Transcriptome analysis reveals key regulatory genes for root growth related to potassium utilization efficiency in rapeseed (Brassica napus L.)

Root system architecture (RSA) is the primary predictor of nutrient intake and significantly influences potassium utilization efficiency (KUE). Uncertainty persists regarding the genetic factors governing root growth in rapeseed. The root transcriptome analysis reveals the genetic basis driving crop root growth. In this study, RNA-seq was used to profile the overall transcriptome in the root tissue of 20 Brassica napus accessions with high and low KUE. 71,437 genes in the roots displayed variable expression profiles between the two contrasting genotype groups. The 212 genes that had varied expression levels between the high and low KUE lines were found using a pairwise comparison approach. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification analysis revealed that the DEGs implicated in hormone and signaling pathways, as well as glucose, lipid, and amino acid metabolism, were all differently regulated in the rapeseed root system. Additionally, we discovered 33 transcription factors (TFs) that control root development were differentially expressed. By combining differential expression analysis, weighted gene co-expression network analysis (WGCNA), and recent genome-wide association study (GWAS) results, four candidate genes were identified as essential hub genes. These potential genes were located fewer than 100 kb from the peak SNPs of QTL clusters, and it was hypothesized that they regulated the formation of the root system. Three of the four hub genes' homologs-BnaC04G0560400ZS, BnaC04G0560400ZS, and BnaA03G0073500ZS-have been shown to control root development in earlier research. The information produced by our transcriptome profiling could be useful in revealing the molecular processes involved in the growth of rapeseed roots in response to KUE.

Differential analysis of transcriptomic and metabolomic of free fatty acid rancidity process in oil palm (Elaeis guineensis) fruits of different husk types

INTRODUCTION

Oil palm is the world's highest yielding oil crop and its palm oil has high nutritional value, making it an oilseed plant with important economic value and application prospects. After picking, oil palm fruits exposed to air will gradually become soft and accelerate the process of fatty acid rancidity, which will not only affect their flavor and nutritional value, but also produce substances harmful to the human body. As a result, studying the dynamic change pattern of free fatty acids and important fatty acid metabolism-related regulatory genes during oil palm fatty acid rancidity can provide a theoretical basis for improving palm oil quality and extending its shelf life.

METHODS

The fruit of two shell types of oil palm, Pisifera (MP) and Tenera (MT), were used to study the changes of fruit souring at different times points of postharvesting, combined with LC-MS/MS metabolomics and RNA-seq transcriptomics techniques to analyze the dynamic changes of free fatty acids during fruit rancidity, and to find out the key enzyme genes and proteins in the process of free fatty acid synthesis and degradation according to metabolic pathways.

RESULTS AND DISCUSSION

Metabolomic study revealed that there were 9 different types of free fatty acids at 0 hours of postharvest, 12 different types of free fatty acids at 24 hours of postharvest, and 8 different types of free fatty acids at 36 hours of postharvest. Transcriptomic research revealed substantial changes in gene expression between the three harvest phases of MT and MP. Combined metabolomics and transcriptomics analysis results show that the expression of SDR, FATA, FATB and MFP four key enzyme genes and enzyme proteins in the rancidity of free fatty acids are significantly correlated with Palmitic acid, Stearic acid, Myristic acid and Palmitoleic acid in oil palm fruit. In terms of binding gene expression, the expression of FATA gene and MFP protein in MT and MP was consistent, and both were expressed higher in MP. FATB fluctuates unevenly in MT and MP, with the level of expression growing steadily in MT and decreasing in MP before increasing. The amount of SDR gene expression varies in opposite directions in both shell types. The above findings suggest that these four enzyme genes and enzyme proteins may play an important role in regulating fatty acid rancidity and are the key enzyme genes and enzyme proteins that cause differences in fatty acid rancidity between MT and MP and other fruit shell types. Additionally, differential metabolite and differentially expressed genes were present in the three postharvest times of MT and MP fruits, with the difference occurring 24 hours postharvest being the most notable. As a result, 24 hours postharvest revealed the most obvious difference in fatty acid tranquility between MT and MP shell types of oil palm. The results from this study offer a theoretical underpinning for the gene mining of fatty acid rancidity of various oil palm fruit shell types and the enhancement of oilseed palm acid-resistant germplasm cultivation using molecular biology methods.

A highly efficient genetic transformation system for broccoli and subcellular localization

INTRODUCTION

Agrobacterium-mediated genetic transformation has been widely used for the identification of functional genes and regulatory and developmental mechanisms in plants. However, there are still some problems of low genetic transformation efficiency and high genotype dependence in cruciferous crops.

METHODS

In this study, broccoli, a worldwide Brassica crop, was used to investigate the effects of genotype, explant type, concentration of hygromycin B used during seedling selection, overexpression vector type, RNAi and CRISPR/cas9 on the genetic transformation efficiency. At the same time, two vectors, PHG-031350 and PHG-CRa, were used for subcellular localization of the glucoraphanin synthesis-related gene FMOGS-OX5 and clubroot resistance gene by a PEG-Ca2+-mediated transient transformation system for broccoli protoplasts. Finally, the Agrobacterium-mediated genetic transformation system of broccoli was optimized and improved.

RESULTS AND DISCUSSION

This study showed that hypocotyl explants are more suitable for Agrobacterium-mediated transgene and CRISPR/Cas9 gene editing of broccoli. In contrast to previous studies, we found that 5 mg/L hygromycin B was more advantageous for the selection of resistant broccoli sprouts, and genotype 19B42 reached the highest transformation rate of 26.96%, which is higher than that in Brassica oleracea crops. In addition, the inbred line 19B42 successfully achieved high genetic transformation of overexpression, RNAi and CRISPR/Cas9 vectors; thus, it is powerful recipient material for the genetic transformation of broccoli. Subcellular localization proved that the glucoraphanin metabolism-related gene Bol031350 and clubroot resistance gene CRa were both expressed in the cytoplasm and nucleus, which provided a scientific basis for studying the regulation of glucosinolate metabolism and clubroot resistance in cruciferous crops. Therefore, these findings will provide new insight into the improvement of the genetic transformation and molecular breeding of Brassica oleracea crops.

Evaluating how lodging affects maize yield estimation based on UAV observations

Timely and accurate pre-harvest estimates of maize yield are vital for agricultural management. Although many remote sensing approaches have been developed to estimate maize yields, few have been tested under lodging conditions. Thus, the feasibility of existing approaches under lodging conditions and the influence of lodging on maize yield estimates both remain unclear. To address this situation, this study develops a lodging index to quantify the degree of lodging. The index is based on RGB and multispectral images obtained from a low-altitude unmanned aerial vehicle and proves to be an important predictor variable in a random forest regression (RFR) model for accurately estimating maize yield after lodging. The results show that (1) the lodging index accurately describes the degree of lodging of each maize plot, (2) the yield-estimation model that incorporates the lodging index provides slightly more accurate yield estimates than without the lodging index at three important growth stages of maize (tasseling, milking, denting), and (3) the RFR model with lodging index applied at the denting (R5) stage yields the best performance of the three growth stages, with R² = 0.859, a root mean square error (RMSE) of 1086.412 kg/ha, and a relative RMSE of 13.1%. This study thus provides valuable insight into the precise estimation of crop yield and demonstra\tes that incorporating a lodging stress-related variable into the model leads to accurate and robust estimates of crop grain yield.

Effects of grazing on vegetation diversity and soil multifunctionality in coconut plantations

Grazing is the main way of utilizing understory vegetation in the tropics. However, the effects of grazing on vegetation diversity and soil functions in coconut plantations remain unclear. Therefore, this study was conducted in a young coconut plantation that was grazed by geese in Wenchang, China. We identified four grazing intensities according to the aboveground biomass, namely, no grazing (CK), light grazing (LG), moderate grazing (MG), and heavy grazing (HG). In April 2022, we used the quadrat method to investigate the composition and traits of vegetation, collected and analyzed 0-40-cm soil samples in each grazing intensity. The results showed that grazing changed the composition of understory species. The predominant species changed from Bidens pilosa to Praxelis clematidea + Paspalum thunbergii and then to P. clematidea with increasing grazing intensity. The richness, Shannon-Wiener index, evenness, modified functional attribute diversity (MFAD), functional divergence (Fdiv), and functional evenness (Feve) of CK were 4.5, 1.0, 0.29, 0.20, 0.84, and 0.80, respectively. Taxonomic diversity did not respond to LG, but responded significantly to MG and HG. Compared with CK, MG and HG increased richness by 96% and 200%, respectively, and Shannon-Wiener index increased by 40% and 98%, respectively. HG increased evenness by 95%. For functional diversity, MG and HG increased MFAD by 164% and 560%, respectively, but Fdiv and Feve did not respond to grazing intensity. The carbon (C) functioning, nitrogen (N) functioning, phosphorus (P) functioning, and multifunctionality in the 0-10-cm topsoil of CK were -0.03, 0.37, -0.06, 0.20, and 0.14, respectively. Grazing increased C functioning, P functioning, and multifunctionality in the 0-10-cm topsoil but decreased N functioning. Multiple linear regression showed that the taxonomic diversity and functional diversity could be used to estimate soil functions, but these vary among soil layers. In general, MG and HG can increase vegetation diversity and soil function. It may be possible to promote even distribution of geese by adding water sources or zoning grazing. Furthermore, quantitative grazing experiments are needed to determine the efficient use pattern of the understory in coconut plantations in tropics.

Integrated multi-omics reveals the molecular mechanisms underlying efficient phosphorus use under phosphate deficiency in elephant grass (Pennisetum purpureum)

Phosphorus (P) is an essential macronutrient element for plant growth, and deficiency of inorganic phosphate (Pi) limits plant growth and yield. Elephant grass (Pennisetum purpureum) is an important fodder crop cultivated widely in tropical and subtropical areas throughout the world. However, the mechanisms underlying efficient P use in elephant grass under Pi deficiency remain poorly understood. In this study, the physiological and molecular responses of elephant grass leaves and roots to Pi deficiency were investigated. The results showed that dry weight, total P concentration, and P content decreased in Pi-deprived plants, but that acid phosphatase activity and P utilization efficiency (PUE) were higher than in Pi-sufficient plants. Regarding Pi starvation-responsive (PSR) genes, transcriptomics showed that 59 unigenes involved in Pi acquisition and transport (especially 18 purple acid phosphatase and 27 phosphate transporter 1 unigenes) and 51 phospholipase unigenes involved in phospholipids degradation or Pi-free lipids biosynthesis, as well as 47 core unigenes involved in the synthesis of phenylpropanoids and flavonoids, were significantly up-regulated by Pi deprivation in leaves or roots. Furthermore, 43 unigenes related to Pi-independent- or inorganic pyrophosphate (PPi)-dependent bypass reactions were markedly up-regulated in Pi-deficient leaves, especially five UDP-glucose pyrophosphorylase and 15 phosphoenolpyruvate carboxylase unigenes. Consistent with PSR unigene expression changes, metabolomics revealed that Pi deficiency significantly increased metabolites of Pi-free lipids, phenylpropanoids, and flavonoids in leaves and roots, but decreased phospholipid metabolites. This study reveals the mechanisms underlying the responses to Pi starvation in elephant grass leaves and roots, which provides candidate unigenes involved in efficient P use and theoretical references for the development of P-efficient elephant grass varieties.

Adsorption of Sulfonamides in Aqueous Solution on Reusable Coconut-Shell Biochar Modified by Alkaline Activation and Magnetization

Biochar is a low-cost adsorbent for sorptive removal of antibiotics from wastewater, but the adsorption efficiency needs to be improved. In this study, coconut-shell biochar was activated with KOH to improve the adsorption efficiency and magnetically modified with FeCl₃ to enable recycling. The amount of KOH and the concentration of FeCl₃ were optimized to reduce the pollution and production cost. The KOH-activated and FeCl₃-magnetized biochar gave good sulfonamide antibiotic (SA) removal. The maximum adsorption capacities for sulfadiazine, sulfamethazine and sulfamethoxazole were 294.12, 400.00 and 454.55 mg g⁻¹, respectively, i.e., five to seven times higher than those achieved with raw biochar. More than 80% of the adsorption capacity was retained after three consecutive adsorption-desorption cycles. A combination of scanning electron microscopy, Brunauer-Emmett-Teller analysis, X-ray diffraction, Fourier-transform infrared and Raman spectroscopies, and magnetic hysteresis analysis showed that KOH activation increased the specific surface area, porosity, and number of oxygen-rich functional groups. Iron oxide particles, which were formed by FeCl₃ magnetization, covered the biochar surface. The SAs were adsorbed on the modified biochar via hydrogen bonds between SA molecules and -OH/-COOH groups in the biochar. Investigation of the adsorption kinetics and isotherms showed that the adsorption process follows a pseudo-second-order kinetic model and a monolayer adsorption mechanism. The adsorption capacity at low pH was relatively high because of a combination of π⁺-π electron-donor-acceptor, charge-assisted hydrogen-bonding, electrostatic, and Lewis acid-base interactions, pore filling, van der Waals forces and hydrophobic interactions. The results of this study show that magnetically modified biochar has potential applications as an effective, recyclable adsorbent for antibiotic removal during wastewater treatment.