Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia

Multilocus digenic linkage disequilibria (LD) and their population structure were investigated in eleven landrace populations of barley (Hordeum vulgare ssp. vulgare L.) in Sardinia, using 134 dominant simple-sequence amplified polymorphism markers. The analysis of molecular variance for these markers indicated that the populations were partially differentiated (F ST = 0.18), and clustered into three geographic areas. Consistent with this population pattern, STRUCTURE analysis allocated individuals from a bulk of all populations into four genetic groups, and these groups also showed geographic patterns. In agreement with other molecular studies in barley, the general level of LD was low (13 % of locus pairs, with P < 0.01) in the bulk of 337 lines, and decayed steeply with map distance between markers. The partitioning of multilocus associations into various components indicated that genetic drift and founder effects played a major role in determining the overall genetic makeup of the diversity in these landrace populations, but that epistatic homogenising or diversifying selection was also present. Notably, the variance of the disequilibrium component was relatively high, which implies caution in the pooling of barley lines for association studies. Finally, we compared the analyses of multilocus structure in barley landrace populations with parallel analyses in both composite crosses of barley on the one hand and in natural populations of wild barley on the other. Neither of these serves as suitable mimics of landraces in barley, which require their own study. Overall, the results suggest that these populations can be exploited for LD mapping if population structure is controlled.

Association mapping of partitioning loci in barley

Background: Association mapping, initially developed in human disease genetics, is now being applied to plant species. The model species Arabidopsis provided some of the first examples of association mapping in plants, identifying previously cloned flowering time genes, despite high population sub-structure. More recently, association genetics has been applied to barley, where breeding activity has resulted in a high degree of population sub-structure. A major genotypic division within barley is that between winter- and spring-sown varieties, which differ in their requirement for vernalization to promote subsequent flowering. To date, all attempts to validate association genetics in barley by identifying major flowering time loci that control vernalization requirement (VRN-H1 and VRN-H2) have failed. Here, we validate the use of association genetics in barley by identifying VRN-H1 and VRN-H2, despite their prominent role in determining population sub-structure. Results: By taking barley as a typical inbreeding crop, and seasonal growth habit as a major partitioning phenotype, we develop an association mapping approach which successfully identifies VRN-H1 and VRN-H2, the underlying loci largely responsible for this agronomic division. We find a combination of Structured Association followed by Genomic Control to correct for population structure and inflation of the test statistic, resolved significant associations only with VRN-H1 and the VRN-H2 candidate genes, as well as two genes closely linked to VRN-H1 (HvCSFs1 and HvPHYC). Conclusion: We show that, after employing appropriate statistical methods to correct for population sub-structure, the genome-wide partitioning effect of allelic status at VRN-H1 and VRN-H2 does not result in the high levels of spurious association expected to occur in highly structured samples. Furthermore, we demonstrate that both VRN-H1 and the candidate VRN-H2 genes can be identified using association mapping. Discrimination between intragenic VRN-H1 markers was achieved, indicating that candidate causative polymorphisms may be discerned and prioritised within a larger set of positive associations. This proof of concept study demonstrates the feasibility of association mapping in barley, even within highly structured populations. A major advantage of this method is that it does not require large numbers of genome-wide markers, and is therefore suitable for fine mapping and candidate gene evaluation, especially in species for which large numbers of genetic markers are either unavailable or too costly.

Statistical methods for examining genetic influences of resistance to anti-epileptic drugs

It is generally accepted that genetics may be an important factor in explaining the variation between patients’ responses to certain drugs. However, identification and confirmation of the responsible genetic variants is proving to be a challenge in many cases. A number of difficulties that maybe encountered in pursuit of these variants, such as non-replication of a true effect, population structure and selection bias, can be mitigated or at least reduced by appropriate statistical methodology. Another major statistical challenge facing pharmacogenetics studies is trying to detect possibly small polygenic effects using large volumes of genetic data, while controlling the number of false positive signals. Here we review statistical design and analysis options available for investigations of genetic resistance to anti-epileptic drugs.

Reduced height (Rht) and photoperiod insensitivity (Ppd) allele associations with establishment and early growth of wheat in contrasting production systems

Near isogenic lines (NILs) varying for genes for reduced height (Rht) and photoperiod insensitivity (Ppd-D1a) in a cv. Mercia background (rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht8c + Ppd-D1a, Rht-D1c, Rht12) were compared at one field site but within contrasting ('organic' vs. 'conventional') rotational and agronomic contexts, in each of 3 years. In the final year, further NILs (rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht-B1b + Rht-D1b, Rht-D1b + Rht-B1c) in both Maris Huntsman and Maris Widgeon backgrounds were added together with 64 lines of a doubled haploid (DH) population [Savannah (Rht-D1b) x Renesansa (Rht-8c + Ppd-D1a)]. Assessments included laboratory tests of germination and coleoptile length, and various field measurements of crop growth between emergence and pre jointing [plant population, tillering, leaf length, ground cover (GC), interception of photosynthetically active radiation (PAR), crop dry matter (DM) and nitrogen accumulation (N), far red: red reflectance ratio (FR:R), crop height, and weed dry matter]. All of the dwarfing alleles except Rht12 in the Mercia background and Rht8c in the DHs were associated with reduced coleoptile length. Most of the dwarfing alleles (depending on background) reduced seed viability. Severe dwarfing alleles (Rht-B1c, Rht-D1c and Rht12) were routinely associated with fewer plant numbers and reduced early crop growth (GC, PAR, DM, N, FR:R), and in 1 year, increased weed DM. In the Mercia background and the DHs the semi-dwarfing allele Rht-D1b was also sometimes associated with reductions in early crop growth; no such negative effects were associated with the marker for Rht8c. When significant interactions between cropping system and genotype did occur it was because differences between lines were more exaggerated in the organic system than in the conventional system. Ppd-D1a was associated positively with plant numbers surviving the winter and early crop growth (GC, FR:R, DM, N, PAR, height), and was the most significant locus in a QTL analysis. We conclude that, within these environmental and system contexts, genes moderating development are likely to be more important in influencing early resource capture than using Rht8c as an alternative semi-dwarfing gene to Rht-D1b.

Biodiversity of Collembola in urban soils and the use of Folsomia candida to assess soil 'quality'

The effects of metal contamination on natural populations of Collembola in soils from five sites in the Wolverhampton area ( West Midlands, England) were examined. Analysis revealed that metal concentrations were elevated above background levels at all sites. One location in particular (Ladymoor, a former smelting site) was highly contaminated with Cd, Cu, Pb and Zn at more than 20 times background levels. Biodiversity indices ( Shannon - Weiner, Simpson index, Margalef index, alpha index, species richness, Shaneven ( evenness) and Berger - Parker dominance) were calculated. Of these indices, estimates of species richness and evenness were most effective at highlighting the differences between the Collembola communities. Indeed, the highest number of species were found at the most contaminated site, although the Collembola population also had a comparatively low evenness value, with just two species dominating. The number of individuals per species were allocated into geometric classes and plotted against the cumulative number of species as a percentage. At Ladymoor, there were more geometric classes, and the slope of the line was shallower than at the other four sites. This characteristic is a feature of polluted sites, where a few species are dominant and most species are rare. The Ladymoor soil also had a dominance of Isotomurus palustris, and was the only site in which Ceratophysella denticulata was found. Previous studies have shown that these two species are often found in sites subject to high metal contamination. Survival and reproduction of the "standard'' test springtail, Folsomia candida (Willem), were determined in a 4 week exposure test to soils from all five sites. Mortality was significantly increased in adults and reproduction significantly lower in the Ladymoor soil in comparison to the other four sites. This study has shown that severe metal contamination can be related to the population structure of Collembola in the field, and performance of F. candida ( in soils from such sites) in the laboratory.

A model for the evolution of pathogen-induced leaf shedding

A size-structured plant population model is developed to study the evolution of pathogen-induced leaf shedding under various environmental conditions. The evolutionary stable strategy (ESS) of the leaf shedding rate is determined for two scenarios: i) a constant leaf shedding strategy and ii) an infection load driven leaf shedding strategy. The model predicts that ESS leaf shedding rates increase with nutrient availability. No effect of plant density on the ESS leaf shedding rate is found even though disease severity increases with plant density. When auto-infection, that is increased infection due to spores produced on the plant itself, plays a key role in further disease increase on the plant, shedding leaves removes disease that would otherwise contribute to disease increase on the plant itself. Consequently leaf shedding responses to infections may evolve. When external infection, that is infection due to immigrant spores, is the key determinant, shedding a leaf does not reduce the force of infection on the leaf shedding plant. In this case leaf shedding will not evolve. Under a low external disease pressure adopting an infection driven leaf shedding strategy is more efficient than adopting a constant leaf shedding strategy, since a plant adopting an infection driven leaf shedding strategy does not shed any leaves in the absence of infection, even when leaf shedding rates are high. A plant adopting a constant leaf shedding rate sheds the same amount of leaves regardless of the presence of infection. Based on the results we develop two hypotheses that can be tested if the appropriate plant material is available.

Responses of invertebrate trophic level, feeding guild and body size to the management of improved grassland field margins

P>1. Management of lowland mesotrophic grasslands in north-west Europe often makes use of inorganic fertilizers, high stocking densities and silage-based forage systems to maximize productivity. The impact of these practices has resulted in a simplification of the plant community combined with wide-scale declines in the species richness of grassland invertebrates. We aim to identify how field margin management can be used to promote invertebrate diversity across a suite of functionally diverse taxa (beetles, planthoppers, true bugs, butterflies, bumblebees and spiders). 2. Using an information theoretic approach we identify the impacts of management (cattle grazing, cutting and inorganic fertilizer) and plant community composition (forb species richness, grass species richness and sward architecture) on invertebrate species richness and body size. As many of these management practices are common to grassland systems throughout the world, understanding invertebrate responses to them is important for the maintenance of biodiversity. 3. Sward architecture was identified as the primary factor promoting increased species richness of both predatory and phytophagous trophic levels, as well as being positively correlated with mean body size. In all cases phytophagous invertebrate species richness was positively correlated with measures of plant species richness. 4. The direct effects of management practices appear to be comparatively weak, suggesting that their impacts are indirect and mediated though the continuous measures of plant community structure, such as sward architecture or plant species richness. 5. Synthesis and applications. By partitioning field margins from the remainder of the field, economically viable intensive grassland management can be combined with extensive management aimed at promoting native biodiversity. The absence of inorganic fertilizer, combined with a reduction in the intensity of both cutting and grazing regimes, promotes floral species richness and sward architectural complexity. By increasing sward architecture the total biomass of invertebrates also increased (by c. 60% across the range of sward architectural measures seen in this study), increasing food available for higher trophic levels, such as birds and mammals.

Grazing management of calcareous grasslands and its implications for the conservation of beetle communities

Calcareous grasslands are an important habitat for floral and faunal communities in the UK and Europe. Declines due to changes in management, scrub invasion and agricultural improvement have left much of the remnants of this habitat in a degraded and fragmented state. Grazing, by cattle or sheep, is one of the main management practices used to maintain and improve the floral and faunal quality of calcareous grassland. The long-term impacts of different grazing regimes, however, are poorly understood, particularly in terms of the invertebrate communities. This study contrasted the impacts of recently introduced and long-term sheep or cattle grazing on beetle communities present on one of the largest areas of calcareous grassland in Europe, the Salisbury Plain military training Area, UK. No effects of grazing management on beetle abundance, species. richness or evenness were found, but plant diversity and overall percentage cover of grasses did influence beetle diversity. Proportions of the total number of individuals and overall species richness within beetle guilds (predatory, phytophagous, flower/seed feeders, root feeders and foliage feeders) were strongly influenced by both the duration and type of grazing animal. At the species level, beetle community structure showed significant differences between ungrazed, long-term cattle and long-term sheep grazing treatments. Changes in plant community structure were found to influence beetle community structure. The significance of these results is discussed in terms of the long-term impacts of grazing on beetle community structure, and the benefits of different grazing regimes for the conservation management of calcareous grasslands. (c) 2005 Elsevier Ltd. All rights reserved.

Effects of a sex-ratio distorting endosymbiont on mtDNA variation in a global insect pest

Background: Patterns of mtDNA variation within a species reflect long-term population structure, but may also be influenced by maternally inherited endosymbionts, such as Wolbachia. These bacteria often alter host reproductive biology and can drive particular mtDNA haplotypes through populations. We investigated the impacts of Wolbachia infection and geography on mtDNA variation in the diamondback moth, a major global pest whose geographic distribution reflects both natural processes and transport via human agricultural activities. Results: The mtDNA phylogeny of 95 individuals sampled from 10 countries on four continents revealed two major clades. One contained only Wolbachia-infected individuals from Malaysia and Kenya, while the other contained only uninfected individuals, from all countries including Malaysia and Kenya. Within the uninfected group was a further clade containing all individuals from Australasia and displaying very limited sequence variation. In contrast, a biparental nuclear gene phylogeny did not have infected and uninfected clades, supporting the notion that maternally-inherited Wolbachia are responsible for the mtDNA pattern. Only about 5% (15/306) of our global sample of individuals was infected with the plutWBI isolate and even within infected local populations, many insects were uninfected. Comparisons of infected and uninfected isofemale lines revealed that plutWBI is associated with sex ratio distortion. Uninfected lines have a 1:1 sex ratio, while infected ones show a 2:1 female bias. Conclusion: The main correlate of mtDNA variation in P. xylostella is presence or absence of the plutWBI infection. This is associated with substantial sex ratio distortion and the underlying mechanisms deserve further study. In contrast, geographic origin is a poor predictor of moth mtDNA sequences, reflecting human activity in moving the insects around the globe. The exception is a clade of Australasian individuals, which may reflect a bottleneck during their recent introduction to this region.

API-CALC 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives

Individual identification via DNA profiling is important in molecular ecology, particularly in the case of noninvasive sampling. A key quantity in determining the number of loci required is the probability of identity (PIave), the probability of observing two copies of any profile in the population. Previously this has been calculated assuming no inbreeding or population structure. Here we introduce formulae that account for these factors, whilst also accounting for relatedness structure in the population. These formulae are implemented in API-CALC 1.0, which calculates PIave for either a specified value, or a range of values, for F-IS and F-ST.

Recent developments in genetic data analysis: what can they tell us about human demographic history?

Over the last decade, a number of new methods of population genetic analysis based on likelihood have been introduced. This review describes and explains the general statistical techniques that have recently been used, and discusses the underlying population genetic models. Experimental papers that use these methods to infer human demographic and phylogeographic history are reviewed. It appears that the use of likelihood has hitherto had little impact in the field of human population genetics, which is still primarily driven by more traditional approaches. However, with the current uncertainty about the effects of natural selection, population structure and ascertainment of single-nucleotide polymorphism markers, it is suggested that likelihood-based methods may have a greater impact in the future.

Biodiversity of Collembola in urban soils and the use of Folsomia candida to assess soil 'quality'

The effects of metal contamination on natural populations of Collembola in soils from five sites in the Wolverhampton area ( West Midlands, England) were examined. Analysis revealed that metal concentrations were elevated above background levels at all sites. One location in particular (Ladymoor, a former smelting site) was highly contaminated with Cd, Cu, Pb and Zn at more than 20 times background levels. Biodiversity indices ( Shannon - Weiner, Simpson index, Margalef index, alpha index, species richness, Shaneven ( evenness) and Berger - Parker dominance) were calculated. Of these indices, estimates of species richness and evenness were most effective at highlighting the differences between the Collembola communities. Indeed, the highest number of species were found at the most contaminated site, although the Collembola population also had a comparatively low evenness value, with just two species dominating. The number of individuals per species were allocated into geometric classes and plotted against the cumulative number of species as a percentage. At Ladymoor, there were more geometric classes, and the slope of the line was shallower than at the other four sites. This characteristic is a feature of polluted sites, where a few species are dominant and most species are rare. The Ladymoor soil also had a dominance of Isotomurus palustris, and was the only site in which Ceratophysella denticulata was found. Previous studies have shown that these two species are often found in sites subject to high metal contamination. Survival and reproduction of the "standard'' test springtail, Folsomia candida (Willem), were determined in a 4 week exposure test to soils from all five sites. Mortality was significantly increased in adults and reproduction significantly lower in the Ladymoor soil in comparison to the other four sites. This study has shown that severe metal contamination can be related to the population structure of Collembola in the field, and performance of F. candida ( in soils from such sites) in the laboratory.

A model for the evolution of pathogen-induced leaf shedding

A size-structured plant population model is developed to study the evolution of pathogen-induced leaf shedding under various environmental conditions. The evolutionary stable strategy (ESS) of the leaf shedding rate is determined for two scenarios: i) a constant leaf shedding strategy and ii) an infection load driven leaf shedding strategy. The model predicts that ESS leaf shedding rates increase with nutrient availability. No effect of plant density on the ESS leaf shedding rate is found even though disease severity increases with plant density. When auto-infection, that is increased infection due to spores produced on the plant itself, plays a key role in further disease increase on the plant, shedding leaves removes disease that would otherwise contribute to disease increase on the plant itself. Consequently leaf shedding responses to infections may evolve. When external infection, that is infection due to immigrant spores, is the key determinant, shedding a leaf does not reduce the force of infection on the leaf shedding plant. In this case leaf shedding will not evolve. Under a low external disease pressure adopting an infection driven leaf shedding strategy is more efficient than adopting a constant leaf shedding strategy, since a plant adopting an infection driven leaf shedding strategy does not shed any leaves in the absence of infection, even when leaf shedding rates are high. A plant adopting a constant leaf shedding rate sheds the same amount of leaves regardless of the presence of infection. Based on the results we develop two hypotheses that can be tested if the appropriate plant material is available.

Escherichia coli isolates from extraintestinal organs of livestock animals harbour diverse virulence genes and belong to multiple genetic lineages

Escherichia coli, the most common cause of bacteraemia in humans in the UK, can also cause serious diseases in animals. However the population structure, virulence and antimicrobial resistance genes of those from extraintestinal organs of livestock animals are poorly characterised. The aims of this study were to investigate the diversity of these isolates from livestock animals and to understand if there was any correlation between the virulence and antimicrobial resistance genes and the genetic backbone of the bacteria and if these isolates were similar to those isolated from humans. Here 39 E. coli isolates from liver (n=31), spleen (n=5) and blood (n=3) of cattle (n=34), sheep (n=3), chicken (n=1) and pig (n=1) were assigned to 19 serogroups with O8 being the most common (n=7), followed by O101, O20 (both n=3) and O153 (n=2). They belong to 29 multi-locus sequence types, 20 clonal complexes with ST23 (n=7), ST10 (n=6), ST117 and ST155 (both n=3) being most common and were distributed among phylogenetic group A (n=16), B1 (n=12), B2 (n=2) and D (n=9). The pattern of a subset of putative virulence genes was different in almost all isolates. No correlation between serogroups, animal hosts, MLST types, virulence and antimicrobial resistance genes was identified. The distributions of clonal complexes and virulence genes were similar to other extraintestinal or commensal E. coli from humans and other animals, suggesting a zoonotic potential. The diverse and various combinations of virulence genes implied that the infections were caused by different mechanisms and infection control will be challenging.

Viruses in soils: morphological diversity and abundance in the rhizosphere

Soil viruses are potentially of great importance as they may influence the ecology and evolution of soil biological communities through both an ability to transfer genes from host to host and as a potential cause of microbial mortality. Despite this importance, the area of soil virology is understudied. Here, we report the isolation and preliminary characterisation of viruses from soils in the Dundee area of Scotland. Different virus morphotypes including tailed, polyhedral (spherical), rod shaped, filamentous and bacilliform particles were detected in the soil samples. An apparent predominance of small spherical and filamentous bacteriophages was observed, whereas tailed bacteriophages were significantly less abundant. In this report, we also present observations and characterisation of viruses from different soil functional domains surrounding wheat roots: rhizosheath, rhizosphere and bulk soil. In spite of the differences in abundance of bacterial communities in these domains, no significant variations in viral population structure in terms of morphology and abundance were found. Typically, there were approximately 1.1–1.2 × 109 virions g−1 dry weight, implicating remarkable differences in virus-to-bacteria ratios in domains close to roots, rhizosphere and rhizosheath (approximately 0.27) and in bulk soil (approximately 4.68).