because of their success in colonizing and spreading into new areas, the factors underlying this success often remain obscure. In this sense, studies on population genetics and phylogenetic relationships of invasive species could offer insights into mechanisms of invasions. Originally from Africa, the terrestrial orchid Oeceoclades maculata, considered an invasive plant, is the only species of the genus throughout the Americas. Considering the lack of information on population genetics of this species, the aim of this study was to evaluate the genetic diversity and structure of Brazilian populations of O. maculata. We used 13 inter-simple sequence repeat primers to assess the genetic diversity of 152 individuals of O. maculata distributed in five sampled sites from three Brazilian states (São Paulo, Mato Grosso and Paraná). Low diversity was found within samples, with estimates of the Shannon index (H) ranging from 0.0094 to 0.1054 and estimates of Nei's gene diversity (He) ranging from 0.0054 to 0.0668. However, when evaluated together, the sampling locations showed substantially higher diversity estimates (H = 0.3869, He = 0.2556), and most of the genetic diversity was found among populations (ΦST = 0.933). Both clustering and principal coordinate analysis indicate the existence of five distinct groups, corresponding to the sampled localities, and which were also recovered in the Bayesian analysis. A substructure was observed in one of the localities, suggesting a lack of gene flow even between very small distances. The patterns of genetic structure found in this study may be understood considering the interaction of several probable reproductive strategies with its history of colonization involving possible genetic drift, selective pressures and multiple introductions.

Distribution, management and diversity of yam local varieties in Brazil: a study on Dioscorea alata L

Widely spread in the tropics, yams were introduced into Brazil during the colonial period and are currently grown throughout the country. Despite its importance as a pharmacological and food source, there is a lack of studies describing how and where this tuber is grown in Brazil. The aim of this study was to provide an overview of the cultivation and distribution of Dioscorea alata in different Brazilian regions. A total of 63 farmers were visited in different municipalities and communities in four regions in the country: South, Southeast, Northeast and Midwest. Semi-structured interviews were conducted to collect socio-economic, use, management and diversity data for this crop. The majority of interviewers were men, married, with children, using retirement benefits and agriculture as income and family labour as the main support in the yam cultivation. A wide distribution of this species was found, with the occurrence of D. alata in the four sampled regions. A variety of vernacular names for this species was collected, differing according to the region where it is cultivated. Most farmers cultivate yams in fields, however an increased usage of home gardens for the cultivation of this tuber was found. Also, most farmers cultivate yams in association with other crops in areas of different sizes and slash and burn practices, although mostly disappearing, are still being used by many farmers. The results of this study provide more concrete data on the distribution and diversity of this important crop.

Isolation and characterization of microsatellites for the yam Dioscorea cayenensis (Dioscoreaceae) and cross-amplification in D. rotundata

Dioscorea cayenensis and Dioscorea rotundata are among the most important yam species for the humid and sub-humid tropics. We isolated nine polymorphic microsatellite markers using a microsatellite-enriched genomic library technique. The nine primer pairs were validated in 22 D. cayenensis accessions, and were tested for transferability in 26 D. rotundata accessions. The number of bands ranged from 2 to 4, with a mean of 3.11. D. cayenensis gave primer polymorphism information content values ranging from 0.37 to 0.62, while for D. rotundata the values ranged from 0.15 to 0.66. The D parameter in D. cayenensis ranged from 0.14 to 0.40, while in D. rotundata it ranged from 0.05 to 0.34. These SSR markers will be useful to characterize genetic diversity in D. cayenensis and D. rotundata accessions.

Genetic structure and diversity in the Dioscorea cayenensis/D. rotundata complex revealed by morphological and isozyme markers

Of the 600 known yam species, only 10 are utilized as food, and the Dioscorea cayenensis/D. rotundata species complex is among the most cultivated. In Brazil, these species are commercially cultivated in the northeast region and are cultivated in the south and southeast regions as subsistence crops by traditional agriculturists. This study aimed to evaluate the genetic diversity of 21 local varieties of D. cayenensis and 2 D. rotundata accessions using 7 isozymic loci and 24 morphological markers, and to investigate the diversity distribution in different levels of organization, such as swidden fields and communities of Vale do Ribeira. Cluster analyses for both the isozymic and morphological data separated the 2 D. rotundata accessions from the D. cayenensis accessions from Vale do Ribeira. The analysis with morphological characteristics showed the presence of 2 subgroups (Iguape and Cananéia) within group I, which included all of the local varieties from Vale do Ribeira; this result may indicate the influence of the cultural units on the morphological variation. Molecular analysis of variance indicated that most of the isozymic variability was concentrated among swiddens within communities (42.5%) and within communities (40.3%). Most of the morphological variability was also concentrated among swidden fields within communities (44.8%). The correlation between geographic and genetic distances indicated that neither morphological (r = 0.17) nor isozymic diversity (r = -0.15) is structured in space. Thus, the traditional agriculturists of Vale do Ribeira maintain and manage a great diversity of D. cayenensis varieties in their communities.

Simple-sequence repeat markers of Cattleya coccinea (Orchidaceae), an endangered species of the Brazilian Atlantic Forest

Microsatellite markers were developed for the endangered Brazilian orchid species Cattleya coccinea to describe its genetic diversity and structure and to support conservation studies. Nine microsatellite loci were isolated and characterized using an enriched genomic library. All loci are polymorphic at least in the 2 populations sampled, except for loci Cac05 and Cac09 for the Petrópolis population. The mean number of alleles per locus was 8.8 between populations. The mean values of the observed and expected heterozygosities were 0.541 (ranging from 0 to 1) and 0.639 (ranging from 0 to 0.9), respectively. Cross-amplifications were performed in 7 additional Epidendroideae species, and at least 2 loci were successful in 3 additional Cattleya species, Epidendrum secundum, and Brasiliorchis gracilis. All markers described herein will be useful in further studies evaluating the genetic diversity, population dynamics, and conservation genetics of C. coccinea and related species.

Microsatellite loci for tucumã of Amazonas (Astrocaryum aculeatum) and amplification in other Arecaceae

PREMISE OF THE STUDY

Microsatellite loci were developed for tucumã of Amazonas (Astrocaryum aculeatum), and cross-species amplification was performed in six other Arecaceae, to investigate genetic diversity and population structure and to provide support for natural populations management. •

METHODS AND RESULTS

Fourteen microsatellite loci were isolated from a microsatellite-enriched genomic library and used to characterize two wild populations of tucumã of Amazonas (Manaus and Manicoré cities). The investigated loci displayed high polymorphism for both A. aculeatum populations, with a mean observed heterozygosity of 0.498. Amplification rates ranging from 50% to 93% were found for four Astrocaryum species and two additional species of Arecaceae. •

CONCLUSIONS

The information derived from the microsatellite markers developed here provides significant gains in conserved allelic richness and supports the implementation of several molecular breeding strategies for the Amazonian tucumã.

Microsatellite polymorphisms in cassava landraces from the Cerrado biome, Mato Grosso do sul, Brazil

Using nine microsatellite loci, we investigated genetic structure and diversity in 83 Brazilian cassava accessions, including several landraces, in the Cerrado biome in Mato Grosso do Sul, Brazil. All nine loci were polymorphic, averaging 6.00 alleles per locus. Treating each of seven municipalities as a cassava group or population, they averaged 3.5 alleles per locus, with 97% polymorphic loci, high values for observed heterozygosity (0.32) and gene diversity (0.56). Total genetic variability was high (0.668), and most of this genetic variability was concentrated within municipalities (0.577). Cluster and structure analyses divided accessions into two major clusters or populations (K = 2). Also, a significant genetic versus geographic correlation was found (r = 0.4567; P < 0.0260). Migratory routes in the Cerrado are considered main contributors to the region's high cassava diversity and spatial genetic structure, amplifying interactions between traditional farmers and the evolutionary dynamics of this crop.

Genetic characterization of cassava (Manihot esculenta) landraces in Brazil assessed with simple sequence repeats

Based on nine microsatellite loci, the aim of this study was to appraise the genetic diversity of 42 cassava (Manihot esculenta) landraces from selected regions in Brazil, and examine how this variety is distributed according to origin in several municipalities in the states of Minas Gerais, São Paulo, Mato Grosso do Sul, Amazonas and Mato Grosso. High diversity values were found among the five above-mentioned regions, with 3.3 alleles per locus on an average, a high percentage of polymorphic loci varying from 88.8% to 100%, an average of 0.265 for observed heterozygosity and 0.570 for gene diversity. Most genetic diversity was concentrated within the regions themselves (H_S = 0.52). Cluster analysis and principal component based scatter plotting showed greater similarity among landraces from São Paulo, Mato Grosso do Sul and Amazonas, whereas those from Minas Gerais were clustered into a sub-group within this group. The plants from Mato Grosso, mostly collected in the municipality of General Carneiro, provided the highest differentiation. The migration of human populations is one among the possible reasons for this closer resemblance or greater disparity among plants from the various regions.

Elevada diversidade genética interpopulacional em Oryza glumaepatula Steud. (Poaceae) avaliada com microssatélites

Marcadores microssatélites foram usados para caracterizar a diversidade genética entre e dentro de sete populações naturais de Oryza glumaepaula. Seis dessas populações são originárias da bacia hidrográfica da Amazônia e uma do rio Paraguai no Pantanal Matogrossense. Utilizando sete locos de microssatélites, observou-se diversidade genética intrapopulacional média de 1,98 alelos por loco, 56,2% de locos polimórficos, Ho = 0,026 e He = 0,241. Elevada diferenciação interpopulacional foi observada pelo índice de fixação de Wright e pelo parâmetro de divergência de Slatkin (F ST = 0,715 e R ST = 0,595, respectivamente), bem como elevado nível de endogamia total (F IT = 0,963), em grande parte influenciada pelo sistema reprodutivo (F IS = 0,858). Verificou-se que nenhuma população estava em equilíbrio de Hardy-Weinberg, devido ao predomínio da autofertilização, o que também pôde ser verificado pela taxa média aparente de cruzamentos: t a = 0,055. Consequentemente, o fluxo gênico entre populações foi praticamente nulo o que contribuiu para o elevado nível de divergência interpopulacional. De modo geral, as taxas de cruzamento foram muito baixas ou nulas nas populações da Amazônia. Entretanto, a população PG-3 do Rio Paraguai, originária do Pantanal Matogrossense, apresentou taxa de cruzamento mais elevada (13,2%), indicando sistema reprodutivo misto com predomínio de autogamia. Como a diversidade intrapopulacional foi baixa, os resultados indicam que a amostragem de elevado número de populações é a estratégia mais adequada para a conservação ex situ desta espécie. Para a conservação in situ, com base na riqueza alélica, recomenda-se como prioridade as populações PG-3, TA-3, SO-17 e NE-7, originárias das bacias hidrográficas dos Rios Paraguai, Tapajós, Solimões e Negro, respectivamente.

Variation in the loss of seed dormancy during after-ripening of wild and cultivated rice species

BACKGROUND AND AIMS

The aim of this paper was to verify the variation in the loss of seed dormancy during after-ripening and the interspecific and interpopulation variability in the degree of dormancy of seven wild and two cultivated rice species comprising 21 populations and two cultivars.

METHODS

Four wild rice species from South America, Oryza glumaepatula, O. latifolia, O. grandiglumis and O. alta, and two O. sativa cultivars were tested in one experiment. In a second experiment, five wild species, O. punctata, O. eichingeri, O.rufipogon, O. latifolia and O. glumaepatula, and one cultivated species (O. glaberrima) were evaluated. Initial germination tests were performed soon after the seeds were harvested and subsequently at 2-month intervals, for a total of six storage periods in the first experiment and three in the second. All tests were conducted in the dark at a temperature of 27 degrees C.

KEY RESULTS

Different patterns of after-ripening among populations within and between species were observed.

CONCLUSIONS

The cultivated species (O. sativa and O. glaberrima) and, amongst the wild species, the tetraploids O. latifolia, O. grandiglumis and the diploids O. eichingeri and O. punctata, had weak dormancy, losing it completely 2 months after harvest, while O. rufipogon and O. glumaepatula exhibited pronounced dormancy. The latter showed different patterns of after-ripening between populations indigenous to the Amazon region and those originating in the Paraguay River system. Seeds of Solimoes (Amazon) and Japura origin showed weak dormancy whereas those of Paraguay origin showed deep dormancy. Ecological differences among natural habitats may be involved in such differentiation.