Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)

Background Cultivated peanut or groundnut (Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut. Results A microsatellite-enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable amplicon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecies hypogaea were grouped together in one cluster, while the genotypes belonging to subspecies fastigiata were grouped mainly under two clusters. Conclusion Newly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be very useful for germplasm analysis, linkage mapping, diversity studies and phylogenetic relationships in cultivated groundnut as well as related Arachis species

Monitoring the threat of unintentional transgene flow into maize gene banks and breeding materials

The use of transgenic crops is steadily increasing around the world, led by soybean (based on total area) and maize (in terms of total number of countries). Transgenic maize is grown in at least 17 countries across four continents: Africa, America, Asia and Europe. The comprehensive global spread of transgenic maize has significant implications for organizations involved in germplasm conservation and genetic enhancement; particularly as some countries require a GMO-free declaration when receiving shipments of maize germplasm. This article describes the protocol used by the International Maize and Wheat Improvement Center (CIMMYT) for monitoring unintentional transgene flow in maize genebank and breeding plots. The protocol is based on polymerase chain reaction (PCR) markers for detecting specific recombinant DNA sequences in bulked samples collected from sentinel plots. To date, no unintentional transgene flow has been detected in CIMMYT fields of maize genebank accessions or breeding materials

Playing safe: Assessing the risk of sexual abuse to elite child athletes

Young athletes frequently suffer from being seen as athletes first and children second. This has consequences for their legal, civil and human rights as children (Kelly et al., 1995) and for the way in which sport organisations choose to intervene on their behalf to protect them from physical, psychological and sexual abuses (Brackenridge, 1994). Sport careers peak at different ages depending on the sport: in some, children as young as 12 or 13 may reach the highest levels of competitive performance; in others, full maturity as an athlete may come late into adulthood or even middle age. Recognition of this variation has given rise to the concept of ‘sport age’ (Kirby, 1986) referring to sport-specific athlete development. This concept is of significance in helping to identify the developmental process in terms of athletic, rather than chronological, maturity. The risk of sexual abuse in sport, formerly ignored or denied, has now been documented in a number of studies, using both quantitative and qualitative methods (Kirby & Greaves, 1996; Brackenridge, 1997; Volkwein, 1996). Drawing on data from these studies and from the previous work on sport age and athletic maturation, this paper proposes a possible means of identifying and assessing relative risk of sexual abuse to elite young athletes in selected sports. The concept of a ‘stage of imminent achievement’ (SIA) is proposed as the period of peak vulnerability of young athletes to sexual abuse

A Brauer's theorem and related results

Given a square matrix A, a Brauer's theorem [Brauer A., Limits for the characteristic roots of a matrix. IV. Applications to stochastic matrices, Duke Math. J., 1952, 19(1), 75-91] shows how to modify one single eigenvalue of A via a rank-one perturbation without changing any of the remaining eigenvalues. Older and newer results can be considered in the framework of the above theorem. In this paper, we present its application to stabilization of control systems, including the case when the system is noncontrollable. Other applications presented are related to the Jordan form of A and Wielandt's and Hotelling's deflations. An extension of the aforementioned Brauer's result, Rado's theorem, shows how to modify r eigenvalues of A at the same time via a rank-r perturbation without changing any of the remaining eigenvalues. The same results considered by blocks can be put into the block version framework of the above theorem. © 2012 Versita Warsaw and Springer-Verlag Wien.This work is supported by Fondecyt 1085125, Chile, the Spanish grant DGI MTM2010-18228 and the Programa de Apoyo a la Investigacion y Desarrollo (PAID-06-10) of the UPV.Bru García, R.; Cantó Colomina, R.; Soto, RL.; Urbano Salvador, AM. (2012). A Brauer's theorem and related results. Central European Journal of Mathematics. 10(1):312-321. https://doi.org/10.2478/s11533-011-0113-0S312321101Brauer A., Limits for the characteristic roots of a matrix. IV. Applications to stochastic matrices, Duke Math. J., 1952, 19(1), 75–91Crouch P.E., Introduction to Mathematical Systems Theory, Mathematik-Arbeitspapiere, Bremen, 1988Delchamps D.F., State-Space and Input-Output Linear Systems, Springer, New York, 1988Hautus M.L.J., Controllability and observability condition of linear autonomous systems, Nederl. Akad. Wetensch. Indag. Math., 1969, 72, 443–448Kailath T., Linear Systems, Prentice Hall Inform. System Sci. Ser., Prentice Hall, Englewood Cliffs, 1980Langville A.N., Meyer C.D., Deeper inside PageRank, Internet Math., 2004, 1(3), 335–380Perfect H., Methods of constructing certain stochastic matrices. II, Duke Math. J., 1955, 22(2), 305–311Saad Y., Numerical Methods for Large Eigenvalue Problems, Classics Appl. Math., 66, SIAM, Philadelphia, 2011Soto R.L., Rojo O., Applications of a Brauer theorem in the nonnegative inverse eigenvalue problem, Linear Algebra Appl., 2006, 416(2–3), 844–856Wilkinson J.H., The Algebraic Eigenvalue Problem, Clarendon Press, Oxford, 196

Laboratory Information Management Software for genotyping workflows: Applications in high throughput crop genotyping

Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp

Modeling the Subsurface Structure of Sunspots

While sunspots are easily observed at the solar surface, determining their subsurface structure is not trivial. There are two main hypotheses for the subsurface structure of sunspots: the monolithic model and the cluster model. Local helioseismology is the only means by which we can investigate subphotospheric structure. However, as current linear inversion techniques do not yet allow helioseismology to probe the internal structure with sufficient confidence to distinguish between the monolith and cluster models, the development of physically realistic sunspot models are a priority for helioseismologists. This is because they are not only important indicators of the variety of physical effects that may influence helioseismic inferences in active regions, but they also enable detailed assessments of the validity of helioseismic interpretations through numerical forward modeling. In this paper, we provide a critical review of the existing sunspot models and an overview of numerical methods employed to model wave propagation through model sunspots. We then carry out an helioseismic analysis of the sunspot in Active Region 9787 and address the serious inconsistencies uncovered by \citeauthor{gizonetal2009}~(\citeyear{gizonetal2009,gizonetal2009a}). We find that this sunspot is most probably associated with a shallow, positive wave-speed perturbation (unlike the traditional two-layer model) and that travel-time measurements are consistent with a horizontal outflow in the surrounding moat.Comment: 73 pages, 19 figures, accepted by Solar Physic

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes

Surface-focused Seismic Holography of Sunspots: I. Observations

We present a comprehensive set of observations of the interaction of p-mode oscillations with sunspots using surface-focused seismic holography. Maps of travel-time shifts, relative to quiet-Sun travel times, are shown for incoming and outgoing p modes as well as their mean and difference. We compare results using phase-speed filters with results obtained with filters that isolate single p-mode ridges, and further divide the data into multiple temporal frequency bandpasses. The f mode is removed from the data. The variations of the resulting travel-time shifts with magnetic-field strength and with the filter parameters are explored. We find that spatial averages of these shifts within sunspot umbrae, penumbrae, and surrounding plage often show strong frequency variations at fixed phase speed. In addition, we find that positive values of the mean and difference travel-time shifts appear exclusively in waves observed with phase-speed filters that are dominated by power in the low-frequency wing of the p1 ridge. We assess the ratio of incoming to outgoing p-mode power using the ridge filters and compare surface-focused holography measurements with the results of earlier published p-mode scattering measurements using Fourier-Hankel decomposition.Comment: Solar Physics, accepte