Lydia Smith

Population-Based Resequencing Reveals That the Flowering Time Adaptation of Cultivated Barley Originated East of the Fertile Crescent

Gene resequencing and association analysis present new opportunities to study the evolution of adaptive traits in crop plants. Here we apply these tools to an extensive set of barley accessions to identify a component of the molecular basis of the flowering time adaptation, a trait critical to plant survival. Using an association-based study to relate variation in flowering time to sequence-based polymorphisms in the Ppd-H1 gene, we identify a causative polymorphism (SNP48) that accounts for the observed variation in barley flowering time. This polymorphism also shows latitude-dependent geographical distribution, consistent with the expected clinal variation in phenotype with the nonresponsive form predominating in the north. Networks, genealogies, and phylogenetic trees drawn for the Ppd-H1 haplotypes reveal population structure both in wild barley and in domesticated barley landraces. The spatial distribution of these population groups indicates that phylogeographical analysis of European landraces can provide information relevant to the Neolithic spread of barley cultivation and also has implications for the origins of domesticated barley, including those with the nonresponsive ppd-H1 phenotype. Haplotypes containing the nonresponsive version of SNP48 are present in wild barley accessions, indicating that the nonresponsive phenotype of European landraces originated in wild barley. The wild accessions whose nonresponsive haplotypes are most closely similar to those of landraces are found in Iran, within a region suggested as an area for domestication of barley east of the Fertile Crescent but which has previously been thought to have contributed relatively little to the diversity of European cultivars.

Sainfoin (Onobrychis viciifolia): A beneficial forage legume

The Onobrychis genus comprises a few agronomically important forage legume species, with sainfoin ( Onobrychis viciifolia ) being the most widespread. O. viciifolia has a long history of traditional culture worldwide, but its use has declined in western countries over the last decades. It suffers from low productivity and is more difficult to maintain than other legumes but is known to have valuable characteristics such as palatability and drought tolerance. Recent studies suggest that it has several other highly beneficial properties due to its unique tannin and polyphenol composition. Condensed tannins present in Onobrychis species have been shown to confer anthelmintic properties, increase protein utilization and prevent bloating; they may also have the potential to reduce greenhouse gas emissions. Positive effects on wildlife and honey production could also be advantageous in the context of sustainable farming. Modern breeding programmes have not been a priority, leading to a lack of genetic knowledge in comparison to extensively used forage legumes. It is expected that potential for O. viciifolia improvements could be achieved by rigorous characterization of the available germplasm and utilization of characters derived from close relatives of the genus. Breeding priorities for the future would include enhanced germination and improved early establishment, allied to the best anthelmintic properties observed in some varieties.

Enhancement of artemisinin concentration and yield in response to optimization of nitrogen and potassium supply to Artemisia annua

BACKGROUND AND AIMS The resurgence of malaria, particularly in the developing world, is considerable and exacerbated by the development of single-gene multi-drug resistances to chemicals such as chloroquinone. Drug therapies, as recommended by the World Health Organization, now include the use of antimalarial compounds derived from Artemisia annua--in particular, the use of artemisinin-based ingredients. Despite our limited knowledge of its mode of action or biosynthesis there is a need to secure a supply and enhance yields of artemisinin. The present study aims to determine how plant biomass can be enhanced while maximizing artemisinin concentration by understanding the plants nutritional requirements for nitrogen and potassium. METHODS Experiments were carried out, the first with differing concentrations of nitrogen, at 6, 31, 56, 106, 206 or 306 mg L(-1) being applied, while the other differing in potassium concentration (51, 153 or 301 mg L(-1)). Nutrients were supplied in irrigation water to plants in pots and after a growth period biomass production and leaf artemisinin concentration were measured. These data were used to determine optimal nutrient requirements for artemisinin yield. KEY RESULTS Nitrogen nutrition enhanced plant nitrogen concentration and biomass production successively up to 106 mg N L(-1) for biomass and 206 mg N L(-1) for leaf nitrogen; further increases in nitrogen had no influence. Artemisinin concentration in dried leaf material, measured by HPLC mass spectroscopy, was maximal at a nitrogen application of 106 mg L(-1), but declined at higher concentrations. Increasing potassium application from 51 to 153 mg L(-1) increased total plant biomass, but not at higher applications. Potassium application enhanced leaf potassium concentration, but there was no effect on leaf artemisinin concentration or leaf artemisinin yield. CONCLUSIONS Artemisinin concentration declined beyond an optimal point with increasing plant nitrogen concentration. Maximization of artemisinin yield (amount per plant) requires optimization of plant biomass via control of nitrogen nutrition.

Approaches and constraints of using existing landrace and extant plant material to understand agricultural spread in prehistory

The potential for the phylogeographical analysis of cereal landraces to determine the initial patterns of agricultural spread through Europe is discussed in relation to two of the first cereals to be domesticated, emmer wheat (Triticum turgidum subsp. dicoccum) and barley (Hordeum vulgare). Extant landraces available from germplasm collections have a patchy distribution, largely being confined to regions of rugged upland topography, and the phylogeographical patterns observed may be due to ‘overstamping’ by more recent crop movements. Phylogeographical studies of non-viable historical landrace material held in herbarium and old seed collections and found in historical buildings have the potential to fill in the gaps in time and space. We explore the importance of precise geographical provenance and the limitations of this in extant and historical material. Additionally, we consider the effect of various chemicals and the preservation of DNA in the historical material.

In vitro effects of extracts and purified tannins of sainfoin (Onobrychis viciifolia) against two cattle nematodes.

Sainfoin (Onobrychis viciifolia) is a condensed tannin (CT)-containing legume and has anthelmintic potential against gastrointestinal nematodes of ruminants. This study investigated in vitro effects of acetone/water extracts and derived CT fractions from different types of sainfoin (i.e. accessions) against larvae of Cooperia oncophora and Ostertagia ostertagi by applying the larval feeding inhibition assay (LFIA). Seven sainfoin accessions were extracted and tested with L1 larvae at 10 and 40 μg extract/ml. In addition, CT in extracts from 4 accessions were fractionated according to polymer size and tested by LFIA at two concentrations (2 and 10 μg CT fraction/ml). All sainfoin extracts caused significant inhibition of L1-feeding of both C. oncophora and O. ostertagi with varying intensity compared to the control (phosphate buffered saline). For both nematode species the in vitro effect was positively correlated with CT content in the extracts, but not with any of the structural CT parameters. In contrast, the 16 CT fractions revealed significant correlations between in vitro effect and CT content, polymer size (mean degree of polymerisation, mDP) and monomeric composition (prodelphinidin percentage, % PD). These differences between crude extracts and purified fractions may stem from the fact that extracts contain complex CT mixtures, which may mask and thus suppress CT structural effects. This study provides the first indication that, apart from CT and % PD content, polymer size also contributes to anthelmintic activity of CTs. The results, therefore, suggest that the inter-accession variability in CT content and composition needs to be taken into account in future plant breeding programmes which seek to enhance the anthelmintic properties of sainfoin.

Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces

BackgroundUnderstanding the evolution of cultivated barley is important for two reasons. First, the evolutionary relationships between different landraces might provide information on the spread and subsequent development of barley cultivation, including the adaptation of the crop to new environments and its response to human selection. Second, evolutionary information would enable landraces with similar traits but different genetic backgrounds to be identified, providing alternative strategies for the introduction of these traits into modern germplasm.ResultsThe evolutionary relationships between 651 barley landraces were inferred from the genotypes for 24 microsatellites. The landraces could be divided into nine populations, each with a different geographical distribution. Comparisons with ear row number, caryopsis structure, seasonal growth habit and flowering time revealed a degree of association between population structure and phenotype, and analysis of climate variables indicated that the landraces are adapted, at least to some extent, to their environment. Human selection and/or environmental adaptation may therefore have played a role in the origin and/or maintenance of one or more of the barley landrace populations. There was also evidence that at least some of the population structure derived from geographical partitioning set up during the initial spread of barley cultivation into Europe, or reflected the later introduction of novel varieties. In particular, three closely-related populations were made up almost entirely of plants with the daylength nonresponsive version of the photoperiod response gene PPD-H1, conferring adaptation to the long annual growth season of northern Europe. These three populations probably originated in the eastern Fertile Crescent and entered Europe after the initial spread of agriculture.ConclusionsThe discovery of population structure, combined with knowledge of associated phenotypes and environmental adaptations, enables a rational approach to identification of landraces that might be used as sources of germplasm for breeding programs. The population structure also enables hypotheses concerning the prehistoric spread and development of agriculture to be addressed.

Polyphenol metabolism provides a screening tool for beneficial effects of Onobrychis viciifolia (sainfoin)

Onobrychis viciifolia (sainfoin) is a traditional fodder legume showing multiple benefits for the environment, animal health and productivity but weaker agronomic performance in comparison to other legumes. Benefits can be mainly ascribed to the presence of polyphenols. The polyphenol metabolism in O. viciifolia was studied at the level of gene expression, enzyme activity, polyphenol accumulation and antioxidant activity. A screening of 37 accessions regarding each of these characters showed a huge variability between individual samples. Principal component analysis revealed that flavonols and flavan 3-ols are the most relevant variables for discrimination of the accessions. The determination of the activities of dihydroflavonol 4-reductase and flavonol synthase provides a suitable screening tool for the estimation of the ratio of flavonols to flavan 3-ols and can be used for the selection of samples from those varieties that have a specific optimal ratio of these compounds for further breeding.

Phylogenetic characterisation of Onobrychis species with special focus on the forage crop Onobrychis viciifolia Scop.

Sainfoin (Onobrychis viciifolia Scop.) is a perennial forage legume that possesses beneficial properties in the context of sustainable agriculture. In order to initiate a pre-breeding programme, we have assembled a germplasm collection of O. viciifolia from many geographic regions, as well as a collection of Onobrychis species that might be crossed with O. viciifolia to improve its biological and agronomic properties. The objective of this study was to obtain DNA sequences from a representative sample of these accessions in order to characterise their genetic diversity and to assess the robustness of the Onobrychis taxonomy. Because of potential problems with copurification of tannins and polyphenols from Onobrychis leaf tissue, three methods for DNA extraction were assessed and the most appropriate one identified. DNA sequences were obtained for the nuclear internal transcribed spacer region and the trnH-psbA and trnT-trnL intergenic spacers of the chloroplast genome. Neighbour joining trees were constructed and accessions were assigned to operational taxonomic units. The results indicated that there is substantial genetic diversity among Onobrychis species. Redundancies in species nomenclature were identified, as well as possible overlap between some of the sections into which the Onobrychis genus has been divided. A genetic distinction was apparent between O. viciifolia accessions from western Europe and those from eastern Europe and Asia, reflecting a similar division based on agronomic properties. Recognition of these different though related germplasms will be valuable in the design of breeding programmes for the rational improvement of sainfoin as a forage crop for sustainable agriculture.

DNA evidence for multiple introductions of barley into Europe following dispersed domestications in Western Asia

It has long been recognised that the Neolithic spread across Europe via two separate routes, one along the Mediterranean coasts, the other following the axis of the major rivers. But did these two streams have a common point of origin in south-west Asia, at least with regard to the principal plant and animals species that were involved? This study of barley DNA shows that the domesticated barley grown in Neolithic Europe falls into three separate types (groups A, B and C), each of which may have had a separate centre of origin in south-west Asia. Barley was relatively rarely cultivated by the early Linearbandkeramik farmers of Central and Northern Europe, but became more common during the fifth and fourth millennia BC. The analysis reported here indicates that a genetic variety of barley more suitable for northern growing conditions was introduced from south-west Asia at this period. It also suggests that the barley grown in south-eastern Europe at the very beginning of the Neolithic may have arrived there by different routes from two separate centres of domestication in south-west Asia. The multiple domestications that this pattern reveals imply that domestication may have been more a co-evolutionary process between plants and people than an intentional human action.

Screening a diverse collection of Artemisia annua germplasm accessions for the antimalarial compound, artemisinin

The anti-malarial drug artemisinin is commercially extracted from the medicinal plant Artemisia annua (L.). Here we report the screening of seventy A. annua individuals sourced from around the world, identifying individuals containing > 2% artemisinin, concentrations approximately twice as high as have been previously reported. These extremely high yielding individuals have been maintained as propagational clones, and represent promising parental lines for future A. annua breeding programmes.