Comparative analysis of 343 plastid genomes of Solanum section Petota: Insights into potato diversity,phylogeny, and species discrimination

Common potato (Solanum tuberosum L.) and its wild relatives belong to Solanum section Petota. This section's phylogeny and species delimitation are complicated due to various ploidy levels, high heterozygosity, and frequent interspecific hybridization. Compared to the nuclear genome, the plastid genome is more conserved, has a haploid nature, and has a lower nucleotide substitution rate, providing informative alternative insights into the phylogenetic study of section Petota. Here, we analyzed 343 potato plastid genomes from 53 wild and four cultivated species. The diversity of sequences and genomes was comprehensively analyzed. A total of 24 species were placed in a phylogenetic tree based on genomic data for the first time. Overall, our results not only confirmed most existing clades and species boundaries inferred by nuclear evidence but also provided some distinctive species clade belonging and the maternally inherited evidence supporting the hybrid origin of some species. Furthermore, the divergence times between the major potato clades were estimated. In addition, the species discriminatory power of universal barcodes, nuclear ribosomal DNA, and whole and partial plastid genomes and their combinations were thoroughly evaluated; the plastid genome performed best but had limited discriminatory power for all survey species (40%). Overall, our study provided not only new insights into phylogeny and DNA barcoding of potato but also provided valuable genetic data resources for further systematical research of Petota.     

Stimulation of shoot elongation in Salix pentandra by gibberellin A9; activity appears to be dependent upon hydroxylation to GAl via GA20

Cessation of shoot elongation in seedlings of Salix pentandra L. is induced by short photoperiod. Gibbereliin A₉ (GA₉) applied either to the apical bud or injected into a mature leaf, induced shoot elongation under a short photoperiod of 12 h, and GA₉ could completely substitute for a transfer to a long photoperiod. When [³H]GA₉ or [²H₂]GA₉ was injected into a leaf, no [³H]GA₉ was detected in the elongating apex and only traces of [³H]GA₉ were found in the shoot above the treated leaf. By the use of gas chromatography-mass spectrometry (GC-MS), [²H₂]GA₂₀ was identified as the main metabolite of [²H₂]GA₉ in both the shoot and the treated leaf. In addition, [²H₂]GA₁ and [²H₂]GA₂₉ were also identified as metabolites of [²H₂]GA₉. These results are consistent with the hypothesis that exogenous GA, promotes shoot elongation in Salix through its metabolism to GA₂₀ and GA,.     

Ultrastructural changes associated with June Yellows in strawberry and with leaf yellowing symptoms of viral and genetic origin in Fragaria, Rubus and Ribes

Light and electron microscopy was used to study the ultrastructural effects of June Yellows (JY) in leaves of strawberry. Four cultivars of strawberry, affected to different extents by JY, were compared with healthy (JY-free) cv. Cambridge Favourite and with strawberry infected with strawberry crinkle rhabdovirus, Fragaria vesca infected with strawberry mottle virus (SMotV), raspberry and black currant showing virus-induced yellowing and with strawberry and raspberry showing chaemeric yellow sectors in the leaves. Except for isometric virus-like particles detected in SMotV-infected F. vesca, no virus-like particles or structures of other pathogenic agents were found in any of the tissues examined. Leaf cells of JY-affected strawberry showed severe disruption of chloroplasts and plasmalemma, whorls of membranous vesicles and decreased vacuole size. The extent and severity of these abnormalities increased with increased severity of JY symptoms but, even in leaves with mild JY symptoms, chloroplast abnormalities were obvious. In the most severely affected leaves, the cells lacked discrete vacuoles and extensive hypertrophy was seen in other organelles such as nuclei and mitochondria. Few, if any, ultrastructural abnormalities were observed in virus-infected strawberry or F. vesca, or in chaemeric leaves of strawberry and raspberry. By contrast, in raspberry and black currant with yellowed leaves caused by virus infection, the cells showed enlarged chloroplasts, decreased vacuole size and vesicle formation. However, chloroplast enlargement and disruption in this material seemed due to increased size of starch grains which were largely absent from swollen chloroplasts of JY-affected strawberry. The ultrastructural abnormalities observed in JY-affected strawberry are, therefore, not inconsistent with the possibility that a pathogenic agent may be involved in the condition.     

Episodic exposure to acid and aluminium in soft water: survival and recovery of brown trout,Salmo trutta L.

Yolk-sac fry, swim-up fry and 1–2 yr juveniles of brown trout, Sulmo trutta L., were exposed to episodes of aluminium and low pH, maximum aluminium concentration 12 μmol l⁻¹ (323 μg l⁻¹), minimum pH 4.5, total duration up to 54 h (yolk-sac fry) or up to 78 h (swim-up fry and juveniles), in an artificial soft water medium, [Ca] 20 μmol l⁻¹ (0–8 mg l⁻¹) (nominal baseline: pH 5.6, zero aluminium concentration). Yolk-sac fry mortality was nil or very low. A marked increase in susceptibility, with high mortalities, occurred when the yolk was fully absorbed. Mortality of juveniles exposed to two successive episodes was lower than would have been expected on the basis of comparisons with mortalities in single episodes, and mortality declined as the interval between the two episodes was increased. Disturbance of sodium, potassium or calcium balance or gill damage in surviving yolk-sac fry or juveniles was still evident 5 to 6 days after the end of a single episode.     

CALLING SONG DISPLACEMENT IN A ZONE OF OVERLAP AND HYBRIDIZATION

The ground crickets Allonemobius fasciatus and A. socius meet in a mosaic zone of overlap and hybridization stretching from the East Coast to at least Illinois. To test whether male calling song differences were enhanced in sympatry, we analyzed the songs of crickets from inside and outside the zone of overlap along two transects. No evidence of calling song displacement was found in A. socius males from populations within the zone of overlap. On the other hand, A. fasciatus displayed calling song displacement in three populations. Our results are consistent with the hypothesis that the selective pressure exerted by the challenge from a related species is frequency dependent. While not a conclusive demonstration, the observed shifts in calling song are strongly suggestive of reproductive character displacement.     

Genotype and phenotype associations with drought tolerance in barley tested in North Africa

A review is presented of genetic strategies deployed in a 3-yr project on drought tolerance in barley. Data were collected on genetic, physiological and agronomic traits in non-irrigated and irrigated field trials in Egypt, Morocco and Tunisia. A wide range of barley germplasm (developed from African and European cultivars, adapted landraces and wild barleys) was tested, and positive traits were found in each gene pool. The contrasting environments of the three North African countries had major effects on plant/genotype performance. Genetic effects were also detected, as were genotype × environment interactions. A range of strategies were deployed to investigate the physiology and genetics of quantitative traits associated with field performance. Quantitative trait locus (QTL) analysis was performed using backcross lines, recombinant inbred lines and doubled haploid mapping populations. A detailed genetic map was generated in the Tadmor × (ER/Apm) recombinant inbred lines, an important mapping population specifically developed by ICARDA (Centre for Agricultural Research in Dry Areas) and CIMMYT (International Maize and Wheat Improvement Center) to study drought. Quantitative trait loci (QTLs) for grain yield and other important morphological and physiological traits were also identified in a population of doubled haploids derived from F2BCj plants from a cross between a cultivar and a wild barley accession. Significantly, the wild parental line was found to contribute a number of positive alleles for yield. Effects of major developmental genes could explain many of the responses observed. QTLs were found to cluster around major genes controlling flowering time (sghI), plant stature (sdwI and arie.GP) and ear type (vrsl), and it is highly likely that the associations represent pleiotropic effects. Some QTLs were associated with candidate genes such as dehydrins and rubisco activase. One of the most significant results was the identification and generation of material that out performed the best local standards in the three participating North African countries; the selected lines have now entered local breeding programmes. The strategies adopted provided information on physiological traits, genotypes and genetic markers that could be used for marker-assisted selection. Target QTLs and their associated genetic markers may be deployed in marker assisted selection programmes to match crop phenology to the field environment.     

Effect of salinisation of soil on growth and macro- and micro-nutrient accumulation in seedlings of Acacia catechu (Mimosaceae)

The effects of salinisation of soil on Acacia catechu (Mimosaceae) were studied by means of emergence and growth of seedlings and pattern of mineral accumulation. A mixture of chlorides and sulphates of Na, K, Ca and Mg was added to the soil and salinity was maintained at 4.1, 6.3, 8.2,10.1 and 12.2 dSm⁻¹. A negative relationship between proportion of seed germination and salt concentration was obtained. Seedlings did not emerge when soil salinity exceeded 10.1 dSm⁻¹. Results suggested that this tree species is salt tolerant at the seed germination stage. Seedlings survived and grew up to soil salinity of 10.1 dSm⁻¹, which suggests that this species is salt tolerant at the seedling stage too. Elongation of stem and root was retarded by increasing salt stress. Among the tissues, young roots and stem were most tolerant to salt stress and were followed by old roots and leaves, successively. Leaf tissue exhibited maximum reduction in dry mass production in response to increasing salt stress. However, production of young roots and death of old roots were found to be continuous and plants apparently use this process as an avoidance mechanism to remove excess ions and delay onset of ion accumulation in this tissue. This phenomenon, designated “fine root turnover”, is of importance to the mechanisms of salt tolerance. Plants accumulated Na in roots and were able to regulate transfer of Na ions to leaves. Stem tissues were a barrier for translocation of Na from root to leaf. Moreover, K was affected in response to salinity; it rapidly decreased in root tissues with increased salinisation. Nitrogen content decreased in all tissues (leaf, stem and root) in response to low water treatment and salinisation of soil. Phosphorus content significantly decreased, while Ca increased in leaves as soil salinity increased. Changes in tissue and whole plant accumulation patterns of the other elements tested, as well as possible mechanisms for avoidance of Na toxicity in this tree species during salinisation, are discussed.     

Factors influencing the effectiveness of an attracticide formulation against the Oriental fruit moth, Grapholita molesta

An attracticide formulation, LastCall?OFM, was tested against the Oriental fruit moth Grapholita molesta (Busck) (Lepidoptera: Tortricidae) in replicated small plot field trials in apple, Malus domestica (Borkhausen), orchards in South‐eastern Pennsylvania, USA. Attracticide treatments were applied using a calibrated hand pump, and treated plots were compared to similar untreated plots. Male moth activity was monitored using virgin female‐baited traps, and the potential for reduction in mating activity was assessed using sentinel virgin females. A comparison of application rates showed that 1500 droplets per ha of the attracticide formulation was as effective as 3000 droplets per ha, and both application rates reduced captures in synthetic pheromone‐baited traps for prolonged periods. Droplets placed either at high or low positions within the canopy significantly reduced trap capture and mating with sentinel females. In addition, the only sentinel females that mated in the treated plots were located in the untreated portion of the tree canopy. Mate finding behaviour was equally disrupted by formulations with and without insecticide. Therefore, under the test conditions, the mechanism by which the attracticide formulation worked was by disruption of male orientation, and not by the removal of males due to insecticide poisoning. Two field cage experiments tested the impact of population density on the competitiveness of the attracticide formulation compared to virgin females. A significant proportion of males were captured in female‐baited traps at the highest female‐to‐droplet ratio tested. Equal proportions of males were captured in attracticide‐baited traps at male moth densities of 10, 20, 40, and 80 males per cage. These results clarify some of the factors influencing the effectiveness and possible mechanisms of an attracticide management tactic against the Oriental fruit moth.     

Summer Epidemics of Apple Scab: The Relationship between Measurements and their Implications for the Development of Predictive Models and Threshold Levels under Different Disease Control Regimes

A 2‐year study on epidemic progress of apple scab was conducted at Randwijk, the Netherlands, in 1998 and 1999. The summer epidemic caused by conidia was studied instead of the well‐described spring season epidemic originating from ascospores. The aim was to investigate relationships between disease measurements, i.e. disease incidence and severity measures of apple scab, and their implications for the development of predictive models and threshold levels. The study characterized good relationships between the measurements on cultivar Jonagold using regression analyses in three disease control regimes (untreated, organic and integrated). For fruit quality prediction, the relationship between fruit incidence (I_f) and leaf incidence (I_l) in the organic control regime was given by I_f = 1.966 + 0.402 × (I_l) (R² = 0.92). As a result of low level of disease in the integrated control regime, shoot incidence (I_s), with higher values than leaf incidence, was better suited for prediction. The relationship was given by I_f = ?0.162 + 0.028 × (I_s) (R² = 0.91). For the integrated control regime, disease threshold levels were constructed for timing of the final fungicide application. If an apple grower wants to keep fruit infection under 1% incidence (harvest scab threshold), the timing of the final fungicide application (action threshold) should correspond to 4% shoot scab incidence at the beginning of August. The results are compared with similar studies and their biological interpretation is discussed.     

Soil-surface carbon dioxide efflux and microbial biomass in relation to tree density 13 years after a stand replacing fire in a lodgepole pine ecosystem

The effects of fire on soil‐surface carbon dioxide (CO₂) efflux, F_S, and microbial biomass carbon, C_mic, were studied in a wildland setting by examining 13‐year‐old postfire stands of lodgepole pine differing in tree density (< 500 to > 500 000 trees ha^?1) in Yellowstone National Park (YNP). In addition, young stands were compared to mature lodgepole pine stands (～110‐year‐old) in order to estimate ecosystem recovery 13 years after a stand replacing fire. Growing season F_S increased with tree density in young stands (1.0 µmol CO₂ m^?2 s^?1 in low‐density stands, 1.8 µmol CO₂ m^?2 s^?1 in moderate‐density stands and 2.1 µmol CO₂ m^?2 s^?1 in high‐density stands) and with stand age (2.7 µmol CO₂ m^?2 s^?1 in mature stands). Microbial biomass carbon in young stands did not differ with tree density and ranged from 0.2 to 0.5 mg C g^?1 dry soil over the growing season; C_mic was significantly greater in mature stands (0.5–0.8 mg C g^?1 dry soil). Soil‐surface CO₂ efflux in young stands was correlated with biotic variables (above‐ground, below‐ground and microbial biomass), but not with abiotic variables (litter and mineral soil C and N content, bulk density and soil texture). Microbial biomass carbon was correlated with below‐ground plant biomass and not with soil carbon and nitrogen, indicating that plant activity controls not only root respiration, but C_mic pools and overall F_S rates as well. These findings support recent studies that have demonstrated the prevailing importance of plants in controlling rates of F_S and suggest that decomposition of older, recalcitrant soil C pools in this ecosystem is relatively unimportant 13 years after a stand replacing fire. Our results also indicate that realistic predictions and modeling of terrestrial C cycling must account for the variability in tree density and stand age that exists across the landscape as a result of natural disturbances.