Data analysis for molecular characterization of plant genetic resources

Characterizations of plant genetic resources based on molecular markers have been increased in the last years. Studies using a broad range of markers applied on hundreds of plant species are the theoretical basis for inferring genetic diversity to propose both breeding and conservation strategies. Despite increased importance of molecular characterization in plant genetic resources, there is scarce information about analysis of this type of data. To fill this gap of information, this review discuss the rationale behind analyses achieved to study genetic relationship among accessions (within and between groups) and to identify accession, and also discuss the adequacy of some analyses and/or parameters for specific purposes. Genetic diversity within groups may be either quantified for the whole group (parameters to choose will depend on type of marker), or quantified and visualized for the relationships among individuals. Quantification parameters will be chosen depending on type of marker, reproduction mode and relatedness of individuals. Visualization is achieved by hierarchical and non-hierarchical methods. Genetic diversity between groups should be quantified either by analysis of molecular variance, or Nei’s parameters, or Wright’s F-statistics. Efficiency of accession identification can be evaluated by maximal probability of identical match by chance and number of resolved genotypes.     

Differential resistance of switchgrass <Emphasis Type="Italic">Panicum virgatum</Emphasis> L. lines to fall armyworms <Emphasis Type="Italic">Spodoptera frugiperda</Emphasis> (J. E. Smith)

Six cultivars of switchgrass Panicum virgatum L., a plant native to North America that has potential as a bioenergy source, were evaluated for resistance to feeding by the fall armyworm Spodoptera frugiperda (J. E. Smith). Although no mortality was noted, seedlings of the cultivar ‘Trailblazer’ and older plants of the cultivar ‘Blackwell’ were among the most resistant to feeding by S. frugiperda. Some field-collected samples from natural habitat were fed upon by S. frugiperda as readily as were the cultivars, while others caused high mortality after 2 days. Enzyme assays indicated relative differences in expression of two peroxidases thought to be involved in insect resistance in maize, but not in two chitinolytic enzymes. Genomic searches based on maize-sequence templates for the aforementioned genes identified homologs in switchgrass. Sequencing of cDNA coding for these genes identified some differences, especially in the cationic peroxidase, which could influence relative activity. These results indicate switchgrass germplasm has varying resistance to fall armyworms which could be a function of gene sequence diversity, as well as of variation in gene expression due to differences in ploidy levels or other factors.     

Color analysis of storage roots from the USDA,ARS sweetpotato (<Emphasis Type="Italic">Ipomoea batatas</Emphasis>) germplasm collection

The United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit in Griffin, GA maintains the United States germplasm collection for Ipomoea spp. (Convolvulaceae). During 2012–2014, 737 sweetpotato, Ipomoea batatas (L.) Lam., plant introductions (PI) were acquired as tissue-culture plantlets and then acclimated to greenhouse conditions at the USDA, ARS, U. S. Vegetable Laboratory (USVL), Charleston, SC. Single plants were transferred to plastic-covered plant beds to produce cuttings for replicated field trials. Storage roots were harvested from 690 PIs grown in the field and 695 PIs grown in pots. Color coordinates were obtained for each PI using a tristimulus colorimeter. Hue angle values (h*) ranged from 8.2° to 88.3° (\( \bar{x} \) = 54.9°) for the periderm (peel or skin) of field-grown storage roots (n = 690 PIs) and ? 9.4° (= 350.6°) to 96.2° (\( \bar{x} \) = 51.3°) for pot-grown roots (n = 695 PIs). The red–green coordinate (a*) ranged from 0.8 to 30.7 (\( \bar{x} \) = 12.8) for the periderm of field-grown roots and ? 2.0 to 44.9 (\( \bar{x} \) = 16.1) for pot-grown roots. The yellow–blue coordinate (b*) ranged from 2.8 to 33.1 (\( \bar{x} \) = 19.4) for the periderm of field-grown roots and ? 7.4 to 38.1 (\( \bar{x} \) = 19.3) for pot-grown roots. Color saturation (chroma, C*) ranged from 13.7 to 35.8 (\( \bar{x} \) = 24.9) for the periderm of field-grown roots and 14.9–45.5 (\( \bar{x} \) = 29.3) for pot-grown roots. Lightness (white–black, L*) ranged from 32.6 to 81.7 (\( \bar{x} \) = 54.6) for the periderm of field-grown roots and 32.1–88.2 (\( \bar{x} \) = 64.0) for pot-grown roots. Hue angles ranged from ? 13.1° (= 346.9°) to 100.9° (\( \bar{x} \) = 80.9°) for the stele (flesh) of field-grown storage roots (n = 672 PIs) and ? 29.9° to 103.5° (\( \bar{x} \) = 81.6°) for pot-grown roots (n = 676 PIs); a* ranged from ? 5.6 to 35.0 (\( \bar{x} \) = 8.0) for the stele of field-grown roots and ? 6.0 to 41.0 (\( \bar{x} \) = 7.6) for pot-grown roots; and b* ranged from ? 7.7 to 56.1 (\( \bar{x} \) = 34.6) for the stele of field-grown roots and ? 12.6 to 56.1 (\( \bar{x} \) = 31.8) for pot-grown roots. C* ranged from 12.7 to 65.8 (\( \bar{x} \) = 37.2) for the stele of field-grown roots and 8.9–65.7 (\( \bar{x} \) = 34.5) for pot-grown roots; and L* ranged from 27.8 to 91.1 (\( \bar{x} \) = 77.7) for the stele of field-grown roots and 28.2–91.9 (\( \bar{x} \) = 80.4) for pot-grown roots. There were significant relationships between stele color (h*) and percent dry matter, with orange stele having a significantly lower % dry matter (\( \bar{x} \) = 25.6%, n = 183) compared with roots with cream/white stele (\( \bar{x} \) = 30.8%, n = 373). There appears to be wide genetic diversity for root color characteristics for the United States sweetpotato germplasm collection.     

Blue honeysuckle (<Emphasis Type="Italic">Lonicera caerulea</Emphasis> L.) vegetative growth cessation and leaf drop phenological adaptation to a temperate climate

Blue honeysuckle (Lonicera caerulea L.) is a northern-adapted crop species with extremely early phenology and cold hardiness. Restricted adaptation to temperate climates is a current limitation to the crop’s mainstream potential for large-scale production. Based on the broad germplasm base at the University of Saskatchewan, vegetative growth cessation and leaf drop phenology were characterized to complement analysis of spring phenological adaptation in a temperate climate. A multi-trial site of three foundation groups and a single-site trial of three improved groups compared with their parental foundation genotypes were conducted in the Fraser Valley, British Columbia, Canada in 2012 and 2013. The current study shows that blue honeysuckle germplasm contains considerable phenological variation that will permit adaptation to temperate climates. It also demonstrates that breeding for improved adaptation is possible using the existing germplasm resources. For Russian germplasm with the earliest phenology, adaptation to northern latitudes and short growing seasons results in early floral initiation, which presents an indirect limitation to production in more southern latitudes due to secondary flowering. Early leaf drop indirectly limits production and is related to poor adaptation to high chill environments. Skew toward later leaf drop in improved groups, produced from hybridization with Japanese and Kuril germplasm with intermediate and late phenologies, respectively, shows that development of better adaptation to southern latitudes can be achieved.     

Electrophoretic variation in seed proteins and interrelationships of species in the genus <Emphasis Type="Italic">Oryza</Emphasis>

Comparative studies of two cultivated and sixteen wild species of the genus Oryza were carried out using one- and two-dimensional gel electrophoresis for variation in their seed proteins for interrelationships of these species. A number of polypeptides in the range of molecular weight 13–110 kDa were seen to vary. Under reducing conditions, polypeptides spread over the regions of mol. wt. 33–40.5, 25–27 and 19–21.5 kDa exhibited maximum variation in their patterns. Two-dimensional gel electrophoresis revealed the occurrence of disulphide-linked glutelin polypeptide pairs of mol. wt. 60, 58, 52 and 25 kDa breaking into a large and a small subunit each in the range of mol. wt. 18–40.5 and 16–25 kDa respectively in Oryza sativa. The number of such polypeptide pairs varied from 2 to 6 in different species and also in O. sativa showed variation in mol. wts. of their constituent subunits. The UPGMA dendrogram revealed that most of the Oryza species occurred in different clusters and subclusters and thus did not share very close relationships. The undisputed and closest relationship observed was that of cultivated rice O. sativa with the O. rufipogon followed by that with O. nivara. The African cultivated O. glaberrima occurring on the nearest branch of the same subcluster, thereby, supporting the phylogenetic of these species suggested in earlier studies. Eight diploid species and seven tetraploid species were included in one part of the dendrogram while the remaining two species with AA genome i.e. O. glumaepatula and O. meridionalis and one with FF i.e. O. brachyantha stood separately from these as scattered in the group of seven tetraploid species with BBCC, CCDD and HHJJ genomes. The tetraploids O. alta, O. latifolia and O. grandiglumis with CCDD genomes which occurred on the farthest part were distantly related with O. sativa. The cyanogen bromide peptide maps and two dimensional gel electrophoresis also supported the closest relationship between O. sativa and O. rufipogon.     

Hydroxyl Radical Generation and Contaminant Removal from Water by the Collapse of Microbubbles Under Different Hydrochemical Conditions

The present study addresses the mechanism of hydroxyl radical (·OH) generation by the collapse of microbubbles in water solution. The influence of gas supply and flow rate, solution pH, and ionic strength on the aeration efficiency, free radical generation, and contaminant removal (take methylene blue as an example) are elucidated. The results showed that the degradation rate of methylene blue by ·OH increased with flow rate as well as in acidic or alkaline solutions compared to that in neutral conditions. ·OH was shown to be produced by the reaction between protons and oxygen radicals generated by the decomposition of O₂ rather than water molecules. A greater concentration of O₂ or H⁺ thus promoted the reaction, resulting in effective removal at a high flow rate or low pH. Nevertheless, there was considerable methylene blue removal at high pH, driven by the production of the dye cation through the dissociation of methylene blue and the high electronegativity of bubbles at high pH, thus enhancing interface adsorption and degradation, as well as by the high ionic strength of the solution helping to generate ultrafine bubbles and maintaining them through ionic shielding. The current work provides useful insights into the application of microbubble as a promising technique.     

Prevalence of Concentrated Flow Paths in Agricultural Fields in Southern Illinois

Literature on prevalence of concentrated flow paths (CPFs) in agricultural fields are limited at field scale with only few studies that address occurrence of CFPs at large geographic extent. This study used high-resolution Light Detection and Ranging (LiDAR) data to identify CFPs in agricultural fields and calculate the percentage of the fields drained by CFPs at a county scale. In 389 agricultural fields across Jackson County, southern Illinois, this study also investigated the association between field characteristics and CFP formation using multiple regression and CART analysis. The mean number of CFPs in a field was 5 with a minimum of 0 and maximum of 17 CFPs. The majority of the CFPs fell under the large category for CFP length and drainage area that corresponds with high mean percent (81%) of field area drained by the CFPs. Further, 85% of the fields had more than 70% of their area drained by CFPs. The multiple regression and CART analysis showed slope as an important factor influencing CFP characteristics such as number of CFPs and CFP length. Both analyses also indicated physical soil properties such as bulk density, soil erodibility factor, saturated hydraulic conductivity, LS factor, organic matter, and percent sand were also predictors of the CFP characteristics. However, these factors explained only 2 to 12% of the variation observed. The significant presence of CFP’s has important implications for water quality since current conservation practices such as riparian buffers were not designed to address concentrated flow from agricultural fields.     

Peroxicoagulation and Solar Peroxicoagulation for Landfill Leachate Treatment Using a Cu–Fe System

Leachates, particularly those from mature landfills, are difficult to treat by biological processes because of their high toxicity and low biodegradability. Therefore, the development of new treatment technology is necessary. The treatment of landfill leachate by peroxicoagulation and solar peroxicoagulation using a batch electrolytic reactor with a Fe cathode and a Cu anode is proposed. The tested operational variables included pH (2.8 and 8.2), current density (11 and 16 mA cm^?2), treatment time (5, 10, 15, 20, 25, and 30 min), and presence of solar ultraviolet (UV) light and were collected using a compound parabolic collector. The optimum conditions were a pH, current density, and treatment time of 2.8, 16 mA cm^?2, and 10 min, respectively. The presence of UV did not have a significant effect. The chemical oxygen demand and biochemical oxygen demand removed were 62.3% and 55.5%, respectively. The results of UV-visible absorption, fluorescence, and Fourier transform infrared spectroscopy measurements confirm the oxidation process.     

Small Area Estimation of Proportions with Constraint for National Resources Inventory Survey

Motivated by the need to produce small area estimates for the National Resources Inventory survey, we develop a spatial hierarchical model based on the generalized Dirichlet distribution to construct small area estimators of compositional proportions in several mutually exclusive and exhaustive landcover categories. At the observation level, the standard design-based estimators of the proportions are assumed to follow the generalized Dirichlet distribution. After proper transformation of the design-based estimators, beta regression is applicable. We consider a logit mixed model for the expectation of the beta distribution, which incorporates covariates through fixed effects and spatial effect through a conditionally autoregressive process. In a design-based evaluation study, the proposed model-based estimators are shown to have smaller root-mean-square error and relative root-mean-square error than design-based estimators and multinomial model-based estimators. Supplementary materials accompanying this paper appear online.