Current Plant Biology最新文献

Sorghum, also known as great millet, is a major cereal crop that feeds over 500 million people in more than 100 countries, especially in Africa and Asia. It can grow well under harsh environmental conditions, such as drought, heat, salinity, and soils that are nutritionally poor. The crop is water- and nitrogen-efficient with C₄ photosynthesis system and a relatively small genome of about 730 Mb. Its genome has been sequenced and annotated, revealing significant genetic variation and genomics resources. Despite being drought tolerant, there is a great degree of variation among the diverse lines of germplasm for drought and drought associated traits, and hence resilience to drought and other stresses need to be studied through the integration of phenomics and genomics technologies. There is an urgent need to adopt advanced genomics and high-throughput technologies to find candidate genes and alleles for crop traits, develop molecular markers and genomic selection (GS) models, create new genetic variation and design sorghum ideotypes that suit to the changing climate.

Jojoba (Simmondsia chinensis) is a desert shrub with an ability to survive in extremely arid environments. The exceptional drought tolerance of jojoba includes traits that could be useful in developing drought tolerant crop plants. This study characterized changes in gene expression in jojoba under water-stress during a controlled-environment experiment. A large number of transcripts (10,936) were identified as differentially expressed under contrasting water stress conditions. These included transcripts corresponding to antioxidant activity-related genes such as superoxide dismutase, defense response genes such as Pathogenesis-Related 4 (PR4), water molecule bio-channels such as aquaporins, cell membrane protectants such as Late Embryogenesis Abundant (LEA), and growth regulators such as 1-aminocyclopropane-1-carboxylic acid (ACC). A total of 880 novel transcripts were identified as representing possible novel genes associated with jojoba subjected to water stress. There were also many transcripts linked to transcriptional regulation that were expressed in response to water-stress in jojoba. Many male-specific transcripts corresponding to stress-related genes and transcription regulators were differentially expressed under water-stress with 1928 differentially expressed transcripts that aligned to the two Y chromosome-specific regions Y1 and Y2. The water-stress related genes detected may help explain the drought tolerance of jojoba and provide a valuable source of genes for exploitation in providing tolerance to water stress in other species.

Target of rapamycin (TOR) signaling is an essential nutrient-dependent pathway controlling cell growth in all eukaryotes. TOR signaling is well characterized in yeast and animals but remains poorly investigated in plants. The hormonal action of gibberellic acid (GA) is a crucial factor for wheat germination by inducing the synthesis of α-amylase in wheat aleurone cells. Here we showed that GA promotes the activation of Triticum aestivum TOR (TaTOR) signaling as evidenced by increased phosphorylation of T. aestivum S6K1 (TaS6K1) on its conserved hydrophobic motif together with proteasomal degradation of growth-inhibitory factor Rht-1. GA-dependent activation of TaTOR signaling led to α-amylase synthesis and Rht-1 proteasomal degradation because both GA-dependent events were sensitive to TaTOR inhibition. Using antibodies specific to TaTOR, we successfully identified the presence of endogenous TaTOR protein in terminally differentiated wheat aleurone layers. Additionally, by examining the rapamycin-sensitive phosphorylation of S6K1 as a reliable indicator of endogenous TOR kinase activity, we demonstrated that the activity of TaTOR in aleurone layers is enhanced by GA. Importantly, this stimulation is not associated with the regulation of either TaTOR transcription or the accumulation of TaTOR protein. In yeast and pull-down assays, a robust interaction between TaS6K1 and the N terminus of Rht-1 (amino acids 1–234) was observed, a finding further supported by co-immunoprecipitation of endogenous Rht-1 and TaS6K1. Furthermore, the administration of mTOR inhibitors significantly attenuated GA-induced degradation of endogenous Rht-1 and prolonged the persistence of the complex formed by these two proteins. We propose that TaTOR-TaS6K1 signaling contributes to GA-dependent wheat germination by mediating α-amylase synthesis and controlling proteasomal degradation of Rht-1 in wheat aleurone cells.

The ZIP (Zn-regulated, iron-regulated transporter-like protein) gene family is a novel metal transporter that is capable of absorbing and transporting a variety of metal cations, including zinc (Zn), iron (Fe), manganese (Mn), and cadmium (Cd). Quercus dentata Thunb. is a candidate plant species for the phytoremediation of heavy metal contaminated soil. A chromosome-scale genome assembly is reported recently for Q. dentata, however, genome-wide analysis of ZIP genes has not been performed. In this study, we identified 29 ZIP genes in Q. dentata genome using bioinformatics tools. The sequence homology, chromosomal distribution and phylogenetic relationship of these genes with ZIP genes from other plants indicated potential gene duplication during Q. dentata genome evolution. Sequence analysis revealed 23 conserved motifs in QdZIP proteins and 11 types of high-frequency cis-acting elements in the promoters of QdZIP genes. QdZIP proteins were predicted to localize on cell membrane except QdZIP7. QdZIP7 was predicted to be a chloroplast protein, which was confirmed using microscopic observation of QdZIP7-GFP fusion protein. QdZIP gene expression patterns in roots and exophytic mycorrhiza, leaves, stems and fruits were obtained from transcriptome data, and the responsiveness of QdZIP7 to excessive heavy metal Zn was detected using qRT-PCR. In summary, our study provided a basic sights on the ZIP gene family in Q. dentata, laying the foundation for in-depth investigation on the roles of the ZIP proteins in heavy metal transport.

The development of sequencing methods has resulted in the investigation of many unexplored research areas. Among the different sequencing methods, single-cell transcriptomics is versatile and has completely changed the researchers' perception of biological processes from tissue to single-cell. Single-cell transcriptomic is applied in various fields to reveal cell-cell interaction, phytopathogenic interactions, cell-specific genetic expression, regulatory pathways, and the effects of drugs on cells. Single-cell transcriptomics was initially applied to the model organisms, such as mice and Arabidopsis thaliana, and then later expanded to other non-model species. Recently, single-cell transcriptomics is revolutionizing plant and animal research. The direct application of single-cell transcriptomics has become simple with advanced sequencing methods and data analysis tools available. This review summarizes the latest knowledge on single-cell transcriptomics in plant and animal research. We emphasize various sequencing methods, bioinformatics software development, comparison between plant and animal single-cell transcriptomics studies, and the limitations and future prospectus.

Improving the forage quality of alfalfa in terms of digestibility and crude content is essential for any alfalfa quality breeding programs. Arabidopsis thaliana orphan gene QQS (Qua-Quine Starch) has been shown to improve protein content and alter carbohydrate composition in different food crops. However, there are significant differences in agronomic traits and nutritional conditions between alfalfa and other food crops. To explore the biological function and molecular mechanisms of QQS in alfalfa, we generated QQS transgenic plants and their segregated population (T1 generation), and evaluated their performance under normal- and nitrogen-deficient conditions. Our findings indicate that QQS can significantly enhance the total nitrogen and crude protein content of alfalfa and increase nodule weight under low-nitrogen conditions. Furthermore, QQS transgenic lines also showed reduced levels of neutral detergent fiber (NDF) and lignin, improving forage digestibility. By RNA sequencing and RT-qPCR analysis, we found that QQS affected the expression of genes involved in carbon and nitrogen metabolism, lignin biosynthesis and amino acid biosynthesis and degradation pathways in alfalfa. In addition, QQS also improved alfalfa biomass yield by increasing branch number and plant height in both greenhouse and field conditions. Our results demonstrate that QQS as a useful molecular tool can improve alfalfa biomass yield and overall forage quality and could have significant implications for the alfalfa breeding industry in satisfying the constant demands for high-quality and high-yielding forage.

Brassica juncea L. is an important oilseed crop that yields edible oil and biofuel. Improving B. juncea seed traits is a primary breeding target, but these traits are genetically complex. MicroRNAs (miRNAs) regulate seed development by modulating gene expression at the post-transcriptional or translational level and are excellent candidates for improving seed traits. However, the roles of miRNAs in B. juncea seed development are yet to be investigated. Here, we report small RNA profiling and miRNA identification from developing seeds of two contrasting varieties of B. juncea, Early Heera2 (EH2) and Pusa Jaikisan (PJK). We identified 326 miRNAs, including 127 known and 199 novel miRNAs, of which 103 exhibited inter-varietal differential expression. Integrating miRNAome and our previous transcriptome data identified 13,683 putative miRNA-target modules. Segregation of differentially expressed miRNAs into different groups based on variety-wise upregulation, followed by comprehensive functional analysis of targets using pathway mapping, gene ontology, transcription factor mapping, and candidate gene analysis, revealed at least 11, 6, and 7 miRNAs as robust candidates for the regulation of seed size, seed coat color, and oil content, respectively. Further, co-localization with previously reported quantitative trait loci (QTL) proffered 29 and 15 miRNAs overlapping with seed weight and oil content QTLs, respectively. Our study is the first comprehensive report of miRNAome expression dynamics from developing seeds and provides candidate miRNAs and target genes for engineering seed traits in B. juncea.

Being a preparative step for germination, seed imbibition is a hydration process that involves the release of seed molecules into the environment, an essential ecological aspect of this phase. On one side this leakage leads to unlocking the seed dormancy by removing abscisic acid and other pro-dormancy molecules, on the other side, it releases small molecules such as vitamins, amino acids, flavonoids, and proteins contributing to supporting germination by attracting symbionts, contrasting pathogens, and facilitating nutrients uptake. Here the proteome associated with the imbibition spillage of chickpea seeds emerges as a probe to understand the early events during germination and (pre-) symbiosis, providing a proxy to disclose the influence that the seed applies to the environment for optimal achievement of its eco-physiological needs. This proteome is clustered into two main groups that differ in chemical-physical properties and function. Most proteome entries belong to biochemical pathways that directly influence germination by enhancing nutrient uptake, protecting against stresses of various origins, and promoting symbiosis. A fraction of this proteome was found to be associated with accidental pathways due to the loss of proteins from teguments and fractured tissues. Here, germination, protection, and symbiosis emerge as a balanced proteomic triad aimed at enhancing and sustaining seedling emergence and plant growth.

Zinc oxide nanoparticles (ZnO NPs) are currently being used in a number of applications, including agriculture. In agricultural regions all throughout the world, drought poses a serious danger to crop production and development. The outcome of this experiment showed that the treatment of 250 ppm ZnO NPs provides drought resistance by considerably improving physiological and biochemical traits, viz., shoot and root length, RWC, MSI, Zn content, total chlorophyll and protein content, biomass accumulation, osmolytes content, and antioxidant enzyme activities. Similar results were found by gene expression analysis. The expression of drought-responsive genes (DHN, DREB, P5CS, BADH, SOD, CAT, APX, bZIP and NAC) were highly upregulated in ZnO- treated plants compared with non-ZnO treated root and leaf tissues of plants under stress and non-stress conditions. The osmoregulation-related genes (P5CS and BADH) were highly expressed in ZnO treated plants over non-ZnO treated samples in both conditions (stress and control). However, the relative accumulation of these genes was higher root tissues compared to leaf tissues. According to the results, ZnO NPs caused an instantaneous rise in P5CS and BADH expression, which function as stress signaling molecules and trigger the production of genes that are responsive to drought. This results in the activation of the defense system and a greater ability to withstand stress. ZnO NPs in general may, under drought conditions, influence the expression of genes that are drought-inducible via both ABA-dependent and ABA-independent pathways.

Proline/P5C cycle between mitochondria and cytosol, play important roles in energy supply and ROS (Reactive oxygen species) generation in mammalian cell. Recently, in plant, proline-dependent ROS via proline/P5C cycle was proposed to be involved in hypersensitive reaction during plant response to avirulent pathogens. However, much remains to be elucidated about the regulation of proline/P5C cycle upon pathogen infection. Here, we reported the isolation and characterization of an Arabidopsis mutant proline resistance 2 (pre2), with a single dominant mutation in a single gene. Our results showed that the proline resistance phenotype of pre2 is not due to decreased intracellular proline content, when treated with exogenous proline. Upon proline treatment, pre2 showed reduced induction of PDH transcript level and enhanced induction of that of P5CDH, accompanied by lower level of mitochondrial ROS, suggesting an attenuated proline/P5C cycle activity. Proline-induced SA (Salicylic acid) signaling was also less activated in pre2, as evidenced by reduced free SA content and PR1 transcript level, compared to the WT. On the other hand, SA activation on the proline/P5C activity is to a lesser extent in pre2 than in WT. Significantly, pre2 demonstrated increased susceptibility to infection by avirulent pathogen Pst. DC3000 (avrRps4), accompanied also by lesser induced proline/P5C cycle activity by the pathogen. Our results indicated that there is a correlation between proline/P5C cycle and plant response to avirulent pathogen.