Measuring variation in potato roots in both field and glasshouse: the search for useful yield predictors and a simple screen for root traits

Aims Potatoes have an inadequate rooting system for efficient acquisition of water and minerals and use disproportionate amounts of irrigation and fertilizer. This research determines whether significant variation in rooting characteristics of potato exists, which characters correlate with final yield and whether a simple screen for rooting traits could be developed. Methods Twenty-eight genotypes of Solanum tuberosum groups Tuberosum and Phureja were grown in the field; eight replicate blocks to final harvest, while entire root systems were excavated from four blocks. Root classes were categorised and measured. The same measurements were made on these genotypes in the glasshouse, 2 weeks post emergence. Results In the field, total root length varied from 40 m to 112 m per plant. Final yield was correlated negatively with basal root specific root length and weakly but positively with total root weight. Solanum tuberosum group Phureja genotypes had more numerous roots and proportionally more basal than stolon roots compared with Solanum tuberosum, group Tuberosum genotypes. There were significant correlations between glasshouse and field measurements. Conclusions Our data demonstrate that variability in rooting traits amongst commercially available potato genotypes exists and a robust glasshouse screen has been developed. By measuring potato roots as described in this study, it is now possible to assess rooting traits of large populations of potato genotypes.

Assessing the spatial and temporal variation in the skill of precipitation forecasts from an NWP model

It is becoming increasingly important to be able to verify the spatial accuracy of precipitation forecasts, especially with the advent of high-resolution numerical weather prediction (NWP) models. In this article, the fractions skill score (FSS) approach has been used to perform a scale-selective evaluation of precipitation forecasts during 2003 from the Met Office mesoscale model (12 km grid length). The investigation shows how skill varies with spatial scale, the scales over which the data assimilation (DA) adds most skill, and how the loss of that skill is dependent on both the spatial scale and the rainfall coverage being examined. Although these results come from a specific model, they demonstrate how this verification approach can provide a quantitative assessment of the spatial behaviour of new finer-resolution models and DA techniques.

Pharmacometabonomic characterization of xenobiotic and endogenous metabolic phenotypes that account for inter-individual variation in isoniazid-induced toxicological response

An NMR-based pharmacometabonomic approach was applied to investigate inter-animal variation in response to isoniazid (INH; 200 and 400 mg/kg) in male Sprague-Dawley rats, alongside complementary clinical chemistry and histopathological analysis. Marked inter-animal variability in central nervous system (CNS) toxicity was identified following administration of a high dose of INH, which enabled characterization of CNS responders and CNS non-responders. High-resolution post-dose urinary (1)H NMR spectra were modeled both by their xenobiotic and endogenous metabolic information sets, enabling simultaneous identification of the differential metabolic fate of INH and its associated endogenous metabolic consequences in CNS responders and CNS non-responders. A characteristic xenobiotic metabolic profile was observed for CNS responders, which revealed higher urinary levels of pyruvate isonicotinylhydrazone and β-glucosyl isonicotinylhydrazide and lower levels of acetylisoniazid compared to CNS non-responders. This suggested that the capacity for acetylation of INH was lower in CNS responders, leading to increased metabolism via conjugation with pyruvate and glucose. In addition, the endogenous metabolic profile of CNS responders revealed higher urinary levels of lactate and glucose, in comparison to CNS non-responders. Pharmacometabonomic analysis of the pre-dose (1)H NMR urinary spectra identified a metabolic signature that correlated with the development of INH-induced adverse CNS effects and may represent a means of predicting adverse events and acetylation capacity when challenged with high dose INH. Given the widespread use of INH for the treatment of tuberculosis, this pharmacometabonomic screening approach may have translational potential for patient stratification to minimize adverse events.

Seasonal variation in the fatty acid composition of milk available at retail in the United Kingdom and implications for dietary intake

Milk and dairy products are major sources of fat in the human diet, but there are few detailed reports on the fatty acid composition of retail milk, trans fatty acids in particular, and how these change throughout the year. Semi-skimmed milk was collected monthly for one year from five supermarkets and analysed for fatty acid composition. Relative to winter, milk sold in the summer contained lower total saturated fatty acid (SFA; 67 vs 72 g/100 g fatty acids) and higher cis-monounsaturated fatty acid (MUFA; 23 vs 21 g/100 g fatty acids) and total trans fatty acid (6.5 vs 4.5 g/100 g fatty acids) concentrations. Concentrations of most trans-18:1 and -18:2 isomers also exhibited seasonal variation. Results were applied to national dietary intakes, and indicated that monthly variation in the fatty acid composition of milk available at retail has limited influence on total dietary fatty acid consumption by UK adults.

Some numerical experiments on the effect of the variation of static stability in two-layer quasi-geostrophic models

A method to solve a quasi-geostrophic two-layer model including the variation of static stability is presented. The divergent part of the wind is incorporated by means of an iterative procedure. The procedure is rather fast and the time of computation is only 60–70% longer than for the usual two-layer model. The method of solution is justified by the conservation of the difference between the gross static stability and the kinetic energy. To eliminate the side-boundary conditions the experiments have been performed on a zonal channel model. The investigation falls mainly into three parts: The first part (section 5) contains a discussion of the significance of some physically inconsistent approximations. It is shown that physical inconsistencies are rather serious and for these inconsistent models which were studied the total kinetic energy increased faster than the gross static stability. In the next part (section 6) we are studying the effect of a Jacobian difference operator which conserves the total kinetic energy. The use of this operator in two-layer models will give a slight improvement but probably does not have any practical use in short periodic forecasts. It is also shown that the energy-conservative operator will change the wave-speed in an erroneous way if the wave-number or the grid-length is large in the meridional direction. In the final part (section 7) we investigate the behaviour of baroclinic waves for some different initial states and for two energy-consistent models, one with constant and one with variable static stability. According to the linear theory the waves adjust rather rapidly in such a way that the temperature wave will lag behind the pressure wave independent of the initial configuration. Thus, both models give rise to a baroclinic development even if the initial state is quasi-barotropic. The effect of the variation of static stability is very small, qualitative differences in the development are only observed during the first 12 hours. For an amplifying wave we will get a stabilization over the troughs and an instabilization over the ridges.

Variation in root-associated phosphatase activities in wheat contributes to the utilization of organic P substrates in vitro, but does not explain differences in the P-nutrition of plants when grown in soils

To understand whether genotypic variation in root-associated phosphatase activities in wheat impacts on its ability to acquire phosphorus (P), various phosphatase activities of roots were measured in relation to the utilization of organic P substrates in agar, and the P-nutrition of plants was investigated in a range of soils. Root-associated phosphatase activities of plants grown in hydroponics were measured against different organic P substrates. Representative genotypes were then grown in both agar culture and in soils with differing organic P contents and plant biomass and P uptake were determined. Differences in the activities of both root-associated and exuded phosphodiesterase and phosphomonoesterase were observed, and were related to the P content of plants supplied with either ribonucleic acid or glucose 6-phosphate, respectively, as the sole form of P. When the cereal lines were grown in different soils, however, there was little relationship between any root-associated phosphatase activity and plant P uptake. This indicates that despite differences in phosphatase activities of cereal roots, such variability appears to play no significant role in the P-nutrition of the plant grown in soil, and that any benefit derived from the hydrolysis of soil organic P is common to all genotypes.

Genetic variation at flowering time loci in wild and cultivated barley

The worldwide spread of barley cultivation required adaptation to agricultural environments far distant from those found in its centre of domestication. An important component of this adaptation is the timing of flowering, achieved predominantly in response to day length and temperature. Here, we use a collection of cultivars, landraces and wild barley accessions to investigate the origins and distribution of allelic diversity at four major flowering time loci, mutations at which have been under selection during the spread of barley cultivation into Europe. Our findings suggest that while mutant alleles at the PPD-H1 and PPD-H2 photoperiod loci occurred pre-domestication, the mutant vernalization non-responsive alleles utilized in landraces and cultivars at the VRN-H1 and VRN-H2 loci occurred post-domestication. The transition from wild to cultivated barley is associated with a doubling in the number of observed multi-locus flowering-time haplotypes, suggesting that the resulting phenotypic variation has aided adaptation to cultivation in the diverse ecogeographic locations encountered. Despite the importance of early-flowering alleles during the domestication of barley in Europe, we show that novel VRN alleles associated with early flowering in wild barley have been lost in domesticates, highlighting the potential of wild germplasm as a source of novel allelic variation for agronomic traits.

Variation in genome organization of the plant pathogenic fungus Colletotrichum lindemuthianum

The genome structure of Colletotrichum lindemuthianum in a set of diverse isolates was investigated using a combination of physical and molecular approaches. Flow cytometric measurement of genome size revealed significant variation between strains, with the smallest genome representing 59% of the largest. Southern-blot profiles of a cloned fungal telomere revealed a total chromosome number varying from 9 to 12. Chromosome separations using pulsed-field gel electrophoresis (PFGE) showed that these chromosomes belong to two distinct size classes: a variable number of small (< 2.5 Mb) polymorphic chromosomes and a set of unresolved chromosomes larger than 7 Mb. Two dispersed repeat elements were shown to cluster on distinct polymorphic minichromosomes. Single-copy flanking sequences from these repeat-containing clones specifically marked distinct small chromosomes. These markers were absent in some strains, indicating that part of the observed variability in genome organization may be explained by the presence or absence, in a given strain, of dispensable genomic regions and/or chromosomes.

Exploring variation in proanthocyanidin composition and content of sainfoin (Onobrychis viciifolia)

To maximise the potential benefits to ruminants from sainfoin, plant breeding should focus on developing varieties with predictable condensed tannin (CT) profiles. Little is known about whether and to what extent accession and environment influence sainfoin CT structures. We sought to investigate the likely extent of accession and environment effects on CT characteristics of sainfoin. Four single-flowering (Communis) accessions and two multiple-flowering (Bifera) accessions, grown at three sites and collected at two harvest times were used. Sainfoin CTs were characterised by thiolytic degradation and by high-performance liquid chromatography-gel permeation chromatography (HPLC-GPC). Also, CT concentration measured earlier by the HCl-butanol method was compared with that from thiolysis

Variation, asymmetry and working memory in the process of second language acquisition

Calls for understanding the interface between L2 linguistic knowledge and development (Gregg 1996; Carroll 2001; Towell 2003) provide a context for analysing the role of memory (Paradis 2004), specifically working memory (Baddeley 1986, 2003) in L2 development. Miyake and Friedman (1998) have claimed that Working Memory (WM) may be the key to L2 acquisition, especially in explaining individual variation in L2 acquisition. Recent findings found a robust connection between greater working memory (WM) capacity and rapid, successful acquisition of L2 vocabulary, reading and oral fluency (Service 1992; Harrington and Sawyer 1992; Fortkamp 1999). This study adds to the growing body of research by investigating correlations between WM and variation in grammatical development, focusing on asymmetries in processing L2 English wh-constructions in an immersion setting.

Variation in the shoot calcium content of angiosperms

This study describes the variation in the mean relative shoot Ca content within the angiosperms at the ordinal level. Data were derived from studies in the literature in which the shoot Ca content of two or more species had been compared, and from a hydroponic experiment in which plants were selected to represent the relative number of species within each angiosperm order. Across all angiosperms, most of the variation in shoot Ca content occurred at and above the level of the order. Relative shoot Ca contents and variances correlated between literature and experimental data. In general, orders of commelinoid monocots had lower Ca contents than other monocot or eudicot orders. These results are used to illustrate how physiological and ecological hypotheses can be formulated using literature data.

Phylogenetic variation in the shoot mineral concentration of angiosperms

The calcium (Ca) concentration of plant shoot tissues varies systematically between angiosperm orders. The phylogenetic variation in the shoot concentration of other mineral nutrients has not yet been described at an ordinal level. The aims of this study were (1) to quantify the shoot mineral concentration of different angiosperm orders, (2) to partition the phylogenetic variation in shoot mineral concentration between and within orders, (3) to determine if the shoot concentration of different minerals are correlated across angiosperm species, and (4) to compare experimental data with published ecological survey data on 81 species sampled from their natural habitats. Species, selected pro rata from different angiosperm orders, were grown in a hydroponic system under a constant external nutrient regime. Shoots of 117 species were sampled during vegetative growth. Significant variation in shoot carbon (C), calcium (Ca), potassium (K), and magnesium (Mg) concentration occurred between angiosperm orders. There was no evidence for systematic differences in shoot phosphorus (P) or organic-nitrogen (N) concentration between orders. At a species level, there were strong positive correlations between shoot Ca and Mg concentration, between shoot P and organic-N concentration, and between shoot K concentration and shoot fresh weight:dry weight ratio. Shoot C and cation concentration correlated negatively at a species level. Species within the Poales and the Caryophyllales had distinct shoot mineralogies in both the designed experiment and in the ecological survey.

Natural genetic variation in caesium (Cs) accumulation by Arabidopsis thaliana

Ingestion of caesium (Cs) radioisotopes poses a health risk to humans. Crop varieties that accumulate less Cs in their edible tissues may provide a useful countermeasure. This study was performed to determine whether quantitative genetics on a model plant (Arabidopsis thaliana) might inform such 'safe'-crop strategies. Arabidopsis accessions and recombinant inbred lines (RILs), from Landsberg erecta (Ler) x Cape Verdi Island (Cvi), Ler x Columbia (Col), and Niederzenz (Nd) x Col mapping populations, were grown on agar supplemented with subtoxic levels of Cs. Shoot Cs concentration varied up to three-fold, and shoot f. wt varied up to 25-fold within populations. The heritability of growth and Cs accumulation traits ranged from 0.06 to 0.28. Four quantitative trait loci (QTL) accounted for > 80 of the genetic contribution to the total phenotypic variation in shoot Cs concentration in the Ler x Col population. QTL identified in this study, in particular, QTL co-localizing to the top and bottom regions of Chromosomes I and V in two different mapping populations, are amenable to positional cloning and, through collinearity, may inform selection or breeding strategies for the development of 'safe' crops.

Variation in rice cadmium related to human exposure.

Cereal grains are the dominant source of cadmium in the human diet, with rice being to the fore. Here we explore the effect of geographic, genetic, and processing (milling) factors on rice grain cadmium and rice consumption rates that lead to dietary variance in cadmium intake. From a survey of 12 countries on four continents, cadmium levels in rice grain were the highest in Bangladesh and Sri Lanka, with both these countries also having high per capita rice intakes. For Bangladesh and Sri Lanka, there was high weekly intake of cadmium from rice, leading to intakes deemed unsafe by international and national regulators. While genetic variance, and to a lesser extent milling, provide strategies for reducing cadmium in rice, caution has to be used, as there is environmental regulation as well as genetic regulation of cadmium accumulation within rice grains. For countries that import rice, grain cadmium can be controlled by where that rice is sourced, but for countries with subsistence rice economies that have high levels of cadmium in rice grain, agronomic and breeding strategies are required to lower grain cadmium.

Geographical variation in total and inorganic arsenic content of polished (white) rice

An extensive data set of total arsenic analysis for 901 polished (white) grain samples, originating from 10 countries from 4 continents, was compiled. The samples represented the baseline (i.e., not specifically collected from arsenic contaminated areas), and all were for market sale in major conurbations. Median total arsenic contents of rice varied 7-fold, with Egypt (0.04 mg/kg) and India (0.07 mg/kg) having the lowest arsenic content while the U.S. (0.25 mg/kg) and France (0.28 mg/kg) had the highest content. Global distribution of total arsenic in rice was modeled by weighting each country’s arsenic distribution by that country’s contribution to global production. A subset of 63 samples from Bangladesh, China, India, Italy, and the U.S. was analyzed for arsenic species. The relationship between inorganic arsenic content versus total arsenic content significantly differed among countries, with Bangladesh and India having the steepest slope in linear regression, and the U.S. having the shallowest slope. Using country-specific rice consumption data, daily intake of inorganic arsenic was estimated and the associated internal cancer risk was calculated using the U.S. Environmental Protection Agency (EPA) cancer slope. Median excess internal cancer risks posed by inorganic arsenic ranged 30-fold for the 5 countries examined, being 0.7 per 10,000 for Italians to 22 per 10,000 for Bangladeshis, when a 60 kg person was considered.