Genomic variability of Pantoea ananatis in maize white spot lesions assessed by AFLP markers.

Measures to control maize white spot (MWS) caused by Pantoea ananatis are preferentially based on resistant cultivars. A lack of knowledge on the genetic variability of pathogens could interfere with the development and utilization of controlling strategies in this pathosystem. The main goals of this study were to investigate the genetic variability of 90 P. ananatis isolates from three different eco-geographical regions of Brazil by amplified fragment length polymorphism (AFLP), and to determine the presence of a universal P. ananatis plasmid in isolates from tropical Brazil. Analysis of genetic similarity by AFLP allowed us to categorize the 90 isolates into two groups. However, no correlation between the collecting sites and genetic groupings was observed. The polymorphism percentage found in P. ananatis ranged between 24.64 and 92.46%, and genetic diversity was calculated to be 0.07-0.09. The analysis of molecular variance showed that 99.18% of genetic variability was within the populations, providing evidence that evolutionary forces were acting on these populations. All P. ananatis isolates showed the P. ananatis universal plasmid (280 or 352 kb). This is the first report on the presence of a universal P. ananatis plasmid from MWS lesions in the tropical area.

Population genetic structure in Phyla scaberrima from Mexico and Colombia assessed by AFLP markers and implications for conservation.

Phyla scaberrima (Verbenaceae) is a herbaceous perennial species that is distributed from Mexico (center of origin) to Colombia, growing in forest and swamp edges or grasslands from sea level up to an altitude of 1800 m. The chemical properties and uses in popular medicine have drastically affected the population size of this species. In this study, we investigated genetic variability in populations of P. scaberrima using AFLP markers. Three AFLP primer combinations rendered a total of 997 markers in a sample of 131 individuals from five populations, including two populations from Mexico and three from Colombia. The average percentage of polymorphic loci, gene diversity and Shannon-Wiener index were 46.62, 0.0695, and 0.119, respectively. Analysis of molecular variance showed that the distribution of the genetic variability within populations (85.41%) was higher than between groups (8.11%) and between populations (6.48%). Principal coordinate analysis and Bayesian analysis for the K number of clusters showed that the individuals were dispersed in five (K= 5) clusters. The low levels of genetic diversity observed in these populations demonstrated that the populations from Mexico and Colombia need urgent management to recover their genetic variability.

Isolation and characterization of simple sequence repeat markers for the herbaceous species Phyla scaberrima (Verbenaceae).

Phyla scaberrima (Verbenaceae) is a herbaceous species distributed from Mexico to Panama. Because of its well-known sweet properties and other medicinal uses, this species is cultivated in South America and the Caribbean. Phyla scaberrima has been arbitrarily extracted from nature, resulting in a severe reduction in its gene pool. In this study, we developed and characterized 11 simple sequence repeat markers for P. scaberrima to determine the genetic variability and patterns of population structure of the species. Fifty-six alleles were detected in a sample of 48 individuals belonging to 3 different populations. The average number of alleles per locus was 5.09, while the polymorphic information content ranged from 0.000-0.587. The observed and expected heterozygosities varied from 0.000-0.543 and from 0.000-0.651, respectively. Two loci exhibited significant deviation of the expected Hardy-Weinberg proportion. The 11 primer pairs were also tested for cross-amplification to 6 species of the related genus Lippia. The transferability rate ranged from 4 loci in Lippia florida and L. rotundifolia to 6 loci in L. corymbosa and L. microcephala. The 11 primer sets were shown to be valuable tools for population genetic studies in P. scaberrima and in species of the genus Lippia in which primer transferability was detected.

Isolation and characterization of 8 microsatellite loci from Chrysophyllum gonocarpum (Sapotaceae).

Chrysophyllum gonocarpum is a tropical tree species that is very important in the recovery of heterogeneous forests and of degraded areas of permanent preservation. We identified microsatellite loci for C. gonocarpum to assess the genetic variability and the patterns of the population structure of the species. We isolated 8 microsatellite primers by using CT- and GT-enriched genomic libraries. We detected 2-4 alleles with 2.9 alleles per locus on average, by polymerase chain reaction. Test for cross-amplification showed that some loci were successfully amplified in 2 other Chrysophyllum species. The microsatellites can be used to assess the genetic diversity and population structure of C. gonocarpum. Some primer pairs can be amplified in C. marginatum and C. splendens.

Characterization of nine microsatellite loci for the tree species Parapiptadenia rigida (Fabaceae-Mimosoideae) and their transferability.

Parapiptadenia rigida, locally known as angico, is a tropical tree common in the semideciduous Brazilian forest. Its wood is naturally resistant to insect attack and is useful for construction. Extracts from the tree have medicinal properties. We characterized nine microsatellite loci for P. rigida. Thirty-five alleles were detected in a sample of 45 individuals from 3 different populations, with an average of 3.9 alleles per locus. The average polymorphic information content ranged from 0.099 to 0.640. Observed and expected heterozygosities varied from 0.111 to 0.489 and from 0.106 to 0.707, respectively. One locus exhibited significant deviation from Hardy-Weinberg equilibrium and four pairs of loci showed significant linkage disequilibrium. All nine primers were tested for cross-amplification in species from the Fabaceae-Mimosoidea family, yielding a transferability success rate of 7 loci in Stryphnodendron adstringens to 0 transferred loci in Pithecellobium incuriale and Inga marginata. These microsatellites will be valuable to study population genetics of this and other species where primer transferability was detected.

Population genetic structure of the tropical tree species Aegiphila sellowiana (Lamiaceae).

The Tibagi River, located in southern Brazil, is associated with a significant degree of environmental heterogeneity, along its 550 km extension. There is concern about the integrity of this river's ecosystem, as human interference has been increasing. Aegiphila sellowiana (Lamiaceae) is an important pioneer tree species, commonly found near rivers; the fruit is consumed by avifauna. We studied this species along three ecological gradients, comprising the upper, middle, and lower regions of the Tibagi River basin. The genetic structure of nine subpopulations of A. sellowiana distributed along these gradients was investigated using RAPDs. Moderate levels of gene diversity (ranging from 0.091 to 0.132) were identified, inferred by a traditional approach and a Bayesian model-based method. The F-statistic, G(ST) parameters and molecular variance analysis showed high genetic differentiation among the three regions (39.5 to 50.26%). Analysis of molecular variance revealed high levels of genetic variation between populations (50.26%), while lower values of genetic variation (ranging from 9.56 to 16.35%) were seen between subpopulations within the upper, middle, and lower regions of the Tibagi River basin. The validity of these results was confirmed by principal coordinate analysis. Linear regression analysis showed significant correlations (r = 0.621, P = 0.0001) between the genetic and geographical distances. The differences observed in genetic variation between regions are probably due to habitat fragmentation; for conservation purposes, we recommend that at least one subpopulation from each region of the Tibagi River should be maintained.

Genetic differentiation in Aspidosperma polyneuron (Apocynaceae) over a short geographic distance as assessed by AFLP markers.

Studies on intraspecific variation can contribute to the development of conservation strategies by identifying units of conservation for threatened species. Aspidosperma polyneuron is a tropical tree of seasonal semideciduous forests that is currently endangered and protected because it has been heavily logged for lumber, although it was once common in Brazil and neighboring countries. We investigated genetic structure in two samples of A. polyneuron collected from steep hillsides and from flat areas of a natural forest fragment in northern Paraná State, Brazil. Seven AFLP primer combinations yielded 200 markers, with a polymorphic rate of 88.5% for samples from the flat area and 99% for samples from the high declivity area. Total genetic diversity (H(T)) was 0.387, while the genetic diversity within the populations (H(S)) was 0.307 and 0.372, for samples from the flat and the high declivity areas, respectively. Genetic differentiation between samples was high, with a mean F(ST) of 0.265 and a genetic distance of 0.148, indicative of a high degree of genetic structure over a short distance. Principal coordinate analysis separated the samples into three groups of individuals; the first group included individuals from the high declivity area, the second group consisted of individuals only from the flat area, and the third group had individuals from both areas. Bayesian analysis also showed K = 3 clusters. The unexpected high level of intraspecific variation of A. polyneuron in this small forest fragment should be taken into account when evaluating the genetic impact of forest degradation on this species in other semideciduous forest fragments.

Genetic diversity and flooding survival in Aegiphila sellowiana (Lamiaceae), a typical tree species from upland riparian forests.

Saplings of Aegiphila sellowiana were submitted to flooding and analysis of genetic diversity in order to investigate flooding tolerance as well as its genetic determination. This response is important because it means that some lines could be planted in degraded riparian areas. Leaves were sampled from each plant, and they were submitted to different flooding periods. Mortality of saplings was 40, 80, 50, 53.3, 33.3, and 33.3% in flooding for 15, 18, 25, 50, 80 days, and flooding for 50 days followed by re-aeration for 30 days, respectively. From the total number of flooded plants, 46.7% died in the first seven days of treatment, while 53.3% survived the flooding. The percentage of polymorphic loci (P(p)), Nei's genetic diversity (H) and the Shannon index (I) were slightly higher for the group that survived the stress of flooding (surviving: P(p) (%) = 67.48, H = 0.184, I = 0.287; not surviving: P(p) (%) = 66.67, H = 0.165, I = 0.261). Analysis of molecular variance showed that 5.88% of the genetic variability was due to the differences between groups of plants surviving and not surviving flooding, while 94.12% was due to genetic differences between individuals within these groups. Similar results were obtained by principal coordinate analysis. Based on these results, we can assume the existence of environment-specific genotypes and the genetic determination of flooding tolerance in A. sellowiana. Thus, some lines of A. sellowiana could be used in the reforestation of riparian habitats, especially in uplands along riverbanks.

Anatomy and genetic diversity of two populations of Schinus terebinthifolius (Anacardiaceae) from the Tibagi River basin in Paraná, Brazil.

Knowledge of the effects of flooding on plant survival is relevant for the efficiency of management and conservation programs. Schinus terebinthifolius is a tree of economic and ecological importance that is common in northeast Brazil. Flooding tolerance and genetic variation were investigated in two riparian populations of S. terebinthifolius distributed along two different ecological regions of the Tibagi River basin. Flooding tolerance was evaluated through the investigation of young plants, submitted to different flooding intensities to examine the morphological and anatomical responses to this stress. The growth rate of S. terebinthifolius was not affected by flooding, but total submersion proved to be lethal for 100% of the plants. Morphological alterations such as hypertrophied lenticels were observed in both populations and lenticel openings were significantly higher in plants from one population. Genetic analysis using DNA samples obtained from both populations showed a moderate degree of genetic variation between populations (13.7%); most of the variation was found within populations (86.3%). These results show that for conservation purposes and management of degraded areas, both populations should be preserved and could be used in programs that intend to recompose riparian forests.