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Background Long non-coding RNAs (lncRNAs), as important regulators, play important roles in plant growth and development. The expression and epigenetic regulation of lncRNAs remain uncharacterized generally in plant seeds, especially in the transient endosperm of the dicotyledons. Results In this study, we identified 11,840 candidate lncRNAs in 12 day-after-pollination sunflower endosperm by analyzing RNA-seq data. These lncRNAs were evenly distributed in all chromosomes and had specific features that were distinct from mRNAs including tissue-specificity expression, shorter and fewer exons. By GO analysis of protein coding genes showing strong correlation with the lncRNAs, we revealed that these lncRNAs potential function in many biological processes of seed development. Additionally, genome-wide DNA methylation analyses revealed that the level of DNA methylation at the transcription start sites was negatively correlated with gene expression levels in lncRNAs. Finally, 36 imprinted lncRNAs were identified including 32 maternally expressed lncRNAs and four paternally expressed lncRNAs. In CG and CHG context, DNA methylation levels of imprinted lncRNAs in the upstream and gene body regions were slightly lower in the endosperm than that in embryo tissues, which indicated that the maternal demethylation potentially induce the paternally bias expression of imprinted lncRNAs in sunflower endosperm. Conclusion Our findings not only identified and characterized lncRNAs on a genome-wide scale in the development of sunflower endosperm, but also provide novel insights into the parental effects and epigenetic regulation of lncRNAs in dicotyledonous seeds.

Drought tolerance in maize is a complex and polygenic trait, especially in the seedling stage. In plant breeding, such traits can be improved by genomic selection (GS), which has become a practical and effective tool. In the present study, a natural maize population named Northeast China core population (NCCP) consisting of 379 inbred lines were genotyped with diversity arrays technology (DArT) and genotyping-by-sequencing (GBS) platforms. Target traits of seedling emergence rate (ER), seedling plant height (SPH), and grain yield (GY) were evaluated under two natural drought environments in northeast China. adequate genetic variants have been found for genomic selection, they are not stable enough between two years. Similarly, the heritability of the three traits is not stable enough, and the heritabilities in 2019 (0.88, 0.82, 0.85 for ER, SPH, GY) are higher than that in 2020 (0.65, 0.53, 0.33) and cross-two-year (0.32, 0.26, 0.33). The current research obtained two kinds of marker sets: the SilicoDArT markers were from DArT-seq, and SNPs were from the GBS and DArT-seq. In total, a number of 11,865 SilicoDArT, 7,837 DArT's SNPs, and 91,003 GBS SNPs were used for analysis after quality control. The results of phylogenetic trees showed that the population was rich in consanguinity. Genomic prediction results showed that the average prediction accuracies estimated using the DArT SNP dataset under the 2-fold cross-validation scheme were 0.27, 0.19, and 0.33, for ER, SPH, and GY, respectively. The result of SilicoDArT is close to the SNPs from DArT-seq, those were 0.26, 0.22, and 0.33. For SPH, the prediction accuracies using SilicoDArT were more than ones using DArT SNP, In some cases, alignment to the reference genome results in a loss to the prediction. The trait with lower heritability can improve the prediction accuracy using filtering of linkage disequilibrium. For the same trait, the prediction accuracy estimated with two types of DArT markers was consistently higher than those estimated with the GBS SNPs under the same genotyping cost. Our results show the prediction accuracy has been improved in some cases of controlling population structure and marker quality, even when the density of the marker is reduced. In the initial maize breeding cycle, Silicodart markers can obtain higher prediction accuracy with a lower cost. However, higher marker density platforms i.e. GBS may play a role in the following breeding cycle for the long term. The natural drought experimental station can reduce the difficulty of phenotypic identification in a water-scarce environment. The accumulation of more yearly data will help to stabilize the heritability and improve predictive accuracy in maize breeding. The experimental design and model for drought resistance also need to be further developed.

While it is generally accepted that different maize varieties respond in various ways to cadmium (Cd) stress, the physiological mechanisms that determine how they respond are not well-defined. We do know, however, that antioxidant systems and sucrose metabolism help plants to cope with abiotic stresses, including stress from Cd. Seed is sensitive to Cd stress during germination stage. In this study, we investigated how the antioxidant systems, sucrose metabolism, abscisic acid (ABA) and gibberellin (GA3) concentration in two maize varieties with low (FY9) or high (SY33) sensitivities to Cd changed when Cd was added at 20 mg L−1 over different germination stages (3, 6, and 9 days). As Cd accumulated, the germination rate decreased, and growth was inhibited. The O2•-, malondialdehyde (MDA), and proline (Pro) concentrations, and the superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and lipoxygenase (LOX) activities increased compared to the CK (without Cd). The expression levels of three genes (ZmOPR2, ZmOPR5 and ZmPP2C6) that respond to oxidative stress increased differently in two varieties under Cd stress. The activity of the antioxidant system including the transcript levels of oxidative stress response genes were higher in Cd-tolerant variety, FY9, than in sensitive variety, SY33. And then, we also examined sucrose metabolism levels that were increased compared to the CK. However, it was more active in the Cd-sensitive variety, SY33. Therefore, these results also suggest that antioxidant systems are first respond to Cd stress in maize plants, and sucrose metabolism is cooperation and complement that are exposed to Cd.

Fertility restoration of cytoplasmic male sterility (CMS) in Capsicum annuum is controlled by multiple alleles of Restorer-of-fertility (Rf) genes. The isolation of additional Rf genes should therefore enrich the knowledge of CMS/Rf systems and accelerate their exploitation in hybrid seed production. In this study, the fertility restorer gene CaRfm of ‘0601 M’, a non-pungent bell pepper, was genetically mapped to a 1.2-cM region flanked by KASP markers S761 and S183. CaRfm was then physically mapped to a 128.96-Kb interval predicted from 24 recombinants with two co-segregated markers, S423 and S424. CaPPR6 encoding a pentatricopeptide repeat (PPR) protein was suggested as the most likely candidate gene for the CaRfm locus on the basis of sequence alignment as well as genotyping of tightly linked markers. In addition, molecular markers S1597 and S1609, which are immediately adjacent to CaRfm at 15.7 and 57.8-Kb respectively, were developed and applied to marker-assisted selection. The results provided friendly markers for breeding pepper restorer lines and laid the foundation for elucidating the male fertility restoration mechanism. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01109-9.

The CCT gene family plays important roles in diurnal rhythm and abiotic stress response, affecting crop growth and development, and thus yield. However, little information is available on the CCT family in foxtail millet (Setaria italica). In the present study, we identified 37 putative SiCCT genes from the foxtail millet genome. A phylogenetic tree was constructed from the predicted full-length SiCCT amino acid sequences, together with CCT proteins from rice and Arabidopsis as representatives of monocotyledonous and dicotyledonous plants, respectively. Based on the conserved structure and phylogenetic relationships, 13, 5, and 19 SiCCT proteins were classified in the COL, PRR, and CMF subfamilies, respectively. The gene structure and protein conserved motifs analysis exhibited highly similar compositions within the same subfamily. Whole-genome duplication analysis indicated that segmental duplication events played an important role in the expansion of the CCT gene family in foxtail millet. Analysis of transcriptome data showed that 16 SiCCT genes had significant diurnal rhythm oscillations. Under abiotic stress and exogenous hormonal treatment, the expression of many CMF subfamily genes was significantly changed. Especially after drought treatment, the expression of CMF subfamily genes except SiCCT32 was significantly up-regulated. This work provides valuable information for further study of the molecular mechanism of diurnal rhythm regulation, abiotic stress responses, and the identification of candidate genes for foxtail millet molecular breeding.

The sugar will eventually be exported transporters (SWEET) family is an important group of transport carriers for carbon partitioning in plants and has important functions in growth, development, and abiotic stress tolerance. Although the SWEET family is an important sugar transporter, little is known of the functions of the SWEET family in maize (Zea mays), especially in response to abiotic stresses. To further explore the response pattern of maize SWEET to abiotic stress, a bioinformatics-based approach was used to predict and identify the maize SWEET gene (ZmSWEET) family. Twenty-four ZmSWEET genes were identified using the MaizeGDB database. Phylogenetic analysis resolved these twenty-four genes into four clades. One tandem and five segmental duplication events were identified, which played a major role in ZmSWEET family expansion. Synteny analysis provided insight into the evolutionary characteristics of the ZmSWEET genes with those of three graminaceous crop species. A heatmap showed that most ZmSWEET genes responded to at least one type of abiotic stress. By an abscisic acid signaling pathway, among which five genes were significantly induced under NaCl treatment, eight were obviously up-regulated under PEG treatment and five were up-regulated under Cd stress, revealing their potential functions in response to abiotic stress. These findings will help to explain the evolutionary links of the ZmSWEET family and contribute to future studies on the functional characteristics of ZmSWEET genes, and then improve abiotic stress tolerance in maize through molecular breeding.

Sucrose metabolism contributes to the growth and development of plants and helps plants cope with abiotic stresses, including stress from Cd. Many of these processes are not well-defined, including the mechanism underlying the response of sucrose metabolism to Cd stress. In this study, we investigated how sucrose metabolism in maize varieties with low (FY9) and high (SY33) sensitivities to Cd changed in response to different levels of Cd (0 (control), 5, 10, and 20 mg L−1 Cd). The results showed that photosynthesis was impaired, and the biomass decreased, in both varieties of maize at different Cd concentrations. Cd inhibited the activities of sucrose phosphate synthase (SPS) and sucrose synthase (SS) (sucrose synthesis), and stimulated the activities of acid invertase (AI) and SS (sucrose hydrolysis). The total soluble sugar contents were higher in the Cd-treated seedlings than in the control. Also, Cd concentrations in the shoots were higher in SY33 than in FY9, and in the roots were lower in SY33 than in FY9. The decreases in the photosynthetic rate, synthesis of photosynthetic products, enzyme activity in sucrose synthesis direction, and increases in activity in hydrolysis direction were more obvious in SY33 (the sensitive variety) than in FY9 (the tolerant variety), and more photosynthetic products were converted into soluble sugar in SY33 than in FY9 as the Cd stress increased. The transcript levels of the sugar transporter genes also differed between the two varieties at different concentrations of Cd. These results suggest that sucrose metabolism may be a secondary response to Cd additions, and that the Cd-sensitive variety used more carbohydrates to defend against Cd stress rather than to support growth than the Cd-tolerant variety.

The interaction between 5-sulfosalicylic acid (SSA) and bovine serum albumin (BSA) at pH 7.40 was studied by fluorescence and UV–vis absorption spectroscopy at different temperatures. The results revealed that SSA caused the fluorescence quenching of BSA through a static quenching procedure. The binding constant K was measured by fluorescence quenching method. The thermodynamic parameters, ΔH and ΔS, were calculated to be 23.16 kJ mol−1>0 and 162.37 J mol−1 K−1>0, respectively, which suggested that the hydrophobic force played a major role in the reaction of SSA on BSA. The distance r between donor (BSA) and acceptor (SSA) was obtained according to the Forster non-radiation energy transfer theory. The results of synchronous fluorescence spectra, three-dimensional fluorescence spectra and far-UV circular dichroism spectra showed that the interaction between BSA and SSA induced conformational changes in BSA.

Previous video summarization studies focused on monocular videos, and the results would not be good if they were applied to multi-view videos directly, due to problems such as the redundancy in multiple views. In this paper, we present a method for summarizing multi-view videos. We construct a spatio-temporal shot graph and formulate the summarization problem as a graph labeling task. The spatio-temporal shot graph is derived from a hypergraph, which encodes the correlations with different attributes among multi-view video shots in hyperedges. We then partition the shot graph and identify clusters of event-centered shots with similar contents via random walks. The summarization result is generated through solving a multi-objective optimization problem based on shot importance evaluated using a Gaussian entropy fusion scheme. Different summarization objectives, such as minimum summary length and maximum information coverage, can be accomplished in the framework. Moreover, multi-level summarization can be achieved easily by configuring the optimization parameters. We also propose the multi-view storyboard and event board for presenting multi-view summaries. The storyboard naturally reflects correlations among multi-view summarized shots that describe the same important event. The event-board serially assembles event-centered multi-view shots in temporal order. Single video summary which facilitates quick browsing of the summarized multi-view video can be easily generated based on the event board representation.

We present a full pipeline for computing the medial axis transform of an arbitrary 2D shape. The instability of the medial axis transform is overcome by a pruning algorithm guided by a user-defined Hausdorff distance threshold. The stable medial axis transform is then approximated by spline curves in 3D to produce a smooth and compact representation. These spline curves are computed by minimizing the approximation error between the input shape and the shape represented by the medial axis transform. Our results on various 2D shapes suggest that our method is practical and effective, and yields faithful and compact representations of medial axis transforms of 2D shapes., Comment: GMP14 (Geometric Modeling and Processing)

Equilibrium, thermodynamic and kinetic studies were carried out for the biosorption of Pb(2+), Cd(2+) and Ni(2+) ions from aqueous solution using the grafted copolymerization-modified orange peel (OPAA). Langmuir and Freundlich isotherm models were applied to describe the biosorption of the metal ions onto OPAA. The influences of pH and contact time of solution on the biosorption were studied. Langmuir model fitted the equilibrium data better than the Freundlich isotherm. According to the Langmuir equation, the maximum uptake capacities for Pb(2+), Cd(2+) and Ni(2+) ions were 476.1, 293.3 and 162.6 mg g(-1), respectively. Compared with the unmodified orange peel, the biosorption capacity of the modified biomass increased 4.2-, 4.6- and 16.5-fold for Pb(2+), Cd(2+) and Ni(2+), respectively. The kinetics for Pb(2+), Cd(2+) and Ni(2+) ions biosorption followed the pseudo-second-order kinetics. The free energy changes (ΔG°) for Pb(2+), Cd(2+) and Ni(2+) ions biosorption process were found to be -3.77, -4.99 and -4.22 kJ mol(-1), respectively, which indicates the spontaneous nature of biosorption process. FTIR demonstrated that carboxyl and hydroxyl groups were involved in the biosorption of the metal ions. Desorption of Pb(2+), Cd(2+) and Ni(2+) ions from the biosorbent was effectively achieved in a 0.05 mol L(-1) HCl solution.