Analysis of >3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration-diversification routes

Eggplant (Solanum melongena) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild relatives, consisting of 3499 accessions from seven worldwide genebanks, originating from 105 countries in five continents. The combination of genotypic and passport data points to the existence of at least two main centers of domestication, in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The wild and weedy eggplant ancestor S. insanum shows admixture with domesticated S. melongena, similar to what was described for other fruit-bearing Solanaceous crops such as tomato and pepper and their wild ancestors. After domestication, migration and admixture of eggplant populations from different regions have been less conspicuous with respect to tomato and pepper, thus better preserving ‘local’ phenotypic characteristics. The data allowed the identification of misclassified and putatively duplicated accessions, facilitating genebank management. All the genetic, phenotypic, and passport data have been deposited in the Open Access G2P-SOL database, and constitute an invaluable resource for understanding the domestication, migration and diversification of this cosmopolitan vegetabl

Phase-locking of a 2.7-THz quantum cascade laser to a mode-locked erbium-doped fibre laser

We demonstrate phase-locking of a 2.7-THz metalmetal waveguide quantum cascade laser (QCL) to an external microwave signal. The reference is the 15th harmonic, generated by a semiconductor superlattice nonlinear device, of a signal at 182 GHz, which itself is generated by a multiplier-chain (x2x3x2) from a microwave synthesizer at 15 GHz. Both laser and reference radiations are coupled into a hot electron bolometer mixer, resulting in a beat signal, which is fed into a phase-lock loop. Spectral analysis of the beat signal (see fig. 1) confirms that the QCL is phase locked. This result opens the possibility to extend heterodyne interferometers into the far-infrared range

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.Peer reviewe

Entwicklung eines modularen gedrückten Ge:Ga Photoleiter-Fokalebenen-Array Prototypen

Die im Institut für Weltraumsensorik und Planetenerkundung des DLR vorgeschlagene Spektral-photometrische Infrarot-Kamera SPICA für SOFIA wird den mittleren und fern-infraroten Wellenlängenbereich von ca. 20-210 mm detektieren können. Auf SOFIA soll SPICA als eines der Deutschen Instrumente räumlich beugungsbegrenzt bei niedriger spektraler Auflösung (l/Dl=50) zum Einsatz kommen. Dieser Wellenlängenbereich ist nicht mit einem einzigen Detektorsystem abzudecken, so dass für den längstwelligen Bereich von ca. 100-210 mm gedrückte, Gallium-dotierte Germanium-Kristalle (Ge:Ga) als Photoleiter verwendet werden. Gallium hat in Germanium eine Störstellenbindungsenergie von 10.8 meV oberhalb des Valenzbandes, was einer Absorptionswellenlänge von 115 mm entspricht. Wenn der Kristall unter uniaxialen Druck in [100]-Richtung nahe der Bruchgrenze gesetzt wird, hebt sich die Entartung der schweren und leichten Löcher des Valenzbandes auf und das leichte-Löcher-Band rückt energetisch näher an die Störstelle heran. Dies drückt sich in einer längerwelligen Absorptionskante aus, die je nach Grösse des Drucks dann bis zu 220 mm betragen kann. Wie bereits in mehreren astronomischen Projekten wie dem Infrared Space Observatory (ISO, 2x2-Array), dem Kuiper Airborne Observatory (KAO, 5x5-Array) u. a. erfolgreich gezeigt, eignen sich diese gedrückten Ge:Ga-Photoleiter gut als Detektoren in der Fokalebene der jeweiligen Teleskope. Da der erforderliche Druck auf die Kristalle jedoch nahe der Bruchgrenze bei etwa 700 N/mm² liegt und die Detektoren bei einer Temperatur von etwa 2 K betrieben werden, sind die mechanischen Details eines solchen bei Kryotemperaturen arbeitenden Detektors unter Umständen sehr delikat. Dazu kommt, dass grossformatige Arrays solcher Detektoren die Fokalebenen bevölkern sollen, was besondere Anforderungen an die Packungsdichte solcher Druckmechanismen stellt. In dieser Arbeit wird anhand der Entwicklung eines Prototyps eines solchen linearen, zu zweidimensionalen Arrays stapelbaren Druckmoduls die Machbarkeit eines grossformatigen gedrückten Detektorarrays gezeigt. Die Pixel eines solchen Moduls haben einen Abstand von 4 mm, was aufgrund der Airy-Scheibe in der Fokalebene ausreichend für beugungsbegrenztes Nyquist-Sampling ist. Erstmalig mit dieser Arbeit werden zwölf Detektorpixel in einer Reihe zu einem linearen Array zusammengesetzt. Ein lineares Array besteht aus zwei Detektorstapeln zu je sechs Detektoren, die jeweils gleichzeitig unter mechanischen Druck gesetzt werden, wobei der Druckmechanismus so einfach wie möglich gehalten wird: Eine Schraube an den beiden Köpfen der zwei Detektorstapel baut einen Teil des Drucks auf, wogegen der Rest des erforderlichen Drucks durch differentielle Schrumpfung von Detektorgehäuse und Detektorstapel erbracht wird. Die zwei Detektorstapel erlauben Redundanz bezüglich Versagen der Detektoren: Bruch eines Detektorkristalls resultiert höchstens im Ausfall eines halben Moduls. Wichtige zu testende Eigenschaften dabei sind Stärke des erreichten Drucks im Kalten, Uniformität des Drucks von Detektor zu Detektor, sowie Uniformität innerhalb eines Detektorkristalls und Stabilität des Detektorgehäuses im Kryobetrieb. Wichtige zu lösende Probleme bei der Entwicklung dieses modularen Arrays sind im Design eingeflossen. Erste Tests am Prototypen werden mit Trans-Impedanz Verstärkern durchgeführt, welche akzeptablen Dunkelstrom und eine Performance limitiert vom Photonenrauschen ergeben. Damit sind Detektor- und Verstärkerrauschquellen kleiner als das natürliche Rauschen eines etwaigen astronomischen Signals. Experimentelle Verifikation des erreichten Drucks durch Messung der FIR-Absorptionskante mit Hilfe eines Michelson-Interferometers sowie der Stabilität des Drucks über mehrere Kühlzyklen wird erbracht und diskutiert. Dabei wird festgestellt, dass der mechanische Druck von Kühlzyklus zu Kühlzyklus abnimmt, was auf entweder den Fluss duktilen Materials oder Bruch einzelner Detektorkristalle schliessen lässt. Verbesserungsmöglichkeiten für ein über das Prototypenstadium hinausgehendes Flug-Modell werden ebenfalls aus den Messungen abgeleitet und diskutiert.A Spectral-Photometric Infrared CAmera (SPICA) proposed at DLR's Institute for Space Sensor Technology and Planetary Exploration will cover the wavelength range from mid- to far-infrared (20-210 mm). SPICA is one of the German instruments on SOFIA and shall perform observations with diffraction-limited performance at low spectral resolution (l/Dl=50). Currently this wavelength range can not be covered with a single detection system, so several detectors have to be employed independently. For the longest wavelengths from about 100-210 mm stressed Gallium-doped Germanium crystals will be used as detectors. In the band gap of Germanium, Gallium has an ionization potential of 10.8 meV above the valence band, which corresponds to an absorption wavelength of 115 mm. If the crystal is stressed under uniaxial pressure close to the yield stress, the degeneracy of the light and heavy holes in the valence band is split and the light-hole-band energetically moves closer to the impurity, rendering a smaller ionization potential or, equivalently, a longer absorption wavelength. Depending on the magnitude of the stress, the longest-wavelength-cut-off can be as long as 220 mm. As already shown at several astronomical projects like the Infrared Space Observatory (ISO, 2x2-Array), the Kuiper Airborne Observatory (KAO, 5x5-Array) and others, this kind of focal plane detectors are well suited as focal plane arrays for FIR telescopes. Since the required stress is close to the yield stress of 700 N/mm² and these detectors work at temperatures at 2 K, the mechanical details of a cryogenic detector become quite delicate. Above that large arrays of these detectors shall populate the focal planes, which poses other requirements on packaging the stressing mechanism. In this work the feasibility of a large-format focal plane array is shown with help of a prototype of a linear, stackable detector module. The pixels of this module have a pitch of 4 mm, which is sufficient for diffraction-limited Nyquist sampling due to the Airy-disk at the focal plane. In this work for the first time twelve detector elements are arranged in two collinear stacks of six detectors each, that can be stressed individually with a simplest-possible stressing mechanism: A ram screw squashes the detectors up to certain fraction of the required stress, whereas the remainder of the stress is applied during cool-down by differential shrinkage of the detector housing. The two stacks also allow for redundancy: Fracture of a detector crystal results in failure of half a detector module only (6 pixels). Important to verify are the final stress at the cold operating temperature, uniformity of the stress from detector to detector, uniformity within a single detector crystal and stability of the stressing harness at cryogenic temperatures. The tests of the prototype were conducted with trans-impedance amplifiers, which yields acceptable dark current and photon-noise-limited performance. Thus the noise sources of the detector's and amplifier's noise sources are smaller than the fluctuations of an astronomical signal. Experimental verification of the stress reached by measuring the absorption edge with help of a Michelson interferometer as well as the stability of the stress during serveral cooling cycles is shown and discussed. It is noticed that the stress decreases from cycle to cycle which can be attributed to ductile material or fracture of components under stress. From the measurements improvement strategies for a flight model after the prototype are derived and discussed

Analysis of >3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration‐diversification routes

SUMMARY Eggplant ( Solanum melongena ) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild relatives, consisting of 3499 accessions from seven worldwide genebanks, originating from 105 countries in five continents. The combination of genotypic and passport data points to the existence of at least two main centers of domestication, in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The wild and weedy eggplant ancestor S. insanum shows admixture with domesticated S. melongena , similar to what was described for other fruit‐bearing Solanaceous crops such as tomato and pepper and their wild ancestors. After domestication, migration and admixture of eggplant populations from different regions have been less conspicuous with respect to tomato and pepper, thus better preserving ‘local’ phenotypic characteristics. The data allowed the identification of misclassified and putatively duplicated accessions, facilitating genebank management. All the genetic, phenotypic, and passport data have been deposited in the Open Access G2P‐SOL database, and constitute an invaluable resource for understanding the domestication, migration and diversification of this cosmopolitan vegetable.Significance Statement Genotypic, passport and geographical origin data from 3499 worldwide accessions of eggplant and its wild relatives were collected, curated, analyzed, and deposited in a ‘one stop shop’ Open Access database. The identified polymorphisms and georeferencing data led to the identification of two main centers of domestication of eggplant – in Southeast Asia and the Indian subcontinent – and of its migration and diversification routes. Identification of putatively duplicated and misclassified accessions will facilitate genebank management

GREAT: The German first light heterodyne instrument for SOFIA

GREAT, the German REceiver for Astronomy at Terahertz frequencies, is a first generation SOFIA dual channel heterodyne PI-instrument for high resolution spectroscopy. The system is developed by a cosortium of German research institutes. The receiver will allow simultaneous observations in two out of the following three far-infrared frequency bands: - a 1.4-1.9 THz channel for e.g. the fine-stucture line of ionized carbon [CII] at 158µm; - a 2.4-2.7 THz channel for e.g. the 112µm transition of HD; and - a 4.7 THz channel for the 63µm fine-structure line of neutral atomic oxygen. Hot electron bolometers (HEB) mixers provide state of the art sensitivity. A spectral resolving power of up to 108 is achieved with chirp transform spectrometers, and a total bandwidth of 4 GHz at 1 MHz resolution is reached with wide band acousto-optical spectrometers. The modular concept of GREAT allows to observe with any combination of two out of the three channels aboard SOFIA. A more complete frequency coverage of the THz regime by adding additional GREAT channels is possible in the future. The adaptation of new LO-, mixer- or backend-techniques is easily possible. We describe details of the receiver and the results of first performance tests of the system at 1.9 THz

A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture

Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%–3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.Funding was provided by the Max Planck Society and the President's Strategic Initiative Fund of ASU. T.M.B. is supported by BFU2017‐86471‐P (MINECO/FEDER, UE), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880) and C.F. is supported by a La Caixa PhD Fellowship