PEPC of sugarcane regulated glutathione S-transferase and altered carbon-nitrogen metabolism under different N source concentrations in Oryza sativa

Wild soybean cotyledons at the emergence stage tolerate alkali stress by maintaining carbon and nitrogen metabolism, and accumulating organic acids

Soil alkalization is a global ecological problem that constrains food security and sustainable socio-economic development. As a wild relative of soybean, wild soybean (Glycine soja) exhibits strong salt and alkali stress resistance and its cotyledons play a key role during the emergence (VE) stage. This study aimed to compare variations in growth parameters, cotyledon ultrastructure, photosynthetic physiology, mineral ion and metabolite contents, and gene expression in two ecotypes of wild soybean to elucidate the regulatory mechanisms underlying alkali stress resistance in salt-tolerant wild soybean cotyledons during the VE stage. The results showed that salt-tolerant wild soybean cotyledons exhibited relatively stable growth parameters, dense and orderly chloroplast structure, high photosynthetic rates, as well as high K+ and Ca2+ contents under alkali stress. Metabolomics, transcriptomics, and weighted gene co-expression network analyses revealed that salt-tolerant wild soybean cotyledons adapted to alkali stress during the VE stage by enhancing photosynthetic carbon assimilation pathways, increasing methionine and proline biosynthesis, and enhancing gamma-aminobutyric acid biosynthesis, thereby maintaining a stable carbon and nitrogen balance. In addition, upregulation of the expression of ICL, MS, and ACO2 led to the accumulation of various organic acids, such as pyruvic, aconitic, succinic, oxalic, malic, and fumaric acids, thereby promoting the synthesis of organic acid metabolism modules. This study provides novel insights into the key metabolic modules by which wild soybeans resist alkali stress.

Toxic effects of atmospheric deposition in mining areas on wheat seedlings

Storage and transportation of coal, as well as operation of coal-fired power plants, produce amounts of metallic exhaust that may lead to different atmospheric environment in the overlapped areas of farmland and coal resource (OAFCR) environment. To investigate the effects of different atmospheric environment in the OAFCR region (north of Xuzhou) on wheat seedlings (AK-58), a box experiment was conducted and compared to an area far from the OAFCR (south of Xuzhou). The study revealed that (1) compared to the southern suburb of Xuzhou, the fresh and dry weight, activities of photosynthetic enzymes and POD of wheat seedlings in the OAFCR reduced obviously. (2) Significantly higher levels of Cr, Cd, Pb, Zn, and Cu were found in the shoots and roots of wheat seedlings in the OAFCR, with lower transfer factor for heavy metals (except Cd and As) in comparison to those in the southern suburb. And the bioconcentration factors of heavy metals (except As) in wheat seedlings in the OAFCR were significantly higher. (3) Nearly 90% of heavy metals (Pb, Cu, Cd, Zn, and Cr) absorbed by wheat were stored in cell walls and soluble fractions, with significantly higher contents of Cu and Cr in wheat seedlings' cell walls and higher contents of Pb, Zn, and Cd in soluble components found in the OAFCR. Our results showed that atmospheric deposition in the mining area has a certain toxic effect on wheat seedlings, and this study provides a theoretical basis for OAFCR crop toxicity management.

The response of nutrient cycle, microbial community abundance and metabolic function to nitrogen fertilizer in rhizosphere soil of Phellodendron chinense Schneid seedlings

Nitrogen (N) as an essential macronutrient affects the soil nutrient cycle, microbial community abundance, and metabolic function. However, the specific responses of microorganisms and metabolic functions in rhizosphere soil of Phellodendron chinense Schneid seedlings to N addition remain unclear. In this study, four treatments (CK, N5, N10 and N15) were conducted, and the soil physicochemical properties, enzyme activities, microbial community abundances and diversities, metabolism, and gene expressions were investigated in rhizosphere soil of P. chinense Schneid. The results showed that N addition significantly decreased rhizosphere soil pH, among which the effect of N10 treatment was better. N10 treatment significantly increased the contents of available phosphorus (AP), available potassium (AK), ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N) and sucrase (SU) activity, as well as fungal diversity and the relative expression abundances of amoA and phoD genes in rhizosphere soil, but observably decreased the total phosphorus (TP) content, urease (UR) activity and bacterial diversity, among which the pH, soil organic matter (SOM), AP, NH4+-N and NO3--N were the main environmental factors for affecting rhizosphere soil microbial community structure based on RDA and correlation analyses. Meanwhile, N10 treatment notably enhanced the absolute abundances of the uracil, guanine, indole, prostaglandin F2α and γ-glutamylalanine, while reduced the contents of D-phenylalanine and phenylacetylglycine in rhizosphere soil of P. chinense Schneid seedlings. Furthermore, the soil available nutrients represented a significant correlation with soil metabolites and dominant microorganisms, suggesting that N10 addition effectively regulated microbial community abundance and metabolic functions by enhancing nutrient cycle in the rhizosphere soil of P. chinense Schneid seedlings.

Silencing of SbPPCK1-3 Negatively Affects Development, Stress Responses and Productivity in Sorghum

Phosphoenolpyruvate carboxylase (PEPC) plays central roles in photosynthesis, respiration, amino acid synthesis, and seed development. PEPC is regulated by different post-translational modifications. Between them, the phosphorylation by PEPC-kinase (PEPCk) is widely documented. In this work, we simultaneously silenced the three sorghum genes encoding PEPCk (SbPPCK1-3) by RNAi interference, obtaining 12 independent transgenic lines (Ppck1-12 lines), showing different degrees of SbPPCK1-3 silencing. Among them, two T2 homozygous lines (Ppck-2 and Ppck-4) were selected for further evaluation. Expression of SbPPCK1 was reduced by 65% and 83% in Ppck-2 and Ppck-4 illuminated leaves, respectively. Expression of SbPPCK2 was higher in roots and decreased by 50% in Ppck-2 and Ppck-4 in this tissue. Expression of SbPPCK3 was low and highly variable. Despite the incomplete gene silencing, it decreased the degree of phosphorylation of PEPC in illuminated leaves, P-deficient plants, and NaCl-treated plants. Both leaves and seeds of Ppck lines had altered metabolic profiles and a general decrease in amino acid content. In addition, Ppck lines showed delayed flowering, and 20% of Ppck-4 plants did not produce flowers at all. The total amount of seeds was lowered by 50% and 36% in Ppck-2 and Ppck-4 lines, respectively. The quality of seeds was lower in Ppck lines: lower amino acid content, including Lys, and higher phytate content. These data confirm the relevance of the phosphorylation of PEPC in sorghum development, stress responses, yield, and quality of seeds.

Differential physiological response of marine and freshwater microalgae to polystyrene microplastics

Effects of microplastics on microalgae have not been compared from different habitat. To answer this question, three marine microalgae species (Chlorella marined, Nannochloropsis oculate, and Phaeodactylum tricornutum) and two freshwater species (Chlorella vulgaris and Tetradesmus obliquus) were selected and exposed to the environment relevant concentrations of polystyrene microplastics. The results indicated that microplastics have a significant concentration effect on the growth of microalgae. The attachment of microalgae to microplastics surface and the aggregation of microalgae with each other were observed. Under exposure of microplastics, the photosynthesis of microalgae was inhibited while the antioxidant system was activated, indicating that microplastics had a negative impact on microalgae. At the end of exposure, the oxidative stress status caused by microplastics in marine microalgae were alleviated, but the antioxidant system of freshwater microalgae was still at high levels, indicating a stress response. In addition, integrated biomarker response (IBR) indicated that the effects of microplastics on freshwater microalgae were severer than marine microalgae, which might relate to their differences in removing reactive oxygen species (ROS) effectively and membrane structure. Our study provides a reliable data for understanding the complex effects of microplastics on microalgae, and especially for comparing the differential effects of microplastics among different microalgae.

Estimation of intrinsic water-use efficiency from δ13C signature of C3 leaves: Assumptions and uncertainty

Carbon isotope composition (δ¹³C) has been widely used to estimate the intrinsic water-use efficiency (iWUE) of plants in ecosystems around the world, providing an ultimate record of the functional response of plants to climate change. This approach relies on established relationships between leaf gas exchange and isotopic discrimination, which are reflected in different formulations of ¹³C-based iWUE models. In the current literature, most studies have utilized the simple, linear equation of photosynthetic discrimination to estimate iWUE. However, recent studies demonstrated that using this linear model for quantitative studies of iWUE could be problematic. Despite these advances, there is a scarcity of review papers that have comprehensively reviewed the theoretical basis, assumptions, and uncertainty of ¹³C-based iWUE models. Here, we 1) present the theoretical basis of ¹³C-based iWUE models: the classical model (iWUE_sim), the comprehensive model (iWUE_com), and the model incorporating mesophyll conductance (iWUE_mes); 2) discuss the limitations of the widely used iWUE_sim model; 3) and make suggestions on the application of the iWUE_mes model. Finally, we suggest that a mechanistic understanding of mesophyll conductance associated effects and post-photosynthetic fractionation are the bottlenecks for improving the ¹³C-based estimation of iWUE.

Overexpression of Setaria italica phosphoenolpyruvate carboxylase gene in rice positively impacts photosynthesis and agronomic traits

C₄ plants have the inherent capacity to concentrate atmospheric CO₂ in the vicinity of RuBisCo, thereby increasing carboxylation, and inhibiting photorespiration. Carbonic anhydrase (CA), the first enzyme of C₄ photosynthesis, converts atmospheric CO₂ to HCO₃^-, which is utilized by PEPC to produce C₄ acids. Bioengineering of C₄ traits into C₃ crops is an attractive strategy to increase photosynthesis and water use efficiency. In the present study, we isolated the PEPC gene from the C₄ plant Setaria italica and transferred it to C₃ rice. Overexpression of SiPEPC resulted in a 2-6-fold increment in PEPC enzyme activity in transgenic lines with respect to non-transformed control. Photosynthetic efficiency was enhanced in transformed plants, which was associated with increased ФPSII, ETR, lower NPQ, and higher chlorophyll accumulation. Water use efficiency was increased by 16-22% in PEPC transgenic rice lines. Increased PEPC activity enhanced quantum yield and carboxylation efficiency of PEPC transgenic lines. Transgenic plants exhibited higher light saturation photosynthesis rate and lower CO₂ compensation point, as compared to non-transformed control. An increase in net photosynthesis increased the yield by (23-28.9%) and biomass by (24.1-29%) in transgenic PEPC lines. Altogether, our findings indicate that overexpression of C_4-specific SiPEPC enzyme is able to enhance photosynthesis and related parameters in transgenic rice.

Optimized potassium application rate increases foxtail millet grain yield by improving photosynthetic carbohydrate metabolism

Photosynthetic carbohydrate metabolism is an important biochemical process related to crop production and quality traits. Potassium (K) critically contributes to the process of photosynthetic carbon assimilation and carbohydrate metabolism. We explored the effects of potassium fertilization on physiological mechanisms including carbohydrate metabolism in foxtail millet and its yield. Field experiments were performed using two foxtail millet (Setaria italica L.) cultivars: 1) Jingu 21 (low-K sensitive); and 2) Zhangza 10 (low-K tolerant). Effect of five different potassium fertilizer (K₂O) rates (0, 60, 120, 180, and 240 kg·hm^-2) were tested in two consecutive years, 2020 and 2021. We found that potassium application significantly increases the K content, dry matter accumulation and yield. Jingu 21 and Zhangza 10 had maximum yields at 180 kg·hm^-2 K application, which were 29.91% and 31.51% larger than without K application, respectively. Excessive K application (K₂₄₀) did not further improve their yields. The suitable K fertilizer application of Jingu 21 and Zhangza 10 are 195.25-204.27 and 173.95-175.87 kg·K2O·hm^-2, respectively. The net photosynthetic rate (P_n), ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco), phosphoenolpyruvate carboxylase (PEPC), and fructose-1,6-bisphosphatase (FBPase) were positively correlated with the potassium content. Potassium application improved the availability of carbon sources for carbohydrate synthesis. Compared with the K₀ treatment, variations in the activities of sucrose phosphate synthase (SPS) and sucrose synthase (SuSy) in potassium-treated Jingu 21 (K₆₀, K₁₂₀, K₁₈₀, and K₂₄₀) were 17.94%-89.93% and 22.48%-182.10%, respectively, which were greater than those of Zhangza 10 (11.34%-71.12% and 16.18%-109.13%, respectively) and indicate that Jingu 21 is more sensitive to potassium application. The sucrose contents in the Jingu 21 and Zhangza 10 grains were 0.97%-1.15% and 1.04%-1.23%, respectively. The starch contents were 28.99%-37.75% and 24.81%-34.62%, respectively. The sucrose: ratio of Jingu 21 was smaller than that of Zhangza 10, indicating that Jingu 21 utilized nutrients better than Zhangza 10. Stepwise regression and path analysis showed that leaf and grain SuSy activity, by coordinating the source-sink relationship, have the greatest direct effect on Jingu 21 yield, whereas leaf SuSy activity, by promoting the generation of photosynthates at the source leaf, plays a leading role in Zhangza 10 yield increase. In conclusion, optimized K application can increase foxtail millet grain yield by improving photosynthesis and promoting carbohydrate accumulation and distribution.

Understanding complex genetic architecture of rice grain weight through QTL-meta analysis and candidate gene identification

Quantitative trait loci (QTL) for rice grain weight identified using bi-parental populations in various environments were found inconsistent and have a modest role in marker assisted breeding and map-based cloning programs. Thus, the identification of a consistent consensus QTL region across populations is critical to deploy in marker aided breeding programs. Using the QTL meta-analysis technique, we collated rice grain weight QTL information from numerous studies done across populations and in diverse environments to find constitutive QTL for grain weight. Using information from 114 original QTL in meta-analysis, we discovered three significant Meta-QTL (MQTL) for grain weight on chromosome 3. According to gene ontology, these three MQTL have 179 genes, 25 of which have roles in developmental functions. Amino acid sequence BLAST of these genes indicated their orthologue conservation among core cereals with similar functions. MQTL3.1 includes the OsAPX1, PDIL, SAUR, and OsASN1 genes, which are involved in grain development and have been discovered to play a key role in asparagine biosynthesis and metabolism, which is crucial for source-sink regulation. Five potential candidate genes were identified and their expression analysis indicated a significant role in early grain development. The gene sequence information retrieved from the 3 K rice genome project revealed the deletion of six bases coding for serine and alanine in the last exon of OsASN1 led to an interruption in the synthesis of α-helix of the protein, which negatively affected the asparagine biosynthesis pathway in the low grain weight genotypes. Further, the MQTL3.1 was validated using linked marker RM7197 on a set of genotypes with extreme phenotypes. MQTL that have been identified and validated in our study have significant scope in MAS breeding and map-based cloning programs for improving rice grain weight.

Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage

BACKGROUND

Heterosis is widely used in many crops and is important for global food safety, and maize is one of the most successful crops to take advantage of heterosis. Gene expression patterns control the development of the maize ear, but the mechanisms by which heterosis affects transcriptional-level control are not fully understood.

RESULTS

In this study, we sampled ear inflorescence meristems (IMs) from the single-segment substitution maize (Zea mays) line lx9801^hlEW2b, which contains the heterotic locus hlEW2b associated with ear width, as well as the receptor parent lx9801, the test parent Zheng58, and their corresponding hybrids Zheng58 × lx9801^hlEW2b (HY) and Zheng58 × lx9801 (CK). After RNA sequencing and transcriptomic analysis, 2531 unique differentially expressed genes (DEGs) were identified between the two hybrids (HY vs. CK). Our results showed that approximately 64% and 48% of DEGs exhibited additive expression in HY and CK, whereas the other genes displayed a non-additive expression pattern. The DEGs were significantly enriched in GO functional categories of multiple metabolic processes, plant organ morphogenesis, and hormone regulation. These essential processes are potentially associated with heterosis performance during the maize ear developmental stage. In particular, 125 and 100 DEGs from hybrids with allele-specific expression (ASE) were specifically identified in HY and CK, respectively. Comparison between the two hybrids suggested that ASE genes were involved in different development-related processes that may lead to the hybrid vigor phenotype during maize ear development. In addition, several critical genes involved in auxin metabolism and IM development were differentially expressed between the hybrids and showed various expression patterns (additive, non-additive, and ASE). Changes in the expression levels of these genes may lead to differences in auxin homeostasis in the IM, affecting the transcription of core genes such as WUS that control IM development.

CONCLUSIONS

Our research suggests that additive, non-additive, and allele-specific expression patterns may fine-tune the expression of crucial DEGs that modulate carbohydrate and protein metabolic processes, nitrogen assimilation, and auxin metabolism to optimal levels, and these transcriptional changes may play important roles in maize ear heterosis. The results provide new information that increases our understanding of the relationship between transcriptional variation and heterosis during maize ear development, which may be helpful for clarifying the genetic and molecular mechanisms of heterosis.