Genomic prediction of crown rust resistance in Lolium perenne

peer-reviewedBackground Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.This work received funding from the Irish Department of Agriculture Food and the Marine DAFM (RSF 11/S/109) and Teagasc core funding. SKA is supported by a Teagasc PhD Walsh Fellowship. SLB has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 658031

Sequencing the potato genome: outline and first results to come from the elucidation of the sequence of the world's third most important food crop

Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potat

A Genetic Strategy for Probing the Functional Diversity of Magnetosome Formation

Model genetic systems are invaluable, but limit us to understanding only a few organisms in detail, missing the variations in biological processes that are performed by related organisms. One such diverse process is the formation of magnetosome organelles by magnetotactic bacteria. Studies of model magnetotactic α-proteobacteria have demonstrated that magnetosomes are cubo-octahedral magnetite crystals that are synthesized within pre-existing membrane compartments derived from the inner membrane and orchestrated by a specific set of genes encoded within a genomic island. However, this model cannot explain all magnetosome formation, which is phenotypically and genetically diverse. For example, Desulfovibrio magneticus RS-1, a δ-proteobacterium for which we lack genetic tools, produces tooth-shaped magnetite crystals that may or may not be encased by a membrane with a magnetosome gene island that diverges significantly from those of the α-proteobacteria. To probe the functional diversity of magnetosome formation, we used modern sequencing technology to identify hits in RS-1 mutated with UV or chemical mutagens. We isolated and characterized mutant alleles of 10 magnetosome genes in RS-1, 7 of which are not found in the α-proteobacterial models. These findings have implications for our understanding of magnetosome formation in general and demonstrate the feasibility of applying a modern genetic approach to an organism for which classic genetic tools are not available

La educación inclusiva frente a las desigualdades sociales: un estado de la cuestion y algunas reflexiones geograficas

Este artículo establece un estado de la cuestión e la educación inclusiva en el mundo y sugiere algunas reflexiones al respecto. El primer apartado recuerda las conexiones ineludibles entre las preocupaciones educativas por la educación inclusiva y las preocupaciones más generales por la desigualdad. El segundo consigna los criterios de búsqueda de las publicaciones académicas, y observa dos grandes temas en sus contenidos: sobre todo, el cambio interno de las escuelas atrae las miradas, pero en segundo plano también el entorno territorial despierta algunas inquietudes. El tercero anota los criterios de búsqueda de la documentación del Banco Mundial, la OCDE y la UNESCO. En este ámbito los simposios de la Oficina Internacional de la Educación de UNESCO revelan una interpretación dispar, aunque convergente, del concepto de educación inclusiva en las distintas regiones mundiales. Asimismo, todas las publicaciones oficiales muestran una atención prioritaria a las dinámicas internas de las escuelas, puesto que apenas algunas esbozan ciertas relaciones entre la educación inclusiva y las políticas públicas. El último apartado adelanta varios argumentos a favor de una mayor consideración de las escalas local y estatal de la educación inclusiva. Las principales razones para atender a la dimensión local provienen de la causalidad acumulativa de las privaciones sociales, de la necesidad de articular la acción de las escuelas y de la posibilidad de abrir un espacio significativo para la participación ciudadana. Asimismo, las principales razones para atender a la dimensión estatal surgen de las posibles sinergias entre la educación inclusiva y la expansión educativa (p. ej. ¿es correlativo el avance de la escolarización en los distintos ciclos escolares?) como también entre la educación inclusiva y la protección social (p. ej. ¿tienen una implicación pedagógica consistente las abundantes condiciones educativas de las transferencias sociales?

Making sense of joint commissioning: three discourses of prevention, empowerment and efficiency

Background: In recent years joint commissioning has assumed an important place in the policy and practice of English health and social care. Yet, despite much being claimed for this way of working there is a lack of evidence to demonstrate the outcomes of joint commissioning. This paper examines the types of impacts that have been claimed for joint commissioning within the literature. Method: The paper reviews the extant literature concerning joint commissioning employing an interpretive schema to examine the different meanings afforded to this concept. The paper reviews over 100 documents that discuss joint commissioning, adopting an interpretive approach which sought to identify a series of discourses, each of which view the processes and outcomes of joint commissioning differently. Results: This paper finds that although much has been written about joint commissioning there is little evidence to link it to changes in outcomes. Much of the evidence base focuses on the processes of joint commissioning and few studies have systematically studied the outcomes of this way of working. Further, there does not appear to be one single definition of joint commissioning and it is used in a variety of different ways across health and social care. The paper identifies three dominant discourses of joint commissioning – prevention, empowerment and efficiency. Each of these offers a different way of seeing joint commissioning and suggests that it should achieve different aims. Conclusions: There is a lack of clarity not only in terms of what joint commissioning has been demonstrated to achieve but even in terms of what it should achieve. Joint commissioning is far from a clear concept with a number of different potential meanings. Although this ambiguity can be helpful in some ways in the sense that it can bring together disparate groups, for example, if joint commissioning is to be delivered at a local level then more specificity may be required in terms of what they are being asked to deliver

Considering tradeoffs in “local” food policies: examples from school feeding programmes

City, national, and multinational governments are increasingly leveraging nutrition programme spending, specifically pursuing policies that require or incentive “local” procurement, to meet a myriad of goals. However, these policies involve tradeoffs that are often not fully considered by government officials, planners, and advocates. This perspective article provides some examples of those tradeoffs from the peer-reviewed literature, which, we argue, are useful to consider in setting school feeding programme policies to achieve sustainability goals

Maltese teachers’ beliefs concerning the integration of children’s literature in mathematics teaching and learning

This exploratory mixed-methods study set out to explore Maltese primary school teachers’ perceived barriers to, and enablers for, the integration of children’s literature in mathematics teaching. Data were collected by means of an online questionnaire and semi-structured interviews, and analysed thematically using Ajzen’s Theory of Planned Behaviour. The responses given by the participants showed that integration of mathematics and stories was not a common practice. The perceived barriers were categorised as Resource Constraint, Time Constraint, Lack of Pedagogical Knowledge and Confidence, Doubts about Outcome Expectancy, and Inhibiting Social Norms while the three perceived enablers identified were Pedagogical Benefits, Love of Stories, and Enabling Social Norms. Given that the majority of the participating teachers acknowledged the potential benefits of the approach and expressed a wish for training, one key recommendation of the study is for teaching mathematics through stories to be explicitly included in pre-service and in-service professional development programmes

Unsigned magnetic flux as a proxy for radial-velocity variations in Sun-like stars

A major obstacle to detecting and characterizing long-period, low-mass exoplanets is the intrinsic radial-velocity (RV) variability of host stars. To better understand RV variability, we estimate disk-averaged RV variations of the Sun over its magnetic cycle, from the Fe I line observed by SDO/HMI, using a physical model for rotationally modulated magnetic activity that was previously validated against HARPS-N solar observations. We estimate the unsigned magnetic flux and show that a linear fit to it reduces the RMSof RV variations by 62%, i.e., a factor of 2.6. We additionally apply the FF′ method, which predicts RV variations based on a star’s photometric variations. At cycle maximum, we find that additional processes must be at play beyond suppression of convective blueshift and velocity imbalances resulting from brightness inhomogeneities, in agreement with recent studies of RV variations. By modeling RV variations over the magnetic cycle using a linear fit to the unsigned magnetic flux, we recover injected planets at a period of ≈300 days with RV semi-amplitudes down to 0.3 ms−1. To reach 0.1 ms−1, we will need to identify and model additional phenomena that are not well traced by Bobs ∣ ˆ ∣or FF′. This study motivates ongoing and future efforts to develop observation and analysis techniques to measure the unsigned magnetic flux at high precision in slowly rotating, relatively inactive stars like the Sun. We conclude that the unsigned magnetic flux is an excellent proxy for rotationally modulated, activity-induced RV variations, and could become key to confirming and characterizing Earth analogs