Mitochondrial DNA evolution in the genus Equus

Employing mitochondrial DNA (mtDNA) restriction-endonuclease maps as the basis of comparison, we have investigated the evolutionary affinities of the seven species generally recognized as the genus Equus. Individual species' cleavage maps contained an average of 60 cleavage sites for 16 enzymes, of which 29 were invariant for all species. Based on an average divergence rate of 2%/Myr, the variation between species supports a divergence of extant lineages from a common ancestor approximately 3.9 Myr before the present. Comparisons of cleavage maps between Equus przewalskii (Mongolian wild horse) and E. caballus (domestic horse) yielded estimates of nucleotide sequence divergence ranging from 0.27% to 0.41%. This range was due to intraspecific variation, which was noted only for E. caballus. For pairwise comparisons within this family, estimates of sequence divergence ranged from 0% (E. hemionus onager vs. E. h. kulan) to 7.8% (E. przewalskii vs. E. h. onager). Trees constructed according to the parsimony principle, on the basis of 31 phylogenetically informative restriction sites, indicate that the three extant zebra species represent a monophyletic group with E. grevyi and E. burchelli antiquorum diverging most recently. The phylogenetic relationships of E. africanus and E. hemionus remain enigmatic on the basis of the mtDNA analysis, although a recent divergence is unsupported.      

Cassava leaf harvesting as vegetables; a cause of vulnerability of cassava plant to cassava mosaic disease and eventual yield reduction: Ernte von cassavablättern als gemüse; eine ursache für die anfälligkeit der cassavapflanze für die cassava-mosaikkrankheit und für spätere ertragseinbußen

The consequence of harvesting young leaves of cassava as vegetable on the vulnerability of the crop to cassava mosaic disease (CMD) and on storage root yield was investigated using 30 cassava genotypes planted in IITA fields located in the humid forest (Port Harcourt?:?Onne), forest-savannah transition (Ibadan), southern guinea savannah (Mokwa) and northern guinea savannah (Zaria) agroecologies in Nigeria. Tender apical leaves and shoots of the cassava genotypes were removed from forty plants per cassava genotype with the same number of plants considered as control. Whitefly infestation, disease incidence (DI) and symptom severity (ISS) of the disease were assessed at monthly interval for six months and also at the ninth month after planting (MAP). Yield reduction due to this treatment was calculated as percentage harvest index (HI). Whitefly population fluctuated throughout the period of observation at all locations with higher population obtained generally for treated plants compared to control plants. Sprouting leaves of some treated genotypes were observed with severe mosaic symptoms, while corresponding control showed no mosaic symptoms. Contrarily, no remarkable difference was observed in Zaria between the mean ISS of treated and control cassava genotypes. There was a highly significant difference (P?<?0.01) in DI and ISS among cassava genotypes across all locations. Also, there was a highly significant interaction (P?<?0.01) in symptom severity between location (loc) and genotype, genotype and treatment (trt), loc and trt. Interaction between loc, genotypes and trt with regard to DI was highly significant at 2, 3 and 4 MAP, while with ISS, the interaction was highly significant all through the counting period. There was a positive relationship between DI and ISS on plants of genotypes 96/1039 and ISU. The percentage HI (27.4) of treated plants of genotype 95/0166 in Ibadan was remarkably lower than the value obtained for corresponding control (41.9) plants. Also, sharp distinction in% HI of treated (39.5) and control (43.8) ISU was observed in Onne with their respective ISS values as 3.7 and 3.2. Therefore, harvesting tender apical leaves and shoots of cassava as vegetables should be discouraged as it increases the severity of CMD infection in the regenerating shoots of cassava with attendant storage root yield reduction.     

Biomarkers of toxicity in Clarias gariepinus exposed to sublethal concentrations of polycyclic aromatic hydrocarbons

Physiological, biochemical and histological indices in Clarias gariepinus broodstock, and teratogenic indices in embryos exposed to sublethal concentrations of naphthalene, phenanthrene and pyrene were investigated in 2014 using a static-renewal bioassay protocol. Phenanthrene (1.41 mg l^?1) was the most toxic, followed by pyrene (1.53 mg l^?1) and naphthalene (7.21 mg l^?1), based on 96 h LC50 values. Hepatosomatic indices were significantly higher in naphthalene- and pyrene-treated males compared with solvent controls, whereas fecundity in females was significantly lower by factors of 2.4 (naphthalene), 2.8 (phenanthrene) and 2.4 (pyrene), compared with controls. Catalase levels were lower in female phenanthrene-treated fish compared with controls. Histological alterations observed in PAH-treated fish include oedema, inflammatory cells, epithelial lifting and hyperplasia in the gills, vacuolation, haemosiderin pigments and sinusoidal congestion in the liver, and degenerated zona radiata in the ovary. Teratogenic effects were not observed, as evidenced by the lack of histological alterations in embryos spawned from pre-exposed broodstock. Sex-specific responses and the utility of biomarkers at cellular and individual levels of organisation are therefore demonstrated for holistic evaluations of polycyclic aromatic hydrocarbons in ecotoxicological studies.     

Natural Genetic Variation in Selected Populations of Arabidopsis thaliana Is Associated with Ionomic Differences

Controlling elemental composition is critical for plant growth and development as well as the nutrition of humans who utilize plants for food. Uncovering the genetic architecture underlying mineral ion homeostasis in plants is a critical first step towards understanding the biochemical networks that regulate a plant''s elemental composition (ionome). Natural accessions of Arabidopsis thaliana provide a rich source of genetic diversity that leads to phenotypic differences. We analyzed the concentrations of 17 different elements in 12 A. thaliana accessions and three recombinant inbred line (RIL) populations grown in several different environments using high-throughput inductively coupled plasma- mass spectroscopy (ICP-MS). Significant differences were detected between the accessions for most elements and we identified over a hundred QTLs for elemental accumulation in the RIL populations. Altering the environment the plants were grown in had a strong effect on the correlations between different elements and the QTLs controlling elemental accumulation. All ionomic data presented is publicly available at www.ionomicshub.org.     

Association and Linkage Analysis of Aluminum Tolerance Genes in Maize

Background

Aluminum (Al) toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two important mechanisms for Al tolerance in maize, but little is known about the underlying genetics.

Methodology

An association panel of 282 diverse maize inbred lines and three F₂ linkage populations with approximately 200 individuals each were used to study genetic variation in this complex trait. Al tolerance was measured as net root growth in nutrient solution under Al stress, which exhibited a wide range of variation between lines. Comparative and physiological genomics-based approaches were used to select 21 candidate genes for evaluation by association analysis.

Conclusions

Six candidate genes had significant results from association analysis, but only four were confirmed by linkage analysis as putatively contributing to Al tolerance: Zea mays Alt_SB like (ZmASL), Zea mays aluminum-activated malate transporter2 (ALMT2), S-adenosyl-L-homocysteinase (SAHH), and Malic Enzyme (ME). These four candidate genes are high priority subjects for follow-up biochemical and physiological studies on the mechanisms of Al tolerance in maize. Immediately, elite haplotype-specific molecular markers can be developed for these four genes and used for efficient marker-assisted selection of superior alleles in Al tolerance maize breeding programs.     

Physiological and Genetic Characterization of End-of-Day Far-Red Light Response in Maize Seedlings

Developmental responses associated with end-of-day far-red light (EOD-FR) signaling were investigated in maize (Zea mays subspecies mays) seedlings. A survey of genetically diverse inbreds of temperate and tropical/semitropical origins, together with teosinte (Zea mays subspecies parviglumis) and a modern hybrid, revealed distinct elongation responses. A mesocotyl elongation response to the EOD-FR treatment was largely absent in the tropical/semitropical lines, but both hybrid and temperate inbred responses were of the same magnitude as in teosinte, suggesting that EOD-FR-mediated mesocotyl responses were not lost during the domestication or breeding process. The genetic architecture underlying seedling responses to EOD-FR was investigated using the intermated B73 × Mo17 mapping population. Among the different quantitative trait loci identified, two were consistently detected for elongation and responsiveness under EOD-FR, but none were associated with known light signaling loci. The central role of phytochromes in mediating EOD-FR responses was shown using a phytochromeB1 phytochromeB2 (phyB1 phyB2) mutant series. Unlike the coleoptile and first leaf sheath, EOD-FR-mediated elongation of the mesocotyl appears predominantly controlled by gibberellin. EOD-FR also reduced abscisic acid (ABA) levels in the mesocotyl for both the wild type and phyB1 phyB2 double mutants, suggesting a FR-mediated but PHYB-independent control of ABA accumulation. EOD-FR elongation responses were attenuated in both the wild type and phyB1 phyB2 double mutants when a chilling stress was applied during the dark period, concomitant with an increase in ABA levels. We present a model for the EOD-FR response that integrates light and hormonal control of seedling elongation.Plants utilize a complex network of photoreceptors to monitor the spectral quality, fluence, direction, and duration of light (Smith, 1995). These photosensory pigments include phytochromes that sense red light (R; 580–690 nm) and far-red light (FR; 690–800 nm) and the cryptochromes, phototropins, and zeitlupes for blue light (380–495 nm) and UV-A light (320–380 nm). The light reflected and transmitted by the vegetation creates a canopy characterized by reductions in both the R-to-FR ratio (R:FR) and the photosynthetically active radiation (400–700 nm). This light environment induces adaptive biochemical and morphological responses known as the shade avoidance syndrome (Smith and Whitelam, 1997). These responses can be induced early in development, before canopy closure, through FR reflected from adjacent neighbor plants (Ballare et al., 1990) or from low-lying weeds (Rajcan and Swanton, 2001), which can negatively impact yields in maize (Zea mays subspecies mays; Rajcan et al., 2004), even if only present early in the growing season (Liu et al., 2009).R:FR signals are transduced by the phytochrome family of photoreceptors (Franklin and Whitelam, 2007b). In rice (Oryza sativa) and sorghum (Sorghum bicolor), three genes constitute the phytochrome family: PhytochromeA (PhyA), PhytochromeB (PhyB), and PhytochromeC (PhyC). In maize, an ancient alloploidization has doubled the family size to six: PhyA1, PhyA2, PhyB1, PhyB2, PhyC1, and PhyC2 (Sheehan et al., 2004). Although many similarities are apparent between maize and Arabidopsis (Arabidopsis thaliana) light response, there are significant differences between members of the phytochrome gene family in copy number and selection pressures that have resulted in the divergence of phytochrome signaling networks (Sawers et al., 2005; Sheehan et al., 2007). Thus far, only three phytochrome mutants have been characterized in maize: elongated mesocotyl1 (elm1), phyB1, and phyB2. The elm1 mutant carries a mutation in phytochromobilin synthase, necessary for the biosynthesis of the chromophore common to all phytochromes (Sawers et al., 2004). The mutation severely reduces the total phytochrome pool, but the weak nature of the allele enables a partial responsiveness to R and FR (Markelz et al., 2003). At maturity, elm1 mutants have elongated internodes, pale green leaves, and flower early (Sawers et al., 2002). Mutations at phyB1 and phyB2 also impair light signal transduction. At maturity, both PHYB1 and PHYB2 contribute to plant height, stem diameter, and sheath-internode length, but PHYB2 predominates in the control of flowering (Sheehan et al., 2007). Like the sorghum and rice phyB mutants (Childs et al., 1997; Takano et al., 2005; Kebrom et al., 2010), both elm1 and phyB1 phyB2 double mutants constitutively display several traits associated with low R:FR response (Sawers et al., 2002; Markelz et al., 2003; Sheehan et al., 2007).In Arabidopsis, R/FR-mediated responses are developmentally complex and involve the PIF proteins (Duek and Fankhauser, 2005) and many hormones including auxins (Tao et al., 2008), ethylene (Khanna et al., 2007), jasmonate (Moreno et al., 2009), and GA (Djakovic-Petrovic et al., 2007). In particular, there is a direct interaction between PIF and DELLA proteins that govern phytochrome-mediated elongation (de Lucas et al., 2008; Feng et al., 2008; Lorrain et al., 2008). DELLA proteins also regulate FR inhibition of germination by abscisic acid (ABA; Piskurewicz et al., 2009), suggesting an interaction between the PIFs and ABA signaling. Complex cross talk between light and temperature has also been reported (Franklin, 2009). In Arabidopsis, colder temperatures can repress the early-flowering phenotype of the phyB mutant (Halliday et al., 2003). These studies suggest a complex interplay between light, hormone, and temperature to fine-tune the elongation response.The end-of-day far-red light (EOD-FR) treatment consists of a pulse of FR given at subjective dusk (Kasperbauer, 1971) and triggers a circadian clock-gated response (Salter et al., 2003). EOD-FR treatments result in a minimal pool of active Pfr during the dark period (Fankhauser and Casal, 2004), and plants submitted to daily treatments display similar developmental responses to those elicited by a continuous photoperiod with low R:FR (Smith, 1994). One of the key features that contributed to the discovery of the phytochromes is the photoreversibility of the response (Borthwick et al., 1952). These low-fluence responses (LFRs) are induced or repressed by alternating R and FR treatments (Mancinelli, 1994). The LFR nature of EOD-FR in maize was previously demonstrated in 5-d-old mesocotyl and coleoptile tissues (Gorton and Briggs, 1980). The EOD-FR treatment offers several advantages over growing plants in continuous low R:FR, including exposing plants to relatively brief treatment periods, thus potentially reducing genotype × environment effects. It also facilitates kinetic assays of phytochrome response, as treatments are limited to a single point in the diurnal cycle and can be delivered at any stage in plant development. Finally, as relatively low fluences of light are needed to saturate EOD-FR responses, large populations of seedlings can be screened without the need for large numbers of FR light-emitting diodes (LEDs) or sophisticated light chambers.Here, we have examined EOD-FR-mediated responses in maize and its closest relative, teosinte (Zea mays subspecies parviglumis). A survey of genetically diverse maize and teosinte accessions revealed extensive tissue-specific variations in mesocotyl, coleoptile, and first leaf sheath elongation. EOD-FR responses were greatly attenuated in tropical/semitropical (TS) accessions but present in teosinte, temperate inbreds, and a modern commercial hybrid, suggesting that the EOD-FR response is plastic in Z. mays. To investigate the genetic regulation underlying seedling responses to EOD-FR, we performed a quantitative trait locus (QTL) analysis using the intermated B73 × Mo17 (IBM) recombinant inbred population. We identified several QTLs that regulate mesocotyl and first leaf sheath response to EOD-FR and show that these QTLs mediate tissue-specific responses. The phyB1 phyB2 mutant series was also evaluated, indicating that the two PhyB paralogs are largely redundant in mediating the EOD-FR response. Pharmacological assays revealed a major role for GA in promoting mesocotyl, but not coleoptile or first leaf sheath, elongation in response to EOD-FR treatments. In contrast, EOD-FR reduced mesocotyl ABA levels. A chill treatment (10°C) applied during dark breaks attenuated EOD-FR elongation responses. Based on these observations, we discuss a model that integrates temperature, light, and hormonal inputs in the regulation of mesocotyl elongation.     

The Physiology, Genetics and Molecular Biology of Plant Aluminum Resistance and Toxicity

Aluminum (Al) toxicity is the primary factor limiting crop production on acidic soils (pH values of 5 or below), and because 50% of the world’s potentially arable lands are acidic, Al toxicity is a very important limitation to worldwide crop production. This review examines our current understanding of mechanisms of Al toxicity, as well as the physiological, genetic and molecular basis for Al resistance. Al resistance can be achieved by mechanisms that facilitate Al exclusion from the root apex (Al exclusion) and/or by mechanisms that confer the ability of plants to tolerate Al in the plant symplasm (Al tolerance). Compelling evidence has been presented in the literature for a resistance mechanism based on exclusion of Al due to Al-activated carboxylate release from the growing root tip. More recently, researchers have provided support for an additional Al-resistance mechanism involving internal detoxification of Al with carboxylate ligands (deprotonated organic acids) and the sequestration of the Al-carboxylate complexes in the vacuole. This is a field that is entering a phase of new discovery, as researchers are on the verge of identifying some of the genes that contribute to Al resistance in plants. The identification and characterization of Al resistance genes will not only greatly advance our understanding of Al-resistance mechanisms, but more importantly, will be the source of new molecular resources that researchers will use to develop improved crops better suited for cultivation on acid soils.     

Using Metabolomics To Estimate Unintended Effects in Transgenic Crop Plants: Problems, Promises, and Opportunities

Transgenic crops are widespread in some countries and sectors of the agro-economy, but are also highly contentious. Proponents of transgenic crop improvement often cite the “substantial equivalence” of transgenic crops to the their nontransgenic parents and sibling varieties. Opponents of transgenic crop improvement dismiss the substantial equivalence standard as being without statistical basis and emphasize the possible unintended effects to food quality and composition due to genetic transformation. Systems biology approaches should help consumers, regulators, and other stakeholders make better decisions regarding transgenic crop improvement by characterizing the composition of conventional and transgenically improved crop species and products. In particular, metabolomic profiling via mass spectrometry and nuclear magnetic resonance can make broad and deep assessments of food quality and content. The metabolome observed in a transgenic variety can then be assessed relative to the consumer and regulator accepted phenotypic range observed among conventional varieties. I briefly discuss both targeted (closed architecture) and nontargeted (open architecture) metabolomics with respect to the transgenic crop debate and highlight several challenges to the field. While most experimental examples come from tomato (Solanum lycoperiscum), analytical methods from all of systems biology are discussed.     

<i>Streptomyces</i> PRIO41 as plant growth promoter of jalapeño pepper plants and as biocontrol agent of <i>Fusarium</i>

Chili pepper is one of the main crops of economic importance in Mexico, and Fusarium wilting is a disease that limits its production. In addition, the inappropriate use of agrochemicals in farming activities generate environmental and health problems. Therefore, in this study the effectiveness of Streptomyces sp PRIO41 was evaluated as a (1) biocontrol agent of Fusarium spp and (2) plant growth promoter bacteria. Assays of pathogenicity and virulence of Fusarium spp. in jalapeño pepper seeds, and interactions of these pathogens with Streptomyces PRIO41 were evaluated under two nutritional conditions. In the greenhouse, the effectiveness of Streptomyces sp. PRIO41 was determined as a (1) biocontrol of Fusarium, and (2) plant growth promoter of wilt of pepper plants. The results showed that all fungal isolates caused symptoms in pepper seeds and seedlings with different degrees of virulence. Interactions in vitro showed that Streptomyces showed the most effective range of virulence against Fusarium isolates in the poor medium (37.6%-100%), with fungicidal effects in some cases. In the greenhouse, Streptomyces PRIO41 reduced Fusarium wilting up to a 40%, and positively affected all vegetative growth parameters, particularly plant height, leaf area, root length, and leaf and root dry biomasses. This study showed the potential of Streptomyces PRIO41 as a biocontrol agent of Fusarium spp., and as a biofertilizer of pepper plants.     

Mechanisms of metal resistance in plants: aluminum and heavy metals

Plants have evolved sophisticated mechanisms to deal with toxic levels of metals in the soil. In this paper, an overview of recent progress with regards to understanding fundamental molecular and physiological mechanisms underlying plant resistance to both aluminum (Al) and heavy metals is presented. The discussion of plant Al resistance will focus on recent advances in our understanding of a mechanism based on Al exclusion from the root apex, which is facilitated by Al-activated exudation of organic acid anions. The consideration of heavy metal resistance will focus on research into a metal hyperaccumulating plant species, the Zn/Cd hyperaccumulator, Thlaspi caerulescens, as an example for plant heavy metal research. Based on the specific cases considered in this paper, it appears that quite different strategies are used for Al and heavy metal resistance. For Al, our current understanding of a resistance mechanism based on excluding soil-borne Al from the root apex is presented. For heavy metals, a totally different strategy based on extreme tolerance and metal hyperaccumulation is described for a hyperaccumulator plant species that has evolved on naturally metalliferous soils. The reason these two strategies are the focus of this paper is that, currently, they are the best understood mechanisms of metal resistance in terrestrial plants. However, it is likely that other mechanisms of Al and/or heavy metal resistance are also operating in certain plant species, and there may be common features shared for dealing with Al and heavy resistance. Future research may uncover a number of novel metal resistance mechanisms in plants. Certainly the complex genetics of Al resistance in some crop plant species, such as rice and maize, suggests that a number of presently unidentified mechanisms are part of an overall strategy of metal resistance in crop plants.