Integrating genetic maps in bambara groundnut [Vigna subterranea (L) Verdc.] and their syntenic relationships among closely related legumes

Background Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for minor and underutilised crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata). From these comparisons we identify conserved synteny blocks corresponding to the Linkage Groups (LGs) in bambara groundnut genetic maps and evaluate the potential to identify genes in conserved syntenic locations in a sequenced genome that underlie a QTL position in the underutilised crop genome. Results Two individual intraspecific linkage maps consisting of DArTseq markers were constructed in two bambara groundnut (2n = 2x = 22) segregating populations: 1) The genetic map of Population IA was derived from F2 lines (n = 263; IITA686 x Ankpa4) and covered 1,395.2 cM across 11 linkage groups; 2) The genetic map of Population TD was derived from F3 lines (n = 71; Tiga Nicuru x DipC) and covered 1,376.7 cM across 11 linkage groups. A total of 96 DArTseq markers from an initial pool of 142 pre-selected common markers were used. These were not only polymorphic in both populations but also each marker could be located using the unique sequence tag (at selected stringency) onto the common bean, adzuki bean and mung bean genomes, thus allowing the sequenced genomes to be used as an initial ‘pseudo’ physical map for bambara groundnut. A good correspondence was observed at the macro synteny level, particularly to the common bean genome. A test using the QTL location of an agronomic trait in one of the bambara groundnut maps allowed the corresponding flanking positions to be identified in common bean, mung bean and adzuki bean, demonstrating the possibility of identifying potential candidate genes underlying traits of interest through the conserved syntenic physical location of QTL in the well annotated genomes of closely related species. Conclusions The approach of adding pre-selected common markers in both populations before genetic map construction has provided a translational framework for potential identification of candidate genes underlying a QTL of trait of interest in bambara groundnut by linking the positions of known genetic effects within the underutilised species to the physical maps of other well-annotated legume species, without the need for an existing whole genome sequence of the study species. Identifying the conserved synteny between underutilised species without complete genome sequences and the genomes of major crops and model species with genetic and trait data is an important step in the translation of resources and information from major crop and model species into the minor crop species. Such minor crops will be required to play an important role in future agriculture under the effects of climate change

A High Density Consensus Map of Rye (Secale cereale L.) Based on DArT Markers

L.) is an economically important crop, exhibiting unique features such as outstanding resistance to biotic and abiotic stresses and high nutrient use efficiency. This species presents a challenge to geneticists and breeders due to its large genome containing a high proportion of repetitive sequences, self incompatibility, severe inbreeding depression and tissue culture recalcitrance. The genomic resources currently available for rye are underdeveloped in comparison with other crops of similar economic importance. The aim of this study was to create a highly saturated, multilocus linkage map of rye via consensus mapping, based on Diversity Arrays Technology (DArT) markers.Recombinant inbred lines (RILs) from 5 populations (564 in total) were genotyped using DArT markers and subjected to linkage analysis using Join Map 4.0 and Multipoint Consensus 2.2 software. A consensus map was constructed using a total of 9703 segregating markers. The average chromosome map length ranged from 199.9 cM (2R) to 251.4 cM (4R) and the average map density was 1.1 cM. The integrated map comprised 4048 loci with the number of markers per chromosome ranging from 454 for 7R to 805 for 4R. In comparison with previously published studies on rye, this represents an eight-fold increase in the number of loci placed on a consensus map and a more than two-fold increase in the number of genetically mapped DArT markers.Through the careful choice of marker type, mapping populations and the use of software packages implementing powerful algorithms for map order optimization, we produced a valuable resource for rye and triticale genomics and breeding, which provides an excellent starting point for more in-depth studies on rye genome organization

Influence of imperfections in a wedged multilayer Laue lens for the focusing of X-rays investigated by beam propagation method

Using a beam propagation method the focusing properties of a one-dimensional wedged multilayer Laue lens with imperfections have been investigated theoretically. The calculations were done for a lens focusing 20 keV X-rays to <5 nm spot. Our simulations of the intensity in the focal plane and at the far screen show that the systematic errors degrade the performance more than the stochastic ones and that a proper image at the far screen is not a proof for a good quality beam in the focus

Bucking the trend in wolf-dog hybridization: first evidence from europe of hybridization between female dogs and male wolves.

Studies on hybridization have proved critical for understanding key evolutionary processes such as speciation and adaptation. However, from the perspective of conservation, hybridization poses a concern, as it can threaten the integrity and fitness of many wild species, including canids. As a result of habitat fragmentation and extensive hunting pressure, gray wolf (Canis lupus) populations have declined dramatically in Europe and elsewhere during recent centuries. Small and fragmented populations have persisted, but often only in the presence of large numbers of dogs, which increase the potential for hybridization and introgression to deleteriously affect wolf populations. Here, we demonstrate hybridization between wolf and dog populations in Estonia and Latvia, and the role of both genders in the hybridization process, using combined analysis of maternal, paternal and biparental genetic markers. Eight animals exhibiting unusual external characteristics for wolves - six from Estonia and two from Latvia - proved to be wolf-dog hybrids. However, one of the hybridization events was extraordinary. Previous field observations and genetic studies have indicated that mating between wolves and dogs is sexually asymmetrical, occurring predominantly between female wolves and male dogs. While this was also the case among the Estonian hybrids, our data revealed the existence of dog mitochondrial genomes in the Latvian hybrids and, together with Y chromosome and autosomal microsatellite data, thus provided the first evidence from Europe of mating between male wolves and female dogs. We discuss patterns of sexual asymmetry in wolf-dog hybridization

One dimensional focusing with high numerical aperture multilayer Laue lens

Multilayer Laue lenses (MLLs) capitalize on the developments in multilayer deposition technologies for fabricating reflective coatings, specifically undertaken for EUV lithography, where layer thicknesses of several nanometers can be achieved. MLLs are deposited layer by layer, with their thicknesses following the zone plate law, and then pieces are sliced and extracted for use in focusing. Rays are reflected in the Laue geometry. The efficiency of a MLL can be very high, and is maximized by making the slice equal to about a half Pendellosung period so that most energy is transferred from the undiffracted to the diffracted beam, and by ensuring that the Bragg condition is met at each point in the zone plate. This latter condition requires that the layers are tilted to the beam by an amount that varies with layer position; e.g. for focusing a collimated beam, the layers should be normal to a cylinder of radius of twice the focal length. We have fabricated such tilted-zone MLLs and find that they exhibit improved efficiency across their entire pupil as compared with parallel-zone MLLs. This leads to a higher effective NA of the optic and hence higher resolution

One dimensional focusing with high numerical aperture multilayer Laue lens

Multilayer Laue lenses (MLLs) capitalize on the developments in multilayer deposition technologies for fabricating reflective coatings, specifically undertaken for EUV lithography, where layer thicknesses of several nanometers can be achieved. MLLs are deposited layer by layer, with their thicknesses following the zone plate law, and then pieces are sliced and extracted for use in focusing. Rays are reflected in the Laue geometry. The efficiency of a MLL can be very high, and is maximized by making the slice equal to about a half Pendellosung period so that most energy is transferred from the undiffracted to the diffracted beam, and by ensuring that the Bragg condition is met at each point in the zone plate. This latter condition requires that the layers are tilted to the beam by an amount that varies with layer position; e.g. for focusing a collimated beam, the layers should be normal to a cylinder of radius of twice the focal length. We have fabricated such tilted-zone MLLs and find that they exhibit improved efficiency across their entire pupil as compared with parallel-zone MLLs. This leads to a higher effective NA of the optic and hence higher resolution

Sampling locations of wolves (small open circles) and wolf-dog hybrids (black triangles 1–8, see also <b>Table 1</b>) in Estonia (Taebla) and Latvia (Dikli), hunted during the winter period of 2008–2009.

<p>The approximate ranges of wolves are with dark green (Estonia) and light green (Latvia).</p

First-generation (F1) wolf-dog hybrids from Wildlife Park Kadzidlowo, Poland: female wolf×male Polish Spaniel (left); female wolf×West Siberian Laika (right) (photos: A. Krzywinski).

<p>First-generation (F1) wolf-dog hybrids from Wildlife Park Kadzidlowo, Poland: female wolf×male Polish Spaniel (left); female wolf×West Siberian Laika (right) (photos: A. Krzywinski).</p

Bayesian phylogenetic tree of wolves, dogs and wolf-dog hybrids (from this study and homologous sequences from GenBank) based on the analysis of mtDNA control region sequences (1134 bp).

<p>Nodes with posterior probability values ≥0.80 are shown. Colours: green – dogs, blue – wolves, red – hybrids. Haplotypes representing more than one individual are numbered (circles 1–15). More detailed information about different haplotypes can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046465#pone.0046465.s004" target="_blank">Table S3</a>.</p