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

Waveform Memory for Real-Time FPGA Test of Fiber-Optic Receiver DSPs

Verification of advanced circuit implementations poses many challenges. For complex digital signal processing (DSP) circuits, logic simulations may be prohibitively slow when non-stationary scenarios are considered. A real-time emulation technique like the Fiber-on-Chip (FoC) approach can significantly speed up DSP logic verification. However, a potential weakness with this type of emulation is that it does not use data obtained from experiments, but synthetically creates test data. We introduce a waveform memory, which can be integrated with FoC systems and similar emulators, and which allows measured waveforms to be stored and fed to DSP circuits under test. We perform real-time FPGA experiments where we evaluate a carrier-phase recovery (CPR) module that is tested using either waveform data or synthetic data. Our results for the two different data sets show that the CPR module behaves similarly, both qualitatively and quantitatively, which indicates that the synthetic phase-noise model is a valid replacement of measured data

The Reliability of Hybrid Functionals for Accurate Fundamental and Optical Gap Prediction of Bulk Solids and Surfaces

Hybrid functionals have been considered insufficiently reliable for the prediction of band gaps in solids and surfaces. We revisit this issue with a new generation of optimally tuned range-separated hybrid functionals, focusing on the reconstructed Si(111)-(2×1) and Ge(111)-(2×1) surfaces. We show that certain hybrid functionals can accurately predict the surface-state and bulk fundamental and optical gaps, as well as projected band structures of these surfaces, by combining ground-state and time-dependent density functional theory

Electronic structure and optical properties of halide double perovskites from a Wannier-localized optimally-tuned screened range-separated hybrid functional

Halide double perovskites are a chemically diverse and growing class of compound semiconductors that are promising for optoelectronic applications. However, the prediction of their fundamental gaps and optical properties with density functional theory (DFT) and ab initio many-body perturbation theory has been a significant challenge. Recently, a nonempirical Wannier-localized optimally tuned screened range-separated hybrid (WOT-SRSH) functional has been shown to accurately produce the fundamental band gaps of a wide set of semiconductors and insulators, including lead halide perovskites. Here, we apply the WOT-SRSH functional to five halide double perovskites and compare the results with those obtained from other known functionals and previous GW calculations. We also use the approach as a starting point for GW calculations and we compute the band structures and optical absorption spectrum for Cs2AgBiBr6, using both time-dependent DFT and the GW-Bethe-Salpeter equation approach. We show that the WOT-SRSH functional leads to accurate fundamental and optical band gaps, as well as optical absorption spectra, consistent with spectroscopic measurements, thereby establishing WOT-SRSH as a viable method for the accurate prediction of optoelectronic properties of halide double perovskites

Electronic structure and optical properties of halide double perovskites from a Wannier-localized optimally-tuned screened range-separated hybrid functional

Halide double perovskites are a chemically-diverse and growing class of compound semiconductors that are promising for optoelectronic applications. However, the prediction of their fundamental gaps and optical properties with density functional theory (DFT) and {\it ab initio} many-body perturbation theory has been a significant challenge. Recently, a nonempirical Wannier-localized optimally-tuned screened range-separated hybrid (WOT-SRSH) functional has been shown to accurately produce the fundamental band gaps of a wide set of semiconductors and insulators, including lead halide perovskites. Here we apply the WOT-SRSH functional to five halide double perovskites, and compare the results with those obtained from other known functionals and previous $GW$ calculations. We also use the approach as a starting point for $GW$ calculations and we compute the band structures and optical absorption spectrum for Cs\textsubscript{2}Ag{Bi}Br\textsubscript{6}, using both time-dependent DFT and the $GW$-Bethe-Salpeter equation approach. We show that the WOT-SRSH functional leads to accurate fundamental and optical band gaps, as well as optical absorption spectra, consistent with spectroscopic measurements, thereby establishing WOT-SRSH as a viable method for the accurate prediction of optoelectronic properties of halide double perovskites

Optical absorption spectra of metal oxides from time-dependent density functional theory and many-body perturbation theory based on optimally-tuned hybrid functionals

Using both time-dependent density functional theory (TDDFT) and the ``single-shot" $GW$ plus Bethe-Salpeter equation ($GW$-BSE) approach, we compute optical band gaps and optical absorption spectra from first principles for eight common binary and ternary closed-shell metal oxides (MgO, Al$_2$O$_3$, CaO, TiO$_2$, Cu$_2$O, ZnO, BaSnO$_3$, and BiVO$_4$), based on the non-empirical Wannier-localized optimally-tuned screened range-separated hybrid functional. Overall, we find excellent agreement between our TDDFT and $GW$-BSE results and experiment, with a mean absolute error less than 0.4 eV, including for Cu$_2$O and ZnO, traditionally considered to be challenging for both methods

Uso de marcadores SSR para identificaci\uf3n de germoplasma de papa en el programa de mejoramiento de INIA de Chile

Molecular markers based on Simple Sequence Repeats (SSR) are a very efficient tool for potato ( Solanum tuberosum L. ) genotype identification and can be very useful for germplasm conservation and management. With the purpose of incorporate this technology into the potato breeding program of the National Institute of Agricultural Research (INIA) Chile, a set of 26 SSR markers was evaluated on a sample of 71 potato genotypes. Each marker was characterized for number and combinations of alleles, scoring quality, polymorphic information content (PIC) and discrimination power (D). From the total, only 21 SSR markers showed up scoreable products and the allele number ranged between 2 and 17. The observed allelic combinations among the different potato genotypes ranged from 2 to 47; however, unique genotypes detected by each SSR marker ranged from 0 to 38. The observed (Do) and expected (Dj) discriminatory power ranged from 0.23 to 0.98 and from 0.43 to 0.92, respectively. The seven SSR markers which showed the highest Do scores were STM1009 (0.98), STM1020 (0.97), STM0031 (0.97), STM2013 (0.96), STM1008 (0.94), STM1052 (0.93) and STM0019 (0.91). The STM1009, STM1020 and STM1008 markers are multi-loci SSR, where each one amplifies more than one locus of the potato genome. The utilization of the multi-loci type of marker, or combinations of several SSR markers in either PCR-multiplex or pseudo-multiplex reactions, are good options to increase the speed and reduce the cost of SSR markers application.Los marcadores moleculares basados en Secuencias Simples Repetidas (SSR) constituyen una herramienta altamente eficaz para la identificaci\uf3n de genotipos de papa ( Solanum tuberosum L. ) y pueden ser de gran utilidad en la conservaci\uf3n y manejo de germoplasma. Con el prop\uf3sito de incorporar esta tecnolog\ueda al Programa de Mejoramiento de Papa del Instituto de Investigaciones Agropecuarias (INIA) de Chile, se evalu\uf3 un grupo de 26 marcadores SSR sobre una muestra de 71 genotipos de papa. Cada marcador se caracteriz\uf3 seg\ufan su n\ufamero de alelos y sus respectivas combinaciones, calidad de lectura, contenido de informaci\uf3n polim\uf3rfica (PIC) y poder discriminatorio (D). Del total s\uf3lo 21 marcadores SSR mostraron productos legibles con un n\ufamero de alelos que vari\uf3 entre 2 y 17. Las combinaciones al\ue9licas observadas variaron desde 2 a 47; sin embargo, los genotipos \ufanicos detectados por cada marcador fueron desde 0 a 38. El poder discriminatorio observado (Do) y esperado (Dj) estuvo entre 0,23 a 0,98 y entre 0,43 a 0,92, respectivamente. Los siete marcadores que presentaron mayor Do fueron STM1009 (0,98), STM1020 (0.97), STM0031 (0,97), STM2013 (0,96), STM1008 (0,94), STM1052 (0,93) y STM0019 (0,91). Los marcadores STM1009, STM1020 y STM1008 corresponden a SSR multi-loci, donde cada uno amplifica m\ue1s de un locus desde distintas regiones del genoma de la papa. La utilizaci\uf3n de este tipo de marcadores multi-loci, o de combinaciones de varios SSR en reacciones de PCR-m\ufaltiplex o pseudos-m\ufaltiplex son una buena alternativa para aumentar rapidez y disminuir costo en la aplicaci\uf3n de marcadores SSR