Development of an SNP marker set for marker-assisted backcrossing using genotyping-by-sequencing in tetraploid perilla.

High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2326 and 2454 SNP markers that spanned a total genetic distance of 2133 cM across 16 linkage groups and 2169 cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.

Transcriptome Analysis of Differentially Expressed Genes Associated with Salt Stress in Cowpea (Vigna unguiculata L.) during the Early Vegetative Stage.

Cowpea (Vigna unguiculata (L.), 2n = 22) is a tropical crop grown in arid and semiarid regions that is tolerant to abiotic stresses such as heat and drought. However, in these regions, salt in the soil is generally not eluted by rainwater, leading to salt stress for a variety of plant species. This study was conducted to identify genes related to salt stress using the comparative transcriptome analysis of cowpea germplasms with contrasting salt tolerance. Using the Illumina Novaseq 6000 platform, 1.1 billion high-quality short reads, with a total length of over 98.6 billion bp, were obtained from four cowpea germplasms. Of the differentially expressed genes identified for each salt tolerance type following RNA sequencing, 27 were shown to exhibit significant expression levels. These candidate genes were subsequently narrowed down using reference-sequencing analysis, and two salt stress-related genes (Vigun_02G076100 and Vigun_08G125100) with single-nucleotide polymorphism (SNP) variation were selected. Of the five SNPs identified in Vigun_02G076100, one that caused significant amino acid variation was identified, while all nucleotide variations in Vigun_08G125100 was classified as missing in the salt-resistant germplasms. The candidate genes and their variation, identified in this study provide, useful information for the development of molecular markers for cowpea breeding programs.

Strong and Tough Nacre-Inspired Graphene Oxide Composite with Hierarchically Similar Structure.

We report a graphene oxide (GO)-based composite, featuring GO/cross-linking agent (CA) nanoparticles, inspired by a nacre-like hierarchical structure present in nature. The as-prepared GO/CA composite was powdered to nanoscale particles and then mixed with pure GO to be GO/CA/GO (GCG) composite forming hierarchical GO/CA nanoasperities on the GO surface. The strength and toughness of the nacre-inspired GCG composite films were simultaneously improved by adjusting the nanoparticle concentration and hierarchical level of the GO-based films. Compared to pristine GO films and GO/CA composites, which exhibit a low level of hierarchy in their structures, the tensile strength and toughness of the GCG composites with higher hierarchy were enhanced 3.1 and 1.6 times and 47.6 and 10.9 times, respectively. Furthermore, a plausible mechanism of increasing mechanical properties based on nanoscale asperities and homogeneous interactions between GO and CA has been discussed.

Asymmetric Dichroic Colors in Stretchable Film with Embedded Au/Ag Alloy Nanoparticles.

We present a new type of stretchable dichroic film in which Au and Ag alloy nanoparticles (NPs) are dispersed in polydimethylsiloxane (PDMS). The alloy NPs are synthesized with different atomic compositions and sizes to modulate their plasmonic resonance frequencies and absorption and scattering cross sections. The PDMS dichroic film in which 100 nm alloy NPs with a Au/Ag ratio of 7:3 are dispersed shows exotic optical properties under tensile strain. When 40% tensile strain is applied, the film exhibits a strain-sensitive transmission and strain-insensitive reflection behavior in which the transmittance is increased up to 2.6 times, whereas the reflectance remains unchanged. Moreover, we demonstrate a stretchable anticounterfeiting film and a flexible dichroic sculpture fabricated with the PDMS composite. This work demonstrates a new type of plasmonic application that has great potential in various applications, such as special-purpose optical films, security patterns, and smart windows.

Angle-Insensitive Transmission and Reflection of Nanopatterned Dielectric Multilayer Films for Colorful Solar Cells.

Aesthetically appealing photovoltaic (PV) panels with colorful layers are used in numerous applications involving color matching with the surroundings. To develop a colored film for a PV system, appropriate optical properties such as high transparency and low angle sensitivity are necessary because the colored layers can reduce the efficiency of the PV system by causing variations in the transmittance and angle of incidence. Herein, we propose a facile fabrication method for bioinspired three-dimensional (3D) photonic crystal (PC) films that exhibit broad angle-insensitive transmission and reflection, for application in colorful PV. This structure, patterned on a sequentially stacked 11-layer film of SiO2 and TiO2, is fabricated via nanoimprint lithography and a one-step dry-etching process, without using a metal mask. The changes in transmission and reflection are observed via ultraviolet-visible spectroscopy and from the reflected images obtained under various angles. The transmittance dips of the 3D PC film shift by less than 10 nm in wavelength, for angles from 0 to 45°, indicating low angle dependency. In addition, the change in the observed color, with respect to the viewing position, is less in the fabricated film. Once the 3D PC film was added to a commercial PV cell, it exhibited a higher efficiency (approximately 6% upper) when compared to a cell with a one-dimensional PC film, during the duration of the experiment, from 0 to 30°. Thus, the proposed method demonstrates excellent potential for developing structural color films for achieving aesthetically appealing PV cells.

Identification of quantitative trait loci associated with flowering time in perilla using genotyping-by-sequencing.

Understanding the transition to the reproductive period is important for crop breeding. This information can facilitate the production of novel varieties that are better adapted to local environments or changing climatic conditions. Here, we report the development of a high-density linkage map based on genotyping-by-sequencing (GBS) for the genus perilla. Through GBS library construction and Illumina sequencing of an F2 population, a total of 9607 single-nucleotide polymorphism (SNP) markers were developed. The ten-group linkage map of 1309.39 cM contained 2518 markers, with an average marker density of 0.56 cM per linkage group (LG). Using this map, a total of six QTLs were identified. These quantitative trait loci (QTLs) are associated with three traits related to flowering time: days to visible flower bud, days to flowering, and days to maturity. Ortholog analysis conducted with known genes involved in the regulation of flowering time among different crop species identified GI, CO and ELF4 as putative perilla orthologs that are closely linked to the QTL regions associated with flowering time. These results provide a foundation that will be useful for future studies of flowering time in perilla using fine mapping, and marker-assisted selection for the development of new varieties of perilla.

Iridescent and Glossy Effect on Polymer Surface Using Micro-/Nanohierarchical Structure: Artificial Queen of the Night Tulip Petals.

Many petals in nature have a hierarchical structure that imparts various optical properties. Among these, the petals of the Queen of the Night tulip exhibit an iridescent and glossy color due to the diffraction and scattering of light. Herein, we report a bioinspired micro-/nanohierarchical structure that mimics Queen of the Night tulip petal surfaces. Using a method that combined soft lithography and UV-ozone treatment, we fabricated nanoscale line patterns with a linewidth of 600 nm on microwrinkles of 15 µm width and 3 µm height. Using optical microscopy in the dark-field mode and monochromatic light diffraction measurements, we found that these hierarchical structures on a poly(dimethylsiloxane) (PDMS) substrate synergistically improved the scattering and diffraction effects, unlike the pristine, nano-, and microstructures. In addition, using a dye-colored PDMS material, we fabricated artificial Queen of the Night petals with iridescent and glossy effects. They show great potential for a range of applications, such as coloring, smart displays, dynamic gratings, and light-control devices.

Surface-diffusion-limited growth of atomically thin WS2 crystals from core-shell nuclei.

Atomically thin transition metal dichalcogenides (TMDs) have recently attracted great attention since the unique and fascinating physical properties have been found in various TMDs, implying potential applications in next-generation devices. The progress towards developing new functional and high-performance devices based on TMDs, however, is limited by the difficulty in producing large-area monolayer TMDs due to a lack of knowledge of the growth processes of monolayer TMDs. In this work, we have investigated the growth processes of monolayer WS2 crystals using a thermal chemical vapor deposition method, in which the growth conditions were adjusted in a systematic manner. It was found that, after forming WO3-WS2 core-shell nanoparticles as nucleation sites on a substrate, the growth of three-dimensional WS2 islands proceeds by ripening and crystallization processes. Lateral growth of monolayer WS2 crystals subsequently occurs by the surface diffusion process of adatoms toward the step edge of the three-dimensional WS2 islands. Our results provide understanding of the growth processes of monolayer WS2 by using chemical vapor deposition methods.

Nacre-Mimetic Graphene Oxide/Cross-Linking Agent Composite Films with Superior Mechanical Properties.

We report a graphene oxide/cross-linking agent (GO/CA) composite inspired by the nacre structure. Based on the "brick-and-mortar" concept of nacre, graphene oxide and a cross-linking agent are covalently conjugated in the form of nacre. The mechanical characteristics of the nacre-mimetic GO/CA composite film can be controlled by adjusting the preparation method, degree of cross-linking, and cross-linking times. As a result, the cross-linking strategy can drastically enhance the tensile strength [142.9 ± 6.4 MPa (∼2.3-fold)], modulus [4.7 ± 0.36 GPa (∼15.7-fold)], and hardness [917.4 ± 85.7 MPa (∼9.0-fold)], which are superior to those of pristine materials. The cross-linking agent-based chemical bonding method for mechanically improved integration is mainly attributed to the formation of strong cross-linked networks between the GO-based 2D interfaces and CA. The facile fabrication process provides many opportunities to design advanced, robust, and integrated nacre-like GO/CA composites, which can be applied to future aerospace utilizations, electronic protectors, robotic elements, and permeable membranes.

A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae.

It is necessary for molecular breeders to overcome the difficulties in applying abundant genomic information to crop breeding. Candidate orthologs would be discovered more efficiently in less-studied crops if the information gained from studies of related crops were used. We developed a comparative analysis tool and web-based genome viewer to identify orthologous genes based synteny as well as sequence similarity between tomato, pepper and potato. The tool has a step-by-step interface with multiple viewing levels to support the easy and accurate exploration of functional orthologs. Furthermore, it provides access to single nucleotide-polymorphism markers from the massive genetic resource pool in order to accelerate the development of molecular markers for candidate orthologs in the Solanaceae. This tool provides a bridge between genome data and breeding by supporting effective marker development, data utilization and communication.Database URL: http://tgsol.seeders.co.kr/scomp/.

Molecular characterization of proton beam-induced mutations in soybean using genotyping-by-sequencing.

Proton beam irradiation is a next-generation technique to develop mutant crop varieties. The mutagenic effects and molecular mechanisms of radiation are important multi-disciplinary research subjects. This study was conducted to investigate the types of mutations induced in the soybean genome by proton beam irradiation. In total, 22 plants, including 10 M2 plants treated with proton beam irradiation at 118 and 239 Gy, each, and two wild-type plants (Daepung) were sequenced by genotyping-by-sequencing (GBS). In total, 7453 single nucleotide polymorphisms (SNPs) were detected in the 20 M2 plants, compared with the two wild-type controls. The SNP frequency was 1/36,976 bp with proton beam irradiation at 118 Gy, and 1/32,945 bp at 239 Gy. Of these, 3569 SNPs were detected in genic regions. We observed that proton beam irradiation induced more substitutions than small insertion-deletions (INDELs). Based on the mutagenic effect of proton beam irradiation, the frequency of transition mutations was shown to be higher than that of transversions. The proton beam-induced SNPs were distributed uniformly in most of the chromosomes. Gene ontology (GO) analysis showed that there were many genes involved in protein metabolic process under biological process, intracellular membrane-bounded organelle under cellular component, and nucleic acid binding under molecular function. This study could provide valuable information for investigating the potential mechanisms of mutation, and guidance for developing soybeans cultivars using mutation breeding.

Stomata-Inspired Photomechanical Ion Nanochannels Modified by Azobenzene Composites.

A low-powered and highly selective photomechanical sensor system mimicking stomata in the epidermis of leaves harvested from nature is demonstrated. This device uses a light-responsive composite consisting of 4-amino-1,1'-azobenzene-3,4'-disulfonic acid monosodium salt (AZO) and poly(diallyldimethylammonium chloride) (PDDA) coated on a membrane with tens of nanometer-size pores. The ionic current change through the pore channels as a function of pore size variation is then measured. The tran-cis isomerism of AZO-PDDA during light irradiation and the operation mechanism of photomechanical ion channel sensor are discussed and analyzed using UV-vis spectroscopy and atomic force microscopy analysis. It presents the discriminative current levels to the different light wavelengths. The response time of the photoreceptor is about 0.2 s and it consumes very low operating power (≈15 nW) at 0.1 V bias. In addition, it is found that the change of the pore diameter during the light irradiation is due to the photomechanical effect, which is capable of distinguishing light intensity and wavelength.

Effect of interlayer interactions on exciton luminescence in atomic-layered MoS2 crystals.

The atomic-layered semiconducting materials of transition metal dichalcogenides are considered effective light sources with both potential applications in thin and flexible optoelectronics and novel functionalities. In spite of the great interest in optoelectronic properties of two-dimensional transition metal dichalcogenides, the excitonic properties still need to be addressed, specifically in terms of the interlayer interactions. Here, we report the distinct behavior of the A and B excitons in the presence of interlayer interactions of layered MoS2 crystals. Micro-photoluminescence spectroscopic studies reveal that on the interlayer interactions in double layer MoS2 crystals, the emission quantum yield of the A exciton is drastically changed, whereas that of the B exciton remains nearly constant for both single and double layer MoS2 crystals. First-principles density functional theory calculations confirm that a significant charge redistribution occurs in the double layer MoS2 due to the interlayer interactions producing a local electric field at the interfacial region. Analogous to the quantum-confined Stark effect, we suggest that the distinct behavior of the A and B excitons can be explained by a simplified band-bending model.

Whole-transcriptome analyses of the Sapsaree, a Korean natural monument, before and after exercise-induced stress.

BACKGROUND: The Sapsaree (Canis familiaris) is a Korean native dog that is very friendly, protective, and loyal to its owner, and is registered as a natural monument in Korea (number: 368). To investigate large-scale gene expression profiles and identify the genes related to exercise-induced stress in the Sapsaree, we performed whole-transcriptome RNA sequencing and analyzed gene expression patterns before and after exercise performance. RESULTS: We identified 525 differentially expressed genes in ten dogs before and after exercise. Gene Ontology classification and KEGG pathway analysis revealed that the genes were mainly involved in metabolic processes, such as programmed cell death, protein metabolic process, phosphatidylinositol signaling system, and cation binding in cytoplasm. The ten Sapsarees could be divided into two groups based on the gene expression patterns before and after exercise. The two groups were significantly different in terms of their basic body type (p ≤ 0.05). Seven representative genes with significantly different expression patterns before and after exercise between the two groups were chosen and characterized. CONCLUSIONS: Body type had a significant effect on the patterns of differential gene expression induced by exercise. Whole-transcriptome sequencing is a useful method for investigating the biological characteristics of the Sapsaree and the large-scale genomic differences of canines in general.

Identification of candidate genes for an early-maturing soybean mutant by genome resequencing analysis.

Flowering is indicative of the transition from vegetative to reproductive phase, a critical event in the life cycle of plants. In this study, we performed whole genome resequencing by Illumina HiSeq to identify changes in flowering genes using an early-flowering phenotype of soybean mutant line Josaengserori (JS) derived from Korean landrace, Seoritae (SR), and we obtained mapped reads of 131,769,690 and 167,669,640 bp in JS and SR, respectively. From the whole genome sequencing results between JS and SR, we identified 332,821 polymorphic SNPs and 65,178 indels, respectively. Among these, 30 flowering genes were in SNPs and 25 were in indels. Among 30 flowering genes detected in SNPs, Glyma02g33040, Glyma06g22650, Glyma10g36600, Glyma13g01290, Glyma14g10530, Glyma16g01980, Glyma17g11040, Glyma18g53690, and Glyma20g29300 were non-synonymous substitutions between JS and SR. Changes in Glyma10g36600 (GI), Glya02g33040 (AGL18), Glyma17g11040 (TOC1), and Glyma14g10530 (ELF3) in JS affected the expression of GmFT2a and resulted in early flowering. These results provide insight into the regulatory pathways of flowering in soybean mutants and help to improve our knowledge of soybean mutation breeding.

De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa.

Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family.

High-throughput sequencing and de novo assembly of Brassica oleracea var. Capitata L. for transcriptome analysis.

BACKGROUND: The cabbage, Brassica oleracea var. capitata L., has a distinguishable phenotype within the genus Brassica. Despite the economic and genetic importance of cabbage, there is little genomic data for cabbage, and most studies of Brassica are focused on other species or other B. oleracea subspecies. The lack of genomic data for cabbage, a non-model organism, hinders research on its molecular biology. Hence, the construction of reliable transcriptomic data based on high-throughput sequencing technologies is needed to enhance our understanding of cabbage and provide genomic information for future work. METHODOLOGY/PRINCIPAL FINDINGS: We constructed cDNAs from total RNA isolated from the roots, leaves, flowers, seedlings, and calcium-limited seedling tissues of two cabbage genotypes: 102043 and 107140. We sequenced a total of six different samples using the Illumina HiSeq platform, producing 40.5 Gbp of sequence data comprising 401,454,986 short reads. We assembled 205,046 transcripts (≥ 200 bp) using the Velvet and Oases assembler and predicted 53,562 loci from the transcripts. We annotated 35,274 of the loci with 55,916 plant peptides in the Phytozome database. The average length of the annotated loci was 1,419 bp. We confirmed the reliability of the sequencing assembly using reverse-transcriptase PCR to identify tissue-specific gene candidates among the annotated loci. CONCLUSION: Our study provides valuable transcriptome sequence data for B. oleracea var. capitata L., offering a new resource for studying B. oleracea and closely related species. Our transcriptomic sequences will enhance the quality of gene annotation and functional analysis of the cabbage genome and serve as a material basis for future genomic research on cabbage. The sequencing data from this study can be used to develop molecular markers and to identify the extreme differences among the phenotypes of different species in the genus Brassica.

Genome-wide SNP calling using next generation sequencing data in tomato.

The tomato (Solanum lycopersicum L.) is a model plant for genome research in Solanaceae, as well as for studying crop breeding. Genome-wide single nucleotide polymorphisms (SNPs) are a valuable resource in genetic research and breeding. However, to do discovery of genome-wide SNPs, most methods require expensive high-depth sequencing. Here, we describe a method for SNP calling using a modified version of SAMtools that improved its sensitivity. We analyzed 90 Gb of raw sequence data from next-generation sequencing of two resequencing and seven transcriptome data sets from several tomato accessions. Our study identified 4,812,432 non-redundant SNPs. Moreover, the workflow of SNP calling was improved by aligning the reference genome with its own raw data. Using this approach, 131,785 SNPs were discovered from transcriptome data of seven accessions. In addition, 4,680,647 SNPs were identified from the genome of S. pimpinellifolium, which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of S. pimpinellifolium. Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the sufficient genome-wide SNP markers and very sensitive SNP calling method allow for application of marker assisted breeding and genome-wide association studies.

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species.

Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.

Ectopic expression of Capsicum-specific cell wall protein Capsicum annuum senescence-delaying 1 (CaSD1) delays senescence and induces trichome formation in Nicotiana benthamiana.

Secreted proteins are known to have multiple roles in plant development, metabolism, and stress response. In a previous study to understand the roles of secreted proteins, Capsicum annuum secreted proteins (CaS) were isolated by yeast secretion trap. Among the secreted proteins, we further characterized Capsicum annuum senescence-delaying 1 (CaSD1), a gene encoding a novel secreted protein that is present only in the genus Capsicum. The deduced CaSD1 contains multiple repeats of the amino acid sequence KPPIHNHKPTDYDRS. Interestingly, the number of repeats varied among cultivars and species in the Capsicum genus. CaSD1 is constitutively expressed in roots, and Agrobacterium-mediated transient overexpression of CaSD1 in Nicotiana benthamiana leaves resulted in delayed senescence with a dramatically increased number of trichomes and enlarged epidermal cells. Furthermore, senescence- and cell division-related genes were differentially regulated by CaSD1-overexpressing plants. These observations imply that the pepper-specific cell wall protein CaSD1 plays roles in plant growth and development by regulating cell division and differentiation.