Sphingolipid metabolism, transport, and functions in plants: Recent progress and future perspectives

Sphingolipids, which comprise membrane systems together with other lipids, are ubiquitous in cellular organisms. They show a high degree of diversity across plant species and vary in their structures, properties, and functions. Benefiting from the development of lipidomic techniques, over 300 plant sphingolipids have been identified. Generally divided into free long-chain bases (LCBs), ceramides, glycosylceramides (GlcCers) and glycosyl inositol phosphoceramides (GIPCs), plant sphingolipids exhibit organized aggregation within lipid membranes to form raft domains with sterols. Accumulating evidence has revealed that sphingolipids obey certain trafficking and distribution rules and confer unique properties to membranes. Functional studies using sphingolipid biosynthetic mutants demonstrate that sphingolipids participate in plant developmental regulation, stimulus sensing, and stress responses. Here, we present an updated metabolism/degradation map and summarize the structures of plant sphingolipids, review recent progress in understanding the functions of sphingolipids in plant development and stress responses, and review sphingolipid distribution and trafficking in plant cells. We also highlight some important challenges and issues that we may face during the process of studying sphingolipids.

Streamflow calculation for medium-to-small rivers in data scarce inland areas

Inland streamflow estimation is essential in global water supply and environment protection. In data-scarce areas a highly efficient way of estimating streamflow is through remote sensing methods. However, high requirement of most previous methods on ground-measured data hinder their wide use in data-scarce areas. Therefore, this paper presented a new framework for estimation of streamflow in medium-to-small rivers with few ground measurements by using high-resolution unmanned aerial vehicle (UAV) imagery. A new Virtual Hydraulic Radius (VHR) method was proposed to complement AMHG (at-many-stations hydraulic geometry), a method not requiring any ground measurements when global parameters are used (global-AMHG) in large-scaled rivers but yielding great uncertainties in smaller scaled rivers, thus creating a VHR-AMHG method for medium-to-small rivers. The accuracy verification of the proposed method was performed by comparing it to field measurement data and the global parameters of the original AMHG (global-AMHG). Results showed that the root mean square error calculated from VHR-AMHG was 32.15 m³/s, while that from global-AMHG was 305.65 m³/s, indicating that the VHR-AHRG method yields a significantly higher accuracy for streamflow estimation for medium-to-small rivers. We found that regardless of the size of the river, AMHG is not applicable for rivers having excessively small b values in the equation w = aQ^b (low-b rivers). For medium-to-small rivers with b < 0.25, AMHG is not recommended. The accuracy of the original AMHG method is limited by the initial value of the model parameters and the condition that the congruent discharge (Q_c) has to be within the range of observational discharge. The initial value setting of the model parameters significantly impacts the calculation accuracy. The VHR-AMHG method is able to overcome the deficiencies of the original AMHG, i.e. being overly dependent on the initial value setting with long-series known discharge data. It also eliminates the limitation of the Q_c condition, as it achieves a higher accuracy for rivers in which Q_c does not satisfy the condition compared to using global-AMHG on rivers that actually meet the condition, thus greatly expanding its usage scope. Thus VHR-AMHG method can provide detailed data on the spatial and temporal distribution of regional and national streamflow for governments and stakeholders, and offer scientific data support for wisely making water supply polices and sustainably protecting eco-environment.

Optimization of CRISPR/Cas9 genome editing in cotton by improved sgRNA expression

BACKGROUND

When developing CRISPR/Cas9 systems for crops, it is crucial to invest time characterizing the genome editing efficiency of the CRISPR/Cas9 cassettes, especially if the transformation system is difficult or time-consuming. Cotton is an important crop for the production of fiber, oil, and biofuel. However, the cotton stable transformation is usually performed using Agrobacterium tumefaciens taking between 8 and 12 months to generate T₀ plants. Furthermore, cotton is a heterotetraploid and targeted mutagenesis is considered to be difficult as many genes are duplicated in this complex genome. The application of CRISPR/Cas9 in cotton is severely hampered by the long and technically challenging genetic transformation process, making it imperative to maximize its efficiency.

RESULTS

In this study, we provide a new system to evaluate and validate the efficiency of CRISPR/Cas9 cassettes in cotton using a transient expression system. By using this system, we could select the most effective CRISPR/Cas9 cassettes before the stable transformation. We have also optimized the existing cotton CRISPR/Cas9 system to achieve vastly improved mutagenesis efficiency by incorporating an endogenous GhU6 promoter that increases sgRNA expression levels over the Arabidopsis AtU6-29 promoter. The 300 bp GhU6.3 promoter was cloned and validated using the transient expression system. When sgRNAs were expressed under the control of the GhU6.3 promoter in CRISPR/Cas9 cassettes, expression levels were 6-7 times higher than those provided by the AtU6-29 promoter and CRISPR/Cas9-mediated mutation efficiency was improved 4-6 times.

CONCLUSIONS

This study provides essential improvements to maximize CRISPR/Cas9-mediated mutation efficiency by reducing risk and workload for the application of CRISPR/Cas9 approaches in the targeted mutagenesis of cotton.

Identification of genes related to floral organ development in pak choi by expression profiling

Pak choi is a highly nutritious vegetable that is widely grown in China, Southeast Asia, and other parts of the world. Because it reproduces by seed, it is very important to understand the mechanism of floral organ development. Therefore, using the Chinese cabbage genome as a reference, this study analyzed the expression profiles of shoot apex genes at flower bud differentiation stages 1 and 5, in order to identify genes related to floral organ development. The results showed that the proportion of mapped genes was high, with 84.25 and 83.80% of clean reads from the two sample saligned to the reference genome, respectively. A total of 525 differentially expressed genes (DEGs) were identified, 224 of which were upregulated and 301 were downregulated. The expression levels of genes homologous to Chinese cabbage flowering genes were also analyzed at stages 1 and 5; the expression levels of Bra012997 (ap1), Bra000393 (SOC1), and Bra004928 (SOC1) were significantly upregulated at stage 5, suggesting that these three genes positively regulate floral development in pak choi. DEGs involved in floral organ development were analyzed with homologous genes from Arabidopsis thaliana; the homologous genes Bra029281 (AGL42), Bra026577 (ARPN), Bra022954 (SPL3), Bra029293 (ARF2), Bra007978 (AtRLP12), Bra033221 (SPL8), Bra008037 (LOX4), Bra001598 (IAA19), Bra003892 (PATL1), Bra038778 (AT4G21323), Bra025315 (KLCR2), and Bra013906 (DTX35) are directly related to floral organ development in Arabidopsis, suggesting that these genes have corresponding functions during flower organ development in pak choi, and could be candidates for further genetic research. These results provide a foundation for research on the molecular mechanism of flower organ development in pak choi and other Brassica rapa vegetables.