Identification and bioinformatic analysis of the CaCesA/Csls family members and the expression of the CaCslD1 in the flower buds of CMS/Rf system in pepper.

The cellulose synthase gene superfamily contains cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families, which synthesize cellulose and hemicellulose in plant cell walls and play a crucial role in plant growth and development. However, the CesA/Csl gene family has not been reported in pepper. Therefore, the genome-wide research of the CaCesA/CaCsl gene family was conducted in pepper. In this study, a total of 39 CaCesA/CaCsls genes (10 CesAs genes and 29 Csls genes) were identified in pepper and unevenly distributed on 11 chromosomes. These CaCesA/Csls were divided into seven subfamilies (CesAs, CslAs, CslBs, CslCs, CslDs, CslEs, CslGs), and most of CaCesA/Csls genes are closely related to AtCesA/Csls genes. The cis-acting elements in the promoters of CaCesA/Csls genes are mainly related to hormone response and stress response. There are ten collinear gene pairs between the CesA/Csls gene family of pepper and Arabidopsis, and four fragment duplication gene pairs of the CaCesA/Csls genes were discovered. RNA-seq analysis shows that the majority of CaCesA/Csls are expressed in a variety of plant tissues, indicating that most CaCesA/Csls gene expression patterns are not organ-specific, and CaCslD1/D4 have the highest expression in anthers, followed by petal, ovary, and F9. RNA-seq analysis shows that most CaCesA/Csls are responsive to five hormones (IAA, GA3, ABA, SA, and MeJA). The tissue-specific expression analysis of the CaCslD1 gene shows that the CaCslD1 gene is expressed specifically in flowers. In the flower buds IV of cytoplasmic male sterility (CMS) and its restoration of fertility (Rf) system, CaCslD1 reach the highest expression respectively. However, the relative expression level of CaCslD1 in the fertile accessions is extremely significantly higher than in the sterile accessions. This study shows an overall understanding of the CaCesA/Csls gene family and provides a new insight for understanding the function of CaCslD1 in pollen development and exploring the fertility restoration of CMS in pepper.

Comparative transcriptional analysis of Capsicum flower buds between a sterile flower pool and a restorer flower pool provides insight into the regulation of fertility restoration.

BACKGROUND: Cytoplasmic male sterility (CMS) and its restoration of fertility (Rf) system is an important mechanism to produce F1 hybrid seeds. Understanding the interaction that controls restoration at a molecular level will benefit plant breeders. The CMS is caused by the interaction between mitochondrial and nuclear genes, with the CMS phenotype failing to produce functional anthers, pollen, or male gametes. Thus, understanding the complex processes of anther and pollen development is a prerequisite for understanding the CMS system. Currently it is accepted that the Rf gene in the nucleus restores the fertility of CMS, however the Rf gene has not been cloned. In this study, CMS line 8A and the Rf line R1, as well as a sterile pool (SP) of accessions and a restorer pool (RP) of accessions analyzed the differentially expressed genes (DEGs) between CMS and its fertility restorer using the conjunction of RNA sequencing and bulk segregation analysis. RESULTS: A total of 2274 genes were up-regulated in R1 as compared to 8A, and 1490 genes were up-regulated in RP as compared to SP. There were 891 genes up-regulated in both restorer accessions, R1 and RP, as compared to both sterile accessions, 8A and SP. Through annotation and expression analysis of co-up-regulated expressed genes, eight genes related to fertility restoration were selected. These genes encode putative fructokinase, phosphatidylinositol 4-phosphate 5-kinase, pectate lyase, exopolygalacturonase, pectinesterase, cellulose synthase, fasciclin-like arabinogalactan protein and phosphoinositide phospholipase C. In addition, a phosphatidylinositol signaling system and an inositol phosphate metabolism related to the fertility restorer of CMS were ranked as the most likely pathway for affecting the restoration of fertility in pepper. CONCLUSIONS: Our study revealed that eight genes were related to the restoration of fertility, which provides new insight into understanding the molecular mechanism of fertility restoration of CMS in Capsicum.

In-Situ TEM Investigation of Helium Implantation in Ni-SiOC Nanocomposites.

Ni-SiOC nanocomposites maintain crystal-amorphous dual-phase nanostructures after high-temperature annealing at different temperatures (600 °C, 800 °C and 1000 °C), while the feature sizes of crystal Ni and amorphous SiOC increase with the annealing temperature. Corresponding to the dual-phase nanostructures, Ni-SiOC nanocomposites exhibit a high strength and good plastic flow stability. In this study, we conducted a He implantation in Ni-SiOC nanocomposites at 300 °C by in-situ transmission electron microscope (TEM) irradiation test. In-situ TEM irradiation revealed that both crystal Ni and amorphous SiOC maintain stability under He irradiation. The 600 °C annealed sample presents a better He irradiation resistance, as manifested by a smaller He-bubble size and lower density. Both the grain boundary and crystal-amorphous phase boundary act as a sink to absorb He and irradiation-induced defects in the Ni matrix. More importantly, amorphous SiOC ceramic is immune to He irradiation damage, contributing to the He irradiation resistance of Ni alloy.

Crystalline-Amorphous Nanostructures: Microstructure, Property and Modelling.

Crystalline metals generally exhibit good deformability but low strength and poor irradiation tolerance. Amorphous materials in general display poor deformability but high strength and good irradiation tolerance. Interestingly, refining characteristic size can enhance the flow strength of crystalline metals and the deformability of amorphous materials. Thus, crystalline-amorphous nanostructures can exhibit an enhanced strength and an improved plastic flow stability. In addition, high-density interfaces can trap radiation-induced defects and accommodate free volume fluctuation. In this article, we review crystalline-amorphous nanocomposites with characteristic microstructures including nanolaminates, core-shell microstructures, and crystalline/amorphous-based dual-phase nanocomposites. The focus is put on synthesis of characteristic microstructures, deformation behaviors, and multiscale materials modelling.

Genome-wide identification of RUB activating enzyme and conjugating enzyme gene families and their expression analysis under abiotic stresses in Capsicum annuum.

NEDD8/RUB, as a ubiquitin-like protein, participates in the post-translational modification of protein and requires unique E1, E2, and E3 enzymes to bind to its substrate. The RUB E1 activating enzyme and E2 conjugating enzyme play a significant role in the neddylation. However, it is unknown whether RUB E1 and E2 exist in pepper and what its function is. In this study, a total of three putative RUB E1 and five RUB E2 genes have been identified in the pepper genome. Subsequently, their physical and chemical properties, gene structure, conserved domains and motifs, phylogenetic relationship, and cis-acting elements were analyzed. The structure and conserved domain of RUB E1 and E2 are similar to that of Arabidopsis and tomato. The RUB E1 and E2 genes were randomly distributed on seven chromosomes, and there were two pairs of collinearity between pepper and Arabidopsis and eight pairs of collinearity between pepper and tomato. Phylogenetic analysis reveals that RUB E1 and E2 genes of pepper have a closer relationship with that of tomato, potato, and Nicotiana attenuate. The cis-elements of RUB E1 and E2 genes contained hormone response and stress response. RUB E1 and E2 genes were expressed in at least one tissue and CaRCE1.3 and CaRCE2.1 were exclusively expressed in flowers and anthers. Moreover, the expression of RUB E1 genes (CaECR1, CaAXR1.1, and CaAXR1.2) and RUB E2 genes (CaRCE1.1, CaRCE1.2, and CaRCE2.1) was increased to varying degrees under low-temperature, drought, salt, ABA, and IAA treatments, while CaRCE1.3 and CaRCE2.2 were down-regulated under low-temperature treatment. In addition, these genes were hardly expressed under MeJA treatment. In summary, this study provides a theoretical foundation to explore the role of RUB E1 and E2 in the response of plants to stress.

Identification and relative expression analysis of CaFRK gene family in pepper.

Fructokinase is the main catalytic enzyme for fructose phosphorylation and can also act as a glucose receptor and signal molecule to regulate the metabolism of plants, which plays an important role in plant growth and development. In this study, the CaFRK gene family and their molecular characteristics are systematically identified and analyzed, and the specific expression of CaFRKs under different tissues, abiotic stresses and hormone treatments were explored. Nine FRK genes were authenticated in pepper genome database, which were dispersedly distributed on eight reference chromosomes and predicted to localize in the cytoplasm. Many cis-acting elements that respond to light, different stresses, hormones and tissue-specific expression were found in the promoters of CaFRKs. FRK proteins of four species including Capsicum annuum, Arabidopsis thaliana, Solanum lycopersicum and Oryza sativa were divided into four groups via phylogenetic analysis. The collinearity analysis showed that there were two collinear gene pairs between CaFRKs and AtFRKs. In addition, it was significantly found that CaFRK9 expressed far higher in flower than other tissues, and the relative expression of CaFRK9 was gradually enhanced with the development of flower buds in fertile accessions, 8B, R1 and F1. Nevertheless, CaFRK9 hardly expressed in all stages of cytoplasmic male sterile lines. Based on the quantitative real-time PCR, most of CaFRK genes showed significant up-regulation under low-temperature, NaCl and PEG6000 treatments. On the contrary, the expression levels of most CaFRKs revealed a various trend in response to hormone treatments (IAA, ABA, GA3, SA and MeJA). This study systematically analyzed CaFRK gene family and studied its expression pattern, which lay the foundation of CaFRK genes cloning and functional verification response to abiotic stresses, and provides new insights into exploring the CaFRK genes on the pollen development in pepper. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03196-1.

Identification and expression analysis of phospholipase C family genes between different male fertility accessions in pepper.

Phospholipase C (PLC) is one of the major lipid-hydrolyzing enzymes, involved in lipid-mediating signal pathway. PLCs have been found to play a significant role in the growth and development of plants. In this study, the genome-wide identification and characteristic analysis of CaPLC family genes in pepper were conducted and the expression of two CaPLC genes were investigated. The results showed that a total of 11 CaPLC family genes were systematically identified, which were distributed on five chromosomes and divided into two groups based on their evolutionary relevance. Some cis-elements responding to different hormones and stresses were screened in the promoters of CaPLC genes. Quantitative real-time PCR indicated that the expression of CaPIPLC1 and CaPIPLC5 in flowers were dozens of times higher than in other tissues. In addition, with the development of flower buds, the relative expressions of CaPIPLC1 and CaPIPLC5 gradually increased in fertile materials R1 and F1. However, no expression of CaPIPLC1 and CaPIPLC5 were detected at all developmental stages of cytoplasmic male sterile lines (CMS) compared with fertile accessions. The study revealed the number and characteristics of the CaPLC family genes, which supplied a basic and systematic understanding of CaPLC family. In addition, these findings provided new insights into the role of CaPLC genes in pollen development and fertility restoration in pepper.

Enhancing strength and ductility via crystalline-amorphous nanoarchitectures in TiZr-based alloys.

Crystalline-amorphous composite have the potential to achieve high strength and high ductility through manipulation of their microstructures. Here, we fabricate a TiZr-based alloy with micrometer-size equiaxed grains that are made up of three-dimensional bicontinuous crystalline-amorphous nanoarchitectures (3D-BCANs). In situ tension and compression tests reveal that the BCANs exhibit enhanced ductility and strain hardening capability compared to both amorphous and crystalline phases, which impart ultra-high yield strength (~1.80 GPa), ultimate tensile strength (~2.3 GPa), and large uniform ductility (~7.0%) into the TiZr-based alloy. Experiments combined with finite element simulations reveal the synergetic deformation mechanisms; i.e., the amorphous phase imposes extra strain hardening to crystalline domains while crystalline domains prevent the premature shear localization in the amorphous phases. These mechanisms endow our material with an effective strength-ductility-strain hardening combination.

Genome-wide identification of superoxide dismutase gene families and their expression patterns under low-temperature, salt and osmotic stresses in watermelon and melon.

The growth and development of watermelon and melon are affected by abiotic stresses such as cold, salinity and drought. Plant superoxide dismutase (SOD) proteins exerted great effects on plant growth, development and response to abiotic stresses. However, little is known about the characteristics of watermelon and melon SOD gene families and their expression patterns under abiotic stresses. In this study, the genome-wide identification of SOD genes and their expression patterns under abiotic stresses has been done in watermelon and melon. Seven SODs were identified in watermelon and melon, respectively. Chromosome location indicated that the SODs were dispersedly distributed on 4-6 chromosomes. Almost all the SOD proteins contained 300 amino acids or less and the intron numbers of SODs ranged from 5 to 7. On the basis of phylogenetic analysis, the SODs were classified into six sub-groups which was also verified by similar motif composition, gene structure and sub-cellular location. Gene ontology analysis displayed that many SOD proteins participated in binding, catalytic, antioxidant activity and stimulus-response. Cis-regulatory elements related to stresses and hormones were found in the promoters of the SODs. Based on the quantitative real-time PCR, most of CmSOD and ClSOD genes showed obvious up-regulation under low-temperature, NaCl and PEG6000 treatments. The abiotic stress-responsive SOD genes were identified to improve watermelon and melon tolerance against abiotic stresses. This was a preliminary study to describe the genome-wide analysis of SOD gene family in watermelon and melon, and the results would facilitate further study of gene cloning and functional verification of SOD genes response to abiotic stresses in watermelon and melon. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02726-7.

A predicted NEDD8 conjugating enzyme gene identified as a Capsicum candidate Rf gene using bulk segregant RNA sequencing.

Cytoplasmic male sterility (CMS) is an important tool for producing F1 hybrids, which can exhibit heterosis. The companion system, restorer-of-fertility (Rf), is poorly understood at the molecular level and would be valuable in producing restorer lines for hybrid seed production. The identity of the Rf gene in Capsicum (pepper) is currently unclear. In this study, using bulked segregant RNA sequencing (BSR-seq), a strong candidate Rf gene, Capana06g002866, which is annotated as a NEDD8 conjugating enzyme E2, was identified. Capana06g002866 has an ORF of 555 bp in length encoding 184 amino acids; it can be cloned from F1 plants from the hybridization of the CMS line 8A and restorer line R1 but is not found in CMS line 8A. With qRT-PCR validation, Capana06g002866 was found to be upregulated in restorer accessions compared to sterile accessions. The relative expression in flower buds increased with the developmental stage in F1 plants, while the expression was very low in all flower bud stages of the CMS lines. These results provide new insights into the Rf gene in pepper and will be useful for other crops utilizing the CMS system.

Histopathology combined with transcriptome analyses reveals the mechanism of resistance to Meloidogyne incognita in Cucumis metuliferus.

Root-knot nematodes (Meloidogyne spp.) cause serious threat to cucumber production. Cucumis metuliferus, a relative of cucumber, is reported to be resistant to Meloidogyne incognita, yet the underlying resistance mechanism remains unclear. In this study, the response of resistant C. metuliferus accession PI482443 following nematode infection was studied in comparison with susceptible C. sativus cv. Jinlv No.3. Roots of selected Cucumis seedings were analysed using histological and biochemical techniques. Transcriptome changes of the resistance reaction were investigated by RNA-seq. The results showed that penetration and development of the nematode in resistant plants were reduced when compared to susceptible plants. Infection of a resistant genotype with M. incognita resulted in a hypersensitive reaction. The induction of phenylalanine ammonia lyase and peroxidase activities after infection was greater in resistant than susceptible roots. Several of the most relevant genes for phenylpropanoid biosynthesis, plant hormone signal transduction, and the plant-pathogen interaction pathway that are involved in resistance to the nematode were significantly altered. The resistance in C. metuliferus PI482443 to M. incognita was associated with reduced nematode penetration, retardation of nematode development, and hypersensitive necrosis. The expression of genes resulting in the deposition of lignin, toxic compounds synthesis, cell wall reinforcement, suppression of nematode feeding and resistance protein accumulation, and activation of several transcription factors might all contribute to the resistance response to the pest. These results may lead to a better understanding of the resistance mechanism and aid in the identification of potential targets resistant to pests for cucumber improvement.