The isolation, characterization, and application of WRKY genes as useful molecular markers in tropical trees

The improvement of tropical tree crops using conventional breeding methods faces challenges due to the length of time involved. Thus, like most crops, there is an effort to utilize molecular genetic markers in breeding programs to select for desirable agronomic traits. Known as marker assisted breeding or marker assisted selection, genetic markers associated with a phenotype of interest are used to screen and select material reducing the time necessary to evaluate candidates. As the focus of this research was improving disease resistance in tropical trees, the usefulness of the WRKY gene superfamily was investigated as candidates for generating useful molecular genetic markers. WRKY genes encode plant-specific transcriptional factors associated with regulating plants' responses to both biotic and abiotic stress. ^ One pair of degenerate primers amplified 48 WRKY gene fragments from three taxonomically distinct, economically important, tropical tree crop species: 18 from Theobroma cacao L., 21 from Cocos nucifera L. and 9 from Persea americana Mill. Several loci from each species were polymorphic because of single nucleotide substitutions present within a putative non-coding region of the loci. Capillary array electrophoresis-single strand conformational polymorphism (CAE-SSCP) mapped four WRKY loci onto a genetic linkage map of a T. cacao F2 population segregating for resistance to witches' broom disease. Additionally, PCR primers specific for four T. cacao loci successfully amplified WRKY loci from 15 members of the Byttneriae tribe. A method was devised to allow the reliable discrimination of alleles by CAE-SSCP using only the mobility assigned to the sample peaks. Once this method was validated, the diversity of three WRKY loci was evaluated in a germplasm collection of T. cacao . One locus displayed high diversity in the collection, with at least 18 alleles detected from mobility differences of the product peaks. The number of WRKY loci available within the genome, ease of isolation by degenerate PCR, codominant segregation demonstrated in the F2 population, and usefulness for screening germplasm collections and closely related wild species demonstrates that the WRKY superfamily of genes are excellent candidates for developing a number of genetic molecular markers for breeding purposes in tropical trees. ^

Molecular markers and human history: A tale of two haplogroup systems

To chronicle demographic movement across African Asian corridors, a variety of molecular (sequence analysis, restriction mapping and denaturing high performance liquid chromatography etc.) and statistical (correspondence analysis, AMOVA, calculation of diversity indices and phylogenetic inference, etc.) techniques were employed to assess the phylogeographic patterns of mtDNA control region and Y chromosomal variation among 14 sub-Saharan, North African and Middle Eastern populations. The patterns of genetic diversity revealed evidence of multiple migrations across several African Asian passageways as well within the African continent itself. The two-part analysis uncovered several interesting results which include the following: (1) a north (Egypt and Middle East Asia) to south (sub-Saharan Africa) partitioning of both mtDNA and Y chromosomal haplogroup diversity, (2) a genetic diversity gradient in sub-Saharan Africa from east to west, (3) evidence in favor of the Levantine Corridor over the Horn of Africa as the major genetic conduit since the Last Glacial Maximum, (4) a substantially higher mtDNA versus Y chromosomal sub-Saharan component in the Middle East collections, (5) a higher representation of East versus West African mtDNA haplotypes in the Arabian Peninsula populations versus no such bias in the Levant groups and lastly, (6) genetic remnants of the Bantu demographic expansion in sub-Saharan Africa. ^

Investigating the origin of PM2.5 in Baltimore using highly time-resolved organic molecular markers measured during the Baltimore PM-supersite

The detailed organic composition of atmospheric fine particles with an aerodynamic diameter smaller than or equal to 2.5 micrometers (PM2.5) is an integral part of the knowledge needed in order to fully characterize its sources and transformation in the environment. For the study presented here, samples were collected at 3-hour intervals. This high time resolution allows gaining unique insights on the influence of short- and long-range transport phenomena, and dynamic atmospheric processes. A specially designed sequential sampler was deployed at the 2002-2003 Baltimore PM-Supersite to collect PM2.5 samples at a 3-hourly resolution for extended periods of consecutive days, during both summer and winter seasons. Established solvent-extraction and GC-MS techniques were used to extract and analyze the organic compounds in 119 samples from each season. Over 100 individual compounds were quantified in each sample. For primary organics, averaging the diurnal ambient concentrations over the sampled periods revealed ambient patterns that relate to diurnal emission patterns of major source classes. Several short-term releases of pollutants from local sources were detected, and local meteorological data was used to pinpoint possible source regions. Biogenic secondary organic compounds were detected as well, and possible mechanisms of formation were evaluated. The relationships between the observed continuous variations of the concentrations of selected organic markers and both the on-site meteorological measurements conducted parallel to the PM2.5 sampling, and the synoptic patterns of weather and wind conditions were also examined. Several one-to-two days episodes were identified from the sequential variation of the concentration observed for specific marker compounds and markers ratios. The influence of the meteorological events on the concentrations of the organic compounds during selected episodes was discussed. It was observed that during the summer, under conditions of pervasive influence of air masses originated from the west/northwest, some organic species displayed characteristics consistent with the measured PM2.5 being strongly influenced by the aged nature of these long-traveling background parcels. During the winter, intrusions from more regional air masses originating from the south and the southwest were more important.

Using soil profiles of seeds and molecular markers as proxies for sawgrass and wet prairie slough vegetation in Shark Slough, Everglades National Park

We measured the abundance of Cladium jamaicense (Crantz) seeds and three biomarkers in freshwater marsh soils in Shark River Slough (SRS), Everglades National Park (ENP) to determine the degree to which these paleoecological proxies reflect spatial and temporal variation in vegetation. We found that C. jamaicense seeds and the biomarkers Paq, total lignin phenols (TLP) and kaurenes analyzed from surface soils were all significantly correlated with extant aboveground C. jamaicense biomass quantified along a vegetation gradient from a C. jamaicense to a wet prairie/slough (WPS) community. Our results also suggest that these individual proxies may reflect vegetation over different spatial scales: Paq and kaurenes correlated most strongly (R 2 = 0.88 and 0.99, respectively) with vegetation within 1 m of a soil sample, while seeds and TLP reflected vegetation 0–20 m upstream of soil samples. These differences in the spatial scale depicted by the different proxies may be complementary in understanding aspects of historic landscape patterning. Soil profiles of short (25 cm) cores showed that downcore variation in C. jamaicense seeds was highly correlated with two of the three biomarkers (Paq, R 2 = 0.84, p<0.005; TLP, R 2 = 0.97, p<0.0001), and all four of the proxies indicated a recent increase in C. jamaicense biomass at the site. Using a preliminary depth-to-age relationship based on matching charcoal peaks with available ENP fire records (1980-present) specific to our coring site, we found that peak-depths in C. jamaicense seed concentration appeared to correspond to recent minimum water levels (e.g., 1989 and 2001), and low seed abundance corresponded to high water levels (e.g., 1995), consistent with the known autecology of C. jamaicense. In summary, the combination of C. jamaicense seeds and biomarkers may be useful for paleoecological reconstruction of vegetation change and ultimately in guaging the success of ongoing efforts to restore historic hydrologic conditions in the South Florida Everglades.

Investigating the origin of PM2.5 in Baltimore using highly time-resolved organic molecular markers measured during the Baltimore PM-supersite

The detailed organic composition of atmospheric fine particles with an aerodynamic diameter smaller than or equal to 2.5 micrometers (PM 2.5) is an integral part of the knowledge needed in order to fully characterize its sources and transformation in the environment. For the study presented here, samples were collected at 3-hour intervals. This high time resolution allows gaining unique insights on the influence of short- and long-range transport phenomena, and dynamic atmospheric processes. A specially designed sequential sampler was deployed at the 2002-2003 Baltimore PM Supersite to collect PM2.5 samples at a 3-hourly resolution for extended periods of consecutive days, during both summer and winter seasons. Established solvent-extraction and GC-MS techniques were used to extract and analyze the organic compounds in 119 samples from each season. Over 100 individual compounds were quantified in each sample. For primary organics, averaging the diurnal ambient concentrations over the sampled periods revealed ambient patterns that relate to diurnal emission patterns of major source classes. Several short-term releases of pollutants from local sources were detected, and local meteorological data was used to pinpoint possible source regions. Biogenic secondary organic compounds were detected as well, and possible mechanisms of formation were evaluated. The relationships between the observed continuous variations of the concentrations of selected organic markers and both the on-site meteorological measurements conducted parallel to the PM2.5 sampling, and the synoptic patterns of weather and wind conditions were also examined. Several one-to-two days episodes were identified from the sequential variation of the concentration observed for specific marker compounds and markers ratios. The influence of the meteorological events on the concentrations of the organic compounds during selected episodes was discussed. It was observed that during the summer, under conditions of pervasive influence of air masses originated from the west/northwest, some organic species displayed characteristics consistent with the measured PM2.5 being strongly influenced by the aged nature of these long-traveling background parcels. During the winter, intrusions from more regional air masses originating from the south and the southwest were more important.

Organic matter dynamics in the Florida coastal Everglades: A molecular marker and isotopic approach

Everglades National Park (ENP) is about to undergo the world's largest wetland restoration with the aim of improving the quality, timing and distribution of water flow. The changes in water flow are hypothesized to alter the nutrient fluxes and organic matter (OM) dynamics within ENP, especially in the estuarine areas. This study used a multi-proxy approach of molecular markers and stable δ 13C isotope measurements, to determine the present day OM dynamics in ENP. ^ OM dynamics in wetland soils/sediments have proved to be difficult to understand using traditional geochemical approaches. These are often inadequate to describe the multitude of OM sources (e.g. higher land plant, emergent vegetation, submerged vegetation) to the soils/sediments and the complex diagenetic processes that can alter the OM characteristics. A multi-proxy approach, however, that incorporates both molecular level and bulk parameter information is ideal to comprehend complex OM dynamics in aquatic environments. Therefore, biomass-specific molecular markers or proxies can be useful in tracing the sources and processing of OM. This approach was used to examine the OM dynamics in the two major drainage basins, Shark River Slough and Taylor River Slough, of ENP. Freshwater to marine transects were sampled in both systems for soils/sediments and suspended particulate organic matter (SPOM) to be characterized through bulk OM analyses, lipid biomarker determinations (e.g. sterols, fatty acids, hydrocarbons and triterpenoids) and compound-specific stable carbon isotope (δ 13C) determinations. ^ One key accomplishment of the research was the assessment of a molecular marker proxy (Paq) to distinguish between emergent/higher plant vegetation from submerged vegetation within ENP. This proxy proved to be quite useful at tracing OM inputs to the soils/sediments of ENP. A second key accomplishment was the development of a 3-way model using vegetation specific molecular markers. This novel, descriptive model was successfully applied to the estuarine areas of Taylor and Shark River sloughs, providing clear evidence of mixing of freshwater, estuarine and marine derived OM in these areas. In addition, diagenetic transformations of OM in these estuaries were found to be quite different between Taylor and Shark Rivers, and are likely a result of OM quality and hydrological differences. ^

Horizontal genetic transfer in asexual fungi

Four aspects of horizontal genetic transfer during heterokaryon formation were examined in the asexual pathogen Fusarium oxysporum f.sp. cubense (Foc): (1) variability based on method of heterokaryon formation; (2) differences in nuclear and mitochondrial inheritance; (3) the occurrence of recombination without nuclear fusion; (4) the occurrence of horizontal genetic transfer between distantly related isolates. The use of non-pathogenic strains of Fusarium oxysporum as biocontrol agents warrants a closer examination at the reproductive life cycle of this fungus, particularly if drug resistance or pathogenicity genes can be transmitted horizontally. Experiments were divided into three phases. Phase I looked at heterokaryon formation by hyphal anastomosis and protoplast fusion. Phase II was a time course of heterokaryon formation to look at patterns of nuclear and mitochondrial inheritance. Phase III examined the genetic relatedness of the different vegetative compatibility groups using a multilocus analysis approach. Heterokaryon formation was evident within and between vegetative compatibility groups. Observation of non-parental genotypes after heterokaryon formation confirmed that, although a rare event, horizontal genetic transfer occurred during heterokaryon formation. Uniparental mitochondria inheritance was observed in heterokaryons formed either by hyphal anastomosis or protoplast fusion. Drug resistance was expressed during heterokaryon formation, even across greater genetic distances than those distances imposed by vegetative compatibility. Phylogenies inferred from different molecular markers were incongruent at a significant level, challenging the clonal origins of Foc. Mating type genes were identified in this asexual pathogen Polymorphisms were detected within a Vegetative Compatibility Group (VCG) suggesting non-clonal inheritance and/or sexual recombination in Foc. This research was funded in part by a NIH-NIGMS (National Institutes of Health-National Institute of General Medical Sciences) Grant through the MBRS (Minority Biomedical Research Support), the Department of Biological Sciences and the Tropical Biology Program at FIU. ^

Genetic individualization of Cannabis sativa by a short tandem repeat multiplex system

Cannabis sativa is the most frequently used of all illicit drugs in the United States. Cannabis has been used throughout history for its stems in the production of hemp fiber, for its seed for oil and food, and for its buds and leaves as a psychoactive drug. Short tandem repeats (STRs), were chosen as molecular markers because of their distinct advantages over other genetic methods. STRs are co-dominant, can be standardized such that reproducibility between laboratories can be easily achieved, have a high discrimination power and can be multiplexed. ^ In this study, six STR markers previously described for Cannabis were multiplexed into one reaction. The multiplex reaction was able to individualize 98 Cannabis samples (14 hemp and 84 marijuana, authenticated as originating from 33 of the 50 United States) and detect 29 alleles averaging 4.8 alleles per loci. The data did not relate the samples from the same state to each other. This is the first study to report a single reaction six-plex and apply it to the analysis of almost 100 Cannabis samples of known geographic collection site. ^

Fatty acids and stable isotopes as indicators of early-life feeding and potential maternal resource dependency in the bull shark Carcharhinus leucas

The degree of reliance of newborn sharks on energy reserves from maternal resource allocation and the timescales over which these animals develop foraging skills are critical factors towards understanding the ecological role of top predators in marine ecosystems. We used muscle tissue stable carbon isotopic composition and fatty acid analysis of bull sharks Carcharhinus leucas to investigate early-life feeding ecology in conjunction with maternal resource dependency. Values of δ13C of some young-of-the-year sharks were highly enriched, reflecting inputs from the marine-based diet and foraging locations of their mothers. This group of sharks also contained high levels of the 20:3ω9 fatty acid, which accumulates during periods of essential fatty acid deficiency, suggesting inadequate or undeveloped foraging skills and possible reliance on maternal provisioning. A loss of maternal signal in δ13C values occurred at a length of approximately 100 cm, with muscle tissue δ13C values reflecting a transition from more freshwater/estuarine-based diets to marine-based diets with increasing length. Similarly, fatty acids from sharks >100 cm indicated no signs of essential fatty acid deficiency, implying adequate foraging. By combining stable carbon isotopes and fatty acids, our results provided important constraints on the timing of the loss of maternal isotopic signal and the development of foraging skills in relation to shark size and imply that molecular markers such as fatty acids are useful for the determination of maternal resource dependency.

Repetitive DNA fragments as taxonomic markers for {\it Penaeus\/} sibling taxa (Decapoda: Dendrobranchiata: Penaeidae) from the southern terminus of the Florida peninsula, U.S.A.

Sympatric populations of P. brasiliensis and P. duorarum from Biscayne Bay, Florida, revealed species-specific satellite DNA organizational patterns with the restriction endonuclease EcoRI. The species-specific satellite DNA patterns can be explained as resulting from differential amplification/deletion events having altered monomer arrays after the divergence of these two species. Two discontinuous populations of P. duorarum (Biscayne Bay and Dry Tortugas) were found to exhibit distinct EcoRI satellite fragment patterns; BamHI repetitive fragments specific to the Dry Tortugas P. duorarum population were also detected. In addition, the evolutionary conservation of the Penaeus (Farfantepenaeus) satellites was investigated. The putative conservation of sequences related to one cloned P. duorarum satellite monomer unit suggests that the FTR satellite DNA family may not only be of use as a genome tag to distinguish between sibling and cryptic Penaeus species but may also serve as a probe to better understand decapod crustacean genome organization and evolution. ^

Molecular phylogenetics of the palm tribe Geonomeae, and differentiation of Geonoma macrostachys western Amazonian varieties

Phylogenetic analyses were performed on six genera and 46 species of the Neotropical palm tribe Geonomeae. The analyses were based on two low copy nuclear DNA sequences from the genes encoding phosphoribulokinase and RNA polymerase II. The basal node of the tribe was polytomous. Pholidostachys formed a monophyletic group. The currently accepted genera Calyptronoma and Calyptrogyne formed a well-supported clade with Calyptronoma resolved as paraphyletic to Calyptrogyne. Geonoma formed a strongly supported monophyletic group consisting of two main clades. ^ An evaluation of the genetic distinctness between Geonoma macrostachys varieties at a local and regional scale using inter-simple sequence repeat (ISSR) markers was performed. Clustering, ordination, and AMOVA suggested a lack of genetic distinctness between varieties at the regional level. A hierarchical AMOVA revealed that the genetic diversity mainly lies among the four localities sampled. A significant genetic differentiation between sympatric varieties occurred in one locality only. The current taxonomy of G. macrostachys, which recognizes only one species, was therefore supported. ^ The preferred habitat of sympatric G. macrostachys varieties with respect to edaphic, topographic, and light factors in three Peruvian lowland forests was studied. The two varieties were mostly encountered in different physiographically defined habitats, with variety acaulis occurring more often in floodplain forest and variety macrostachys in the tierra firme. Comparison of means tests revealed that nine to eleven of the 16 environmental variables were significantly different between varieties. Edaphic factors, mainly soil texture and K content, were better contributors than light conditions to distinguish the habitats occupied by the two varieties in all three study sites. It is concluded that habitat differentiation plays a role in the coexistence of these closely related species taxa. ^

A molecular and stable isotopic approach to investigate the importance of algal and detrital energy pathways in a freshwater marsh

The relative importance of algal and detrital energy pathways remains a central question in wetlands ecology. We used bulk stable isotope analysis and fatty acid composition to investigate the relative contributions of periphyton (algae) and floc (detritus) in a freshwater wetland with the goal of determining the inputs of these resource pools to lower trophic-level consumers. All animal samples revealed fatty acid markers indicative of both microbial (detrital) and algal origins, though the relative contributions varied among species. Vascular plant markers were in low abundance in most consumers. Detritivory is important for chironomids and amphipods, as demonstrated by the enhanced bacterial fatty acids present in both consumers, while algal resources, in the form of periphyton, likely support ephemeropteran larvae. Invertebrates such as amphipods and grass shrimp appear to be important resources for small omnivorous fish, while Poecilia latipinna appear to strongly use periphyton and Ephemeroptera larvae as food sources. Both P. latipinna and Lepomis spp. assimilated small amounts of vascular plant debris, possibly due to unintentional ingestion of floc while foraging for invertebrates and insect larvae. Physid snails, Haitia spp., were characterized by considerably different fatty acid compositions than other taxa examined, and likely play a unique role in Everglades’ food webs.