Genome-wide screening of meta-QTL and candidate genes controlling yield and yield-related traits in barley (Hordeum vulgare L.).

Increasing yield is an important goal of barley breeding. In this study, 54 papers published from 2001-2022 on QTL mapping for yield and yield-related traits in barley were collected, which contained 1080 QTLs mapped to the barley high-density consensus map for QTL meta-analysis. These initial QTLs were integrated into 85 meta-QTLs (MQTL) with a mean confidence interval (CI) of 2.76 cM, which was 7.86-fold narrower than the CI of the initial QTL. Among these 85 MQTLs, 68 MQTLs were validated in GWAS studies, and 25 breeder's MQTLs were screened from them. Seventeen barley orthologs of yield-related genes in rice and maize were identified within the hcMQTL region based on comparative genomics strategy and were presumed to be reliable candidates for controlling yield-related traits. The results of this study provide useful information for molecular marker-assisted breeding and candidate gene mining of yield-related traits in barley.

Ultra-broadband TM-pass polarizer based on anisotropic metamaterials in lithium niobate on an insulator.

An ultra-broadband TM-pass polarizer is designed, fabricated, and experimentally demonstrated based on subwavelength grating (SWG) metamaterials in a lithium niobate on an insulator (LNOI) platform. According to our simulation, the designed device is predicted to work at a 220 nm wavelength range from 1460 to 1680 nm, covering the S-, C-, L-, U-bands of optical fiber communication. By depositing and subsequently etching a silicon nitride thin film atop the LNOI chip, the SWG structures are formed successfully by using complementary metal-oxide semiconductor (CMOS)-compatible fabrication processes. The measured results show a high polarization extinction ratio larger than 20 dB and a relatively low insertion loss below 2.5 dB over a 130 nm wavelength range from 1500 to 1630 nm, mainly limited by the operation bandwidth of our laser source.

Cryogenic lithium-niobate-on-insulator optical filter.

Photonic integrated circuits have garnered significant attention and experienced rapid development in recent years. To provide fundamental building blocks for scalable optical classical and quantum information processing, one important direction is to develop cryogenic compatible photonic integrated devices. Here, we prepare one optical filter on a lithium-niobate-on-insulator (LNOI) platform based on a multimode waveguide grating and verify its availability at temperature from 295 to 7 K. We find that the integrated optical filter still shows good quality under cryogenic conditions, and the shift of the working wavelength at different temperatures is well explained by the index variation of the material. These results advance LNOI integrated optical devices in applications under cryogenic conditions.

Genomic insights into glume pubescence in durum wheat: GWAS and haplotype analysis implicates TdELD1-1A as a candidate gene.

Glume pubescence is an important morphological trait for the characterization of wheat cultivars. It shows tolerance to biotic and abiotic stresses to some extent. Hg1 (formerly named Hg) locus on chromosome 1AS controls glume pubescence in wheat. Its genetic analysis, fine-mapping and candidate gene analysis have been widely studied recently, however, the cloning of Hg1 has not yet been reported. Here, we conducted a GWAS between a dense panel of 171,103 SNPs and glume pubescence (Gp) in a durum wheat population of 145 lines, and further analyzed the candidate genes of Hg1 combined with the gene expression, functional annotation, and haplotype analysis. As a results, TRITD0Uv1G104670 (TdELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was detected as the most promising candidate gene of Hg1 for glume pubescence in durum wheat. Our findings not only contribute to a deeper understanding of its cloning and functional validation but also underscore the significance of accurate genome sequences and annotations. Additionally, our study highlights the relevance of unanchored sequences in chrUn and the application of bioinformatics analysis for gene discovery in durum wheat.

Upgrading pectin methylation for consistently enhanced biomass enzymatic saccharification and cadmium phytoremediation in rice Ospmes site-mutants.

Crop straws provide enormous biomass residues applicable for biofuel production and trace metal phytoremediation. However, as lignocellulose recalcitrance determines a costly process with potential secondary waste liberation, genetic modification of plant cell walls is deemed as a promising solution. Although pectin methylation plays an important role for plant cell wall construction and integrity, little is known about its regulation roles on lignocellulose hydrolysis and trace metal elimination. In this study, we initially performed a typical CRISPR/Cas9 gene-editing for site mutations of OsPME31, OsPME34 and OsPME79 in rice, and then determined significantly upgraded pectin methylation degrees in the young seedlings of three distinct site-mutants compared to their wild type. We then examined distinctively improved lignocellulose recalcitrance in three mutants including reduced cellulose levels, crystallinity and polymerization or raised hemicellulose deposition and cellulose accessibility, which led to specifically enlarged biomass porosity either for consistently enhanced biomass enzymatic saccharification under mild alkali pretreatments or for cadmium (Cd) accumulation up to 2.4-fold. Therefore, this study proposed a novel model to elucidate how pectin methylation could play a unique enhancement role for both lignocellulose enzymatic hydrolysis and Cd phytoremediation, providing insights into precise pectin modification for effective biomass utilization and efficient trace metal exclusion.

Integrated Manipulation and Addressing of Spin Defect in Diamond.

Scalable and addressable integrated manipulation of qubits is crucial for practical quantum information applications. Different waveguides have been used to transport the optical and electrical driving pulses, which are usually required for qubit manipulation. However, the separated multifields may limit the compactness and efficiency of manipulation and introduce unwanted perturbation. Here, we develop a tapered fiber-nanowire-electrode hybrid structure to realize integrated optical and microwave manipulation of solid-state spins at nanoscale. Visible light and microwave driving pulses are simultaneously transported and concentrated along an Ag nanowire. Studied with spin defects in diamond, the results show that the different driving fields are aligned with high accuracy. The spatially selective spin manipulation is realized. And the frequency-scanning optically detected magnetic resonance (ODMR) of spin qubits is measured, illustrating the potential for portable quantum sensing. Our work provides a new scheme for developing compact, miniaturized quantum sensors and quantum information processing devices.

Genomic evidence for climate-linked diversity loss and increased vulnerability of wild barley spanning 28 years of climate warming.

The information on how plant populations respond genetically to climate warming is scarce. Here, landscape genomic and machine learning approaches were integrated to assess genetic response of 10 wild barley (Hordeum vulgare ssp. spontaneum; WB) populations in the past and future, using whole genomic sequencing (WGS) data. The WB populations were sampled in 1980 and again in 2008. Phylogeny of accessions was roughly in conformity with sampling sites, which accompanied by admixture/introgressions. The 28-y climate warming resulted in decreased genetic diversity, increased selection pressure, and an increase in deleterious single nucleotide polymorphism (dSNP) numbers, heterozygous deleterious and total deleterious burdens for WB. Genome-environment associations identified some candidate genes belonging to peroxidase family (HORVU2Hr1G057450, HORVU4Hr1G052060 and HORVU4Hr1G057210) and heat shock protein 70 family (HORVU2Hr1G112630). The gene HORVU2Hr1G120170 identified by selective sweep analysis was under strong selection during the climate warming of the 28-y, and its derived haplotypes were fixed by WB when faced with the 28-y increasingly severe environment. Temperature variables were found to be more important than precipitation variables in influencing genomic variation, with an eco-physiological index gdd5 (growing degree-days at the baseline threshold temperature of 5 °C) being the most important determinant. Gradient forest modelling revealed higher predicted genomic vulnerability in Sede Boqer under future climate scenarios at 2041-2070 and 2071-2100. Additionally, estimates of effective population size (Ne) tracing back to 250 years indicated a forward decline in all populations over time. Our assessment about past genetic response and future vulnerability of WB under climate warming is crucial for informing conservation efforts for wild cereals and rational use strategies.

Polarization-insensitive vortex beam generator by the holographic grating on an integrated multi-layer waveguide.

An integrated polarization-insensitive vortex beam generator is proposed in this study. It is composed of a holographic grating on a multi-layer waveguide, which enables conversion of Transverse Electric (TE) and Transverse Magnetic (TM) waveguide modes to y-polarized and x-polarized optical vortex beams, respectively. The conversion efficiency and the phase fidelity are numerically analyzed, and the working bandwidth is about 100 nm from 1500 nm to 1600 nm with a phase fidelity above 0.7. Moreover, the vortex beam with the superposition of the y-polarization and x-polarization states can be obtained with the incident of the superposition of TE and TM waveguide modes.

Arbitrarily rotated optical axis waveguide induced by a trimming line.

Rotated optical axis waveguides can facilitate on-chip arbitrary wave-plate operations, which are crucial tools for developing integrated universal quantum computing algorithms. In this paper, we propose a unique technique based on femtosecond laser direct writing technology to fabricate arbitrarily rotated optical axis waveguides. First, a circular isotropic main waveguide with a non-optical axis was fabricated using a beam shaping method. Thereafter, a trimming line was used to create an artificial stress field near the main waveguide to induce a rotated optical axis. Using this technique, we fabricated high-performance half- and quarter-wave plates. Subsequently, high-fidelity (97.1%) Pauli-X gate operation was demonstrated via quantum process tomography, which constitutes the basis for the full manipulation of on-chip polarization-encoded qubits. In the future, this work is expected to lead to new prospects for polarization-encoded information in photonic integrated circuits.

Observation of delocalization transition in topological waveguide arrays with long-range interactions.

Topological edge states are a generic feature of topological insulators, and the long-range interactions, which break certain properties of topological edge states, are always non-negligible in real physical systems. In this Letter, we investigate the influence of next-nearest-neighbor (NNN) interactions on the topological properties of the Su-Schrieffer-Heeger (SSH) model by extracting the survival probabilities at the boundary of the photonic lattices. By introducing a series of integrated photonic waveguide arrays with different strengths of long-range interactions, we experimentally observe delocalization transition of light in SSH lattices with nontrivial phase, which is in good agreement with our theoretical predictions. The results indicate that the NNN interactions can significantly affect the edge states, and that the localization of these states can be absent in topologically nontrivial phase. Our work provides an alternative way to investigate the interplay between long-range interactions and localized states, which may stimulate further interest in topological properties in relevant structures.

Coupling of Photon Emitters in Monolayer WS2 with a Photonic Waveguide Based on Bound States in the Continuum.

On-chip light sources are an essential component of scalable photonic integrated circuits (PICs), and coupling between light sources and waveguides has attracted a great deal of attention. Photonic waveguides based on bound states in the continuum (BICs) allow optical confinement in a low-refractive-index waveguide on a high-refractive-index substrate and thus can be employed for constructing PICs. In this work, we experimentally demonstrated that the photoluminescence (PL) from a monolayer of tungsten sulfide (WS2) could be coupled into a BIC waveguide on a lithium-niobate-on-insulator (LNOI) substrate. Using finite-difference time-domain simulations, we numerically obtained a coupling efficiency of ∼2.3% for an in-plane-oriented dipole and a near-zero loss at a wavelength of 620 nm. By breaking through the limits of 2D-material integration with conventional photonic architectures, our work offers a new perspective for light-matter coupling in monolithic PICs.

Ultrathin quantum light source with van der Waals NbOCl2 crystal.

Interlayer electronic coupling in two-dimensional materials enables tunable and emergent properties by stacking engineering. However, it also results in significant evolution of electronic structures and attenuation of excitonic effects in two-dimensional semiconductors as exemplified by quickly degrading excitonic photoluminescence and optical nonlinearities in transition metal dichalcogenides when monolayers are stacked into van der Waals structures. Here we report a van der Waals crystal, niobium oxide dichloride (NbOCl2), featuring vanishing interlayer electronic coupling and monolayer-like excitonic behaviour in the bulk form, along with a scalable second-harmonic generation intensity of up to three orders higher than that in monolayer WS2. Notably, the strong second-order nonlinearity enables correlated parametric photon pair generation, through a spontaneous parametric down-conversion (SPDC) process, in flakes as thin as about 46 nm. To our knowledge, this is the first SPDC source unambiguously demonstrated in two-dimensional layered materials, and the thinnest SPDC source ever reported. Our work opens an avenue towards developing van der Waals material-based ultracompact on-chip SPDC sources as well as high-performance photon modulators in both classical and quantum optical technologies1-4.

Detection of consensus genomic regions and candidate genes for quality traits in barley using QTL meta-analysis.

Improving barley grain quality is a major goal in barley breeding. In this study, a total of 35 papers focusing on quantitative trait loci (QTLs) mapping for barley quality traits published since 2000 were collected. Among the 454 QTLs identified in these studies, 349 of them were mapped onto high-density consensus maps, which were used for QTL meta-analysis. Through QTL meta-analysis, the initial QTLs were integrated into 41 meta-QTLs (MQTLs) with an average confidence interval (CI) of 1. 66 cM, which is 88.9% narrower than that of the initial QTLs. Among the 41 identified MQTLs, 25 were subsequently validated in publications using genome-wide association study (GWAS). From these 25 validated MQTLs, ten breeder's MQTLs were selected. Synteny analysis comparing barley and wheat MQTLs revealed orthologous relationships between eight breeder's MQTLs and 45 wheat MQTLs. Additionally, 17 barley homologs associated with rice quality traits were identified within the regions of the breeder's MQTLs through comparative analysis. The findings of this study provide valuable insights for molecular marker-assisted breeding and the identification of candidate genes related to quality traits in barley.

Identification of QTL underlying the main stem related traits in a doubled haploid barley population.

Lodging reduces grain yield in cereal crops. The height, diameter and strength of stem are crucial for lodging resistance, grain yield, and photosynthate transport in barley. Understanding the genetic basis of stem benefits barley breeding. Here, we evaluated 13 stem related traits after 28 days of heading in a barley DH population in two consecutive years. Significant phenotypic correlations between lodging index (LI) and other stem traits were observed. Three mapping methods using the experimental data and the BLUP data, detected 27 stable and major QTLs, and 22 QTL clustered regions. Many QTLs were consistent with previously reported traits for grain filling rate, internodes, panicle and lodging resistance. Further, candidate genes were predicted for stable and major QTLs and were associated with plant development and adverse stress in the transition from vegetative stage to reproductive stage. This study provided potential genetic basis and new information for exploring barley stem morphology, and laid a foundation for map-based cloning and further fine mapping of these QTLs.

New insights into the evolution of CAF1 family and utilization of TaCAF1Ia1 specificity to reveal the origin of the maternal progenitor for common wheat.

INTRODUCTION: Until now, the most likely direct maternal progenitor (AABB) for common wheat (AABBDD) has yet to be identified. Here, we try to solve this particular problem with the specificity of a novel gene family in wheat and by using large population of rare germplasm resources. OBJECTIVES: Dissect the novelty of TaCAF1Ia subfamily in wheat. Exploit the conservative and specific characteristics of TaCAF1Ia1 to reveal the origin of the maternal progenitor for common wheat. METHODS: Phylogenetic and collinear analysis of TaCAF1 genes were performed to identify the evolutionary specificity of TaCAF1Ia subfamily. The large-scale expression patterns and interaction patterns analysis of CCR4-NOT complex were used to clarify the expressed and structural specificity of TaCAF1Ia subfamily in wheat. The population resequencing and phylogeny analysis of the TaCAF1Ia1 were utilized for the traceability analysis to understand gene-pool exchanges during the transferring and subsequent development from tetraploid to hexaploidy wheat. RESULTS: TaCAF1Ia is a novel non-typical CAF1 subfamily without DEDD (Asp-Glu-Asp-Asp) domain, whose members were extensively duplicated in wheat genome. The replication events had started and constantly evolved from ancestor species. Specifically, it was found that a key member CAF1Ia1 was highly specialized and only existed in the subB genome and S genome. Unlike CAF1s reported in other plants, TaCAF1Ia genes may be new factors for anther development. These atypical TaCAF1s could also form CCR4-NOT complex in wheat but with new interaction sites. Utilizing the particular but conserved characteristics of the TaCAF1Ia1 gene, the comparative analysis of haplotypes composition for TaCAF1Ia1 were identified among wheat populations with different ploidy levels. Based on this, the dual-lineages origin model of maternal progenitor for common wheat and potential three-lineages domestication model for cultivated tetraploid wheat were proposed. CONCLUSION: This study brings fresh insights for revealing the origin of wheat and the function of CAF1 in plants.

Edge State, Localization Length, and Critical Exponent from Survival Probability in Topological Waveguides.

Edge states in topological phase transitions have been observed in various platforms. To date, verification of the edge states and the associated topological invariant are mostly studied, and yet a quantitative measurement of topological phase transitions is still lacking. Here, we show the direct measurement of edge states and their localization lengths from survival probability. We employ photonic waveguide arrays to demonstrate the topological phase transitions based on the Su-Schrieffer-Heeger model. By measuring the survival probability at the lattice boundary, we show that in the long-time limit, the survival probability is P=(1-e^{-2/ξ_{loc}})^{2}, where ξ_{loc} is the localization length. This length derived from the survival probability is compared with the distance from the transition point, yielding a critical exponent of ν=0.94±0.04 at the phase boundary. Our experiment provides an alternative route to characterizing topological phase transitions and extracting their key physical quantities.

Allelic variation and genetic diversity of HMW glutenin subunits in Chinese wheat (Triticum aestivum L.) landraces and commercial cultivars.

Wheat landraces have abundant genetic variation at the Glu-1 loci, which is desirable germplasms for genetic enhancement of modern wheat varieties, especially for quality improvement. In the current study, we analyzed the allelic variations of the Glu-1 loci of 597 landraces and 926 commercial wheat varieties from the four major wheat-growing regions in China using SDS-PAGE. As results, alleles Null, 7+8, and 2+12 were the dominant HMW-GSs in wheat landraces. Compared to landraces, the commercial varieties contain higher frequencies of high-quality alleles, including 1, 7+9, 14+15 and 5+10. The genetic diversity of the four commercial wheat populations (alleles per locus (A) = 7.33, percent polymorphic loci (P) = 1.00, effective number of alleles per locus (Ae) = 2.347 and expected heterozygosity (He) = 0.563) was significantly higher than that of the landraces population, with the highest genetic diversity found in the Southwestern Winter Wheat Region population. The genetic diversity of HMW-GS is mainly present within the landraces and commercial wheat populations instead of between populations. The landraces were rich in rare subunits or alleles may provide germplasm resources for improving the quality of modern wheat.

Interspecific variation in the temperature response of mesophyll conductance is related to leaf anatomy.

Although mesophyll conductance (gm ) is known to be sensitive to temperature (T), the mechanisms underlying the temperature response of gm are not fully understood. In particular, it has yet to be established whether interspecific variation in gm -T relationships is associated with mesophyll anatomy and vein traits. In the present study, we measured the short-term response of gm in eight crop species, and leaf water potential (Ψleaf ) in five crop species over a temperature range of 15-35°C. The considered structural parameters are surface areas of mesophyll cells and chloroplasts facing intercellular airspaces per unit leaf area (Sm and Sc ), cell wall thickness (Tcw ), and vein length per area (VLA). We detected large interspecific variations in the temperature responses of gm and Ψleaf . The activation energy for gm (Ea,gm ) was found to be positively correlated with Sc , although it showed no correlation with Tcw . In contrast, VLA was positively correlated with the slope of the linear model of Ψleaf -T (a), whereas Ea,gm was marginally correlated with VLA and a. A two-component model was subsequently used to model gm -T relationships, and the mechanisms underlying the temperature response of gm are discussed. The data presented here indicate that leaf anatomy is a major determinant of the interspecific variation in gm -T relationships.

The structural correlations and the physiological functions of stomatal morphology and leaf structures in C3 annual crops.

MAIN CONCLUSION: This study suggests that stomatal and leaf structures are highly correlated, and mesophyll cell size is an important anatomical trait determining the coordination between stomatal size and mesophyll porosity. A comprehensive study of the correlations between the structural traits and on their relationships with gas exchange parameters may provide some useful information into leaf development and improvement in efficiencies of photosynthetic CO2 fixation and transpirational water loss. In the present study, nine plant materials from eight crop species were pot grown in a growth chamber. Leaf structural traits, gas exchange, and leaf nitrogen content were measured. We found that stomatal size, mesophyll cell size (MCS), and mesophyll porosity were positively correlated and that the surface areas of mesophyll cells and chloroplasts facing intercellular air spaces were positively correlated with both stomatal density and stomatal area per leaf area (SA). These results suggested that the developments of stomata and mesophyll cells are highly correlated among different crop species. Additionally, MCS was positively correlated with leaf thickness and negatively correlated with leaf density and leaf mass per area, which indicated that MCS might play an important role in leaf structural investments and physiological functions among species. In summary, this study illustrates the correlations between stomatal and mesophyll structures, and it highlights the importance of considering the covariations among leaf traits with the intent of improving photosynthesis and iWUE.

Near-Field Modulation of Differently Oriented Single Photon Emitters with A Plasmonic Probe.

Single photon emitters (SPEs) are critical components of photon-based quantum technology. Recently, the interaction between surface plasmons and emitters has attracted increasing attention because of its potential to improve the quality of single-photon sources through stronger light-matter interactions. In this work, we use a hybrid plasmonic probe composed of a fiber taper and silver nanowire to controllably modulate the radiation properties of SPEs with differently oriented polarization. For out-of-plane oriented SPEs such as single CdSe quantum dots, the radiation lifetime could be reduced by a factor as large as seven; for in-plane oriented SPEs such as hBN defect SPEs, the average modulation amplitude varied from 0.69 to 1.23, depending on the position of the probe. The experimental results were highly consistent with the simulations and theory. This work provides an efficient approach for optimizing the properties of SPEs for quantum photonic integration.