Construction of a Festuca pratensis BAC library for map-based cloning in Festulolium substitution lines

Introgression in Festulolium is a potentially powerful tool to isolate genes for a large number of traits which differ between Festuca pratensis Huds. and Lolium perenne L. Not only are hybrids between the two species fertile, but the two genomes can be distinguished by genomic in situ hybridisation and a high frequency of recombination occurs between homoeologous chromosomes and chromosome segments. By a programme of introgression and a series of backcrosses, L. perenne lines have been produced which contain small F. pratensis substitutions. This material is a rich source of polymorphic markers targeted towards any trait carried on the F. pratensis substitution not observed in the L. perenne background. We describe here the construction of an F. pratensis BAC library, which establishes the basis of a map-based cloning strategy in L. perenne. The library contains 49,152 clones, with an average insert size of 112 kbp, providing coverage of 2.5 haploid genome equivalents. We have screened the library for eight amplified fragment length polymorphism (AFLP) derived markers known to be linked to an F. pratensis gene introgressed into L. perenne and conferring a staygreen phenotype as a consequence of a mutation in primary chlorophyll catabolism. While for four of the markers it was possible to identify bacterial artificial chromosome (BAC) clones, the other four AFLPs were too repetitive to enable reliable identification of locus-specific BACs. Moreover, when the four BACs were partially sequenced, no obvious coding regions could be identified. This contrasted to BACs identified using cDNA sequences, when multiple genes were identified on the same BAC.

Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome

Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ∼500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene HvbHLH1 identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.

Segmental chromosomal duplications harbouring group IV CONSTANS-like genes in cereals

Comparative mapping is an important component of map-based cloning in large-genome cereal species. We describe evidence of a segmental chromosomal duplication harbouring CONSTANS-like genes in barley that predates the divergence of the Oryzoideae (rice) and Pooideae (brachypodium, barley, wheat) clades, and discuss the implications of such events for comparative mapping and QTL cloning in temperate cereal crops.

Shoot calcium and magnesium concentrations differ between subtaxa, are highly heritable, and associate with potentially pleiotropic loci in Brassica oleracea

Calcium (Ca) and magnesium (Mg) are the most abundant group II elements in both plants and animals. Genetic variation in shoot Ca and shoot Mg concentration (shoot Ca and Mg) in plants can be exploited to biofortify food crops and thereby increase dietary Ca and Mg intake for humans and livestock. We present a comprehensive analysis of within-species genetic variation for shoot Ca and Mg, demonstrating that shoot mineral concentration differs significantly between subtaxa (varietas). We established a structured diversity foundation set of 376 accessions to capture a high proportion of species-wide allelic diversity within domesticated Brassica oleracea, including representation of wild relatives (C genome, 1n = 9) from natural populations. These accessions and 74 modern F-1 hybrid cultivars were grown in glasshouse and field environments. Shoot Ca and Mg varied 2- and 2.3-fold, respectively, and was typically not inversely correlated with shoot biomass, within most subtaxa. The closely related capitata (cabbage) and sabauda (Savoy cabbage) subtaxa consistently had the highest mean shoot Ca and Mg. Shoot Ca and Mg in glasshouse-grown plants was highly correlated with data from the field. To understand and dissect the genetic basis of variation in shoot Ca and Mg, we studied homozygous lines from a segregating B. oleracea mapping population. Shoot Ca and Mg was highly heritable (up to 40). Quantitative trait loci (QTL) for shoot Ca and Mg were detected on chromosomes C2, C6, C7, C8, and, in particular, C9, where QTL accounted for 14 to 55 of the total genetic variance. The presence of QTL on C9 was substantiated by scoring recurrent backcross substitution lines, derived from the same parents. This also greatly increased the map resolution, with strong evidence that a 4-cM region on C9 influences shoot Ca. This region corresponds to a 0.41-Mb region on Arabidopsis (Arabidopsis thaliana) chromosome 5 that includes 106 genes. There is also evidence that pleiotropic loci on C8 and C9 affect shoot Ca and Mg. Map-based cloning of these loci will reveal how shoot-level phenotypes relate to Ca 21 and Mg 21 uptake and homeostasis at the molecular level.

Robust background model for pixel based people counting using a single uncalibrated camera

Several pixel-based people counting methods have been developed over the years. Among these the product of scale-weighted pixel sums and a linear correlation coefficient is a popular people counting approach. However most approaches have paid little attention to resolving the true background and instead take all foreground pixels into account. With large crowds moving at varying speeds and with the presence of other moving objects such as vehicles this approach is prone to problems. In this paper we present a method which concentrates on determining the true-foreground, i.e. human-image pixels only. To do this we have proposed, implemented and comparatively evaluated a human detection layer to make people counting more robust in the presence of noise and lack of empty background sequences. We show the effect of combining human detection with a pixel-map based algorithm to i) count only human-classified pixels and ii) prevent foreground pixels belonging to humans from being absorbed into the background model. We evaluate the performance of this approach on the PETS 2009 dataset using various configurations of the proposed methods. Our evaluation demonstrates that the basic benchmark method we implemented can achieve an accuracy of up to 87% on sequence ¿S1.L1 13-57 View 001¿ and our proposed approach can achieve up to 82% on sequence ¿S1.L3 14-33 View 001¿ where the crowd stops and the benchmark accuracy falls to 64%.

Generation and analysis of the 2005 land cover map for Mexico using 250m MODIS data

Land cover plays a key role in global to regional monitoring and modeling because it affects and is being affected by climate change and thus became one of the essential variables for climate change studies. National and international organizations require timely and accurate land cover information for reporting and management actions. The North American Land Change Monitoring System (NALCMS) is an international cooperation of organizations and entities of Canada, the United States, and Mexico to map land cover change of North America's changing environment. This paper presents the methodology to derive the land cover map of Mexico for the year 2005 which was integrated in the NALCMS continental map. Based on a time series of 250 m Moderate Resolution Imaging Spectroradiometer (MODIS) data and an extensive sample data base the complexity of the Mexican landscape required a specific approach to reflect land cover heterogeneity. To estimate the proportion of each land cover class for every pixel several decision tree classifications were combined to obtain class membership maps which were finally converted to a discrete map accompanied by a confidence estimate. The map yielded an overall accuracy of 82.5% (Kappa of 0.79) for pixels with at least 50% map confidence (71.3% of the data). An additional assessment with 780 randomly stratified samples and primary and alternative calls in the reference data to account for ambiguity indicated 83.4% overall accuracy (Kappa of 0.80). A high agreement of 83.6% for all pixels and 92.6% for pixels with a map confidence of more than 50% was found for the comparison between the land cover maps of 2005 and 2006. Further wall-to-wall comparisons to related land cover maps resulted in 56.6% agreement with the MODIS land cover product and a congruence of 49.5 with Globcover.

Hydraulic modeling of runoff over a rough surface under partial inundation

This study presents a numerical method to derive the Darcy- Weisbach friction coefficient for overland flow under partial inundation of surface roughness. To better account for the variable influence of roughness with varying levels of emergence, we model the flow over a network which evolves as the free surface rises. This network is constructed using a height numerical map, based on surface roughness data, and a discrete geometry skeletonization algorithm. By applying a hydraulic model to the flows through this network, local heads, velocities, and Froude and Reynolds numbers over the surface can be estimated. These quantities enable us to analyze the flow and ultimately to derive a bulk friction factor for flow over the entire surface which takes into account local variations in flow quantities. Results demonstrate that although the flow is laminar, head losses are chiefly inertial because of local flow disturbances. The results also emphasize that for conditions of partial inundation, flow resistance varies nonmonotonically but does generally increase with progressive roughness inundation.

Context-aware visual exploration of molecular databases

Facilitating the visual exploration of scientific data has received increasing attention in the past decade or so. Especially in life science related application areas the amount of available data has grown at a breath taking pace. In this paper we describe an approach that allows for visual inspection of large collections of molecular compounds. In contrast to classical visualizations of such spaces we incorporate a specific focus of analysis, for example the outcome of a biological experiment such as high throughout screening results. The presented method uses this experimental data to select molecular fragments of the underlying molecules that have interesting properties and uses the resulting space to generate a two dimensional map based on a singular value decomposition algorithm and a self organizing map. Experiments on real datasets show that the resulting visual landscape groups molecules of similar chemical properties in densely connected regions.

Quantitative and qualitative differences in morphological traits revealed between diploid Fragaria species

Background and Aims: The aims of this investigation were to highlight the qualitative and quantitative diversity apparent between nine diploid Fragaria species and produce interspecific populations segregating for a large number of morphological characters suitable for quantitative trait loci analysis. Methods: A qualitative comparison of eight described diploid Fragaria species was performed and measurements were taken of 23 morphological traits from 19 accessions including eight described species and one previously undescribed species. A principal components analysis was performed on 14 mathematically unrelated traits from these accessions, which partitioned the species accessions into distinct morphological groups. Interspecific crosses were performed with accessions of species that displayed significant quantitative divergence and, from these, populations that should segregate for a range of quantitative traits were raised. Key Results: Significant differences between species were observed for all 23 morphological traits quantified and three distinct groups of species accessions were observed after the principal components analysis. Interspecific crosses were performed between these groups, and F2 and backcross populations were raised that should segregate for a range of morphological characters. In addition, the study highlighted a number of distinctive morphological characters in many of the species studied. Conclusions: Diploid Fragaria species are morphologically diverse, yet remain highly interfertile, making the group an ideal model for the study of the genetic basis of phenotypic differences between species through map-based investigation using quantitative trait loci. The segregating interspecific populations raised will be ideal for such investigations and could also provide insights into the nature and extent of genome evolution within this group.

Effects of Thomson-scattering geometry on white-light imaging of an interplanetary shock: synthetic observations from forward magnetohydrodynamic modelling

Stereoscopic white-light imaging of a large portion of the inner heliosphere has been used to track interplanetary coronal mass ejections. At large elongations from the Sun, the white-light brightness depends on both the local electron density and the efficiency of the Thomson-scattering process. To quantify the effects of the Thomson-scattering geometry, we study an interplanetary shock using forward magnetohydrodynamic simulation and synthetic white-light imaging. Identifiable as an inclined streak of enhanced brightness in a time–elongation map, the travelling shock can be readily imaged by an observer located within a wide range of longitudes in the ecliptic. Different parts of the shock front contribute to the imaged brightness pattern viewed by observers at different longitudes. Moreover, even for an observer located at a fixed longitude, a different part of the shock front will contribute to the imaged brightness at any given time. The observed brightness within each imaging pixel results from a weighted integral along its corresponding ray-path. It is possible to infer the longitudinal location of the shock from the brightness pattern in an optical sky map, based on the east–west asymmetry in its brightness and degree of polarisation. Therefore, measurement of the interplanetary polarised brightness could significantly reduce the ambiguity in performing three-dimensional reconstruction of local electron density from white-light imaging.

Mid-Holocene and glacial-maximum vegetation geography of the northern continents and Africa.

BIOME 6000 is an international project to map vegetation globally at mid-Holocene (6000 14C yr bp) and last glacial maximum (LGM, 18,000 14C yr bp), with a view to evaluating coupled climate-biosphere model results. Primary palaeoecological data are assigned to biomes using an explicit algorithm based on plant functional types. This paper introduces the second Special Feature on BIOME 6000. Site-based global biome maps are shown with data from North America, Eurasia (except South and Southeast Asia) and Africa at both time periods. A map based on surface samples shows the method’s skill in reconstructing present-day biomes. Cold and dry conditions at LGM favoured extensive tundra and steppe. These biomes intergraded in northern Eurasia. Northern hemisphere forest biomes were displaced southward. Boreal evergreen forests (taiga) and temperate deciduous forests were fragmented, while European and East Asian steppes were greatly extended. Tropical moist forests (i.e. tropical rain forest and tropical seasonal forest) in Africa were reduced. In south-western North America, desert and steppe were replaced by open conifer woodland, opposite to the general arid trend but consistent with modelled southward displacement of the jet stream. The Arctic forest limit was shifted slighly north at 6000 14C yr bp in some sectors, but not in all. Northern temperate forest zones were generally shifted greater distances north. Warmer winters as well as summers in several regions are required to explain these shifts. Temperate deciduous forests in Europe were greatly extended, into the Mediterranean region as well as to the north. Steppe encroached on forest biomes in interior North America, but not in central Asia. Enhanced monsoons extended forest biomes in China inland and Sahelian vegetation into the Sahara while the African tropical rain forest was also reduced, consistent with a modelled northward shift of the ITCZ and a more seasonal climate in the equatorial zone. Palaeobiome maps show the outcome of separate, independent migrations of plant taxa in response to climate change. The average composition of biomes at LGM was often markedly different from today. Refugia for the temperate deciduous and tropical rain forest biomes may have existed offshore at LGM, but their characteristic taxa also persisted as components of other biomes. Examples include temperate deciduous trees that survived in cool mixed forest in eastern Europe, and tropical evergreen trees that survived in tropical seasonal forest in Africa. The sequence of biome shifts during a glacial-interglacial cycle may help account for some disjunct distributions of plant taxa. For example, the now-arid Saharan mountains may have linked Mediterranean and African tropical montane floras during enhanced monsoon regimes. Major changes in physical land-surface conditions, shown by the palaeobiome data, have implications for the global climate. The data can be used directly to evaluate the output of coupled atmosphere-biosphere models. The data could also be objectively generalized to yield realistic gridded land-surface maps, for use in sensitivity experiments with atmospheric models. Recent analyses of vegetation-climate feedbacks have focused on the hypothesized positive feedback effects of climate-induced vegetation changes in the Sahara/Sahel region and the Arctic during the mid-Holocene. However, a far wider spectrum of interactions potentially exists and could be investigated, using these data, both for 6000 14C yr bp and for the LGM.

Interpreters’ perception of linguistic and non linguistic factors affecting quality: a survey through the World Wide Web

This paper will present and discuss the results of an empirical study on perception of quality in interpretation carried out on a sample of 286 interpreters across five continents. Since the 1980’s the field of Interpreting Studies has been witnessing an ever growing interest in the issue of quality in interpretation both in academia and in professional circles, but research undertaken so far is surprisingly lacking in methodological rigour. This survey is an attempt to revise previous studies on interpreters’ perception of quality through the implementation of new Information Technology which allowed us to administer a traditional research tool such as a questionnaire, in a highly innovative way; i.e., through the World Wide Web. Using multidimensional scaling, a perceptual map based upon the results of the manner in which interpreters ranked a list of linguistic and nonlinguistic criteria according to their perception of importance in the interpretative process,was devised.

Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array

Background A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNPbased linkage map of an apple rootstock progeny. Results Of the 7,867 Malus SNP markers on the array, 1,823 (23.2 %) were heterozygous in one of the two parents of the progeny, 1,007 (12.8 %) were heterozygous in both parental genotypes, whilst just 2.8 % of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the ‘Golden Delicious’ genome sequence. A total of 311 markers (13.7 % of all mapped markers) mapped to positions that conflicted with their predicted positions on the ‘Golden Delicious’ pseudo-chromosomes, indicating the presence of paralogous genomic regions or misassignments of genome sequence contigs during the assembly and anchoring of the genome sequence. Conclusions We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the ‘Golden Delicious’ reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.

Integration of retrotransposons-based markers in a linkage map of barley

A deeper understanding of random markers is important if they are to be employed for a range of objectives. The sequence specific amplified polymorphism (S-SAP) technique is a powerful genetic analysis tool which exploits the high copy number of retrotransposon long terminal repeats (LTRs) in the plant genome. The distribution and inheritance of S-SAP bands in the barley genome was studied using the Steptoe × Morex (S × M) double haploid (DH) population. Six S-SAP primer combinations generated 98 polymorphic bands, and map positions were assigned to all but one band. Eight putative co-dominant loci were detected, representing 16 of the mapped markers. Thus at least 81 of the mapped S-SAP loci were dominant. The markers were distributed along all of the seven chromosomes and a tendency to cluster was observed. The distribution of S-SAP markers over the barley genome concurred with the knowledge of the high copy number of retrotransposons in plants. This experiment has demonstrated the potential for the S-SAP technique to be applied in a range of analyses such as genetic fingerprinting, marker assisted breeding, biodiversity assessment and phylogenetic analyses.

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely-related crop species, lentil, and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2 cM interval of Vf chromosome 2 which was highly collinear with Mt3. The obvious candidate gene from 77 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene (Mt3g092830, Mt3g092840) controlling anthocyanin production in Medicago and re-sequencing of the Vf orthologue showed a putative causative deletion of the entire 5’ end of the gene.