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Introduction: The variety of organs carbon concentration may be important for tree survival rate, drought resistance and tree subsequent recovery. However, it remains unclear how drought affect structural carbohydrate (SC) and non-structural carbohydrate (NSC) export and transport on clonal plant, which can be correlated with sustain physiological metabolism and group drought resistance by resource sharing. To better understand the adaption ability of clone plants to drought and the linkage of organ carbon with soil organic carbon (SOC) fractions, we assessed how long-term drought affects organ carbon and its impact on SOC fractions among moso bamboo ( Phyllostachys edulis ) ramets., Methods: Throughfall exclusion included two treatments with simulated drought (TE) and control sample (CK, natural rainfall) by waterproofing panels, which excluded 70-80% of the precipitation. We measured the SC and NSC of leaves, branches and roots as well as soil organic carbon components on three ramets, which emerged in 2017 (grandma, GB), ramets that appeared in 2018 (mother bamboo, MB) and ramets emerging in 2019 (current-year bamboo, CB)., Results: The results showed that there was significant difference on lignin, cellulose: lignin ratio and soluble sugar in leaves and roots ( p <0.05) instead of branches ( p >0.05). Effect of drought on SC and NSC varied with different organs and ramet age. Drought significantly increased soluble sugar concentration of leaves and roots by 15.5-31.0% and 10.6-24.8% for current-year bamboo. Compared with CK, drought decreased SOC by 6.7-19.1%, microbial biomass carbon (MBC) by 55.3-68.7%, readily oxidizable carbon (ROC) by 11.2-29.8%, particulate organic carbon (POC) by 25.1-47.4% but no effect on mineral-associated organic carbon (MOC). Drought changed the relationships of carbon components between plant organs and soil. In the control treatments, SC of leaves were significantly positively correlated with ROC, NSC of branches were positively correlated with ROC and MBC, NSC of roots were significantly positively correlated with SOC., Discussion: Overall, our results suggest that drought strengthened the linkage of plant organ carbon and soil carbon cycling among moso bamboo ramets in ecosystem studies, which are critical for predicting tree resistance and management in subtropical forest under drought., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Ge, Mao, Zhou, Wang and Li.)

Soil salinization represents a significant challenge to the ecological environment in arid areas, and digital mapping of soil salinization as well as exploration of its spatial heterogeneity with crop growth have important implications for national food security and salinization management. However, the machine learning models currently used are deficient in mining local information on salinity and do not explore the spatial heterogeneity of salinity impacts on crops. This study developed soil salinization inversion models using CNN (Convolutional Neural Network), LSTM (Long Short-Term Memory Network), and RF (Random Forest) models based on 97 field samples and feature variables extracted from Landsat-8 imagery. By evaluating the accuracy, the best-performing model was selected to map soil salinity at a 30m resolution for the years 2013 and 2022, and to explore the relationship between soil electrical conductivity (EC) values and the expansion of cotton fields as well as their spatial correlation. The results indicate that:(1) The CNN performs best in prediction, with an R 2 of 0.84 for the training set and 0.73 for the test set, capable of capturing more local salinity information. (2) The expansion of cotton fields has reduced the level of soil salinization, with the area of severely salinized and saline soils in newly added cotton fields decreasing from 177.91 km 2 and 381.46 km 2 to 19.49 km 2 and 1.12 km 2 , respectively. (3) Regions with long-term cotton cultivation and newly reclaimed cotton fields exhibit high sensitivity and vulnerability to soil salinity. This study explores the excellent performance of deep learning in salinity mapping and visualizes the spatial distribution of cotton fields that are highly sensitive to soil salinity, providing a scientific theoretical basis for accurate salinity management., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Zhang, Ding, Wang, Zhang, Tan and Ge.)

Amidst the backdrop of global climate change, it is imperative to comprehend the intricate connections among surface water, vegetation, and climatic shifts within watersheds, especially in fragile, arid ecosystems. However, these relationships across various timescales remain unclear. We employed the Ensemble Empirical Mode Decomposition (EEMD) method to analyze the multifaceted dynamics of surface water and vegetation in the Bosten Lake Watershed across multiple temporal scales. This analysis has shed light on how these elements interact with climate change, revealing significant insights. From March to October, approximately 14.9-16.8% of the areas with permanent water were susceptible to receding and drying up. Both the annual and monthly values of Bosten Lake's level and area exhibited a trend of initial decline followed by an increase, reaching their lowest point in 2013 (1,045.0 m and 906.6 km2, respectively). Approximately 7.7% of vegetated areas showed a significant increase in the Normalized Difference Vegetation Index (NDVI). NDVI volatility was observed in 23.4% of vegetated areas, primarily concentrated in the southern part of the study area and near Lake Bosten. Regarding the annual components (6 < T < 24 months), temperature, 3-month cumulative NDVI, and 3-month-leading precipitation exhibited the strongest correlation with changes in water level and surface area. For the interannual components (T≥ 24 months), NDVI, 3-month cumulative precipitation, and 3-month-leading temperature displayed the most robust correlation with alterations in water level and surface area. In both components, NDVI had a negative impact on Bosten Lake's water level and surface area, while temperature and precipitation exerted positive effects. Through comparative analysis, this study reveals the importance of temporal periodicity in developing adaptive strategies for achieving Sustainable Development Goals in dryland watersheds. This study introduces a robust methodology for dissecting trends within scale components of lake level and surface area and links these trends to climate variations and NDVI changes across different temporal scales. The inherent correlations uncovered in this research can serve as valuable guidance for future investigations into surface water dynamics in arid regions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Ge, Ding, Amantai, Xiong and Wang.)

Plants lack behavioral responses to avoid dramatic environmental changes associated with the annual seasons. For survival, they have evolved complex sensory systems to sense fluctuations in light and optimize their architecture in response to changes in these cues. Phytochrome A (phyA) was initially identified as a photoreceptor that senses far-red light signals. It was then identified as playing a central role in promoting hypocotyl growth, fiber development, and flowering time in a variety of plants including Arabidopsis, rice, soybean and cotton. Under dark conditions, phyA is present in the cytoplasm in the physiologically inactive (Pr) form. Far-red light signals induce the transformation of Pr into the physiologically active (Pfr) form, after which Pfr-phyA is recognized by FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL) and translocated to the nucleus, initiating a series of signaling cascades. The current review comprehensively summarizes recent advances in understanding the function of phyA in plants, including phyA-mediated shade avoidance and flowering time. Remaining issues and possible directions for future research on phyA are also discussed., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Lei, Ma, Zhang, Li, Ning, Wang, Ge, Zhao and Lin.)

Sprouting is an irreversible deterioration of potato quality, which leads to the production of harmful toxins and loss of the commercial value of potatoes. However, there is no report on the changes in different stages of potato sprouting through transcriptome and metabonomics. In this study, 1471 differentially expressed genes (DEGs) were found between DP and BP. In comparison with SP, a total of 6309 DEGs were detected in BP. Additionally, 6624 DEGs were identified between DP and SP. Moreover, 96 and 117 differentially accumulated metabolites (DAMs) were detected between DP and BP and between BP and SP, respectively. Furthermore, 130 DAMs were identified in total between DP and SP. In each group, a correlation analysis of DAMs and DEGs was performed to examine the regulatory network. The results indicated that the sprouting of tubers is mainly regulated by plant hormone signals, and during the sprouting of tubers, significant changes in metabolic products occur in the body. According to the combined analysis of transcriptomics and metabolomics, multiple metabolites were both positive and negative regulated by genes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Zheng, Li, Zhang, Chen, Ge, Li, Tian and Tian.)

Forest gaps play an important role during forest succession in temperate forest ecosystems. However, the differences in spatial distribution and replacement patterns of woody plants (trees and shrubs) between primary and secondary forests remain unclear during the gap-filling processes, especially for temperate forests in Northeast China. We recorded 45,619 regenerated trees and shrubs in young gaps (<10 years), old gaps (10~20 years), and closed forest stands (i.e., filled gaps) in the primary broadleaved Korean pine ( Pinus koraiensis Sieb. Rt Zucc.) forests vs. secondary forests (degraded from primary forests). The gap-filling processes along horizontal (Cartesian coordinate system) and vertical (lower layer: 0~5 m, medium layer: 5~10 m, and upper layer: >10 m) dimensions were quantified by shade tolerance groups of trees and shrubs. We found that gap age, competition between species, and pre-existing regeneration status resulted in different species replacement patterns within gaps in primary vs. secondary forests. Gap formation in both primary and secondary forests increased species richness, with 33, 38, 39, and 41 in the primary closed stands, primary forest gaps, secondary closed stands, and secondary forest gaps, respectively. However, only 35.9% of species in primary forest gaps and 34.1% in secondary forest gaps successfully reached the upper layer. Based on the importance values (IVs) of tree species across different canopy heights, light-demanding trees in the upper layer of the secondary forests were gradually replaced by intermediate and shade-tolerant trees. In the primary forests, Korean pine exhibited intermittent growth patterns at different canopy heights, while it had continuous regeneration along vertical height gradients in the secondary forests. The differences in Korean pine regeneration between the primary and secondary forests existed before gap formation and continued during the gap-filling processes. The interspecific competition among different tree species gradually decreased with increasing vertical height, and compared to the primary forests, the secondary forests showed an earlier occurrence of competition exclusion within gaps. Our findings revealed the species replacement patterns within gaps and provided a further understanding of the competition dynamics among tree species during the gap-filling processes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Wu, Lu, Zhu, Ge, Zhang, Lin, Wang, Liu and Zhang.)

A synthetic octoploid rapeseed, Y3380, induces maternal doubled haploids when used as a pollen donor to pollinate plant. However, the mechanism underlying doubled haploid formation remains elusive. We speculated that double haploid induction occurs as the inducer line's chromosomes pass to the maternal egg cell, and the zygote is formed through fertilization. In the process of zygotic mitosis, the paternal chromosome is specifically eliminated. Part of the paternal gene might have infiltrated the maternal genome through homologous exchange during the elimination process. Then, the zygote haploid genome doubles (early haploid doubling, EH phenomenon), and the doubled zygote continues to develop into a complete embryo, finally forming doubled haploid offspring. To test our hypothesis, in the current study, the octoploid Y3380 line was back bred with the 4122- cp4-EPSPS exogenous gene used as a marker into hexaploid Y3380- cp4-EPSPS as paternal material to pollinate three different maternal materials. The fertilization process of crossing between the inducer line and the maternal parent was observed 48 h after pollination, and the fertilization rate reached 97.92% and 98.72%. After 12 d of pollination, the presence of cp4-EPSPS in the embryo was detected by in situ PCR, and at 13-23 d after pollination, the probability of F 1 embryos containing cp4-EPSPS gene was up to 97.27%, but then declined gradually to 0% at 23-33 d. At the same time, the expression of cp4-EPSPS was observed by immunofluorescence in the 3rd to 29th day embryo. As the embryos developed, cp4-EPSPS marker genes were constantly lost, accompanied by embryonic death. After 30 d, the presence of cp4-EPSPS was not detected in surviving embryos. Meanwhile, SNP detection of induced offspring confirmed the existence of double haploids, further indicating that the induction process was caused by the loss of specificity of the paternal chromosome. The tetraploid-induced offspring showed infiltration of the induced line gene loci, with heterozygosity and homozygosity. Results indicated that the induced line chromosomes were eliminated during embryonic development, and the maternal haploid chromosomes were synchronously doubled in the embryo. These findings support our hypothesis and lay a theoretical foundation for further localization or cloning of functional genes involved in double haploid induction in rapeseed., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Zhao, Huang, Zhang, Zhou, Yang, Shi, Li, Yang, Li, Ge, Gong, Wang, Zou, Tao, Kang, Li, Xiao, Hu and Fu.)

Fruit detection and recognition has an important impact on fruit and vegetable harvesting, yield prediction and growth information monitoring in the automation process of modern agriculture, and the actual complex environment of orchards poses some challenges for accurate fruit detection. In order to achieve accurate detection of green fruits in complex orchard environments, this paper proposes an accurate object detection method for green fruits based on optimized YOLOX&#95;m. First, the model extracts features from the input image using the CSPDarkNet backbone network to obtain three effective feature layers at different scales. Then, these effective feature layers are fed into the feature fusion pyramid network for enhanced feature extraction, which combines feature information from different scales, and in this process, the Atrous spatial pyramid pooling (ASPP) module is used to increase the receptive field and enhance the network's ability to obtain multi-scale contextual information. Finally, the fused features are fed into the head prediction network for classification prediction and regression prediction. In addition, Varifocal loss is used to mitigate the negative impact of unbalanced distribution of positive and negative samples to obtain higher precision. The experimental results show that the model in this paper has improved on both apple and persimmon datasets, with the average precision (AP) reaching 64.3% and 74.7%, respectively. Compared with other models commonly used for detection, the model approach in this study has a higher average precision and has improved in other performance metrics, which can provide a reference for the detection of other fruits and vegetables., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Jia, Xu, Lu, Yin, Pan, Jiang and Ge.)

Cotton is widely grown in many countries around the world due to the huge economic value of the total natural fiber. Verticillium wilt, caused by the soil-borne pathogen Verticillium dahliae , is the most devastating disease that led to extensive yield losses and fiber quality reduction in cotton crops. Developing resistant cotton varieties through genetic engineering is an effective, economical, and durable strategy to control Verticillium wilt. However, there are few resistance gene resources in the currently planted cotton varieties, which has brought great challenges and difficulties for breeding through genetic engineering. Further revealing the molecular mechanism between V. dahliae and cotton interaction is crucial to discovering genes related to disease resistance. In this review, we elaborated on the pathogenic mechanism of V. dahliae and the resistance mechanism of cotton to Verticillium wilt. V. dahliae has evolved complex mechanisms to achieve pathogenicity in cotton, mainly including five aspects: (1) germination and growth of microsclerotia; (2) infection and successful colonization; (3) adaptation to the nutrient-deficient environment and competition of nutrients; (4) suppression and manipulation of cotton immune responses; (5) rapid reproduction and secretion of toxins. Cotton has evolved multiple physiological and biochemical responses to cope with V. dahliae infection, including modification of tissue structures, accumulation of antifungal substances, homeostasis of reactive oxygen species (ROS), induction of Ca 2+ signaling, the mitogen-activated protein kinase (MAPK) cascades, hormone signaling, and PAMPs/effectors-triggered immune response (PTI/ETI). This review will provide an important reference for the breeding of new cotton germplasm resistant to Verticillium wilt through genetic engineering., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Zhu, Zhao, Li, Wang, Liao, Liu, Zhang, Zhao, Liu, Ge and Li.)

Fruit and vegetable picking robots are affected by the complex orchard environment, resulting in poor recognition and segmentation of target fruits by the vision system. The orchard environment is complex and changeable. For example, the change of light intensity will lead to the unclear surface characteristics of the target fruit; the target fruits are easy to overlap with each other and blocked by branches and leaves, which makes the shape of the fruits incomplete and difficult to accurately identify and segment one by one. Aiming at various difficulties in complex orchard environment, a two-stage instance segmentation method based on the optimized mask region convolutional neural network (mask RCNN) was proposed. The new model proposed to apply the lightweight backbone network MobileNetv3, which not only speeds up the model but also greatly improves the accuracy of the model and meets the storage resource requirements of the mobile robot. To further improve the segmentation quality of the model, the boundary patch refinement (BPR) post-processing module is added to the new model to optimize the rough mask boundaries of the model output to reduce the error pixels. The new model has a high-precision recognition rate and an efficient segmentation strategy, which improves the robustness and stability of the model. This study validates the effect of the new model using the persimmon dataset. The optimized mask RCNN achieved mean average precision (mAP) and mean average recall (mAR) of 76.3 and 81.1%, respectively, which are 3.1 and 3.7% improvement over the baseline mask RCNN, respectively. The new model is experimentally proven to bring higher accuracy and segmentation quality and can be widely deployed in smart agriculture., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Jia, Wei, Zhang, Pan, Niu, Yin, Ding and Ge.)

Phosphorus (P) is a nutrient limiting plant growth in subtropical regions. However, our understanding of how soil P responds to an increase in stand age is rather poor. In particular, little is known about how bioavailable P pools (soluble P, exchangeable P, hydrolyzable P, and ligand P) shift with a change in stand age. Moreover, the P cycle in rhizosphere soil has the most direct and significant influence on plants. The aim of the present study was to determine the concentrations of total P in various rhizosphere soil bioavailable P fractions in 5-, 9-, 19-, 29-, and 35-year-old stands of Pinus massoniana Lamb. According to the results, total P (TP) concentration and N:P ratio in rhizosphere soil first decreased, and then increased with an increase in stand age. Soluble P concentration decreased first, and then increased with an increase in stand age; exchangeable P and ligand P decreased first, and then tended to be stable with an increase in stand age, whereas hydrolyzable P increased first, and then decreased. Structural Equation Model results suggested that ligand P and soluble P were the major factor affecting the TP. In addition, soil microorganisms and acid phosphatase-driven hydrolyzable P play a crucial role in soil bioavailable P cycling. Overall, the results of our study provide a mechanistic understanding of soil bioavailable P cycling under low available P conditions, and a basis for an effective P management strategy for the sustainable development of P. massoniana plantations., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer ZJ declared a shared affiliation with the authors at the time of the review., (Copyright © 2022 Xu, Ge, Zhou, Lei and Xiao.)

Accurate detection and segmentation of the object fruit is the key part of orchard production measurement and automated picking. Affected by light, weather, and operating angle, it brings new challenges to the efficient and accurate detection and segmentation of the green object fruit under complex orchard backgrounds. For the green fruit segmentation, an efficient YOLOF-snake segmentation model is proposed. First, the ResNet101 structure is adopted as the backbone network to achieve feature extraction of the green object fruit. Then, the C5 feature maps are expanded with receptive fields and the decoder is used for classification and regression. Besides, the center point in the regression box is employed to get a diamond-shaped structure and fed into an additional Deep-snake network, which is adjusted to the contours of the target fruit to achieve fast and accurate segmentation of green fruit. The experimental results show that YOLOF-snake is sensitive to the green fruit, and the segmentation accuracy and efficiency are significantly improved. The proposed model can effectively extend the application of agricultural equipment and provide theoretical references for other fruits and vegetable segmentation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Jia, Liu, Luo, Wang, Pan, Yang and Ge.)

Sprouting is an irreversible deterioration of potato quality, which not only causes loss in their commercial value but also produces harmful toxins. As a popular disinfectant, ClO 2 can inhibit the sprouting of potato tubers. Using transcriptomic and metabolomic approaches to understand the repressive mechanism of ClO 2 in potato sprouting is yet to be reported. Sequencing the transcriptome and metabolome of potatoes treated with ClO 2 in this study revealed a total of 3,119 differentially expressed genes, with 1,247 and 1,872 genes showing down- and upregulated expression, respectively. The majority of the downregulated genes were associated with plant hormone signal transduction, whereas upregulated differential genes were associated primarily with biological processes, such as phenylpropanoid biosynthesis and the mitogen-activated protein kinase (MAPK) signaling pathway. Metabonomic assays identified a total of 932 metabolites, with 33 and 52 metabolites being down- and upregulated, respectively. Downregulated metabolites were mostly alkaloids, amino acids, and their derivatives, whereas upregulated metabolites were composed mainly of flavonoids and coumarins. Integrated transcriptomic and metabolomic analyses showed that many different metabolites were regulated by several different genes, forming a complex regulatory network. These results provide new insights for understanding the mechanism of ClO 2 -mediated repression of potato sprouting., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflictof interest., (Copyright © 2022 Zheng, Li, Tian, Li, Chen, Zhang, Wu, Ge, Tian, Mu and Song.)

Plant auxin is essential in plant growth and development. However, the molecular mechanisms of auxin involvement in plant immunity are unclear. Here, we addressed the function of the cotton ( Gossypium hirsutum ) miR393-TIR1 module in plant defense against Verticillium dahliae infection via auxin perception and signaling. GhTIR1 was directedly cleaved by ghr-miR393 according to mRNA degradome data, 5'-RACE analysis, and a GUS reporter assay. Ghr-miR393 knockdown significantly increased plant susceptibility to V. dahliae compared to the control, while ghr-miR393 overexpression and GhTIR1 knockdown significantly increased plant resistance. External indole-3-acetic acid (IAA) application significantly enhanced susceptibility to V. dahliae in ghr-miR393 knockdown and control plants compared to mock treatment, and only slightly increased susceptibility in overexpressing ghr-miR393 and GhTIR1-silenced plants. Application of external PEO-IAA (an auxin antagonist) had a contrary trend with IAA application. Based on yeast two-hybrid and bimolecular fluorescence complementation assays, GhTIR1 interacted with GhIAA14 in the nucleus, and GhIAA14 knockdown reduced plant resistance to V. dahliae infection. The results suggested that the ghr-miR393-GhTIR1 module regulates plant defense via auxin perception and signaling. Additionally, simultaneous knockdown of GhTIR1 and GhICS1 significantly increased plant susceptibility to V. dahliae compared to the control, indicating that salicylic acid (SA) accumulation is vital for the ghr-miR393-GhTIR1 module to regulates plant resistance. Transcriptome data also demonstrated that GhTIR1 knockdown significantly downregulated expression of auxin-related genes and upregulated expression of SA-related genes. Overall, the ghr-miR393-GhTIR1 module participates in plant response to V. dahliae infection via IAA perception and signaling partially depending on the SA defense pathway., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Shi, Wang, Wang, Zhan, Tang, Zhao, Li, Ge and Wu.)

During somatic embryogenesis (SE), somatic cells initiate embryogenic development under appropriate conditions. Uniconazole, a plant growth regulator, was found to inhibit the proliferation of callus but promoted the conversion of callus into an embryogenic callus (EC) in cotton. The supplementation of uniconazole in the culture medium significantly suppressed the endogenous auxin [indole acetic acid (IAA)] level in callus tissues in both the callus initiation and proliferation stage but enhanced the abscisic acid (ABA) level only in the callus proliferation stage. Exogenous ABA and uniconazole showed cooperative effects on promoting the differentiation rate of callus into EC. These findings were verified by RNA-seq analysis, which elucidated that the genes involved in the IAA biosynthesis, metabolism, and signaling, and ABA metabolism pathways were regulated by uniconazole during the callus development and SE. Overall, the results suggest that uniconazole could modulate callus proliferation and callus differentiation rate by regulating the endogenous levels of IAA and ABA., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Chen, Yu, Wang, Li, Xing and Ge.)

Detached organs or differentiated tissues could form a mass of pluripotent cells termed as callus on an auxin-rich medium, the underlying molecular mechanism of which remains elusive in cotton. LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor is a key regulator of plant cell totipotency/pluripotency, and a number of cotton GhLBDs with high-level differential expression during the callus induction process have been identified. Their overexpression in cotton calli fostered promotions in and callus induction without exogenous auxin. Expression analysis and histological observation using paraffin sectioning suggested that the first 72 h on culture is a key time point for callus initiation, whereby the GhLBDs showed high transcript abundance and enlarged calli that were rapidly developed from procambium and cambium. GhLBDs' expression level could be precisely modulated by the gradient concentrations of exogenous auxin, whereas auxin transport inhibitor 2,3,5-triiodobenzoic acid could severely inhibit its expression. The LBD-mediated callus formation was also dependent on the expression levels of GhLBDs . Further, a β-estradiol-inducible promoter pER8 was used to drive GhLBD18-1 expression, which led to rapid callus proliferation, suggesting that pER8 / GhLBD18-1 could be used as a selectable marker system to replace the existing antibiotic/herbicide-resistance selectable markers in plant transformation. Our study provides new insights for callus initiation regulatory mechanism and strategies for improving transformation efficiency in cotton., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Wang, Yuan, Wei, Chen, Chen and Ge.)

Plant fine-root decomposition is an important pathway for the reentry of nutrients into the soil. Studies have mainly focused on the loss of fine-root mass and the release characteristics of major elements, including, C, N, and P, but there are few reports on trace elements. In this study, in situ decomposition experiments were conducted to study the dynamic characteristics of mass loss and residual rates of 10 mineral elements in two diameter classes (<2 mm and 2-5 mm) of moso bamboo in the process of fine-root decomposition. The results of the year-long experiment reported herein showed that: (1) fine roots with diameters of less than 2 mm decomposed faster than those with diameters of 2-5 mm; (2) C, N, P, K, Ca, and Mg were released, whereas Fe, Mn, Zn, and Cu were enriched or changed little; (3) decomposition time and root diameter had significant effects on the remaining percentages of C, N, K, Ca, Mg, Mn, Zn, and Cu, and there were interactions among the elements ( P < 0.05). The remaining percentages of P and Fe were only affected by decomposition time. This is the first comprehensive report on the variation in 10 elements during the fine-root decomposition of moso bamboo. The study expands our understanding of the release of mineral nutrients during fine-root decomposition, laying a solid theoretical foundation for further research on fine-root decomposition and plant-soil nutrient cycling., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Xu, Huang, Zhou and Ge.)

Patatin-like proteins (PLPs) have non-specific lipid acyl hydrolysis (LAH) activity, which can hydrolyze membrane lipids into fatty acids and lysophospholipids. The vital role of PLPs in plant growth and abiotic stress has been well documented. However, the function of PLPs in plant defense responses against pathogens is still poorly understood. Here, we isolated and identified a novel cotton ( Gossypium hirsutum ) PLP gene GhPLP2 . The expression of GhPLP2 was induced upon treatment with Verticillium dahliae , the signaling molecules jasmonic acid (JA) and ethylene (ETH) in cotton plants. Subcellular localization revealed that GhPLP2 was localized to the plasma membrane. GhPLP2 -silenced cotton plants were more susceptible to infection by V. dahliae , while the overexpression of GhPLP2 in Arabidopsis enhanced its resistance to V. dahliae , which was apparent as mild symptoms, and a decrease in the disease index and fungal biomass. The hypersensitive response, deposition of callose, and H 2 O 2 accumulation triggered by V. dahliae elicitor were reduced in GhPLP2 -silenced cotton plants. The overexpression of GhPLP2 in Arabidopsis resulted in the accumulation of linoleic acid (LA, 18:2) and α-linolenic acid (ALA, 18:3) and facilitated the biosynthesis of JA and JA-mediated defensive responses. GhPLP2 silencing in cotton plants consistently reduced the accumulation of linoleic acid (LA, 18:2) and α-linolenic acid (ALA, 18:3) and suppressed the biosynthesis of JA and the defensive responses mediated by JA. These results indicate that GhPLP2 is involved in the resistance of cotton to V. dahliae by maintaining fatty acid metabolism pools for JA biosynthesis and activating the JA signaling pathway., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Zhu, Hu, Wang, Gao, Pei, Ge, Ge, Li and Hou.)

Plant-specific TCP transcription factors play vital roles in the controlling of growth, development, and the stress response processes. Extensive researches have been carried out in numerous species, however, there hasn't been any information available about TCP genes in sweet potato ( Ipomoea batatas L.). In this study, a genome-wide analysis of TCP genes was carried out to explore the evolution and function in sweet potato. Altogether, 18 IbTCPs were identified and cloned. The expression profiles of the IbTCPs differed dramatically in different organs or different stages of leaf development. Furthermore, four CIN-clade IbTCP genes contained miR319-binding sites. Blocking IbmiR319 significantly increased the expression level of IbTCP11/17 and resulted in a decreased photosynthetic rate due to the change in leaf submicroscopic structure, indicating the significance of IbmiR319-targeted IbTCPs in leaf anatomical morphology. A systematic analyzation on the characterization of the IbTCPs together with the primary functions in leaf anatomical morphology were conducted to afford a basis for further study of the IbmiR319 / IbTCP module in association with leaf anatomical morphology in sweet potato., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Ren, Wu, Zhang, Ge, Wang, Zhou, Zhang, Ma and Wang.)

Root foraging strategies of plants may be critical to the competition for nutrient resources in the nutrient patches, but little is known about these of co-existing tree species in subtropical regions. This study aimed to elucidate root foraging strategies of three co-existing tree species in nutrient heterogeneous soils by exploring their root distribution, root morphology, photosynthates allocation and nutrient accumulation. Seedlings of the three tree species [moso bamboo ( Phyllostachys edulis ), Chinese fir ( Cunninghamia lanceolata ), and masson pine ( Pinus massoniana )] were grown for 8months under one homogeneous soil [uniform nitrogen (N) plus phosphorus (P)] and three heterogeneous soils (localized N supply, localized P supply, or localized N plus P supply). The biomass, root morphological parameters (i.e., root length and root surface area), specific root length (SRL), non-structural carbohydrates (NSCs, i.e., mobile sugar and starch) in roots, total N and total P of plants were measured. The plasticity and distribution of root system were analyzed by calculating the root response ratio (RRR) and root foraging precision (FP), respectively. The results are as follows (i) Chinese fir tended to forage more N by promoting root proliferation in the N-rich patch, while root proliferation of bamboo and pine did not change. For P, bamboo absorbed more P by promoting root proliferation in the P-rich patch. The total P content of Pine and Chinese fir under localized P supply treatment remain the same despite the fact that the root length in the P-rich patch and the FP increased. (ii) Chinese fir foraged more N by increasing root length and decreasing SRL in the NP-rich patch; bamboo foraged more N and P by increasing root length and SRL in the NP-rich patch. The FP and foraging scale (FS) of both bamboo and Chinese fir were significantly improved under localized N plus P treatment. (iii) The concentrations of NSC were positively correlated with root morphological plasticity for moso bamboo and Chinese fir. Our results indicated that higher morphological plasticity is exhibited in moso bamboo and Chinese fir than masson pine in nutrient heterogeneous soils, allowing them to successfully forage for more nutrients., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Yang, Zhou, Ge, Cao, Brunner, Shi and Li.)

Brassica napus L. (rapeseed, oilseed rape, and canola) and varieties of its two diploid parents, B. oleracea and B. rapa , display a large amount of variation in anthocyanin pigmentation of the leaf, stem, and fruit. Here, we demonstrate that BnaPAP2.A7 , an ortholog of the B. oleracea anthocyanin activator BoMYB2 that confers purple traits, positively regulates anthocyanin biosynthesis in leaves of B. napus . Sequencing of BnaPAP2.A7 and transgenic analysis suggests that activation of this gene in purple rapeseed may result from a single nucleotide and/or 2bp insertion in its promoter region. BnaPAP2.A7 gives rise to three splice variants, designated BnaPAP2.A7-744, BnaPAP2.A7-910 , and BnaPAP2.A7-395 according to the length of the transcripts. While BnaPAP2.A7-744 encodes a full-length R2R3-MYB, both BnaPAP2.A7-910 and BnaPAP2.A7-395 encode truncated proteins that lack both a partial R3 repeat and the complete C terminal domain, and so in vitro are unable to interact with the Arabidopsis bHLH protein AtTT8. Although expression of either BnaPAP2.A7-910 or BnaPAP2.A7-395 in green rapeseed does not result in purple leaves, both genes do modify genome-wide gene expression, with a strong repression of anthocyanin-related genes. We have demonstrated that BnaPAP.A7 regulates anthocyanin accumulation in leaves of B. napus and propose a potential mechanism for modulation of anthocyanin biosynthesis by alternative splicing., (Copyright © 2020 Chen, Liu, Yin, Qiu, Jin, King, Wang, Ge and Li.)

Transcription factors (TFs) and transcriptional regulators are important switches in transcriptional networks. In recent years, the transcriptional regulator TIE1 (TCP interactor containing EAR motif protein 1) was identified as a nuclear transcriptional repressor which regulates leaf development and controls branch development. However, the function and regulatory network of GhTIE1 has not been studied in cotton. Here, we demonstrated that GhTIE1 is functionally conserved in controlling shoot branching in cotton and Arabidopsis . Overexpression of GhTIE1 in Arabidopsis leads to higher bud vigor and more branches, while silencing GhTIE1 in cotton reduced bud activity and increased branching inhibition. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that GhTIE1 directly interacted with subclass II TCPs (GhBRC1, GhBRC2, and GhTCP13) in vivo and in vitro . Overexpression of GhBRC1 , GhBRC2 , and GhTCP13 in mutant brc1 -2 partially rescued the mutant phenotype and decreased the number of branches, showing that these TCPs are functionally redundant in controlling branching. A transient dual-luciferase reporter assay indicated that GhTIE1 repressed the protein activity of GhBRC1 and GhTCP13, and thereby decreased the expression of their target gene GhHB21 . Gene expression level analysis in GhTIE1 -overexpressed and silenced plants also proved that GhTIE1 regulated shoot branching via repressing the activity of BRC1 , HB21 , HB40 , and HB53 . Our data reveals that shoot branching can be controlled via modulation of the activity of the TIE1 and TCP proteins and provides a theoretical basis for cultivating cotton varieties with ideal plant types., (Copyright © 2019 Diao, Zhan, Zhao, Liu, Liu, Wei, Ding, Sajjad, Hu, Wang and Ge.)

Germin-like proteins (GLPs) are water-soluble plant glycoproteins belonging to the cupin superfamily. The important role of GLPs in plant responses against various abiotic and biotic stresses, especially pathogens, is well validated. However, little is known about cotton GLPs in relation to fungal pathogens. Here, a novel GLP gene was isolated from Gossypium hirsutum and designated as GhABP19 . The expression of GhABP19 was upregulated in cotton plants inoculated with Verticillium dahliae and Fusarium oxysporum and in response to treatment with jasmonic acid (JA) but was suppressed in response to salicylic acid treatment. A relatively small transient increase in GhABP19 was seen in H 2 O 2 treated samples. The three-dimensional structure prediction of the GhABP19 protein indicated that the protein has three histidine and one glutamate residues responsible for metal ion binding and superoxide dismutase (SOD) activity. Purified recombinant GhABP19 exhibits SOD activity and could inhibit growth of V. dahliae , F. oxysporum , Rhizoctonia solani , Botrytis cinerea , and Valsa mali in vitro . To further verify the role of GhABP19 in fungal resistance, GhABP19 -overexpressing Arabidopsis plants and GhABP19 -silenced cotton plants were developed. GhABP19-transgenic Arabidopsis lines showed much stronger resistance to V. dahliae and F. oxysporum infection than control (empty vector) plants did. On the contrary, silencing of GhABP19 in cotton conferred enhanced susceptibility to fungal pathogens, which resulted in necrosis and wilt on leaves and vascular discoloration in GhABP19 -silenced cotton plants. The H 2 O 2 content and endogenous SOD activity were affected by GhABP19 expression levels in Arabidopsis and cotton plants after inoculation with V. dahliae and F. oxysporum , respectively. Furthermore, GhABP19 overexpression or silencing resulted in activation or suppression of JA-mediated signaling, respectively. Thus, GhABP19 plays important roles in the regulation of resistance to verticillium and fusarium wilt in plants. These modulatory roles were exerted by its SOD activity and ability to activate the JA pathway. All results suggest that GhABP19 was involved in plant disease resistance.

Novel Brassica napus cytoplasmic male sterility (CMS) with carpelloid stamens ( inap CMS) was produced by intertribal somatic hybridization with Isatis indigotica (Chinese woad), but its RF (restorer of fertility) gene(s) existed in one particular woad chromosome that was carried by one fertile monosomic alien addition line (MAAL) of rapeseed. Herein, the selfed progenies of this MAAL were extensively selected and analyzed to screen the rapeseed-type plants (2 n = 38) with good male fertility and to produce their doubled haploid (DH) lines by microspore culture. From the investigation of fertility restoration in the F 1 hybrids with inap CMS, one DH line (RF 39) was identified to adequately restore male fertility and likely carried one dominant RF gene. Specifically, this restorer produced brown pollen grains, similar to the woad and the MAAL, suggesting that this trait is closely linked with the RF gene(s) and serves as one phenotypic marker for the restorer. This restorer contained 38 chromosomes of rapeseed and no intact chromosomes of woad, but some DNA fragments of woad origin were detected at low frequency. This restorer was much improved for pollen and seed fertility and for low glucosinolate content. The successful breeding of the restorer for inap CMS rendered this new pollination control system feasible for rapeseed hybrid production.

Gossypium hirsutum is an allotetraploid species, meaning that mutants that are difficult to be generated by classical approaches due to gene redundancy. The CRISPR/Cas9 genome editing system is a robust and highly efficient tool for generating target gene mutants, by which the genes of interest may be functionally dissected and applied through genotype-to-phenotype approaches. In this study, the CRISPR/Cas9 genome editing system was developed in G. hirsutum through editing the Gh14-3-3d gene. In T0 transgenic plants, lots of insertions and deletions (indels) in Gh14-3-3d at the expected target site were detected in the allotetraploid cotton At or Dt subgenomes. The results of the PCR, T7EI digestion and sequencing analyses showed that the indels in Gh14-3-3d gene can be stably transmitted to the next generation. Additionally, the indels in the At and Dt subgenomes were segregated in the T1 transgenic plants following Mendelian law, independing on the T-DNA segregation. Two homozygous Gh14-3-3d -edited plants free of T-DNA were chosen by PCR and sequencing assays in the T1 plants, which were called transgene-clean editing plants and were designated ce1 and ce2 in the T2 lines showed higher resistance to Verticillium dahliae infestation compared to the wild-type plants. Thus, the two transgene-clean edited lines can be used as a germplasm to breed disease-resistant cotton cultivars, possibly avoiding complex and expensive safety assessments of the transgenic plants.

Many subunits of the Mediator transcriptional co-activator complex are multifunctional proteins that regulate plant immunity in Arabidopsis . Cotton cyclin-dependent kinase E (GhCDKE), which is a subunit of the cotton ( Gossypium hirsutum ) Mediator complex, has been annotated, but the biological functions of this gene associated with regulating disease resistance have not been characterized. Here, we cloned GhCDKE from cotton and confirmed that GhCDKE belonged to the E-type CDK family in the phylogenetic tree, and, as in other eukaryotes, we found that GhCDKE interacted with C-type cyclin (GhCycC) by yeast two-hybrid and luciferase complementation imaging assays. Expression of GhCDKE in cotton was induced by Verticillium dahliae infection and MeJA treatment, and silencing of GhCDKE expression in cotton led to enhanced susceptibility to V. dahliae , while overexpression of GhCDKE in Arabidopsis thaliana enhanced resistance to this pathogen. Transgenic expression assay demonstrated that the transcriptional activity of GhPDF1.2 pro :LUC in GhCDKE -silenced cotton was dramatically inhibited. In addition, the expression of jasmonic acid (JA)-regulated pathogen-responsive genes was dramatically upregulated in GhCDKE -overexpressed plants after inoculation with V. dahliae , and the roots of GhCDKE -overexpressed A. thaliana were more susceptible to JA treatment. These results indicated that GhCDKE regulates resistance against V. dahliae and that this resistance is mediated by JA response pathway.

Plant height (PH), branch initiation height (BIH), and stem diameter (SD) are three stem-related traits that play crucial roles in plant architecture and lodging resistance. Herein, we show one doubled haploid (DH) population obtained from a cross between Y689 (one Capsella bursa - pastoris derived Brassica napus intertribal introgression) and Westar ( B . napus cultivar) that these traits were significantly positively correlated with one another and with flowering time (FT). Based on a high-density SNP map, a total of 102 additive quantitative trait loci (QTL) were identified across six environments. Seventy-two consensus QTL and 49 unique QTL were identified using a two-round strategy of QTL meta-analysis. Notably, a total of 19 major QTL, including 11 novel ones, were detected for these traits, which comprised two QTL clusters on chromosomes A02 and A07. Conditional QTL mapping was performed to preliminarily evaluate the genetic basis (pleiotropy or tight linkage) of the co-localized QTL. In addition, QTL by environment interactions (QEI) mapping was performed to verify the additive QTL and estimate the QEI effect. In the genomic regions of all major QTL, orthologs of the genes involved in phytohormone biosynthesis, phytohormone signaling, flower development, and cell differentiation in Arabidopsis were proposed as candidate genes. Of these, BnaA02g02560 , an ortholog of Arabidopsis GASA4 , was suggested as a candidate gene for PH, SD, and FT; and BnaA02g08490 , an ortholog of Arabidopsis GNL , was associated with PH, BIH and FT. These results provide useful information for further genetic studies on stem-related traits and plant growth adaptation.

Alien chromosome substitution (CS) lines are treated as vital germplasms for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) was established in the background of natural B. napus genotype "Oro," after the restituted B. rapa (RBR) for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1) in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization. Cs1 exhibited the whole plant morphology similar to RBR except for the defective stamens without fertile pollen grains, but it produced some seeds and progeny plants carrying the C1 chromosome at high rate besides those without the alien chromosome after pollinated by RBR. The viability of the substitution and its progeny for the RBR diploid further elucidated the functional compensation between the chromosome pairs with high homoeology. To reveal the impact of such aneuploidy on genome-wide gene expression, the transcriptomes of MAAL C1, Cs1 and euploid RBR were analyzed. Compared to RBR, Cs1 had sharply reduced gene expression level across chromosome A1, demonstrating the loss of one copy of A1 chromosome. Both additional chromosome C1 in MAAL and substitutional chromosome C1 in Cs1 caused not only cis -effect but also prevalent trans -effect differentially expressed genes. A dominant gene dosage effects prevailed among low expressed genes across chromosome A1 in Cs1, and moreover, dosage effects for some genes potentially contributed to the phenotype deviations. Our results provided novel insights into the transcriptomic perturbation and gene dosage effects on phenotype in CS related to one naturally evolved allopolyploid.

Transgenic glyphosate-tolerant plants overproducing EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) may exhibit enhanced fitness in glyphosate-free environments. If so, introgression of transgenes overexpressing EPSPS into wild relative species may lead to increased competitiveness of crop-wild hybrids, resulting in unpredicted environmental impact. Assessing fitness effects of transgenes overexpressing EPSPS in a model plant species can help address this question, while elucidating how overproducing EPSPS affects the fitness-related traits of plants. We produced segregating T 2 and T 3 Arabidopsis thaliana lineages with or without a transgene overexpressing EPSPS isolated from rice or Agrobacterium ( CP4 ). For each of the three transgenes, we compared glyphosate tolerance, some fitness-related traits, and auxin (indole-3-acetic acid) content in transgene-present, transgene-absent, empty vector (EV), and parental lineages in a common-garden experiment. We detected substantially increased glyphosate tolerance in T 2 plants of transgene-present lineages that overproduced EPSPS. We also documented significant increases in fecundity, which was associated with increased auxin content in T 3 genes, compared with their segregating transgene-absent lineages, EV, and parental controls. Our results from Arabidopsis with nine transgenic events provide a strong support to the hypothesis that transgenic plants overproducing EPSPS can benefit from a fecundity advantage in glyphosate-free environments. Stimulated biosynthesis of auxin, an important plant growth hormone, by overproducing EPSPS may play a role in enhanced fecundity of the transgenic Arabidopsis plants. The obtained knowledge is useful for assessing environmental impact caused by introgression of transgenes overproducing EPSPS from any GE crop into populations of its wild relatives.EPSPS genes, compared with their segregating transgene-absent lineages, EV, and parental controls. Our results from Arabidopsis with nine transgenic events provide a strong support to the hypothesis that transgenic plants overproducing EPSPS can benefit from a fecundity advantage in glyphosate-free environments. Stimulated biosynthesis of auxin, an important plant growth hormone, by overproducing EPSPS may play a role in enhanced fecundity of the transgenic Arabidopsis plants. The obtained knowledge is useful for assessing environmental impact caused by introgression of transgenes overproducing EPSPS from any GE crop into populations of its wild relatives.

Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed ( Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses ( B. rapa ssp. chinesis × O. violaceus ) × B. napus . In present study, a doubled haploid (DH) population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP) array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0-34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs ( cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09 , and cqSL.C09 ) were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related traits were identified.

A novel cytoplasmic male sterility (CMS) in Brassica napus (inap CMS) was selected from the somatic hybrid with Isatis indigotica (Chinese woad) by recurrent backcrossing. The male sterility was caused by the conversion of tetradynamous stamens into carpelloid structures with stigmatoid tissues at their tips and ovule-like tissues in the margins, and the two shorter stamens into filaments without anthers. The feminized development of the stamens resulted in the complete lack of pollen grains, which was stable in different years and environments. The pistils of inap CMS displayed normal morphology and good seed-set after pollinated by B. napus . Histological sections showed that the developmental alteration of the stamens initiated at the stage of stamen primordium differentiation. AFLP analysis of the nuclear genomic composition with 23 pairs of selective primers detected no woad DNA bands in inap CMS. Twenty out of 25 mitochondrial genes originated from I. indigotica , except for cox2-2 which was the recombinant between cox2 from woad and cox2-2 from rapeseed. The novel cox2-2 was transcribed in flower buds of inap CMS weakly and comparatively with the fertile B. napus addition line Me harboring one particular woad chromosome. The restorers of other autoplasmic and alloplasmic CMS systems in rapeseed failed to restore the fertility of inap CMS and the screening of B. napus wide resources found no fertility restoration variety, showing its distinct origin and the related mechanism of sterility. The reasons for the mitochondrial rearrangements and the breeding of the restorer for the novel CMS system were discussed.

The young allotetraploid Brassica napus (2 n = 38, AACC) is one of models to study genomic responses to allopolyploidization. The extraction of AA component from natural B. napus and then restitution of progenitor B. rapa should provide a unique opportunity to reveal the genome interplay for gene expressions during the evolution. Herein, B. napus hybrids (2 n = 19, AC) between the extracted and extant B. rapa (2 n = 20, AA) and the same B. oleracea genotype (2 n = 18, CC) were studied by RNA-seq and compared with natural B. napus donor, to reveal the gene expression changes from hybridization and domestication and the effects of A genome with different origins. Upon the initial merger of two diploid genomes, additive gene expression was prevalent in these two hybrids, for non-additively expressed genes only represented a small portion of total expressed genes. A high proportion of genes exhibited expression level dominance, with no preference to either of the parental genomes. Comparison of homoeolog expressions also showed no bias toward any genomes and the parental expression patterns were often maintained in the hybrids and natural allotetraploids. Although, the overall patterns of gene expression were highly conserved between two hybrids, the extracted B. rapa responded less and appeared more compatible for hybridization than the extant B. rapa . Our results suggested that expression level dominance and homoeolog expressions bias were balanced at the initial stage of genome merger, and such balance were largely maintained during the domestication of B. napus , despite the increased extent over time.

Gene/genome dosage balance is an essential evolutionary mechanism for organisms to ensure a normal function, but the underlying causes of dosage-imbalance regulation remain poorly understood. Herein, the serial Brassica hybrids/polyploids (AC, AAC, CCA, CCAA) with different copies of A and C subgenomes from the same two parents of Brassica rapa and Brassica oleracea were synthesized to investigate the effects of genome dosages on gene expressions and interactions by using RNA-Seq. The expression changes of A- and C-subgenome genes were consistent with dosage alterations. Dosage-dependent and -independent genes were grouped according to the correlations between dosage variations and gene expressions. Expression levels of dosage-dependent genes were strongly correlated with dosage changes and mainly contributed to dosage effects, while those of dosage-independent genes gave weak correlations with dosage variations and mostly facilitated dosage compensation. More protein-protein interactions were detected for dosage-independent genes than dosage-dependent ones, as predicted by the dosage balance hypothesis. Dosage-dependent genes more likely impacted the expressions by trans effects, whereas dosage-independent genes preferred to play by cis effects. Furthermore, dosage-dependent genes were mainly associated with the basic biological processes to maintain the stability of the growth and development, while dosage-independent genes were more enriched in the stress response related processes to accelerate adaptation. The present comprehensive analysis of gene expression dependent/independent on dosage alterations in Brassica polyploids provided new insights into gene/genome dosage-imbalance regulation of gene expressions.

Allopolyploidization with the merger of the genomes from different species has been shown to be associated with genetic and epigenetic changes. But the maintenance of such alterations related to one parental species after the genome is extracted from the allopolyploid remains to be detected. In this study, the genome of Brassica napus L. (2n = 38, genomes AACC) was extracted from its intergeneric allohexaploid (2n = 62, genomes AACCOO) with another crucifer Orychophragmus violaceus (2n = 24, genome OO), by backcrossing and development of alien addition lines. B. napus-type plants identified in the self-pollinated progenies of nine monosomic additions were analyzed by the methods of amplified fragment length polymorphism, sequence-specific amplified polymorphism, and methylation-sensitive amplified polymorphism. They showed modifications to certain extents in genomic components (loss and gain of DNA segments and transposons, introgression of alien DNA segments) and DNA methylation, compared with B. napus donor. The significant differences in the changes between the B. napus types extracted from these additions likely resulted from the different effects of individual alien chromosomes. Particularly, the additions which harbored the O. violaceus chromosome carrying dominant rRNA genes over those of B. napus tended to result in the development of plants which showed fewer changes, suggesting a role of the expression levels of alien rRNA genes in genomic stability. These results provided new cues for the genetic alterations in one parental genome that are maintained even after the genome becomes independent.

The purple leaf pigmentation mainly associated with anthocyanins accumulation is common in Brassica but the mechanisms of its production and its potential physiological functions are poorly understood. Here, we performed the phenotypic, cytological, physiological, and comparative leaves transcriptome analyses of 11 different varieties belonging to five Brassica species with purple or green leaves. We observed that the anthocyanin was accumulated in most of vegetative tissues in all species and also in reproduction organs of B. carinata. Anthocyanin accumulated in different part of purple leaves including adaxial and abaxial epidermal cells as well as palisade and spongy mesophyll cells. Leave transcriptome analysis showed that almost all late biosynthetic genes (LBGs) of anthocyanin, especially Dihydroflavonol 4-Reductase (DFR), Anthocyanidin Synthase (ANS) and Transparent Testa 19 (TT19), were highly up-regulated in all purple leaves. However, only one of transcript factors in anthocyanin biosynthesis pathway, Transparent Testa 8 (TT8), was up regulated along with those genes in all purple leaves, indicating its pivotal role for anthocyanin production in Brassica. Interestingly, with the up-regulation of genes for anthocyanin synthesis, Cytosolic 6-phosphogluconolactonase (PLG5) which involved in the oxidative pentose-phosphate pathway was up-regulated in all purple leaves and three genes FTSH PROTEASE 8 (FTS8), GLYCOLATE OXIDASE 1 (GOX1), and GLUTAMINE SYNTHETASE 1;4 (GLN1;4) related to degradation of photo-damaged proteins in photosystem II and light respiration were down-regulated. These results highlighted the potential physiological functions of anthocyanin accumulation related to photosynthesis which might be of great worth in future.

Polyploidy is popular for the speciation of angiosperms but the initial stage of allopolyploidization resulting from interspecific hybridization and genome duplication is associated with different extents of changes in genome structure and gene expressions. Herein, the transcriptomes detected by RNA-seq in resynthesized Brassica allotetraploids (Brassica juncea, AABB; B. napus, AACC; B. carinata, BBCC) from the pair-wise crosses of the same three diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC) were compared to reveal the patterns of gene expressions from progenitor genomes and the effects of different types of genome combinations and cytoplasm, upon the genome merger and duplication. From transcriptomic analyses for leaves and silique walls, extensive expression alterations were revealed in these resynthesized allotetraploids relative to their diploid progenitors, as well as during the transition from vegetative to reproductive development, for differential and transgressive gene expressions were variable in numbers and functions. Genes involved in glucosinolates and DNA methylation were transgressively up-regulated among most samples, suggesting that gene expression regulation was immediately established after allopolyploidization. The expression of ribosomal protein genes was also tissue-specific and showed a similar expression hierarchy of rRNA genes. The balance between the co-up and co-down regulation was observed between reciprocal B. napus with different types of the cytoplasm. Our results suggested that gene expression changes occurred after initial genome merger and such profound alterations might enhance the growth vigor and adaptability of Brassica allotetraploids.

Brassica rapa includes some of the most important vegetables worldwide as well as oilseed crops. The complete annotated genome sequence confirmed its paleohexaploid origins and provides opportunities for exploring the detailed process of polyploid genome evolution. We generated a genome-wide DNA methylation profile for B. rapa using a modified reduced representation bisulfite sequencing (RRBS) method. This sampling represented 2.24% of all CG loci (2.5 × 10(5)), 2.16% CHG (2.7 × 10(5)), and 1.68% CHH loci (1.05 × 10(5)) (where H = A, T, or C). Our sampling of DNA methylation in B. rapa indicated that 52.4% of CG sites were present as (5m)CG, with 31.8% of CHG and 8.3% of CHH. It was found that genic regions of single copy genes had significantly higher methylation compared to those of two or three copy genes. Differences in degree of genic DNA methylation were observed in a hierarchical relationship corresponding to the relative age of the three ancestral subgenomes, primarily accounted by single-copy genes. RNA-seq analysis revealed that overall the level of transcription was negatively correlated with mean gene methylation content and depended on copy number or was associated with the different subgenomes. These results provide new insights into the role epigenetic variation plays in polyploid genome evolution, and suggest an alternative mechanism for duplicate gene loss.

Aneuploidy with loss of entire chromosomes from normal complement disrupts the balanced genome and is tolerable only by polyploidy plants. In this study, the monosomic and nullisomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome. The monosomics gave a plant phenotype very similar to the original donor, but the nullisomics had much smaller stature and also shorter growth period. By the comparative analyses on the global transcript profiles with the euploid donor, genome-wide alterations in gene expression were revealed in two aneuploids, and their majority of differentially expressed genes (DEGs) resulted from the trans-acting effects of the zero and one copy of C2 chromosome. The higher number of up-regulated genes than down-regulated genes on other chromosomes suggested that the genome responded to the C2 loss via enhancing the expression of certain genes. Particularly, more DEGs were detected in the monosomics than nullisomics, contrasting with their phenotypes. The gene expression of the other chromosomes was differently affected, and several dysregulated domains in which up- or downregulated genes obviously clustered were identifiable. But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss. Some genes and their expressions on C2 were correlated with the phenotype deviations in the aneuploids. These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

Abscisic acid (ABA) and Gibberellic acid (GA) play key roles in regulating seed dormancy and germination. First, when examining germination of different rice cultivars, we found that their germination timing and dormancy status are rather distinct, coupled with different GA/ABA ratio. Second, we studied genomic sequences of ABA and GA dormancy- and germination-associated genes in rice and discovered single nucleotide polymorphisms and insertions/deletions (Indels) in both coding and regulatory sequences. We aligned all these variations to the genome assemblies of 9311 and PA64s and demonstrated their relevance to seed dormancy both quantitatively and qualitatively based on gene expression data. Third, we surveyed and compared differentially expressed genes in dry seeds between 9311 and PA64s to show that these differentially expressed genes may play roles in seed dormancy and germination.