Cis-regulatory elements (CREs) orchestrate the spatiotemporal precision of gene expression that underlies plant development, adaptation, and domestication. Decoding the cis-regulatory grammar of plant genomes remains a central challenge in modern biology, with profound implications for programmable crop engineering. Here, recent conceptual and technological advances are synthesized to reshape our understanding of plant CREs. This review first argues that CRE function is not only an intrinsic property of DNA sequence alone but also emerges from a multidimensional context, including chromatin accessibility, histone modifications, three-dimensional genome topology, and cell type-specific regulatory landscapes. Furthermore, the convergence of single-cell epigenomics, high-throughput functional assays, and CRISPR-based dissection has begun to unravel this contextual grammar, revealing the computational principles governing transcriptional regulation. Critically, we propose that artificial intelligence (AI) platforms are catalyzing an ongoing transition from descriptive discovery to predictive engineering, wherein these platforms outperform natural evolution in designing synthetic CREs. Finally, a roadmap is outlined toward a plant regulatory grammar foundation model, which will enable truly predictive engineering of gene expression when fine-tuned for specific tasks. Collectively, the integration of single-cell resolution maps, precise genome editing, AI-driven design, and regulatory-compliant delivery systems promises to transform our ability to reprogram plant gene regulation for next-generation agriculture, bridging the gap between foundational regulatory biology and tangible crop improvement.

Femtosecond laser processing is an important approach for machining single crystal diamond (SCD), owing to the minimal thermal damage and high machining precision. A thorough understanding of the microscopic interaction mechanisms involved in double pulse femtosecond laser ablation on SCD is of critical importance for improving ablation efficiency under different energy density ratios and pulse delay times. In this work, the microscopic ablation behavior of SCD is investigated based on the two-temperature model and molecular dynamics under varying laser energy density ratios, pulse delay times, and wavelengths. It is found that significantly improved ablation performance of SCD is achieved under double pulse laser irradiation, compared with single pulse irradiation. It is demonstrated that the electron-lattice equilibrium temperature is elevated under an energy density ratio of 0.2:0.8. Correspondingly, more pronounced surface expansion, atomic sputtering, and stress fluctuations in SCD are observed. Meanwhile, effective preservation of the crystal quality in the non-ablated region can also be achieved. In contrast, the influence of the pulse delay time on the ablation behavior of SCD and the stress fluctuations is found to be relatively limited. These findings provide a theoretical basis for deeper understanding of the ablation efficiency improvement under double pulse femtosecond laser irradiation.

The ablation mechanism of single crystal diamond (SCD) is critical for understanding its micro-nanostructured evolution under ultrafast laser irradiation. The ablation behavior of SCD films under varying laser energy densities, pulse widths and wavelengths are investigated by two-temperature model and molecular dynamic (TTM-MD). It is indicated that the effects of energy density and wavelength on ablation are more significant than that of pulse width. The electron-lattice equilibrium temperature increases as the wavelength and energy density increases, and the corresponding ablation are more pronounced. Moreover, it reveals that the number of ejected atoms is increased with increasing energy density and wavelength while only a minor effect is exerted by pulse width. And the crystal quality in the non-ablation region is effectively preserved by laser ablation with long wavelength and high energy density. In addition, the stress in the free layer is influenced slightly by the pulse width, whereas greater stress fluctuations are induced by high energy density and long wavelength. Furthermore, the stress discontinuities are concentrated at the interface between the heated and the free layer of SCD film. These findings provide a theoretical foundation for understanding the microscopic mechanisms in ultrafast laser processing on SCD.

To deepen the understanding of peach aroma, we investigated the changes of volatile organic compound (VOC) profiles during fruit development in three fresh peach cultivars: 'Jiucui (JC)', 'Zhongyoupan No. 9 (ZYP9)' and 'Zhongyou No. 8 (ZY8)'. The classes and contents of VOCs changed significantly during fruit ripening. The representative VOC changes were categorized into three developmental stages, with the lowest volatile content observed during the middle stage. At maturity, ester-related volatiles increased significantly, dominating the VOC profiles and accounting for 78 %, 82 % and 88 % in JC, ZYP9 and ZY8, respectively, while alcohols decreased dramatically. Multivariate analysis identified 23, 21 and 20 potential volatile markers in JC, ZYP9 and ZY8, respectively, with 9 shared markers distinguishing the different developmental stages. Odor activity values (OAVs) and olfactometry analysis highlighted 36, 29, and 26 aroma-active compounds (OAV > 1) across the cultivars, with key contributors to the mature peach aroma including hexyl acetate (OAV 860-2896), (E)-2-hexenyl acetate, (Z)-3-hexenyl acetate, (E)-3-hexenyl acetate, linalool, and gamma-decalactone. The fruity aroma intensified as ripening progressed, with ZY8, a cultivar with a longer maturation cycle, exhibiting the highest odor intensity. This study offers insights into the dynamic changes in VOC profiles during peach development, highlighting key aroma-active compounds and their stage-specific variations.

A core interaction network associated with cluster buds trait was discovered in Brassica napus, and indoleacetic acid-induced protein 8 (IAA8) might affect the shoot apical meristem (SAM) development through IAA8-ARF5 complex → DRN → CLV3 pathway. B. napus is one of the important oilseed crops in China. However, the low level of mechanized production restricts the industry due to the infinite inflorescence characteristics of B. napus. Therefore, the cultivation of new varieties suitable for mechanized harvesting is one of the main objectives of rapeseed breeding. In this study, a screened natural mutant of B. napus with no branching or short branches in the bolting stage and a relatively shorter flowering period showed distinct traits of cluster buds and uniform maturity, which made it suitable for high-density cultivation and mechanized harvesting. Microscopic examination between the wild-type (WT) and the cluster buds mutant (cbm) lines was performed across developmental stages. The results showed that the SAM regions of the mutants were widened and exhibited multiple growth points due to the loss of apical dominance. Transcriptome sequencing of SAM regions in the WT and cbm lines identified 2497 differentially expressed genes (DEGs). Bulk segregant analysis (BSA) pinpointed five significant genomic regions associated with the cluster buds trait and identified 799 candidate genes. Finally, an interaction network associated with the cluster buds trait was constructed, within which IAA8 was revealed as a candidate gene to regulate the SAM development in B. napus. Taken together, the present study elucidates the potential molecular regulation mechanism of cluster buds trait and laid a solid theoretical foundation for the cultivation of new varieties suitable for close planting and mechanized harvesting in B. napus.

Yellow seed coat color (SCC) is a valuable trait in Brassica napus , which is significantly correlated to high seed oil content (SOC) and low seed lignocellulose content (SLC). However, no dominant yellow SCC genes were identified in B. napus . In this study, a dominant yellow SCC B. napus N53-2 was verified, and then 58,981 eQTLs and 25 trans-eQTL hotspots were identified in a double haploid population derived from N53-2 and black SCC material Ken-C8. A rare dominant allele DYSOC1 ( dominant gene of yellow seed coat color and improved seed oil content 1 ) was subsequently cloned in a trans-eQTL hotspot that colocated with SCC, SOC, and SLC QTL hotspot on ChrA09 through QTL fine mapping and multi-omics analysis. Transgenic experiments revealed that the expression of DYSOC1 produced yellow SCC seeds with significantly increased SOC and decreased SLC. Our result provides a rare dominant yellow SCC allele in B. napus , which has excellent potential for yellow SCC and high SOC rapeseed breeding.

Genetically modified (GM) crops have been provided as food and feed in over 70 countries in the world. But the concern is persisting on their comprehensive effects on human health status as feedstock. Physiological indicators detected in human beings or animals were explored to assess the health status after GM crop consumption. Here, a mammalian physiological indicators data set with seven metrics containing 25 physiological indicators was constructed by extracting the experimental raw data from the open access research articles published from January 2000 to September 2024 on GM maize, rice, and soybean consumption. To overcome the experimental heterogeneity in disparate model animals, limited animal number in each independent research, and statistical errors caused by different statistical methods, the multi-sourced data correlation analysis with DerSimonian and Laird random-effect model was employed. The result revealed that the concentration of glucose increased after nutritionally changed maize consumption (GLU, p < .01), but within the safe reference concentration range; the relative weight of liver increased after non-nutritional GM maize consumption (p < .05); the relative weight of kidney was the physiological indicators that significantly increased after nutritionally changed GM rice consumption (p < .05). No pathological characterizations in respective organs were reported. The findings indicated no pathological risks from GM crop consumption, though they emphasized the need for continued research into their metabolic and biochemical effects to ensure comprehensive food safety.

Vibration screening equipment has an extensive application profile in material screening, in which the displacement parameters can reveal the motion state of the material and affect the screening efficiency. These displacement parameters can be obtained by integrating the acceleration signal of the equipment. In this paper, to prevent the noise in the acceleration signal from further amplifying its negative effects on the subsequent integration, the acceleration signal is preprocessed by the complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) and wavelet threshold denoising. Besides, a hybrid integration displacement algorithm is utilized to mitigate the influence of integration errors. The consistent results between simulation and platform experiments demonstrate that CEEMDAN in combination with wavelet threshold denoising can effectively remove noise while retaining the main frequency signal. In addition, the displacement signal obtained by the hybrid integration algorithm proposed in this paper is closer to the original displacement signal. Compared with the 2nd time-domain integration, the 2nd frequency-domain integration, and the empirical mode decomposition integration methods, the integration method proposed in this paper achieves a smaller peak error, mean absolute error, and root mean square error. The experimental results corroborate the superiority of this method in the application of vibration screening equipment.

To explore the formation mechanism of Mg doping point defects in Al0.5Ga0.5N, the first principles methods are used. The formation energies of Al0.5Ga0.5N with Mg doping point defects under p-type condition are calculated and analyzed, and the corresponding donor properties are obtained. The results show that Mgi and VN-MgGa exhibit the lowest formation energies, which are more prone to display donor properties. Then, the charge distribution and bonding states indicate that Mg atom may form weak ionic bonds with N atoms in Al0.5Ga0.5N. Moreover, the band structure and density of states indicate that there appear some bands within the band gap of Al0.5Ga0.5N with VN-MgAl and VN-MgGa, and form some emission peaks, indicating that the VN-MgAl and VN-MgGa may introduce shallow energy levels. Meanwhile, the thermodynamic transition energy levels show that Mgi, MgAl, MgGa, Ali-MgAl, Gai-MgGa, VN-MgAl, and VN-MgGa are prone to undergo thermodynamic transitions near the VBM. Furthermore, the analyses of phonon dispersion spectra and binding energies show that VAl-MgAl is not stable while VN-MgGa exhibits the highest stability. The above studies reveal the formation mechanism of Mg doping point defects in Al0.5Ga0.5N, which is helpful for a deeper understanding of the growth and doping of AlGaN.

For the past decade, research on constructing large-scale plant protein–protein interaction (PPI) networks has mainly focused on model plants, and the capability of experimental-based large-scale PPI networks in these plants was thought to be significantly inferior to the actual number of protein interactions in plants (Altmann et al., 2020; Jones et al., 2014; Smakowska-Luzan et al., 2018; Wang et al., 2023). Currently, there is still a lack of experimentally-derived, large-scale PPI data in plants, especially with respect to protein interaction networks specific to seed organs (Rhee and Mutwil, 2014). In this study, we selected Brassica napus, one of the most important oil crops extensively cultivated worldwide, to construct BnSTINet: an experimental-based seed transcription factor (TF) interaction network. CrY2H-seq is a method that utilizes high-throughput screening of PPIs and relies on precise protein expression libraries (Trigg et al., 2017). Nonetheless, the relatively high cost of this method restricts its extensive application (Pruneda-Paz et al., 2014). We have innovated a method for constructing precise yeast expression vectors, referred to as In-Gate, resulting in a remarkable cost reduction of 93% and a nearly 50% reduction in experimental time compared to the conventional CrY2H-seq method (Figure S1). To screen the candidate TFs for constructing the interaction networks, the developing seeds at the linear embryo, early curved embryo, mid- curved embryo, late curved embryo and green embryo stages were collected for RNA-seq (Figure 1a). The expression patterns of TFs were evaluated, and 10 gene clusters potentially related to seed development and organic accumulation were identified (Figures S2 and S3). Totally, a data set consisting of 932 non-redundant TFs (NRTFs) was proposed to construct the TFs interaction network (Table S1). Almost all NRTFs with FPKMs value greater than 5 were included in the data set (99.1%) (Figure 1b). Those TFs were involved in seed development, such as hormone response, embryo development, seed coat development, lipid metabolism and light response, etc. (Table S2). In total, a precise protein expression library consisting of 1886 Y2H strains expressing TFs was constructed one by one. Identification of self-activating TFs and utilization of nanopore sequencing for detection of interacting recombinant sequences in TF interaction screening enhances the efficiency of detecting protein–protein interactions compared to the original CrY2H-seq (Figure 1c,d). Based on the above optimization and modification of CrY2H-seq technology, we term it mCrY2H-seq which lowers the application threshold for the construction of experimental-based large-scale PPI networks (Figure 1e,f). We loaded a set of 1886 TFs into the mCrY2H-seq pipeline. Self-activating pre-screen showed that 96 TFs were with self-activating characteristics in the bait library (Figure S4; Table S3). Nanopore sequencing generated a total of 64 113 valid reads, while 62 747 of these reads were concurrently mapped to two different TFs, accounting for 97.9% of the entire set of valid reads. Totally, 805 pairs of PPIs were obtained and the unannotated TFs occupied 25.9% of total TFs in the network (Figure 1g; Table S4). The reliability of the interacting pairs within the TF interaction network was confirmed through one-to-one verification using the array yeast two-hybrid method (Figures S5–S11). In the interaction network, multiple interaction subnetworks conserved in model plants were found, such as the Bzip family homodimers, nuclear factor complex, auxin and brassinosteroid (BR) signalling pathway TF interaction network (Figure S12). Some unreported interactions, such as the interaction between indole-3-acetic acid inducible protein 2 (BnaIAA2)/BnaIAA9, auxin response factor 6 (BnaARF6)/BnaIAA18 and BnaARF8/BnaIAA10 (Figure 1h). A total of 24 pairs of direct interactions and 54 pairs of indirect crosstalk were found between IAA, jasmonic acid (JA), abscisic acid (ABA), gibberellic acid (GA), BR and ethylene (ET) hormone signal pathways, which involved direct hormone crosstalk (Figure S13). The BnSTINet can be readily accessed and made available through a publicly accessible website with a simple three-step process (https://yanglab.hzau.edu.cn/BnIR/TF_regulation_network) (Figures 1i and S14). A candidate G-box regulating factor 6 (BnaGRF6) that interacts with WRINKLED1 (BnaWRI1, a star molecule known to control fatty acid synthesis) was selected for the function investigation. The interaction between BnaGRF6 and BnaWRI1 was confirmed by Y2H, bimolecular fluorescence complementation (Figure S15a,b). Overexpression of BnaGRF6 significantly increased seed oil content by 0.9%–4.38% compared with the control (Figure S15c,d). Overexpression of the BnaGRF6 gene in seeds facilitated the elevation of transcriptional levels of downstream regulatory target genes of BnaWRI1 (Figure S15e). In 2274 B. napus germplasm in BnIR, a frameshift mutation from A to ACT in the reading frame of BnaGRF6 homologous gene BnaA03G0592400ZS was found (Figure S 16 a, b and c) (Yang et al., 2023). The frameshift mutation variant mainly appears in semi-winter and spring rapeseed and is distributed in Asia, followed by Europe and North America (Figures 1j and S16d). Among 258 germplasm resources growing in the same environment, the average seed oil content of B. napus germplasm of the mutant variant was 41.74%, which was significantly lower than that of the reference type (43.42%) (Figure 1k). Here, we present a comprehensive research strategy for exploring the functions of polyploid crop genes and achieving molecular breeding advancements. This work was funded by the National Key Research and Development Program of China (2022YFD1200400) and the National Natural Science Foundation of China (32172087, 32072098). The authors declare no conflict of interest. ML and YY designed the research. YY wrote the article. YY, ZG, JJ, HH, WC, NR, JL, YL, HZ and ZL optimized the CrY2H-seq method, the expression vector construction, yeast mating and the recombinant plasmid information sequencing. YY, KC, HL, JH, WZ and YD collected and screened the transcript factors. ML, LZ, CF and YL revised the manuscript. Figure S1 Workflow of the In-Gate method. Figure S2 and S3 NRTF clusters in B. napus seed. Figure S4 Reads number of self-activating TFs in the mCrY2H-seq screen by nanopore sequencing. Figures S5–S11 Point-to-point validation of interactions by array yeast two-hybrid method. Figure S12 Conserved subnetwork within BnSTINet. Figure S13 The hormone crosstalk in BnSTINet. Figure S14 A simplified tutorial on retrieving TF interactions in BnSTINet database. Figure S15 Functional verification of BnaGRF6 affecting seed oil accumulation. Figure S16 Variation and phenotypic distribution of BnaGRF6. Table S1 Comprehensive TF list and expression data used for the BnSTINet construction. Table S2 Enriched metabolic pathways list of the candidate NRTFs for mCrY2H-seq interaction network construction. Table S3 List of self-activated transcription factors detected in the TF interaction network of seeds. Table S4 List of all interaction pairs in the transcription factor interaction network of seeds. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

The complex native point defects in Al0.5Ga0.5N are studied by density functional theory (DFT) and Heyd, Scuseria and Ernzerhof (HSE) hybrid functional. The lower formation energy as well as the donor and acceptor properties of Al0.5Ga0.5N with different complex native point defects are obtained. It is found that VGa-GaN exhibits donor property under p-type conditions while VAl-VN and VGa-VN exhibit acceptor properties under n-type conditions. Then, the density of states studies indicate that the defect peaks in the Al0.5Ga0.5N bandgap are all contributed by the defect atoms or atoms near the defects. Moreover, the charge distribution and bonding states analyses show that the Ali atom in VAl-Ali forms ionic bonds with the N atoms in Al0.5Ga0.5N and the antisite Ga atom in VGa-GaN forms ionic bonds with the N atoms in Al0.5Ga0.5N. Furthermore, the thermodynamic transition energy levels exploration reveals that VGa-GaN is most likely to undergo thermodynamic transitions. Meanwhile, the binding energies analyses elucidate that VGa-GaN is the most stable in Al0.5Ga0.5N. The formation mechanism of complex native point defects in Al0.5Ga0.5N has been revealed, which helps to get a deeper insight to the growth and doping of AlGaN and expands its application in high-power and high-frequency optoelectronic devices.

Isatis indigotica Fort. is a famous medicinal plant that is also used as a natural dye and functional vegetable. The characteristics of the I. indigotica fruit during development are largely unknown, information that is essential for the exploitation and seedlings cultivation of I. indigotica. In this study, the biochemical, metabolite characteristics and gene expression profiling of I. indigotica at four developmental stages were investigated. A total of 428 metabolites were detected and categorized into 17 categories. High contents of anthocyanins, especially cyanidin 3-glucoside, might contribute to the purple colouration of I. indigotica fruits. Moreover, dozens of flavonoid components, including taxifolin, quercetin, astragalin and isovitexin 2″-O-beta-D-glucoside, and several other active components were also up-regulated in mature fruits. The abundance of antioxidants might endow a significantly stronger antioxidant activity of mature I. indigotica fruits compared to many other reported species. Enrichment analyses revealed that flavonoid and anthocyanin biosynthesis genes were mostly enriched in up-regulated gene sets during fruit development. The up-regulated structural genes, including IiCHS, IiCHI, IiF3H, IiDFR, IiANS, IiFLS, IiUGT, and transcription factors such as IiMYBs, IibHLHs and IiNACs were identified as candidate regulators of flavonoid and anthocyanin biosynthetic pathway. Furthermore, biosynthesis of amino acids was enriched in all pairwise comparisons of metabolites in fruits at four developmental stages. The differential accumulation of amino acids might result from the differentially expressed genes involved in amino acid biosynthesis. Taken together, these findings provide a comprehensive understanding of metabolite profiling and gene expression patterns in I. indigotica fruit during maturity, which is useful for pharmaceutical extractions and seedling cultivation of I. indigotica.

Background: Low temperature pose significant challenges to peach cultivation, causing severe damage to peach buds and restricting production and distribution. Ethylene, an important phytohormone, plays a critical role in enhancing plant cold resistance. Structural genes and transcription factors involved in ethylene biosynthesis and signal transduction pathways are associated with cold resistance. However, no research has specifically addressed their roles in peach cold resistance.Methods: In this study, we aimed for cold-resistance gene discovery in cold-sensitive peach cultivar “21Shiji” (21SJ) and cold-resistance cultivar “Shijizhixing” (SJZX) using RNA-seq and gas chromatography.Results: The findings revealed that under cold stress conditions, ethylene biosynthesis in “SJZX” was significantly induced. Subsequently, a structural gene, PpACO1-1, involved in ethylene biosynthesis in peach buds was significantly upregulated and showed a higher correlation with ethylene release rate. To identify potential transcription factors associated with PpACO1-1 expression and ethylene signal transduction, weighted gene co-expression network analysis was conducted using RNA-seq data. Four transcription factors: PpERF2, PpNAC078, PpWRKY65 and PpbHLH112, were identified.Conclusion: These findings provide valuable theoretical insights for investigating the regulatory mechanisms of peach cold resistance and guiding breeding strategies.

To study the ablation mechanism of titanium (Ti) film under ultrafast laser, the irradiation process of Ti film under various pulse widths, energy densities, and wavelengths is analyzed by molecular dynamics combined with a two-temperature model (MD-TTM). The temperature distribution of Ti film under ultrafast laser irradiation is solved based on TTM and the ablation phenomenon is explored through MD simulation. It is found that the energy density and wavelength have a more significant impact on the ablation than pulse width. The shorter the laser wavelength, the smaller the penetration depth, and the more obvious the ablation phenomenon. The higher laser energy density and shorter wavelength result in higher irradiation temperature of the Ti film, wherein the ablation phenomenon becomes more pronounced. Moreover, the stress distribution of Ti film after ultrafast laser irradiation is investigated, and it can be found that the instantaneous laser irradiation induces compressive stress on the entire Ti film. The stress within the non-penetration layer is significantly higher than that within the penetration layer of the Ti film, and stress mutations are mainly concentrated at the interface between the penetration and non-penetration layers of the Ti film. Furthermore, the pulse width has little effect on the stress of the Ti film in the penetration layer while larger energy density and shorter wavelength lead to faster stress release.

Meiotic recombination not only maintains the stability of the chromosome structure but also creates genetic variations for adapting to changeable environments. A better understanding of the mechanism of crossover (CO) patterns at the population level is useful for crop improvement. However, there are limited cost-effective and universal methods to detect the recombination frequency at the population level in Brassica napus. Here, the Brassica 60K Illumina Infinium SNP array (Brassica 60K array) was used to systematically study the recombination landscape in a double haploid (DH) population of B. napus. It was found that COs were unevenly distributed across the whole genome, and a higher frequency of COs existed at the distal ends of each chromosome. A considerable number of genes (more than 30%) in the CO hot regions were associated with plant defense and regulation. In most tissues, the average gene expression level in the hot regions (CO frequency of greater than 2 cM/Mb) was significantly higher than that in the regions with a CO frequency of less than 1 cM/Mb. In addition, a bin map was constructed with 1995 recombination bins. For seed oil content, Bin 1131 to 1134, Bin 1308 to 1311, Bin 1864 to 1869, and Bin 2184 to 2230 were identified on chromosomes A08, A09, C03, and C06, respectively, which could explain 8.5%, 17.3%, 8.6%, and 3.9% of the phenotypic variation. These results could not only deepen our understanding of meiotic recombination in B. napus at the population level, and provide useful information for rapeseed breeding in the future, but also provided a reference for studying CO frequency in other species.

Abiotic stress of plants has serious consequences on the development of the apple industry. Nuclear pore complexes (NPCs) control nucleoplasmic transport and play an important role in the regulation of plant abiotic stress response. However, the effects of NPCs on apple salt and osmotic stress responses have not been reported yet. In this study, we analyzed the expression and function of NUCLEOPORIN 62 ( MdNup62) , a component of apple NPC. MdNup62 expression was significantly increased by salt and mannitol (simulated osmotic stress) treatment. The MdNup62 -overexpressing (OE) Arabidopsis and tomato lines exhibited significantly reduced salt stress tolerance, and MdNup62 -OE Arabidopsis lines exhibited reduced osmotic stress tolerance. We further studied the function of HEAT SHOCK FACTOR A1d (MdHSFA1d), the interacting protein of MdNup62, in salt and osmotic stress tolerance. In contrast to MdNup62 , MdHSFA1d -OE Arabidopsis lines showed significantly enhanced tolerance to salt and osmotic stress. Our findings suggest a possible interaction of MdNup62 with MdHSFA1d in the mediation of nuclear and cytoplasmic transport and the regulation of apple salt and osmotic stress tolerance. These results contribute to the understanding of the salt and osmotic stress response mechanism in apple.

The LncRNAs identified in Chinese sturgeon

Dissecting the complex regulatory mechanism of seed oil content (SOC) is one of the main research goals in Brassica napus. Increasing evidence suggests that genome architecture is linked to multiple biological functions. However, the effect of genome architecture on SOC regulation remains unclear. Here, we used high-throughput chromatin conformation capture to characterize differences in the three-dimensional (3D) landscape of genome architecture of seeds from two B. napus lines, N53-2 (with high SOC) and Ken-C8 (with low SOC). Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci (QTLs)/associated genomic regions (AGRs) for SOC. A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural variations in QTLs/AGRs of B. napus. The candidate gene BnaA09g48250D, which showed structural variation in a QTL/AGR on chrA09, was identified by fine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8. Overexpression and knockout of BnaA09g48250D led to significant increases and decreases in SOC, respectively, in the transgenic lines. Taken together, our results reveal the 3D genome architecture of B. napus seeds and the roles of genome structural variations in SOC regulation, enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.

Chinese sturgeon (Acipenser sinensis) is a critically endangered fish inhabiting the Yangtze River and Chinese coastal waters. Numerous research projects and conservation efforts have focused on artificial propagation and release to restore this endangered species. However, genomic and full-length transcriptomic sequencing of Chinese sturgeon has rarely been reported. In this study, a total of 10 Chinese sturgeon tissues were used for PacBio Iso-seq and RNA-seq analyses. A total of 19,538 full-length transcripts were obtained with sizes from 51 bp to 7,033 bp. Moreover, cluster analysis of gene families and phylogenetic analysis of 14 species were performed. Furthermore, lncRNAs and coding sequence (CDS) were identified in all Chinese sturgeon tissues. Finally, gene expression profiles and differentially expressed genes (DEGs) were analyzed among 10 tissues in Chinese sturgeon. Taken together, full-length transcripts and the gene expression profile from Chinese sturgeon tissues will provide gene sequences and expression information for future functional genomic study and be very helpful for comprehensive understanding of the genetic mechanism of endangerment in Chinese sturgeon.

Background Increasing seed oil content is the most important breeding goal in Brassica napus , and phenotyping is crucial to dissect its genetic basis in crops. To date, QTL mapping for oil content has been based on whole seeds, and the lipid distribution is far from uniform in different tissues of seeds in B. napus . In this case, the phenotype based on whole seeds was unable to sufficiently reveal the complex genetic characteristics of seed oil content. Results Here, the three-dimensional (3D) distribution of lipid was determined for B. napus seeds by magnetic resonance imaging (MRI) and 3D quantitative analysis, and ten novel oil content-related traits were obtained by subdividing the seeds. Based on a high-density genetic linkage map, 35 QTLs were identified for 4 tissues, the outer cotyledon (OC), inner cotyledon (IC), radicle (R) and seed coat (SC), which explained up to 13.76% of the phenotypic variation. Notably, 14 tissue-specific QTLs were reported for the first time, 7 of which were novel. Moreover, haplotype analysis showed that the favorable alleles for different seed tissues exhibited cumulative effects on oil content. Furthermore, tissue-specific transcriptomes revealed that more active energy and pyruvate metabolism influenced carbon flow in the IC, OC and R than in the SC at the early and middle seed development stages, thus affecting the distribution difference in oil content. Combining tissue-specific QTL mapping and transcriptomics, 86 important candidate genes associated with lipid metabolism were identified that underlie 19 unique QTLs, including the fatty acid synthesis rate-limiting enzyme-related gene CAC2 , in the QTLs for OC and IC. Conclusions The present study provides further insight into the genetic basis of seed oil content at the tissue-specific level.