ggComp enables dissection of germplasm resources and construction of a multiscale germplasm network in wheat.

Accurate germplasm characterization is a vital step for accelerating crop genetic improvement, which remains largely infeasible for crops such as bread wheat (Triticum aestivum L.), which has a complex genome that undergoes frequent introgression and contains many structural variations. Here, we propose a genomic strategy called ggComp, which integrates resequencing data with copy number variations and stratified single-nucleotide polymorphism densities to enable unsupervised identification of pairwise germplasm resource-based Identity-By-Descent (gIBD) blocks. The reliability of ggComp was verified in wheat cultivar Nongda5181 by dissecting parental-descent patterns represented by inherited genomic blocks. With gIBD blocks identified among 212 wheat accessions, we constructed a multi-scale genomic-based germplasm network. At the whole-genome level, the network helps to clarify pedigree relationship, demonstrate genetic flow, and identify key founder lines. At the chromosome level, we were able to trace the utilization of 1RS introgression in modern wheat breeding by hitchhiked segments. At the single block scale, the dissected germplasm-based haplotypes nicely matched with previously identified alleles of "Green Revolution" genes and can guide allele mining and dissect the trajectory of beneficial alleles in wheat breeding. Our work presents a model-based framework for precisely evaluating germplasm resources with genomic data. A database, WheatCompDB (http://wheat.cau.edu.cn/WheatCompDB/), is available for researchers to exploit the identified gIBDs with a multi-scale network.

Computational modeling of piezochromism in molecular crystals.

Piezochromic materials, whose luminescence responds to external pressure, have recently garnered much experimental attention. Computational modeling of piezochromism is of high theoretical interest, yet currently lacking. Herein, we present a computational effort to predict the piezochromism for a selection of molecular crystals. The current methodology employs a combination of dispersion-corrected solid-state and gas-phase density-functional theory and Becke's virial exciton model. Our study finds that piezochromism is primarily driven by the modification of intermolecular interactions within the molecular crystal and can be understood from the perspectives of changing polarizability or bandgaps upon the application of mechanical pressure.

Communication: Becke's virial exciton model gives accurate charge-transfer excitation energies.

First singlet (S1) excitations are of primary importance in the photoluminescence spectra of organic chromophores. However, due to the multi-determinantal nature of the singlet excited states, standard Kohn-Sham density-functional theory (DFT) is not applicable. While linear-response time-dependent DFT is the method of choice for the computation of excitation energies, it fails severely for excitations with charge-transfer character. Becke's recent virial exciton model [A. D. Becke, J. Chem. Phys. 148, 044112 (2018)] offers a promising solution to employ standard DFT for calculation of the S1 excitation energy in molecular systems. Here, it is shown that the virial exciton model is free of charge-transfer error. It is equally reliable for S1 excitations with significant charge-transfer character as for other classes of transitions.

Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat.

BACKGROUND: Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. RESULTS: Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency. CONCLUSIONS: This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.

Genome-wide identification and expression analysis of the ZF-HD gene family in pea (Pisum sativum L.).

Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFⅠ-III), and the ZHD subgroup was subdivided into five subclasses (ZHDⅠ-V). The PsZF-HD members were named PsMIF1-PsMIF4 and PsZHD1-PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a low-temperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas.

Fast switching thyristor applied in nanosecond-pulse high-voltage generator with closed transformer core.

For a compact and reliable nanosecond-pulse high-voltage generator (NPHVG), the specification parameter selection and potential usage of fast controllable state-solid switches have an important bearing on the optimal design. The NPHVG with closed transformer core and fast switching thyristor (FST) was studied in this paper. According to the analysis of T-type circuit, the expressions for the voltages and currents of the primary and secondary windings on the transformer core of NPHVG were deduced, and the theoretical maximum analysis was performed. For NPHVG, the rise-rate of turn-on current (di/dt) across a FST may exceed its transient rating. Both mean and maximum values of di/dt were determined by the leakage inductances of the transformer, and the difference is 1.57 times. The optimum winding ratio is helpful to getting higher voltage output with lower specification FST, especially when the primary and secondary capacitances have been established. The oscillation period analysis can be effectively used to estimate the equivalent leakage inductance. When the core saturation effect was considered, the maximum di/dt estimated from the oscillating period of the primary current is more accurate than one from the oscillating period of the secondary voltage. Although increasing the leakage inductance of NPHVG can decrease di/dt across FST, it may reduce the output peak voltage of the NPHVG.