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.

Microsatellite loci and genetic structure of artificial populations of Cotesia flavipes (Hymenoptera, Braconidae).

Cotesia flavipes (Cameron) is a parasitoid wasp used in the biological control of the sugarcane borer (Diatraea saccharalis) (Fabr., 1794). Studies on the genetic diversity of C. flavipes are hampered by the lack of highly polymorphic molecular markers. In this report, a set of 11 microsatellite loci were developed from an enriched library of C. flavipes. Four microsatellite loci were polymorphic and were screened in 212 C. flavipes individuals (183 females and 29 males) that were randomly sampled from seven rearing laboratory populations. The number of alleles ranged from two to three. The average inbreeding coefficient (FIS) among all laboratory populations was 0.120, indicating an excess of homozygotes. The average genetic diversity within the laboratory populations was 0.292, which is lower than the values reported for wild Cotesia spp populations. Genetic diversity was most pronounced within laboratory populations (70 to 90%). Most of the observed alleles were fixed or close to fixation. This low overall genetic diversity may have originated from a founder effect, i.e., the contribution of a small number of individuals (genes and alleles) to the formation of these populations. To our knowledge, this study is the first to provide microsatellite loci and an analysis of the genetic structure of C. flavipes. Our results suggest that new introductions of C. flavipes may increase genetic diversity and improve the efficiency of the biological control of D. saccharalis. In addition, population structure data could be used to estimate the minimum number of wasps to be imported.

Genetic diversity among Puccinia melanocephala isolates from Brazil assessed using simple sequence repeat markers.

Brown rust (causal agent Puccinia melanocephala) is an important sugarcane disease that is responsible for large losses in yield worldwide. Despite its importance, little is known regarding the genetic diversity of this pathogen in the main Brazilian sugarcane cultivation areas. In this study, we characterized the genetic diversity of 34 P. melanocephala isolates from 4 Brazilian states using loci identified from an enriched simple sequence repeat (SSR) library. The aggressiveness of 3 isolates from major sugarcane cultivation areas was evaluated by inoculating an intermediately resistant and a susceptible cultivar. From the enriched library, 16 SSR-specific primers were developed, which produced scorable alleles. Of these, 4 loci were polymorphic and 12 were monomorphic for all isolates evaluated. The molecular characterization of the 34 isolates of P. melanocephala conducted using 16 SSR loci revealed the existence of low genetic variability among the isolates. The average estimated genetic distance was 0.12. Phenetic analysis based on Nei's genetic distance clustered the isolates into 2 major groups. Groups I and II included 18 and 14 isolates, respectively, and both groups contained isolates from all 4 geographic regions studied. Two isolates did not cluster with these groups. It was not possible to obtain clusters according to location or state of origin. Analysis of disease severity data revealed that the isolates did not show significant differences in aggressiveness between regions.

Edge effects enhance selfing and seed harvesting efforts in the insect-pollinated Neotropical tree Copaifera langsdorffii (Fabaceae).

Edge effects may affect the mating system of tropical tree species and reduce the genetic diversity and variance effective size of collected seeds at the boundaries of forest fragments because of a reduction in the density of reproductive trees, neighbour size and changes in the behaviour of pollinators. Here, edge effects on the genetic diversity, mating system and pollen pool of the insect-pollinated Neotropical tree Copaifera langsdorffii were investigated using eight microsatellite loci. Open-pollinated seeds were collected from 17 seed trees within continuous savannah woodland (SW) and were compared with seeds from 11 seed trees at the edge of the savannah remnant. Seeds collected from the SW had significantly higher heterozygosity levels (Ho=0.780; He=0.831) than seeds from the edge (Ho=0.702; He=0.800). The multilocus outcrossing rate was significantly higher in the SW (tm=0.859) than in the edge (tm=0.759). Pollen pool differentiation was significant, however, it did not differ between the SW (=0.105) and the edge (=0.135). The variance effective size within the progenies was significantly higher in the SW (Ne=2.65) than at the edge (Ne=2.30). The number of seed trees to retain the reference variance effective size of 500 was 189 at the SW and 217 at the edge. Therefore, it is preferable that seed harvesting for conservation and environmental restoration strategies be conducted in the SW, where genetic diversity and variance effective size within progenies are higher.

Mendelian inheritance, genetic linkage, and genotypic disequilibrium at nine microsatellite loci of Cariniana legalis (Mart.) O. Kuntze.

Cariniana legalis is one of the largest tropical trees with a wide distribution in the Brazilian Atlantic rainforest. We investigated the Mendelian inheritance, genetic linkage, and genotypic disequilibrium at seven microsatellite loci specifically isolated for C. legalis, and at two previously developed heterologous microsatellite loci. Forty to 100 open-pollinated seeds were collected from 22 seed-trees in two populations. Using the Bonferroni correction, no remarkable deviations from the expected Mendelian segregation, linkage, or genotypic disequilibrium were detected in the nine loci studied. Only 3.7% of the tests were significant for investigations of the Mendelian proportions. On the other hand, only 2.8% of tests for linkage detection showed significance. In addition, among all pairwise tests used for investigating linkage disequilibrium, significance was found in 9.7% of the locus pairs. Our results show clear evidence that the nine simple sequence repeat loci can be used without restriction in genetic diversity, mating system, and parentage analyses.

Genetic structure based on nuclear and chloroplast microsatellite loci of Solanum lycocarpum A. St. Hil. (Solanaceae) in Central Brazil.

Solanum lycocarpum (Solanaceae) is a woody species found in the Brazilian Cerrado. The flowers are pollinated by Xylocopa spp bees, and seeds are dispersed by mammals with distinct home range sizes. As a consequence, relative contributions of pollen and seeds to overall gene flow can vary according to different spatial scales. We studied the genetic structure of four natural populations of S. lycocarpum separated by 19 to 128 km, including individuals located along dirt roads that interlink three of the populations. A total of 294 individuals were genotyped with five nuclear and six chloroplast microsatellite markers. Significant spatial genetic structure was found in the total set of individuals; the Sp statistic was 0.0086. Population differentiation based on the six chloroplast microsatellite markers (θ(pC) = 0.042) was small and similar to that based on the five nuclear microsatellite markers (θ(p) = 0.054). For this set of populations, pollen and seed flow did not differ significantly from one another (pollen-to-seed flow ratio = 1.22). Capability for long distance seed dispersion and colonization of anthropogenic sites contributes to the ability of S. lycocarpum to maintain genetic diversity. Seed dispersion along dirt roads may be critical in preserving S. lycocarpum genetic diversity in fragmented landscapes.

Evaluation of algorithms used to order markers on genetic maps.

When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results.

[Prevalence of hypovitaminosis a in children of peripheral districts of Campinas São Paulo, Brazil]. / Prevalência de hipovitaminose a em crianças da periferia do município de Campinas, São Paulo, Brasil.

The prevalence of hypovitaminosis A among children of the peripheral districts of the city of Campinas, S o Paulo, Brazil, was estimated by determining serum retinol levels by High Performance Liquid Chromatography (HPLC) in a sample of 131 children aged between three and ten years, between April 1991 and February 1992. A prevalence of 17.6% and retinol concentrations in the range of 0.35 to 0.70 micromol/L were found (CI=11.1-24.1; 95%), indicating the existence of public health risk Ophthalmological examinations, however, failed to detect any cases of xerophthalmy. Additional characterization of the sample was obtained from 341 children. The per capita income of the average household was surprisingly high for low-income areas. According to FAO-WHO standards, food consumption was adequate only for protein (133.96%). Adequacy levels were low for energy (87.76%) and particularly for vitamin A (66.13%) and iron (42.14%). Height for-age and weight-for-height anthropometric indices revealed that many children were located below -1 standard deviation.

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.

Implications of the variance effective population size on the genetic conservation of monoecious species.

The concept of variance effective population size [Ne(v)] and other expressions are reviewed and described for specific sampling steps in germplasm collection and regeneration of monoecious species. Special attention is given to procedures for computing the variance of the number of contributed gametes [V(k)] to the next generation. Drift, as it occurs between generations, was considered to contain a component due to the sampling of parents and a subsequent component due to the sampling of gametes. This demonstrates that drift, caused by reduction of seed viability, damages the genetic integrity of accessions stored in germplasm banks. The study shows how mating designs, such as plant-to-plant or chain crossings with additional female gametic control, can partially alleviate this problem. Optimal procedures for increasing Ne(v) when collecting germplasm in the field are also discussed. The effect of different female and male gametic control strategies on Ne(v) is considered under several situations. Practical examples illustrating the use of V(k) and Ne(v) expressions are given.

Genetic structure, mating system, and long-distance gene flow in heart of palm (Euterpe edulis Mart.).

We report a detailed analysis of the population genetic structure, mating system, and gene flow of heart of palm (Euterpe edulis Mart.-Arecaceae) in central Brazil. This palm is considered a keystone species because it supplies fruits for birds and rodents all year and is intensively harvested for culinary purposes. Two populations of this palm tree were examined, using 18 microsatellite loci. The species displays a predominantly outcrossed mating system (tm = 0.94), with a probability of full sibship greater than 70% within open-pollinated families. The following estimates of interpopulation genetic variation were calculated and found significant: FIT = 0.17, FIS = 0.12, FST = 0.06, and RST = 0.07. This low but significant level of interpopulation genetic variation indicates high levels of gene flow. Two adult trees were identified as likely seed parents (P > 99.9%) of juveniles located at a distance of 22 km. Gene flow over such distances has not been reported before for tropical tree species. The establishment and management of in situ genetic reserves or ex situ conservation and breeding populations for E. edulis should contemplate the collection of several hundreds open-pollinated maternal families from relatively few distant populations to maximize the genetic sampling of a larger number of pollen parents.

Practical considerations for maintaining germplasm in maize.

The main goals of genetic resource management are to acquire, maintain, distribute, characterize, regenerate, preserve, evaluate, and utilize the genetic diversity of crops and their wild relatives. The objectives of this study for ex-situ conservation of maize (Zea mays L.) are to review and describe: (1) practical regeneration methods that are based on population genetic theory; (2) practical problems encountered in choosing core subsets of a maize collection. Whenever possible, regeneration procedures should control the number of pollen parents (male gametes; through controlled hand pollination) and the number of female parent gametes (by harvesting equal numbers of kernels from each seed plant). When the number of pollen and seed parents are controlled during regeneration, the effective population size (Ne) is twice the size of the original population (N). Examples of practical methods for controlling the number of male and female parents are presented. The procedure involves random-paired plant crosses and taking equal numbers of seeds from each maize ear. To form a core subset, accessions of a maize race are subdivided through a stratified sampling procedure. Delineation of a core subset from a Tuxpeño racial collection is described as an example.

Genetic diversity and recruitment of the tropical palm, Euterpe edulis Mart., in a natural population from the Brazilian Atlantic Forest.

The genetic diversity and recruitment of plants of heart-of-palm tree (Euterpe edulis Mart.) were investigated in a natural population located in Southern Brazil. Five categories of plants, from seedlings to adults, were analysed using 16 allozymic loci. The results showed an average population level of genetic diversity (He=0.278) greater than the average of plant species already studied. The recruitment process of E. edulis is related to its genetic characteristics. A significant increase in the heterozygote frequency towards the adult stages was observed at three loci (Pgdh-2, G6pdh-1 and Mdh-1). This suggests the possible action of natural selection in promoting such heterozygote increase. In the same way, a linear increase in allele frequencies was observed at four loci (Prx-3, Prx-4, Pgdh-2 and G6pdh-1), indicating that recruitment is also related to a greater survival of individuals that are carriers of certain alleles. The maintenance of high diversity levels, as well as the increase in the heterozygote frequency, are positive aspects for in situ conservation. Furthermore, an increase in heterozygote frequency is favourable to the management of the species, since the maintenance of a stock of reproductive individuals with high heterozygosity levels favours the maintenance of the population dynamic and structure.

Selection for breed-specific growth hormone and IGF-I alleles in a synthetic beef cattle cross, Canchim

Este estudo foi desenvolvido com o objetivo de avaliar as freqüências gênicas em diferentes geraçöes de bovinos da raça sintética Canchim (5/8 Charolês, 3/8 Zebu). Uma amostra de 154 animais, representando três classes de geraçöes de um rebanho da raça Canchim, foi analisada para sete marcadores moleculares. Uma amostra da raça Charolesa (N=36) foi incluída nas análises para permitir comparaçöes. Observou-se um aumento linear, altamente significativo (P < 0,01), na freqüência do alelo que codifica o aminoácido valina na posiçäo 127 do hormônio de crescimento, ao longo das geraçöes de Canchim. Este alelo foi observado na amostra da raça Charolesa e näo é encontrado em raças zebuínas nacionais. Quatro alelos foram observados para o microssatélite localizado na regiäo 5' näo transcrita do gene do fator de crescimento semelhante à insulina do tipo I (IGF-I), com tamanhos variando de 231 a 225 pb. A freqüência do alelo de 225 pb apresentou um aumento significativo (P < 0,05) näo linear ao longo das geraçöes. Este alelo näo foi observado na raça Charolesa e é predominante nas raças zebuínas. Para o microssatélite CSFM50, seis alelos foram observados na raça Canchim, tendo sido verificada uma reduçäo linear (P < 0,05) na freqüência do alelo de 168 bp. A hipótese de acasalamento preferencial com relaçäo ao polimorfismo do hormônio de crescimento foi reforçada pelos resultados da análise de estatística F de Wright. O valor estimado de Fis para este loco foi 0,59 (P < 0,01). O aumento simultâneo de um alelo do hormônio de crescimento característico de Bos taurus e de um alelo de IGF-I característico de Bos indicus sugere que a seleçäo fenotípica tenha favorecido regiöes diferentes de ambos os genomas que entraram na formaçäo dessa raça.