Search

Pepper (Capsicum annuum) is an important vegetable crop that has been subjected to intensive breeding, resulting in limited genetic diversity, especially for sweet peppers. Previous studies have reported pepper draft genome assemblies using short read sequencing, but their capture of the extent of large structural variants (SVs), such as presence-absence variants (PAVs), inversions, and copy-number variants (CNVs) in the complex pepper genome falls short. In this study, we sequenced the genomes of representative sweet and hot pepper accessions by long-read and/or linked-read methods and advanced scaffolding technologies. First, we developed a high-quality reference genome for the sweet pepper cultivar Dempsey and then used the reference genome to identify SVs in 11 other pepper accessions and constructed a graph-based pan-genome for pepper. We annotated an average of 42 972 gene families in each pepper accession, defining a set of 19 662 core and 23 115 non-core gene families. The new pepper pan-genome includes informative variants, 222 159 PAVs, 12 322 CNVs, and 16 032 inversions. Pan-genome analysis revealed PAVs associated with important agricultural traits, including potyvirus resistance, fruit color, pungency, and pepper fruit orientation. Comparatively, a large number of genes are affected by PAVs, which is positively correlated with the high frequency of transposable elements (TEs), indicating TEs play a key role in shaping the genomic landscape of peppers. The datasets presented herein provide a powerful new genomic resource for genetic analysis and genome-assisted breeding for pepper improvement.

To develop plasma-resistant glass materials suitable for semiconductor etching processes, we introduced alkaline earth oxides (ROs) into a Li2O–Al2O3–SiO2 (LAS) glass. Analysis of glass properties with respect to the additives revealed that among the analyzed materials, the LAS material in which Li2O was partially replaced by MgO (MLAS) exhibited the most favorable characteristics, including a low dielectric constant (6.3) and thermal expansion coefficient (2.302 × 10−6/°C). The high performance of MLAS is attributed to the high ionic field strength of Mg2+ ions, which restricts the movement of Li+ ions under the influence of electric fields and thermal vibrations at elevated temperatures. When exposed to CF4/O2/Ar plasma, the etching speed of RO-doped glasses decreased compared with that of quartz and LAS glass, primarily owing to the generation of a high-sublimation-point fluoride layer on the surface. Herein, MLAS demonstrated the slowest etching speed, indicating exceptional plasma resistance. X-ray photoelectron spectroscopy analysis conducted immediately after plasma etching revealed that the oxidation-to-fluorination ratio of Li was the lowest for MLAS. This observation suggests that the presence of Mg2+ ions in the plasma discharge inhibits the migration of Li+ ions toward the surface, thereby contributing to the excellent plasma resistance of MLAS. [ABSTRACT FROM AUTHOR]

Optimization of equipment structure and process conditions is essential to obtain thin films with the required properties, such as film thickness, trapped charge density, leakage current, and memory characteristics, that ensure reliability of the corresponding device. In this study, we fabricated metal–insulator–semiconductor (MIS) structure capacitors using HfO2 thin films separately deposited by remote plasma (RP) atomic layer deposition (ALD) and direct-plasma (DP) ALD and determined the optimal process temperature by measuring the leakage current and breakdown strength as functions of process temperature. Additionally, we analyzed the effects of the plasma application method on the charge trapping properties of HfO2 thin films and properties of the interface between Si and HfO2. Subsequently, we synthesized charge-trapping memory (CTM) devices utilizing the deposited thin films as charge-trapping layers (CTLs) and evaluated their memory properties. The results indicated excellent memory window characteristics of the RP-HfO2 MIS capacitors compared to those of the DP-HfO2 MIS capacitors. Moreover, the memory characteristics of the RP-HfO2 CTM devices were outstanding as compared to those of the DP-HfO2 CTM devices. In conclusion, the methodology proposed herein can be useful for future implementations of multiple levels of charge-storage nonvolatile memories or synaptic devices that require many states. [ABSTRACT FROM AUTHOR]

Summary: The diverse colours of mature pepper (Capsicum spp.) fruit result from the accumulation of different carotenoids. The carotenoid biosynthetic pathway has been well elucidated in Solanaceous plants, and analysis of candidate genes involved in this process has revealed variations in carotenoid biosynthetic genes in Capsicum spp. However, the allelic variations revealed by previous studies could not fully explain the variation in fruit colour in Capsicum spp. due to technical difficulties in detecting allelic variation in multiple candidate genes in numerous samples. In this study, we uncovered allelic variations in six carotenoid biosynthetic genes, including phytoene synthase (PSY1,PSY2), lycopene β‐cyclase, β‐carotene hydroxylase, zeaxanthin epoxidase and capsanthin‐capsorubin synthase (CCS) genes, in 94 pepper accessions by single‐molecule real‐time (SMRT) sequencing. To investigate the relationship between allelic variations in the candidate genes and differences in fruit colour, we performed ultra‐performance liquid chromatography analysis using 43 accessions representing each allelic variation. Different combinations of dysfunctional mutations in PSY1 and CCS could explain variation in the compositions and levels of carotenoids in the accessions examined in this study. Our results demonstrate that SMRT sequencing technology can be used to rapidly identify allelic variation in target genes in various germplasms. The newly identified allelic variants will be useful for pepper breeding and for further analysis of carotenoid biosynthesis pathways. [ABSTRACT FROM AUTHOR]

High contents of cucurbitacin compounds result in a bitter taste in cucumbers. The Bi locus mapped to chromosome 6 is responsible for cucumber bitterness. The Bi gene encodes oxidosqualene cyclase, a key enzyme in the cucurbitacin biosynthetic pathway. Two alleles of the Bi gene responsible for the phenotypic variation in bitterness differ by a single point mutation in the coding region. An efficient genotyping system is necessary to allow breeders to screen for bitterness alleles in their breeding programs. In the present study, the single nucleotide polymorphism located within the Bi gene, which is directly linked to cucumber bitterness, was utilized for gene-based marker development. We developed reliable and cost-effective high-resolution melting (HRM)- and Kompetitive Allele-Specific PCR (KASP)-based molecular markers (BiHRM1 and Bi-KASP). These gene-based markers should enhance the accuracy and effectiveness of marker-assisted selection for bitter-free cucumber lines in cucumber breeding programs. [ABSTRACT FROM AUTHOR]