Deep learning can predict subgenome dominance in ancient but not in neo/synthetic polyploidized genomes.

Deep learning offers new approaches to investigate the mechanisms underlying complex biological phenomena, such as subgenome dominance. Subgenome dominance refers to the dominant expression and/or biased fractionation of genes in one subgenome of allopolyploids, which has shaped the evolution of a large group of plants. However, the underlying cause of subgenome dominance remains elusive. Here, we adopt deep learning to construct two convolutional neural network (CNN) models, binary expression model (BEM) and homoeolog contrast model (HCM), to investigate the mechanism underlying subgenome dominance using DNA sequence and methylation sites. We apply these CNN models to analyze three representative polyploidization systems, Brassica, Gossypium, and Cucurbitaceae, each with available ancient and neo/synthetic polyploidized genomes. The BEM shows that DNA sequence of the promoter region can accurately predict whether a gene is expressed or not. More importantly, the HCM shows that the DNA sequence of the promoter region predicts dominant expression status between homoeologous gene pairs retained from ancient polyploidizations, thus predicting subgenome dominance associated with these events. However, HCM fails to predict gene expression dominance between new homoeologous gene pairs arising from the neo/synthetic polyploidizations. These results are consistent across the three plant polyploidization systems, indicating broad applicability of our models. Furthermore, the two models based on methylation sites produce similar results. These results show that subgenome dominance is associated with long-term sequence differentiation between the promoters of homoeologs, suggesting that subgenome expression dominance precedes and is the driving force or even the determining factor for sequence divergence between subgenomes following polyploidization.

Regional Active Transcription Associates with Homoeologous Exchange Breakpoints in Synthetic Brassica Tetraploids.

Polyploidization plays a crucial role in plant evolution and is becoming increasingly important in breeding. Structural variations and epigenomic repatterning have been observed in synthetic polyploidizations. However, the mechanisms underlying the occurrence and their effects on gene expression and phenotype remain unknown. Here, we investigated genome-wide large deletion/duplication regions (DelDups) and genomic methylation dynamics in leaf organs of progeny from the first eight generations of synthetic tetraploids derived from Chinese cabbage (Brassica rapa L. ssp. pekinensis) and cabbage (Brassica oleracea L. var. capitata). One- or two-copy DelDups, with a mean size of 5.70 Mb (400 kb - 65.85 Mb), occurred from the first generation of selfing and thereafter. The duplication of a fragment in one subgenome consistently coincided with the deletion of its syntenic fragment in the other subgenome, and vice versa, indicating that these DelDups were generated by homoeologous exchanges (HEs). Interestingly, the larger the genomic syntenic region, the higher the frequency of DelDups, further suggesting that the pairing of large homoeologous fragments is crucial for HEs. Moreover, we found that the active transcription of continuously distributed genes in local regions is positively associated with the occurrence of HE breakpoints. In addition, the expression of genes within DelDups exhibited a dosage effect, and plants with extra parental genomic fragments generally displayed phenotypes biased towards the corresponding parent. Genome-wide methylation fluctuated remarkably, which did not clearly affect gene expression on a large scale. Our findings provide insights into the early evolution of polyploid genomes, offering valuable knowledge for polyploidization-based breeding.

Fine mapping of meiotic crossovers in Brassica oleracea reveals patterns and variations depending on direction and combination of crosses.

Meiotic recombination is crucial for assuring proper segregation of parental chromosomes and generation of novel allelic combinations. As this process is tightly regulated, identifying factors influencing rate, and distribution of meiotic crossovers (COs) is of major importance, notably for plant breeding programs. However, high-resolution recombination maps are sparse in most crops including the Brassica genus and knowledge about intraspecific variation and sex differences is lacking. Here, we report fine-scale resolution recombination landscapes for 10 female and 10 male crosses in Brassica oleracea, by analyzing progenies of five large four-way-cross populations from two reciprocally crossed F1s per population. Parents are highly diverse inbred lines representing major crops, including broccoli, cauliflower, cabbage, kohlrabi, and kale. We produced approximately 4.56T Illumina data from 1248 progenies and identified 15 353 CO across the 10 reciprocal crosses, 51.13% of which being mapped to <10 kb. We revealed fairly similar Mb-scale recombination landscapes among all cross combinations and between the sexes, and provided evidence that these landscapes are largely independent of sequence divergence. We evidenced strong influence of gene density and large structural variations on CO formation in B. oleracea. Moreover, we found extensive variations in CO number depending on the direction and combination of the initial parents crossed with, for the first time, a striking interdependency between these factors. These data improve our current knowledge on meiotic recombination and are important for Brassica breeders.

Advances in the Modulation of Potato Tuber Dormancy and Sprouting.

The post-harvest phase of potato tuber dormancy and sprouting are essential in determining the economic value. The intricate transition from dormancy to active growth is influenced by multiple factors, including environmental factors, carbohydrate metabolism, and hormonal regulation. Well-established environmental factors such as temperature, humidity, and light play pivotal roles in these processes. However, recent research has expanded our understanding to encompass other novel influences such as magnetic fields, cold plasma treatment, and UV-C irradiation. Hormones like abscisic acid (ABA), gibberellic acid (GA), cytokinins (CK), auxin, and ethylene (ETH) act as crucial messengers, while brassinosteroids (BRs) have emerged as key modulators of potato tuber sprouting. In addition, jasmonates (JAs), strigolactones (SLs), and salicylic acid (SA) also regulate potato dormancy and sprouting. This review article delves into the intricate study of potato dormancy and sprouting, emphasizing the impact of environmental conditions, carbohydrate metabolism, and hormonal regulation. It explores how various environmental factors affect dormancy and sprouting processes. Additionally, it highlights the role of carbohydrates in potato tuber sprouting and the intricate hormonal interplay, particularly the role of BRs. This review underscores the complexity of these interactions and their importance in optimizing potato dormancy and sprouting for agricultural practices.

Transcriptome Analysis Reveals the Molecular Mechanisms of BR Negative Regulatory Factor StBIN2 Maintaining Tuber Dormancy.

Potato is an important food crop. After harvest, these tubers will undergo a period of dormancy. Brassinosteroids (BRs) are a new class of plant hormones that regulate plant growth and seed germination. In this study, 500 nM of BR was able to break the dormancy of tubers. Additionally, exogenous BR also upregulated BR signal transduction genes, except for StBIN2. StBIN2 is a negative regulator of BR, but its specific role in tuber dormancy remains unclear. Transgenic methods were used to regulate the expression level of StBIN2 in tubers. It was demonstrated that the overexpression of StBIN2 significantly prolonged tuber dormancy while silencing StBIN2 led to premature sprouting. To further investigate the effect of StBIN2 on tuber dormancy, RNA-Seq was used to analyze the differentially expressed genes in OE-StBIN2, RNAi-StBIN2, and WT tubers. The results showed that StBIN2 upregulated the expression of ABA signal transduction genes but inhibited the expression of lignin synthesis key genes. Meanwhile, it was also found that StBIN2 physically interacted with StSnRK2.2 and StCCJ9. These results indicate that StBIN2 maintains tuber dormancy by mediating ABA signal transduction and lignin synthesis. The findings of this study will help us better understand the molecular mechanisms underlying potato tuber dormancy and provide theoretical support for the development of new varieties using related genes.

Impact of family functioning on mental health problems of college students in China during COVID-19 pandemic and moderating role of coping style: a longitudinal study.

BACKGROUND: During the COVID-19 pandemic, college students were required to stay at home and maintain social distance for the entire spring semester of 2020. There is little research on how family functioning influenced mental health problems and how coping styles moderated the relationship between family functioning and mental health problems among college students during their stay-at-home period. METHODS: A total of 13,462 college students (age = 16-29 years) completed four online surveys between February and October 2020, namely the outbreak phase, remission phase, online study phase, and school reopening phase in Guangdong Province, China. Family functioning was assessed by the Family APGAR; coping styles were assessed by the Simplified Coping Style Questionnaire (SCSQ), depression symptoms and anxiety symptoms were evaluated by the Patient Health Questionnaire (PHQ-9) and the Generalized Anxiety Disorder Scale (GAD-7) respectively. Generalized estimating equations were used to assess associations between variables, the logit link function was used to estimate the odds ratio of different subgroups, the Newton-Raphson method was used to estimate parameters, and the Wald test was used to test the main effect and the interaction effect. RESULTS: The incidence rates of depression increased during the stay-at-home period from 33.87%, 95% CI (29.88%, 38.10%) to 40.08% 95% CI (35.76%, 44.55%) after schools reopened, χ2 = 193.68, p < 0.001. The incidence rates of anxiety increased from 17.45%, 95% CI (14.59%, 20.73%) to 26.53%, 95% CI (16.94%, 23.67%) over the entire period, χ2 = 195.74, p < 0.001. The percentages of students with highly functional, moderately dysfunctional and severely dysfunctional family functioning were 48.23%, 43.91 and 7.86% at T1 and 46.20%, 45.28%, and 8.52 at T4, respectively. The percentage of subjects with active coping style was 23.9%, negative coping style was 17.4%, strong response coping was 26.9%, and weak response coping was 31.7%. The incidence rate of depression and anxiety for different family functioning groups varied at different time points, and the interaction effect was significant (χ2 = 52.97, p < 0.001 and χ2 = 51.25, p < 0.001, respectively). The incidence rate of depression and anxiety for different family functioning groups with different coping styles also varied at different time points, the interaction effect was likewise significant (χ2 = 862.09, p < 0.001 and χ2 = 583.29, p < 0.001, respectively). CONCLUSIONS: Having a severely dysfunctional family and a negative coping style increase the incidence rates of depression and anxiety. These findings highlight the importance of paying special attention to college students' family functioning and promoting appropriate coping strategies during and after COVID-19.

StBIN2 Positively Regulates Potato Formation through Hormone and Sugar Signaling.

Potato is an important food crop worldwide. Brassinosteroids (BRs) are widely involved in plant growth and development, and BIN2 (brassinosteroid insensitive 2) is the negative regulator of their signal transduction. However, the function of BIN2 in the formation of potato tubers remains unclear. In this study, transgenic methods were used to regulate the expression level of StBIN2 in plants, and tuber related phenotypes were analyzed. The overexpression of StBIN2 significantly increased the number of potatoes formed per plant and the weight of potatoes in transgenic plants. In order to further explore the effect of StBIN2 on the formation of potato tubers, this study analyzed BRs, ABA hormone signal transduction, sucrose starch synthase activity, the expression levels of related genes, and interacting proteins. The results show that the overexpression of StBIN2 enhanced the downstream transmission of ABA signals. At the same time, the enzyme activity of the sugar transporter and the expression of synthetic genes were increased in potato plants overexpressing StBIN2, which also demonstrated the upregulation of sucrose and the expression of the starch synthesis gene. Apparently, StBIN2 affected the conversion and utilization of key substances such as glucose, sucrose, and starch in the process of potato formation so as to provide a material basis and energy preparation for forming potatoes. In addition, StBIN2 also promoted the expression of the tuber formation factors StSP6A and StS6K. Altogether, this investigation enriches the study on the mechanism through which StBIN2 regulates potato tuber formation and provides a theoretical basis for achieving a high and stable yield of potato.

Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata).

KEY MESSAGE: Correlations between morphological traits of cabbage rosette leaves and heads were found. Genome-wide association studies of these traits identified 50 robust quantitative trait loci in multiple years. Half of these loci affect both organs. Cabbage (Brassica oleracea var. capitata) is an economically important vegetable crop cultivated worldwide. Cabbage plants go through four vegetative stages: seedling, rosette, folding and heading. Rosette leaves are the largest leaves of cabbage plants and provide most of the energy needed to produce the leafy head. To understand the relationship and the genetic basis of leaf development and leafy head formation, 308 cabbage accessions were scored for rosette leaf and head traits in three-year field trials. Significant correlations were found between morphological traits of rosette leaves and heads, namely leaf area with the head area, height and width, and leaf width with the head area and head height, when heads were harvested at a fixed number of days after sowing. Fifty robust quantitative trait loci (QTLs) for rosette leaf and head traits distributed over all nine chromosomes were identified with genome-wide association studies. All these 50 loci were identified in multiple years and generally affect multiple traits. Twenty-five of the QTL were associated with both rosette leaf and leafy head traits. We discuss thirteen candidate genes identified in these QTL that are expressed in heading leaves, with an annotation related to auxin and other phytohormones, leaf development, and leaf polarity that likely play a role in leafy head development or rosette leaf expansion.

Prevalence and associated factors of depression, anxiety and suicidality among Chinese high school E-learning students during the COVID-19 lockdown.

BACKGROUND: The outbreak of Coronavirus disease (COVID-19) in 2019 and the resulting quarantine may have increased the prevalence of mental health problems in adolescents. The aim of this study was to explore the association between the effects of home-based learning during the pandemic and the risks of depression, anxiety, and suicidality among junior and senior high school students. METHODS: An online survey using Patient Health Questionnaire (PHQ-9) and Generalized Anxiety Disorder (GAD-7) was conducted between 12 to 30 April 2020, on a total of 39,751 students. Multivariable logistic regression analysis was used to analyze the risk factors of associated depression, anxiety and suicidality during the pandemic. RESULTS: Prevalence of depression, anxiety symptoms and suicidality found was 16.3% (95% CI: 16.0, 16.7), 10.3% (95% CI: 10.0, 10.6) and 20.3% (95% CI: 19.9, 20.7), respectively. Participants with female gender and in junior high school, with poor overall sleep quality and poor academic performance and very worried about being infected during COVID-19 were highly associated with the risk of depression, anxiety symptoms and suicidal ideation (all P<0.001). CONCLUSIONS: Prevalence of self-reported mental health problems for adolescents using home-based distance learning was high. Implementing measures (e.g., wearing face masks) and spending only moderate time focusing on COVID-19-related information could be protective factors for mental health. These results provide suggestions for teachers and policy makers regarding adolescent improving sleep quality (sufficient sleep) and academic performance and reducing worry about pandemic during quarantine to prevent mental health problems.

The Cysteine-Rich Peptide Snakin-2 Negatively Regulates Tubers Sprouting through Modulating Lignin Biosynthesis and H2O2 Accumulation in Potato.

Potato tuber dormancy is critical for the post-harvest quality. Snakin/Gibberellic Acid Stimulated in Arabidopsis (GASA) family genes are involved in the plants' defense against pathogens and in growth and development, but the effect of Snakin-2 (SN2) on tuber dormancy and sprouting is largely unknown. In this study, a transgenic approach was applied to manipulate the expression level of SN2 in tubers, and it demonstrated that StSN2 significantly controlled tuber sprouting, and silencing StSN2 resulted in a release of dormancy and overexpressing tubers showed a longer dormant period than that of the control. Further analyses revealed that the decrease expression level accelerated skin cracking and water loss. Metabolite analyses revealed that StSN2 significantly down-regulated the accumulation of lignin precursors in the periderm, and the change of lignin content was documented, a finding which was consistent with the precursors' level. Subsequently, proteomics found that cinnamyl alcohol dehydrogenase (CAD), caffeic acid O-methyltransferase (COMT) and peroxidase (Prx), the key proteins for lignin synthesis, were significantly up-regulated in silencing lines, and gene expression and enzyme activity analyses also supported this effect. Interestingly, we found that StSN2 physically interacts with three peroxidases catalyzing the oxidation and polymerization of lignin. In addition, SN2 altered the hydrogen peroxide (H2O2) content and the activities of superoxide dismutase (SOD) and catalase (CAT). These results suggest that StSN2 negatively regulates lignin biosynthesis and H2O2 accumulation, and ultimately inhibits the sprouting of potato tubers.

Design and Synthesis of Polymer Prodrugs for Improving Water-Solubility, Pharmacokinetic Behavior and Antitumor Efficacy of TXA9.

PURPOSE: TXA9, a novel cardiac glycoside, has a potent anti-proliferative effect against A549 human lung cancer cells, however, possesses a poor water-solubility and a rapid metabolic rate in vivo which limited the further development of TXA9. To overcome the shortcomings of TXA9, four polymer prodrugs of TXA9 were designed and synthesized. METHODS: Poly (ethylene glycol) monomethyl ether (mPEG) and α-tocopherol polyethylene glycol succinate (TPGS) were applied to modify TXA9 via carbonate ester and glycine linkers respectively to obtain four polymer prodrugs. The water-solubility and stability of prodrugs were studied in vitro while their pharmacokinetic behaviors and antitumor activity were investigated in vivo. RESULTS: The water-solubility of TXA9 was obviously increased and prodrugs with glycine linkers showed a better stability in rat plasma. Their pharmacokinetic investigation found that the t1/2 and AUC0-∞ of TPGS-Gly-TXA9 was increased by 80- and 9.6-fold compared with that of TXA9, which was more superior than the other three prodrugs. More importantly, the tumor inhibition rate of TPGS-Gly-TXA9 (43.81%) on A549 xenograft nude mice was significantly increased compared with that of TXA9 (25.26%). CONCLUSION: The above results suggested that TPGS-Gly-TXA9 possessed better antitumor efficiency than TXA9 and could be further investigated as an anti-cancer agent.

Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala).

BACKGROUND: Due to its variegated and colorful leaves, ornamental kale (Brassica oleracea L. var. acephala) has become a popular ornamental plant. In this study, we report the fine mapping and analysis of a candidate purple leaf gene using a backcross population and an F2 population derived from two parental lines: W1827 (with white leaves) and P1835 (with purple leaves). RESULTS: Genetic analysis indicated that the purple leaf trait is controlled by a single dominant gene, which we named BoPr. Using markers developed based on the reference genome '02-12', the BoPr gene was preliminarily mapped to a 280-kb interval of chromosome C09, with flanking markers M17 and BoID4714 at genetic distances of 4.3 cM and 1.5 cM, respectively. The recombination rate within this interval is almost 12 times higher than the usual level, which could be caused by assembly error for reference genome '02-12' at this interval. Primers were designed based on 'TO1000', another B. oleracea reference genome. Among the newly designed InDel markers, BRID485 and BRID490 were found to be the closest to BoPr, flanking the gene at genetic distances of 0.1 cM and 0.2 cM, respectively; the interval between the two markers is 44.8 kb (reference genome 'TO1000'). Seven annotated genes are located within the 44.8 kb genomic region, of which only Bo9g058630 shows high homology to AT5G42800 (dihydroflavonol reductase), which was identified as a candidate gene for BoPr. Blast analysis revealed that this 44.8 kb interval is located on an unanchored scaffold (Scaffold000035_P2) of '02-12', confirming the existence of assembly error at the interval between M17 and BoID4714 for reference genome '02-12'. CONCLUSIONS: This study identified a candidate gene for BoPr and lays a foundation for the cloning and functional analysis of this gene.

Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa.

Subgenome dominance is an important phenomenon observed in allopolyploids after whole genome duplication, in which one subgenome retains more genes as well as contributes more to the higher expressing gene copy of paralogous genes. To dissect the mechanism of subgenome dominance, we systematically investigated the relationships of gene expression, transposable element (TE) distribution and small RNA targeting, relating to the multicopy paralogous genes generated from whole genome triplication in Brassica rapa. The subgenome dominance was found to be regulated by a relatively stable factor established previously, then inherited by and shared among B. rapa varieties. In addition, we found a biased distribution of TEs between flanking regions of paralogous genes. Furthermore, the 24-nt small RNAs target TEs and are negatively correlated to the dominant expression of individual paralogous gene pairs. The biased distribution of TEs among subgenomes and the targeting of 24-nt small RNAs together produce the dominant expression phenomenon at a subgenome scale. Based on these findings, we propose a bucket hypothesis to illustrate subgenome dominance and hybrid vigor. Our findings and hypothesis are valuable for the evolutionary study of polyploids, and may shed light on studies of hybrid vigor, which is common to most species.

Retinal detachment with multiple macrocysts in Stickler syndrome: case report and review of the literature.

Background: Stickler syndrome is a hereditary connective tissue disorder associated with ocular, orofacial, musculoskeletal, and auditory impairments. Its main clinical characteristics include retinal detachment, hearing loss, and midface underdevelopment. In clinical practice, macrocyst is rarely reported in retinal detachment cases with Stickler syndrome. Case presentation: We report the case of a 7-year-old child who developed a rhegmatogenous retinal detachment (RRD) in the right eye, accompanied by multiple peripheral macrocysts. The detachment was successfully surgically repaired with vitrectomy, retinal laser photocoagulation, cryotherapy and silicone oil tamponade. During the operation, a mini-retinectomy in the outer layer of each macrocyst was made for vesicular drainage and retinal reattachment. Genetic testing identified a pathogenic point mutation variant (c.1693C>T; p.Arg565Cys) in exon 26 of the COL2A1 gene. Six-months after the operation, the retina remained attached with improvement of best corrected visual acuity to 20/200. Conclusion: Patients with Stickler syndrome may develop RRD of different severity. Macrocyst is rarely reported in previous literature of Stickler syndrome. In this case report, we share our experience in treating with multiple macrocysts in RRD and emphasize the importance of periodic follow-up for patients with Stickler syndrome.

Metabolomic and Transcriptomic Profiles in Diverse Brassica oleracea Crops Provide Insights into the Genetic Regulation of Glucosinolate Profiles.

Glucosinolates (GSLs) are plant secondary metabolites commonly found in the cruciferous vegetables of the Brassicaceae family, offering health benefits to humans and defense against pathogens and pests to plants. In this study, we investigated 23 GSL compounds' relative abundance in four tissues of five different Brassica oleracea morphotypes. Using the five corresponding high-quality B. oleracea genome assemblies, we identified 183 GSL-related genes and analyzed their expression with mRNA-Seq data. GSL abundance and composition varied strongly, among both tissues and morphotypes, accompanied by different gene expression patterns. Interestingly, broccoli exhibited a nonfunctional AOP2 gene due to a conserved 2OG-FeII_Oxy domain loss, explaining the unique accumulation of two health-promoting GSLs. Additionally, transposable element (TE) insertions were found to affect the gene structure of MAM3 genes. Our findings deepen the understanding of GSL variation and genetic regulation in B. oleracea morphotypes, providing valuable insights for breeding with tailored GSL profiles in these crops.

Photovoltaic-driven Ni(ii)/Ni(iii) redox mediator for the valorization of PET plastic waste with hydrogen production.

Electrocatalytic valorization of PET plastic waste provides an appealing route by converting intermittent renewable energy into valuable chemicals and high-energy fuels. Normally, anodic PET hydrolysate oxidation and cathodic water reduction reactions occur simultaneously in the same time and space, which increases the challenges for product separation and operational conditions. Although these problems can be addressed by utilizing membranes or diaphragms, the parasitic cell resistance and high overall cost severely restrict their future application. Herein, we introduce a Ni(ii)/Ni(iii) redox mediator to decouple these reactions into two independent processes: an electrochemical process for water reduction to produce hydrogen fuel assisted by the oxidation of the Ni(OH)2 electrode into the NiOOH counterpart, followed subsequently by a spontaneous chemical process for the valorization of PET hydrolysate to produce formic acid with a high faradaic efficiency of ∼96% by the oxidized NiOOH electrode. This decoupling strategy enables the electrochemical valorization of PET plastic waste in a membrane-free system to produce high-value formic acid and high-purity hydrogen production. This study provides an appealing route to facilitate the transformation process of PET plastic waste into high-value products with high efficiency, low cost and high purity.

OcBSA: An NGS-based bulk segregant analysis tool for outcross populations.

Constructing inbred lines for self-incompatible species and species with long generation times is challenging, making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species. However, there is a lack of dedicated algorithms/tools for rapid quantitative trait locus (QTL) mapping using the F1 populations. To this end, we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations. OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population. Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy. In addition, the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple, pear, peach, citrus, grape, tea, and rice. We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study. The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene, which regulates potato flower color. Taken together, these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species. For ease of use, we have developed both Windows and Linux versions of OcBSA, which are freely available at: https://gitee.com/Bioinformaticslab/OcBSA.

Optimizing the quality of horticultural crop: insights into pre-harvest practices in controlled environment agriculture.

In modern agriculture, Controlled environment agriculture (CEA) stands out as a contemporary production mode that leverages precise control over environmental conditions such as nutrient, temperature, light, and other factors to achieve efficient and high-quality agricultural production. Numerous studies have demonstrated the efficacy of manipulating these environmental factors in the short period before harvest to enhance crop yield and quality in CEA. This comprehensive review aims to provide insight into various pre-harvest practices employed in CEA, including nutrient deprivation, nutrient supply, manipulation of the light environment, and the application of exogenous hormones, with the objective of improving yield and quality in horticultural crops. Additionally, we propose an intelligent pre-harvest management system to cultivate high-quality horticultural crops. This system integrates sensor technology, data analysis, and intelligent control, enabling the customization of specific pre-harvest strategies based on producers' requirements. The envisioned pre-harvest intelligent system holds the potential to enhance crop quality, increase yield, reduce resource wastage, and offer innovative ideas and technical support for the sustainable development of CEA.

Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea.

Brassica oleracea, globally cultivated for its vegetable crops, consists of very diverse morphotypes, characterized by specialized enlarged organs as harvested products. This makes B. oleracea an ideal model for studying rapid evolution and domestication. We constructed a B. oleracea pan-genome from 27 high-quality genomes representing all morphotypes and their wild relatives. We identified structural variations (SVs) among these genomes and characterized these in 704 B. oleracea accessions using graph-based genome tools. We show that SVs exert bidirectional effects on the expression of numerous genes, either suppressing through DNA methylation or promoting probably by harboring transcription factor-binding elements. The following examples illustrate the role of SVs modulating gene expression: SVs promoting BoPNY and suppressing BoCKX3 in cauliflower/broccoli, suppressing BoKAN1 and BoACS4 in cabbage and promoting BoMYBtf in ornamental kale. These results provide solid evidence for the role of SVs as dosage regulators of gene expression, driving B. oleracea domestication and diversification.

The energy conservation and emission reduction co-benefits of China's emission trading system.

Emission Trading System (ETS) is an innovative practice under the progress of green development in China. It is also an important method for China to achieve market-oriented environmental governance in ecological civilization construction. The ETS pilot policy has implemented for more than 10 years. However, the co-benefits of ETS pilot policy by the integration of energy consumption, carbon and sulfur dioxide emissions, and wastewater has not been evaluated. In order to fill this gap, we use the 2003-2017 annual data of 30 China's provinces (municipalities and autonomous regions), and utilize the Difference-in-Differences (DID) model and Propensity Score Matching (PSM-DID) methodology to evaluate the co-benefits of ETS pilot policy on energy conservation and emission reduction. We find that the ETS pilot policy significantly promote energy conservation and emission reduction. Eastern and central China have significantly benefited from the policy, while the western China has not due to the limited technology and innovation as well as an imbalance of the industrial structure. The results provide the policy reference for China's government and institutions as well as the governments and institutions around the world to fulfill their commitments to save energy and reduce emissions, and early achieve the carbon peaking and carbon neutralization.