Genetic variability of garlic accessions as revealed by agro-morphological traits evaluated under different environments

The cultivated garlic (Allium sativum L.) displays a wide phenotypic diversity, which is derived from natural mutations and phenotypic plasticity, due to dependence on soil type, moisture, latitude, altitude and cultural practices, leading to a large number of cultivars. This study aimed to evaluate the genetic variability shown by 63 garlic accessions belonging to Instituto Agronômico de Campinas and the Escola Superior de Agricultura "Luiz de Queiroz" germplasm collections. We evaluated ten quantitative characters in experimental trials conducted under two localities of the State of São Paulo: Monte Alegre do Sul and Piracicaba, during the agricultural year of 2007, in a randomized blocks design with five replications. The Mahalanobis distance was used to measure genetic dissimilarities. The UPGMA method and Tocher's method were used as clustering procedures. Results indicated significant variation among accessions (P < 0.01) for all evaluated characters, except for the percentage of secondary bulb growth in MAS, indicating the existence of genetic variation for bulb production, and germplasm evaluation considering different environments is more reliable for the characterization of the genotypic variability among garlic accessions, since it diminishes the environmental effects in the clustering of genotypes.

Chloroplast diversity of Casearia grandiflora in the Cerrado of Piauí State

Casearia grandiflora (Salicaceae) is a typical Cerrado species adapted to disturbed environments, making it useful for restoration projects. Knowledge of genetic diversity is important for establishing conservation strategies for this species. This study aimed to compare chloroplast haplotype diversity and structure of C. grandiflora, under the assumption that protected areas hold greater genetic diversity than disturbed areas. The populations studied are from Parque Nacional de Sete Cidades Conservation Unit and from the surroundings of the city of Cocal de Telha, both located in the State of Piauí. Molecular analyses were performed with seven chloroplast microsatellite loci. The number of private haplotypes and haplotype diversity were higher in the conservation unit, which reinforces the importance of these areas in maintaining biodiversity. Analysis of molecular variance showed that most of the genetic variation is found within populations, with a moderate divergence between them (F_ST = 0.14). The Bayesian analysis and discriminant analysis of principal components suggested that populations are not structured, revealing that a set of individuals from Parque Nacional de Sete Cidades were more divergent within populations than between them. Since literature has little information on C. grandiflora, the results of this study provide important contribution to a better understanding of the specie's genetic diversity.

Genetic diversity of Casearia sylvestris populations in remnants of the Atlantic Forest

Guaçatonga (Casearia sylvestris) is a native plant of the Atlantic Forest, with high medicinal potential and relevance for reforestation programs. The aim of this study was to characterize, with microsatellite markers, two populations of C. sylvestris from remaining areas of the Atlantic Forest in the State of São Paulo. High allelic variation was found in both populations (N_A = 101 and 117; A_R = 12.5 and 14.4), although with high endogamy coefficients (f = 0.640 and 0.363). Estimates of genetic structure suggested the presence of considerable genetic divergence between the populations (F_ST = 0.103); however, there was no spatial genetic structure within the populations. Genetic divergence may have occurred due to decreased gene flow between the fragmented populations as the result of deforestation. The results of this study demonstrate the importance of genetic diversity and its characterization in native plants within remaining forest areas for the management and restoration of such areas.

Genetic divergence in a soybean (Glycine max) diversity panel based on agro-morphological traits

Owing to the narrow genetic basis of soybean (Glycine max), the incorporation of new sources of germplasm is indispensable when searching for alleles that contribute to a greater diversity of varieties. The alternative is plant introduction, which may increase genetic variability within breeding programs. Multivariate techniques are important tools to study genetic diversity and allow the precise elucidation of variability in a set of genotypes of interest. The agro-morphological traits of 93 soybean accessions from various continents were analyzed in order to assess the genetic diversity present, and to highlight important traits. The experimental design was incomplete blocks (Alpha lattice, 8 x 12) with three replicates. Nine agro-morphological traits were analyzed, and principal component analysis and cluster analysis were performed, the latter by Ward's method. The dendrogram obtained contained eight subgroups, confirming the genetic diversity among the accessions and revealing similarities between 11 national genotypes. The geographical origin of the accessions was not always related to the clusters. The traits evaluated, and the methods used, facilitated the distinction and characterization of genotypes between and within groups, and could be used in Brazilian soybean breeding programs.

QTL mapping of soybean oil content for marker-assisted selection in plant breeding program

The present study was undertaken to detect and map the quantitative trait loci (QTL) related to soybean oil content. We used 244 progenies derived from a bi-parental cross of the Lineage 69 (from Universidade Estadual Paulista "Júlio de Mesquita Filho"/Faculdade de Ciências Agrárias e Veterinárias - Breeding Program) and Tucunaré cultivar. A total of 358 simple sequence repeat (SSR; microsatellite) markers were used to investigate the polymorphism between the parental lines, and for the polymorphic lines all the F2 individuals were tested. Evaluation of the oil content and phenotype was performed with the aid of a Tango equipment by near infra-red reflectance spectroscopy, using single F2 seeds and F2:3 progenies, in triplicate. The data were analyzed by QTL Cartographer program for 56 SSR polymorphic markers. Two oil-content related QTLs were detected on K and H linkage groups. The total phenotypic variation explained by QTLs ranged from 7.8 to 46.75% for oil content. New QTLs were identified for the oil content in addition to those previously identified in other studies. The results reported in this study show that regions different from those already known could be involved in the genetic control of soybean oil content.

Molecular characterization of patchouli (Pogostemon spp) germplasm

Patchouli [Pogostemon cablin (Blanco) Benth.] is an aromatic, herbaceous plant belonging to the Lamiaceae family native to Southeast Asia. Its leaves produce an essential oil regularly used by the perfume and cosmetics industries. However, since patchouli from the Philippines and India were described and named Pogostemon patchouli, there has been a divergence in the identity of these species. The objective of the current study was to study the genetic diversity of patchouli accessions in the Active Germplasm Bank of Universidade Federal de Sergipe using microsatellite and inter simple sequence repeat markers. The results of both types of molecular markers showed that there are two well-defined clusters of accessions that harbor exclusive alleles. It was observed that these two clusters are genetically distant, suggesting that they belong to two different species. Based on the results, two accessions were classified as Pogostemon heyneanus and the remaining accessions were classified as P. cablin.

Populations of Erythrina velutina Willd. at risk of extinction

The goal of this study was to characterize the structure of two natural populations of the coral tree using RAPD and ISSR markers. The study evaluated all individuals in two different areas in the northeastern region of Brazil: the first was in the riparian area, 10 km x 100 m along the edge of the lower São Francisco River, and the second was in the municipality of Pinhão, in a semiarid region between the municipalities of Neópolis and Santana do São Francisco. We used all the coral trees present in those two areas (37 individuals). The results of the RAPD and ISSR markers were highly congruent, supporting the reliability of the techniques used. Similarity was estimated using the Jaccard arithmetic complement index. A dendrogram was constructed using the unweighted pair group method with arithmetic mean cluster algorithm, and the robustness of the data was bootstrapped with 5000 replicates. A principal coordinate analysis was performed on the basis of Jaccard coefficients. The total genetic variation observed was 21%, corresponding to the variation between the populations, and 79% of the variation was observed within the populations.

New loci of Lychnophora ericoides and transferability to Lychnophora pinaster, endangered medicinal species from Brazil

Lychnophora ericoides and Lychnophora pinaster are species used in popular medicine as analgesic or anti-inflammatory agents to treat contusions, rheumatism, and insect bites. In this study, 21 simple sequence repeat loci of L. ericoides were developed and transferred to L. pinaster. Three populations of L. ericoides and 2 populations of L. pinaster were evaluated; they were collected in the State of Minas Gerais. Population parameters were estimated, and the mean values of observed and expected heterozygosity were 0.297 and 0.408 (L. ericoides) and 0.228 and 0.310 (L. pinaster), respectively. Greater genetic variability was observed within populations than between populations of L. ericoides (62 and 37%) and L. pinaster (97 and 2.8%). These results provide information for genetic conservation and taxonomic studies of these endangered species.

Development and characterization of novel microsatellite markers in Hyptis pectinata (Lamiaceae)

A microsatellite-enriched library was constructed and a set of 19 SSR markers were developed to characterize a germplasm collection of Hyptis pectinata (L.) Poit., maintained at the Universidade Federal de Sergipe (UFS). Fifteen markers of 19 ranged from moderately to highly polymorphic. A total of 113 alleles were identified, with a mean of 7.52 alleles per locus. The mean HO and HE were 0.582 and 0.657, respectively. The primers developed were efficient tools for accessing the genetic diversity of the germplasm collection analyzed and may also be useful for other studies involving this species and other species in the genus Hyptis.

Isolation and characterization of microsatellite loci from the tick Amblyomma aureolatum (Acari: Ixodidae)

Amblyomma aureolatum (Pallas) is the main vector of the bacterium Rickettsia rickettsii, the etiological agent of Brazilian spotted fever. This disease is the most lethal human spotted fever rickettsiosis in the world. Microsatellite loci were isolated from a dinucleotide-enriched library produced from A. aureolatum sampled in Southeastern Brazil. Eight polymorphic microsatellites were further characterized among 38 individuals sampled from São Paulo metropolitan region. The number of observed alleles ranged from 2 to 9, observed heterozygosity was 0.184-0.647, and expected heterozygosity was 0.251-0.747. Cross-species amplifications suggested that these loci will be useful for other Amblyomma species.

A modified acidic approach for DNA extraction from plant species containing high levels of secondary metabolites

Purified genomic DNA can be difficult to obtain from some plant species because of the presence of impurities such as polysaccharides, which are often co-extracted with DNA. In this study, we developed a fast, simple, and low-cost protocol for extracting DNA from plants containing high levels of secondary metabolites. This protocol does not require the use of volatile toxic reagents such as mercaptoethanol, chloroform, or phenol and allows the extraction of high-quality DNA from wild and cultivated tropical species.

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.

Microsatellite markers for the Cabreúva tree, Myroxylon peruiferum (Fabaceae), an endangered medicinal species from the Brazilian Atlantic Forest

The Cabreúva tree, Myroxylon peruiferum, is an endangered tropical species from Brazil used in forest restoration projects. It is known for its medicinal properties. Eleven microsatellite markers were developed for this species, from a microsatellite-enriched library. Nine of these markers, characterized in 30 individuals from a semideciduous forest remnant population in southeast Brazil, were polymorphic, with allele numbers ranging from 2 to 8 per locus; expected and observed heterozygosities ranged from 0.103 to 0.757 and 0.107 to 0.704, respectively. One locus (Mpe-C04) showed significant deviation from Hardy-Weinberg equilibrium, probably due to null alleles. Two other loci (Mpe-E09 and Mpe-H07) were monomorphic in this population. These microsatellite loci should be useful for future population genetic studies of this species.

Development and characterization of microsatellite loci for genetic studies of the sugarcane borer, Diatraea saccharalis (Lepidoptera: Crambidae)

We present polymorphic microsatellite markers isolated for genetic studies of the sugarcane borer, Diatraea saccharalis (Fabricius). We isolated 16 microsatellite loci through an enriched genomic library protocol. After characterization, 12 markers showed polymorphic information expressed in the observed number of alleles (ranging from 2 to 7; 5 on average) and in the polymorphism information content (ranging from 0.292 to 0.771; 0.535 on average). These markers can be used in further studies to understand the basic ecological characteristics of the sugarcane borer, e.g., dispersion patterns and population genetic differentiation, associated with distinct geographic scales and host plants.

Low polymorphism revealed in new microsatellite markers for Bemisia tabaci (Hemiptera: Aleyrodidae)

The silverleaf whitefly (Bemisia tabaci) is actually a complex of morphologically indistinct species that vary in their capacity to transmit plant viruses and to induce physiological disorders in plants of economic importance. The worldwide impact of this whitefly has increased greatly, as it is a vector of various types of phytovirus, especially geminiviruses, in plants of economic importance. The adaptability of B. tabaci to many regions of the world has fostered the appearance of various biotypes that attack a broad spectrum of host plants. We developed microsatellite markers to study genetic variability and population structure of this whitefly in Brazil. Thirteen polymorphic microsatellite markers were isolated and characterized in 20 individuals from a natural population that were collected in soybean in Campinas (SP). The number of alleles per locus ranged from one to two, and the expected heterozygosity ranged from 0.000 to 0.505. These microsatellite markers will be useful for studies and management of B. tabaci. The low polymorphism found in these molecular markers is probably associated with homology of genes expressed in these markers.

MtDNA variability in whitefly (Bemisia tabaci) populations in Brazil

Bemisia tabaci (Hemiptera: Aleyrodidae) consists of a complex of morphologically indistinct biotypes that vary mainly in their capacity to transmit plant viruses and to induce physiological disorders in plants of economic importance. The adaptability of B. tabaci to many regions of the world has fostered the appearance of various biotypes and has resulted in a broad spectrum of host plants. Our goal was to identify which biotypes were present in four B. tabaci populations in Brazil. We quantified genetic variability between and within populations. Three individuals were collected from three host plant species: two populations on soybean (Campinas and Rondonópolis), one on pumpkin (Barreiras) and one on tomato (Cruz das Almas) in three States of Brazil (São Paulo, Mato Grosso, and Bahia). We chose one sequence of the B biotype, obtained from GenBank; the Campinas population, which had been previously characterized as biotype B, was used as a control for this biotype. We also included one sequence of the Q biotype, obtained from GenBank, as an outgroup. The COI region of the mtDNA gene was partially amplified with the CI-J-2195 and L2-N-3014 pair of primers, and the reaction products were sequenced. Based on distance-based algorithm analyses, we found that all haplotypes belong to biotype B, which was confirmed by the haplotype network. Genetic structure analyses showed that the host plant species does not influence population structuring of this pest; only the geographic location mattered.

Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis × Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Genetic diversity of turmeric germplasm (Curcuma longa; Zingiberaceae) identified by microsatellite markers

Turmeric (Curcuma longa) is a triploid, vegetatively propagated crop introduced early during the colonization of Brazil. Turmeric rhizomes are ground into a powder used as a natural dye in the food industry, although recent research suggests a greater potential for the development of drugs and cosmetics. In Brazil, little is known about the genetic variability available for crop improvement. We examined the genetic diversity among turmeric accessions from a Brazilian germplasm collection comprising 39 accessions collected from the States of Goiás, Mato Grosso do Sul, Minas Gerais, São Paulo, and Pará. For comparison, 18 additional genotypes were analyzed, including samples from India and Puerto Rico. Total DNA was extracted from lyophilized leaf tissue and genetic analysis was performed using 17 microsatellite markers (single-sequence repeats). Shannon-Weiner indexes ranged from 0.017 (Minas Gerais) to 0.316 (São Paulo). Analyses of molecular variance (AMOVA) demonstrated major differences between countries (63.4%) and that most of the genetic diversity in Brazil is found within states (75.3%). Genotypes from São Paulo State were the most divergent and potentially useful for crop improvement. Structure analysis indicated two main groups of accessions. These results can help target future collecting efforts for introduction of new materials needed to develop more productive and better adapted cultivars.

[Population genetic structure of Bemisia tabaci (Hemiptera: Aleyrodidae) utilizing microsatellite markers]

We aimed to characterize the population genetic structure within and among five Bemisia tabaci (Gennadius) populations collected from different host plants and geographic regions by using microssatelites as a molecular marker. Each population was represented by 19 specimens. The host plants and geographic origins of these populations were described as follows: Pop 1: Squash Barreiras (BA); Pop 2: Cotton Barreiras (BA); Pop 3: Soybean Campinas (SP); Pop 4: Tomato Cruz das Almas (BA); and Pop 5: Soybean Rondonópolis (MT). Six polymorphic loci were observed, which discriminated 31 different alleles in the studied populations, with a mean number of alleles per population of 3.30 (2.67 - 4.00). Using Fisher's Exact test, it was observed that at least three populations were in Hardy-Weinberg equilibrium for most of the studied loci (six). The dendrogram (UPGMA) separated populations into groups mainly related to the geographic origin of the samples. Only population 5 differed from the others at a 0.15 distance (74.5% group consistency). The most similar populations were 1 and 2, with a 0.01 distance (65.3%). This is in agreement with their geographic origins and it was not consistent with host specificity. The results suggest considerable gene flow (7.3%) among all whitefly populations and indicate that a better understanding of the gene flow in populations of B. tabaci associated with different hosts is required for the management of this insect.

Epidemics of Meloidogyne brasilensis in Central Brazil on Processing Tomato Hybrids That Have the Root-Knot Nematode Mi Resistance Gene

The species Meloidogyne brasilensis Charchar & Eisenback 2002 was described as causing root rot, severe wilt, and numerous galls in pea (Pisum sativum L.) in Brasília-Federal District and tomato (Solanum lycopersicum L.) cv. Rossol (known to have the root-knot nematode resistance Mi gene) in Londrina-Paraná State, Brazil. To our knowledge, this current work is the first report of the epidemics on tomato hybrids that have the Mi gene caused by infection of M. brasilensis in central Brazil. Samples were obtained from fields with two commercial hybrids that have the Mi gene ('Calroma' and 'Nemapride') that were cultivated under center-pivot irrigation in Silvânia, Goiás State. These hybrids exhibited slow vegetative development and malformed roots because of the high number of large galls. Symptomatic plants were collected from a tomato crop area of more than 100 ha. Random sampling indicated field sectors with up to 100% of symptomatic plants. Morphological and morphometric evaluations of this Meloidogyne population were carried out with the female perineal pattern, stylet, and excretory pore and also with the male body traits, labial disc, and stylet. The esterase phenotype was unique for this population with four clear bands (J. M. Charchar, unpublished data). Altogether, the morphological and biochemical characteristics of this population were in agreement with that reported for M. brasilensis (1). Koch's postulates were fulfilled using tomato 'Rutgers' (susceptible) and 'Rossol' (with the Mi resistance locus) under greenhouse conditions. The massive use of tomato hybrids with the Mi gene could be a strong selection factor favoring this pathogen under growing conditions in central Brazil. Germplasm screen searching for sources of resistance specific to this nematode species is advisable. Reference: (1) J. M. Charchar and J. D. Eisenback. Nematology 4:629, 2002.

Use of supplementary genotypes in AMMI analysis

Improving stability of crop yield in a target production environment is an important breeding objective. It is well known that selection for better stability generally results in lower mean yields and, conversely, that selection for higher mean yields may lead to poorer stability. This paper explores the equivalence between the singular value decomposition used in AMMI analysis and the spectral decomposition used in principal components analysis. This equivalence enables scores of a "supplementary genotype" made up of the highest yield value within each environment to be obtained, and these may serve as the ideal check treatment for selection purposes. These scores are used to (1) display this check in a biplot graph, thereby providing a qualitative comparison with the real genotypes related to their interaction with environments; (2) obtain estimates of the squared distances from the projection of each real genotype to the projection of the "supplementary treatment", thereby allowing conclusions to be made on the yield stability of each real genotype. This procedure was effective in identifying the most stable soybean cultivars in an example shown for illustration.

Helicobacter pylori-associated gastritis: does it play a role in functional dyspepsia?

OBJECTIVES

The goal of this study is to averiguate whether Helicobacter pylori (Hp)-associated gastritis is involved in the etiology of functional dyspepsia (FD) or, at least in a subset of these patients.

METHODS

103 consecutive FD patients were prospectively analyzed and subdivided according to their main complaints into ulcer-like FD (n = 31), dysmotility-like FD (n = 24) or nonspecific FD (n = 48). After endoscopy with gastric biopsy, gastritis and Hp infection were assessed and graded by histology according to the Sydney System. The prevalence of gastritis, Hp and disease activity were analyzed among the three FD subtypes and against 42 age, sex and race matched controls.

RESULTS

Hp was identified in 64 (62%) of the FD group and in 23 (55%) of the controls (p > 0.20, NS). We neither observed any increased prevalence of the infection among FD subgroups (dysmotility-like 58%, ulcer-like 58%, unspecified 67%), nor in the activity of gastritis among FD subgroups and controls. We conclude that Helicobacter pylori gastritis per se is not associated with functional dyspepsia.

[Intestinal mucosa in rats with iron deficiency anemia]

Eighteen albino rats at the age of 15 days were separated in 2 groups of 9 and fed cow's milk exclusively. The milk supplied to the control rats (group I) was supplemented with iron and copper. The months later, the rats were scarificed. The animals of group II were severely anaemic. In each rat, a histological examination of gastric (in group II, only in 2 rats) and jejunal mucosa as well as measurements of total thickness, villous height, epithelial cell height and mitotic index were made. Histology was normal in all the rats. Measurements gave similar results in both groups except for the epithelial cell height which was significantly higher in anaemic rats than in controls. The authors take issue with the methodology followed in previous studies concerning iron-deficient children and suggest that the causal relation between iron deficiency and structural changes of intestinal mucosa in children has not yet been proven.