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Plastic film mulching has been widely used to increase maize yield in the semiarid area of China. However, whether long-term plastic film mulching is conducive to agricultural sustainability in this region remains controversial. A field experiment was initiated in 2013 with five different film mulching methods: (i) control method, flat planting without mulching (CK), (ii) flat planting with half film mulching (P), (iii) film mulching on ridges and planting in narrow furrows (S), (iv) full film mulching on double ridges (D), and (v) film mulching on ridges and planting in wide furrows (R). The effects on soil organic carbon (SOC) content, storage, and fractions, and on the carbon management index (CMI) were evaluated after nine consecutive years of plastic film mulching. The results showed that long-term plastic film mulching generally maintained the initial SOC level. Compared with no mulching, plastic film mulching increased the average crop yield, biomass yield, and root biomass by 48.38, 35.06, and 37.32%, respectively, which led to the improvement of SOC sequestration. Specifically, plastic film mulching significantly improved CMI, and increased the SOC content by 13.59%, SOC storage by 7.47% and easily oxidizable organic carbon (EOC) by 13.78% on average, but it reduced the other labile fractions. SOC sequestration and CMI were improved by refining the plastic film mulching methods. The S treatment had the best effect among the four mulching methods, so it can be used as a reasonable film mulching method for sustainable agricultural development in the semiarid area.

The occurrence, distribution, and rapid molecular detection technology of Heterodera zeae Koshy et al. 1971, have been reported in China. We explored the biological characteristics of H. zeae sampled in Henan Province, China to understand its interaction with plants. Cysts and second-stage juveniles (J2s) were identified under an optical and scanning electron microscope, internal transcribed spacer (ITS) phylogenetic tree, and sequence characterized amplified region (SCAR)-PCR analyses. The optimum hatching temperatures of H. zeae were 30°C and 28°C, with cumulative hatching rates of 16.5 and 16.1%, respectively, at 30 days post-hatching (dph). The hatching rate of H. zeae eggs was improved by 20- and 50-time maize soil leachate and root juice, and 10-time root exudates. The hatching rate in 10-time root exudates was the highest (25.9%). The 10-time root exudates of maize and millet produced the highest hatching rate at 30 dph (25.9 and 22.9%, respectively), followed by wheat (19.9%), barley (18.3%), and rice (17.6%). Heterodera zeae developed faster in maize than in other crops. Fourth-stage juveniles (J4s) were detected in maize roots 8 days post-inoculation (dpi) at 28°C but not in other crops. Combined with hatching tests, the Huang–Huai–Hai summer maize region and the south and central-southwest mountainous maize areas are highly suitable for H. zeae in China. This is the first systematically study of the hatching and infection characteristics on different plant hosts of corn cyst nematode H. zeae in temperate regions. This study laid a theoretical foundation for the rapid spread and high environmental adaptability of corn cyst nematode.

Xanthomonas spp. cause severe bacterial diseases. However, effective strategies for prevention and management of these diseases are scarce. Thus, it is necessary to improve the efficiency of control of diseases caused by Xanthomonas. In this study, Xanthomonas oryzae pv. oryzae (Xoo), which causes rice bacterial leaf blight, has been studied as a representative. A transposon insertion library of Xoo, comprising approximately 200,000 individual insertion mutants, was generated. Transposon sequencing data indicated that the mariner C9 transposase mapped at 35.7–36.4% of all potential insertion sites, revealing 491 essential genes required for the growth of Xoo in rich media. The results show that, compared to the functions of essential genes of other bacteria, the functions of some essential genes of Xoo are unknown, 25 genes might be dangerous for the Xanthomonas group, and 3 are specific to Xanthomonas. High-priority candidates for developing broad-spectrum, Xanthomonas-specific, and environment-friendly bactericides were identified in this study. In addition, this study revealed the possible targets of dioctyldiethylenetriamine using surface plasmon resonance (SPR) in combination with high performance liquid chromatography–mass spectrometry (HPLC–MS). The study also provided references for the research of some certain bactericides with unknown anti-bacterial mode of action. In conclusion, this study urged a better understanding of Xanthomonas, provided meaningful data for the management of bacterial leaf blight, and disclosed selected targets of a novel bactericide.

Tillering is an important agronomic trait of rice (Oryza sativa) that affects the number of effective panicles, thereby affecting yields. The phytohormone auxin plays a key role in tillering. Here we identified the high tillering and semi-dwarf 1 (htsd1) mutant with auxin-deficiency root characteristics, such as shortened lateral roots, reduced lateral root density, and enlarged root angles. htsd1 showed reduced sensitivity to auxin, but the external application of indole-3-acetic acid (IAA) inhibited its tillering. We identified the mutated gene in htsd1 as AUXIN1 (OsAUX1, LOC_Os01g63770), which encodes an auxin influx transporter. The promoter sequence of OsAUX1 contains many SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) binding sites, and we demonstrated that SPL7 binds to the OsAUX1 promoter. TEOSINTE BRANCHED1 (OsTB1), a key gene that negatively regulates tillering, was significantly downregulated in htsd1. Tillering was enhanced in the OsTB1 knockout mutant, and the external application of IAA inhibited tiller elongation in this mutant. Overexpressing OsTB1 restored the multi-tiller phenotype of htsd1. These results suggest that SPL7 directly binds to the OsAUX1 promoter and regulates tillering in rice by altering OsTB1 expression to modulate auxin signaling.

In order to further improve the utility of unmanned aerial vehicle (UAV) remote-sensing for quickly and accurately monitoring the growth of winter wheat under film mulching, this study examined the treatments of ridge mulching, ridge–furrow full mulching, and flat cropping full mulching in winter wheat. Based on the fuzzy comprehensive evaluation (FCE) method, four agronomic parameters (leaf area index, above-ground biomass, plant height, and leaf chlorophyll content) were used to calculate the comprehensive growth evaluation index (CGEI) of the winter wheat, and 14 visible and near-infrared spectral indices were calculated using spectral purification technology to process the remote-sensing image data of winter wheat obtained by multispectral UAV. Four machine learning algorithms, partial least squares, support vector machines, random forests, and artificial neural network networks (ANN), were used to build the winter wheat growth monitoring model under film mulching, and accuracy evaluation and mapping of the spatial and temporal distribution of winter wheat growth status were carried out. The results showed that the CGEI of winter wheat under film mulching constructed using the FCE method could objectively and comprehensively evaluate the crop growth status. The accuracy of remote-sensing inversion of the CGEI based on the ANN model was higher than for the individual agronomic parameters, with a coefficient of determination of 0.75, a root mean square error of 8.40, and a mean absolute value error of 6.53. Spectral purification could eliminate the interference of background effects caused by mulching and soil, effectively improving the accuracy of the remote-sensing inversion of winter wheat under film mulching, with the best inversion effect achieved on the ridge–furrow full mulching area after spectral purification. The results of this study provide a theoretical reference for the use of UAV remote-sensing to monitor the growth status of winter wheat with film mulching.

Bread wheat (Triticum aestivum) is a staple food crop worldwide. The genetic dissection of important nutrient traits is essential for the biofortification of wheat to meet the nutritional needs of the world’s growing population. Here, 45,298 single-nucleotide polymorphisms (SNPs) from 55K chip arrays were used to genotype a panel of 768 wheat cultivars, and a total of 154 quantitative trait loci (QTLs) were detected for eight traits under three environments by genome-wide association study (GWAS). Three QTLs (qMn-3B.1, qFe-3B.4, and qSe-3B.1/qFe-3B.6) detected repetedly under different environments or traits were subjected to subsequent analyses based on linkage disequilibrium decay and the P-values of significant SNPs. Significant SNPs in the three QTL regions formed six haplotypes for qMn-3B.1, three haplotypes for qFe-3B.4, and three haplotypes for qSe-3B.1/qFe-3B.6. Phenotypic analysis revealed significant differences among haplotypes. These results indicated that the concentrations of several nutrient elements have been modified during the domestication of landraces to modern wheat. Based on the QTL regions, we identified 15 high-confidence genes, eight of which were stably expressed in different tissues and/or developmental stages. TraesCS3B02G046100 in qMn-3B.1 and TraesCS3B02G199500 in qSe-3B.1/qFe-3B.6 were both inferred to interact with metal ions according to the Gene Ontology (GO) analysis. TraesCS3B02G199000, which belongs to qSe-3B.1/qFe-3B.6, was determined to be a member of the WRKY gene family. Overall, this study provides several reliable QTLs that may significantly affect the concentrations of nutrient elements in wheat grain, and this information will facilitate the breeding of wheat cultivars with improved grain properties.

Recently developed ‘super’ rice cultivars with greater yield potentials often suffer from the problem of poor grain filling, especially in inferior spikelets. Here, we studied the activities of enzymes related to starch metabolism in rice stems and grains, and the microstructures related to carbohydrate accumulation and transportation to investigate the effects of different water regimes on grain filling. Two ‘super’ rice cultivars were grown under two irrigation regimes of well-watered (WW) and alternate wetting and moderate soil drying (AWMD). Compared with the WW treatment, the activities of ADP glucose pyrophosphorylase (AGPase), starch synthase (StSase) and starch branching enzyme (SBE), and the accumulation of non-structural carbohydrates (NSCs) in the stems before heading were significantly improved, and more starch granules were stored in the stems in the AWMD treatment. After heading, the activities of α-amylase, β-amylase, sucrose phosphate synthase (SPS) and sucrose synthase in the synthetic direction (SSs) were increased in the stems to promote the remobilization of NSCs for grain filling under AWMD. During grain filling, the enzymatic activities of sucrose synthase in the cleavage direction (SSc), AGPase, StSase and SBE in the inferior spikelets were increased, which promoted grain filling, especially for the inferior spikelets under AWMD. However, there were no significant differences in vascular microstructures. The grain yield and grain weight could be improved by 13.1 and 7.5%, respectively, by optimizing of the irrigation regime. We concluded that the low activities of key enzymes in carbon metabolism is the key limitation for the poor grain filling, as opposed to the vascular microstructures, and AWMD can increase the amount of NSC accumulation in the stems before heading, improve the utilization rate of NSCs after heading, and increase the grain filling, especially in the inferior spikelets, by altering the activities of key enzymes in carbon metabolism.

Formal credit is critical in agricultural production, allowing more expenditure and productive input, thereby improving farmers’ welfare. In pastoral China, formal financial institutions are gradually increasing. However, a limited understanding remains of how formal credit affects herders’ household expenses. Based on a survey of 544 herders from the Qinghai–Xizang Plateau of China, this study adopted the propensity score matching approach to identify the effect of formal credit on herders’ total household expenses, daily expenses, and productive expenses. The results found that average age, grassland mortgage, and other variables significantly affected herders’ participation in formal credit. Formal credit could significantly improve household expenses, especially productive expenses. A heterogeneity analysis showed that formal credit had a greater impact on the household total expense for those at higher levels of wealth; however, it significantly affected the productive expense of herders at lower wealth levels. Moreover, the mediating effect indicated that formal credit could affect herders’ household income, thus influencing their household expenses. Finally, this study suggests that policies should improve herders’ accessibility to formal credit.

Low-density lipoprotein receptor-related protein 2 (LRP2) is a multifunctional endocytic receptor expressed in epithelial cells. In mammals, it acts as an endocytic receptor that mediates the cellular uptake of cholesterol-containing apolipoproteins to maintain lipid homeostasis. However, little is known about the role of LRP2 in lipid homeostasis in insects. In the present study, we investigated the function of LRP2 in the migratory locust Locusta migratoria (LmLRP2). The mRNA of LmLRP2 is widely distributed in various tissues, including integument, wing pads, foregut, midgut, hindgut, Malpighian tubules and fat body, and the amounts of LmLRP2 transcripts decreased gradually in the early stages and then increased in the late stages before ecdysis during the nymphal developmental stage. Fluorescence immunohistochemistry revealed that the LmLRP2 protein is mainly located in cellular membranes of the midgut and hindgut. Using RNAi to silence LmLRP2 caused molting defects in nymphs (more than 60%), and the neutral lipid was found to accumulate in the midgut and surface of the integument, but not in the fat body, of dsLmLRP2-treated nymphs. The results of a lipidomics analysis showed that the main components of lipids (diglyceride and triglyceride) were significantly increased in the midgut, but decreased in the fat body and hemolymph. Furthermore, the content of total triglyceride was significantly increased in the midgut, but markedly decreased in the fat body and hemolymph in dsLmLRP2-injected nymphs. Our results indicate that LmLRP2 is located in the cellular membranes of midgut cells, and is required for lipid export from the midgut to the hemolymph and fat body in locusts.

Bacteria play critical roles in regulating soil phosphorus (P) cycling. The effects of interactions between crops and soil P-availability on bacterial communities and the feedback regulation of soil P cycling by the bacterial community modifications are poorly understood. Here, six soybean (Glycine max) genotypes with differences in P efficiency were cultivated in acidic soils with long-term sufficient or deficient P-fertilizer treatments. The acid phosphatase (AcP) activities, organic-P concentrations and associated bacterial community compositions were determined in bulk and rhizosphere soils. The results showed that both soybean plant P content and the soil AcP activity were negatively correlated with soil organic-P concentration in P-deficient acidic soils. Soil P-availability affected the α-diversity of bacteria in both bulk and rhizosphere soils. However, soybean had a stronger effect on the bacterial community composition, as reflected by the similar biomarker bacteria in the rhizosphere soils in both P-treatments. The relative abundance of biomarker bacteria Proteobacteria was strongly correlated with soil organic-P concentration and AcP activity in low-P treatments. Further high-throughput sequencing of the phoC gene revealed an obvious shift in Proteobacteria groups between bulk soils and rhizosphere soils, which was emphasized by the higher relative abundances of Cupriavidus and Klebsiella, and lower relative abundance of Xanthomonas in rhizosphere soils. Among them, Cupriavidus was the dominant phoC bacterial genus, and it was negatively correlated with the soil organic-P concentration. These findings suggest that soybean growth relies on organic-P mineralization in P-deficient acidic soils, which might be partially achieved by recruiting specific phoC-harboring bacteria, such as Cupriavidus.

Enhancing photosynthetic efficiency is a major goal for improving crop yields under agricultural field conditions and is associated with chloroplast biosynthesis and development. In this study, we demonstrate that Golden2-like 1a (BnGLK1a) plays an important role in regulating chloroplast development and photosynthetic efficiency. Overexpressing BnGLK1a resulted in significant increases in chlorophyll content, the number of thylakoid membrane layers and photosynthetic efficiency in Brassica napus, while knocking down BnGLK1a transcript levels through RNA interference (RNAi) had the opposite effects. A yeast two-hybrid screen revealed that BnGLK1a interacts with the abscisic acid receptor PYRABACTIN RESISTANCE 1-LIKE 1–2 (BnPYL1–2) and CONSTITUTIVE PHOTOMORPHOGENIC 9 SIGNALOSOME 5A subunit (BnCSN5A), which play essential roles in regulating chloroplast development and photosynthesis. Consistent with this, BnGLK1a-RNAi lines of B. napus display hypersensitivity to the abscisic acid (ABA) response. Importantly, overexpression of BnGLK1a resulted in a 10% increase in thousand-seed weight, whereas seeds from BnGLK1a-RNAi lines were 16% lighter than wild type. We propose that BnGLK1a could be a potential target in breeding for improving rapeseed productivity. Our results not only provide insights into the mechanisms of BnGLK1a function, but also offer a potential approach for improving the productivity of Brassica species.

Bone morphogenetic protein 4 (BMP4) can induce the formation of chicken primordial germ cells (PGCs) in vitro; however, its regulatory mechanism in poultry remains unknown. This study aimed to use RNA-seq to analyze PGCs in chicken embryos and iPGCs induced by BMP4 in vitro, clarify the internal regulatory factors of PGCs, analyze the mechanism of the formation of PGCs, and lay a theoretical foundation for the further optimization of PGCs induction systems. Embryonic stem cells (ESCs), PGCs and iPGCs induced by BMP4 in vitro were collected. The transcriptional maps of the three cell types were studied using RNA-seq. The results showed 6,142 genes differentially expressed between PGCs and iPGCs, of which 2,728 were upregulated in iPGCs and 3,414 were downregulated in iPGCs. Compared to that in ESCs, BMP4 was significantly upregulated in PGCs and iPGCs. KEGG results showed that both the TGF-β and Wnt signaling pathways were activated during the formation of PGCs in vitro and in vivo, and the activation was more significant during iPGCs induced by BMP4. The expression of Nodal, an inhibitory factor of TGF-β signaling, was significantly decreased in PGCs and iPGCs, but was not expressed in iPGCs, which further supports our conclusion. Additionally, the Lysosome and PI3K-AKT signaling pathways were significantly enriched in PGCs and iPGCs, respectively. Further, transmission electron microscopy (TEM) results showed that the number of autolysosomes was significantly higher after the addition of BMP4, which is consistent with the KEGG results. Furthermore, the number of PGCs was significantly reduced after ATG14 was interfered in vivo and in vitro. In conclusion, this study screened out the key signaling pathways during the formation of PGCs, aiming to provide help for enriching the mechanism network regulating PGCs formation in chicken and laying a theoretical foundation for further improving the efficiency of inducing PGCs in vitro.

Avian metapneumovirus (aMPV) is a highly contagious pathogen that causes acute upper respiratory tract diseases in chickens and turkeys, resulting in serious economic losses. Subtype B aMPV has recently become the dominant epidemic strain in China. We developed an attenuated aMPV subtype B strain by serial passaging in Vero cells and evaluated its safety and efficacy as a vaccine candidate. The safety test showed that after the 30th passage, the LN16-A strain was fully attenuated, as clinical signs of infection and histological lesions were absent after inoculation. The LN16-A strain did not revert to a virulent strain after five serial passages in chickens. The genomic sequence of LN16-A differed from that of the parent wild-type LN16 (wtLN16) strain and had nine amino acid mutations. In chickens, a single immunization with LN16-A induced robust humoral and cellular immune responses, including the abundant production of neutralizing antibodies, CD4+ T lymphocytes, and the Th1 (IFN-γ) and Th2 (IL-4 and IL-6) cytokines. We also confirmed that LN16-A provided 100% protection against subtype B aMPV and significantly reduced viral shedding and turbinate inflammation. Our findings suggest that the LN16-A strain is a promising live attenuated vaccine candidate that can prevent infection with subtype B aMPV.

Helicoverpa zea is a major target pest of pyramided transgenic crops expressing Cry1, Cry2 and/or Vip3Aa proteins from Bacillus thuringiensis (Bt) in the United States. Laboratory-selected Cry1Ac/Cry2Ab cross resistance and field-evolved practical dual resistance of H. zea to these two toxins have been widely reported. Whether the widespread Cry1Ac/Cy2Ab dual resistance of H. zea has resulted from the selection of one shared or two independent resistance mechanisms by pyramided Bt crops remains unclear. Cadherin is a well-confirmed receptor of Cry1Ac and a suggested receptor of Cry2Ab in at least three Lepidopteran species. To test whether cadherin may serve as one shared mechanism for the cross and dual resistance of H. zea to Cry1Ac and Cry2Ab, we cloned H. zea cadherin (HzCadherin) cDNA and studied its functional roles in the mode of action of Cry1Ac and Cry2Ab by gain- and loss-of-function analyses. Heterologous expression of HzCadherin in H. zea midgut, H. zea fat body and Sf9 cells made all three of these cell lines more susceptible to activated Cry1Ac but not activated Cry2Ab, whereas silencing HzCadherin of H. zea midgut and fat body cells significantly reduced the susceptibility to Cry1Ac but not Cry2Ab. Likewise, suppressing HzCadherin with siRNA made H. zea larvae resistant to Cry1Ac. These results clearly demonstrate that HzCadherin is not a receptor for Cry2Ab, and thus it is unlikely to serve as one shared mechanism for the cross and dual resistance of H. zea to Cry1Ac and Cry2Ab.

Peanut (Arachis hypogaea L.) is a globally important oil crop. Web blotch is one of the most important foliar diseases affecting peanut, which results in serious yield losses worldwide. Breeding web blotch-resistant peanut varieties is the most effective and economically viable method for minimizing yield losses due to web blotch. In the current study, a bulked segregant analysis with next-generation sequencing was used to analyze an F2:3 segregating population and identify candidate loci related to web blotch resistance. Based on the fine-mapping of the candidate genomic interval using kompetitive allele-specific PCR (KASP) markers, we identified a novel web blotch resistance-related locus spanning approximately 169 kb on chromosome 16. This region included four annotated genes, of which only Arahy.35VVQ3 had a non-synonymous single nucleotide polymorphism in the coding region between the two parents. Two markers (Chr.16.12872635 and Chr.16.12966357) linked to this gene were shown to be co-segregated with the resistance of peanut web blotch by 72 randomly selected recombinant inbred lines (RIL), which could be used in marker-assisted breeding of resistant peanut varieties.

China’s crop structure has undergone significant changes in the last two decades since 2000, with an increase in the share of cereals, vegetables, and fruit, squeezing out other crops. As a result, land productivity, nutrient supply, and carbon emissions have changed. How to reallocate limited farmland among crops to achieve the multiple goals of agrifood systems becomes an important issue. This study explores the sources of land productivity and nutrition supply growth and carbon emissions reduction, and identifies the multiple roles of crop structural change from 2003 to 2020 based on a decomposition analysis. The results reveal that the growth within crops is still the primary driver in land productivity and nutrition supply and the reduction in carbon emissions. However, structural change also plays various roles at different periods. From 2003 to 2010, crop structural change increased the total calorie supply but lowered land productivity and contributed at least 70% of the total growth of carbon emissions. The crop structure was relatively stable, and their effects were modest from 2010 to 2015. From 2015 to 2020, the crop structural change began to play a greater role and generate synergistic effects in improving land productivity, micronutrient supply, and reducing carbon emissions, contributing to approximately a quarter of the growth of land productivity and 30% of total carbon emissions reduction. These results suggest that strategies for crop structural change should comprehensively consider its multiple impacts, aiming to achieve co-benefits while minimizing trade-offs.

Presently, integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction accuracy. Here, we set the genomic and transcriptomic data as the training population data, using BSLMM, TWAS, and eQTL mapping to prescreen features according to | ^βb|>0, top 1% of phenotypic variation explained (PVE), expression-associated single nucleotide polymorphisms (eSNPs), and egenes (false discovery rate (FDR)

Excessive use of N fertilizers (driven by high-yield goals) and its consequent environmental problems are becoming increasingly acute in agricultural systems. A 2-year field experiment was conducted to investigate the effects of three N application methods (application of solid granular urea once (OF) or twice (TF), application of solid granular urea mixed with controlled-release urea once (MF)), and six N rates (0, 60, 120, 180, 240, and 300 kg N ha−1) on maize yield, economic benefits, N use efficiency, and soil N balance in the maize (Zea mays L.) film mulching system on the Loess Plateau, China. The grain yield and economic return of maize were significantly affected by the N rate and application method. Compared with the OF treatment, the MF treatment not only increased the maize yield (increased by 9.0–16.7%) but also improved the economic return (increased by 10.9–25.8%). The agronomic N use efficiency (NAE), N partial factor productivity (NPFP) and recovery N efficiency (NRE) were significantly improved by 19.3–66.7, 9.0–16.7 and 40.2–71.5%, respectively, compared with the OF treatment. The economic optimal N rate (EONR) of the OF, TF, and MF was 145.6, 147.2, and 144.9 kg ha−1 in 2019, and 206.4, 186.4, and 146.0 kg ha−1 in 2020, respectively. The apparent soil N loss at EONR of the OF, TF, and MF were 97.1–100.5, 78.5–79.3, and 50.5–68.1 kg ha−1, respectively. These results support MF as a one-time N application method for delivering high yields and economic benefits, with low N input requirements within film mulching spring maize system on the Loess Plateau.

Virus-induced gene silencing (VIGS) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) systems are effective technologies for rapid and accurate gene function verification in modern plant biotechnology. However, the investigation of gene silencing and editing in radish remains limited. In this study, a bleaching phenotype was generated through the knockdown of RsPDS using tobacco rattle virus (TRV)- and turnip yellow mosaic virus (TYMV)-mediated gene silencing vectors. The TYMV-mediated gene silencing efficiency was higher than the TRV-based VIGS system in radish. The expression level of RsPDS was significantly inhibited using VIGS in ‘NAU-067’ radish leaves. The rootless seedlings of ‘NAU-067’ were infected with Agrobacterium rhizogenes using the 2300GN-Ubi-RsPDS-Cas9 vector with two target sequences. Nine adventitious roots were blue with GUS staining, and four of these adventitious roots were edited at target sequence 1 of the RsPDS gene as indicated by Sanger sequencing. Furthermore, albino lines were generated with A. tumefaciens-mediated transformation of radish cotyledons. Five base substitutions and three base deletions occurred at target sequence 2 in Line 1, and three base insertions and three base substitutions occurred at target sequence 1 in Line 2. This study shows that VIGS and CRISPR/Cas9 techniques can be employed to precisely verify the biological functions of genes in radish, which will facilitate the genetic improvement of vital horticultural traits in radish breeding programs.

Winter jujube (Ziziphus jujuba ‘Dongzao’) is greatly appreciated by consumers for its excellent quality, but brand infringement frequently occurs in the market. Here, we first determined a total of 38 elements in 167 winter jujube samples from the main winter jujube producing areas of China by inductively coupled plasma mass spectrometer (ICP-MS). As a result, 16 elements (Mg, K, Mn, Cu, Zn, Mo, Ba, Be, As, Se, Cd, Sb, Ce, Er, Tl, and Pb) exhibited significant differences in samples from different producing areas. Supervised linear discriminant analysis (LDA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA) showed better performance in identifying the origin of samples than unsupervised principal component analysis (PCA). LDA and OPLS-DA had a mean identification accuracy of 87.84 and 94.64% in the testing set, respectively. By using the multilayer perceptron (MLP) and C5.0, the prediction accuracy of the models could reach 96.36 and 91.06%, respectively. Based on the above four chemometric methods, Cd, Tl, Mo and Se were selected as the main variables and principal markers for the origin identification of winter jujube. Overall, this study demonstrates that it is practical and precise to identify the origin of winter jujube through multi-element fingerprint analysis with chemometrics, and may also provide reference for establishing the origin traceability system of other fruits.

Straw mulching is a widespread practice for reducing the soil carbon loss caused by erosion. However, the effects of straw mulching on dissolved organic matter (DOM) runoff loss from black soil are not well studied. How straw mulching affects the composition and loss of runoff DOM by changing soil aggregates remains largely unclear. Here, a straw mulching treatment was compared to a no mulching treatment (as a control) on sloping farmland with black soil erosion in Northeast China. We divided the soil into large macroaggregates (>2 mm), small macroaggregates (0.25–2 mm), and microaggregates (

The Gibberellic Acid-stimulated Arabidopsis (GASA) gene family is involved in the regulation of gene expression and plant growth, development, and stress responses. To investigate the function of loquat GASA genes in the growth and developmental regulation of plants, a loquat EjGASA6 gene homologous to Arabidopsis AtGASA6 was cloned. EjGASA6 expression was induced by gibberellin, and ectopic transgenic plants containing this gene exhibited earlier bloom and longer primary roots since these phenotypic characteristics are related to higher gibberellin content. Transcriptome analysis and qRT-PCR results showed that the expression levels of GA3ox1 and GA20ox1, which encode key enzymes in gibberellin biosynthesis, were significantly increased. Furthermore, we confirmed that EjGASA6 could promote the expression of GA20ox1 via the luciferase reporter system. Overall, our results suggest that EjGASA6 promotes blooming and main-root elongation by positively regulating gibberellin biosynthesis. These findings broaden our understanding of the role of GASAs in plant development and growth, and lay the groundwork for future research into the functions of EjGASA6 in regulating loquat growth and development.

The combined effects of straw incorporation (SI) and polymer-coated urea (PCU) application on soil ammonia (NH3) and nitrous oxide (N2O) emissions from agricultural fields have not been comprehensively evaluated in Northwest China. We conducted a two-year field experiment to assess the effects of combining SI with either uncoated urea (U) or PCU on soil NH3 emissions, N2O emissions, winter wheat yields, yield-scaled NH3 (INH3), and yield-scaled N2O (IN2O). Five treatments were investigated, no nitrogen (N) fertilizer (N0), U application at 150 kg N ha–1 with and without SI (SI+U and S0+U), and PCU application at 150 kg N ha–1 with and without SI (SI+PCU and S0+PCU). The results showed that the NH3 emissions increased by 20.98–34.35% following SI compared to straw removal, mainly due to increases in soil ammonium (NH4+-N) content and water-filled pore space (WFPS). SI resulted in higher N2O emissions than under the S0 scenario by 13.31–49.23% due to increases in soil inorganic N (SIN) contents, WFPS, and soil microbial biomass. In contrast, the PCU application reduced the SIN contents compared to the U application, reducing the NH3 and N2O emissions by 45.99–58.07 and 18.08–53.04%, respectively. Moreover, no significant positive effects of the SI or PCU applications on the winter wheat yield were observed. The lowest INH3 and IN2O values were observed under the S0+PCU and SI+PCU treatments. Our results suggest that single PCU applications and their combination with straw are the optimal agricultural strategies for mitigating gaseous N emissions and maintaining optimal winter wheat yields in Northwest China.

The milk fat globule membrane (MFGM) is a complex structure with numerous functions, and its composition is affected by many factors. There have been few systematic investigations on goat MFGM proteome profiling during lactation. Individual milk samples from 15 healthy dairy goats were obtained at six lactation time points for investigation of the MFGM proteome using both data-independent acquisition (DIA) and data-dependent acquisition (DDA) proteomics techniques combined with multivariate statistical analysis. Using the DIA method, 890 variably abundant MFGM proteins were discovered throughout the lactation cycle. From 1 to 240 d, butyrophilin subfamily 1 member A1, lipoprotein lipase, perilipin-2, and adipose triglyceride lipase were upregulated, while APOE, complement C3, clusterin, and IgG were downregulated. Furthermore, from 1 to 90 d, annexin A1, annexin A2, and antithrombin-III were downregulated, then upregulated by d 240. Albumin had a high degree of connectedness, indicating that it was a key protein, according to protein–protein interaction research. Overall, our findings gave new insights into the biological features of MFGM protein in goat milk throughout lactation, which may aid in the creation of specialized MFGM products and infant formula.

The stamping-out strategy has been used to control highly pathogenic avian influenza viruses in many countries, driven by the belief that vaccination would not be successful against such viruses and fears that avian influenza virus in vaccinated birds would evolve more rapidly and pose a greater risk to humans. In this review, we summarize the successes in controlling highly pathogenic avian influenza in China and make suggestions regarding the requirements for vaccine selection and effectiveness. In addition, we present evidence that vaccination of poultry not only eliminates human infection with avian influenza virus, but also significantly reduces and abolishes some harmful characteristics of avian influenza virus.

Burning biomass on sugarcane plantations can lead to pollution (CO₂ emissions) and degradation in soil properties. Adopting non-burning technology can increase the value of biomass by applying it directly to the soil, although this may result in nutrient immobilization, which can hinder optimal plant growth due to high lignin and cellulose content or high CN ratio. On the contrary, composting waste with a decomposer will boost plant nutrient availability and enhance other soil characteristics. This research was aimed to assess the effect of several types of sugarcane organic matter on improving soil characteristics, growth of sugarcane and the CO₂ emissions. The study was conducted using a Completely Randomized Factorial Design with two factors: type of organic matter (control, fresh litter and compost of sugarcane biomass) and level of drought stress (100, 75, 50 and 25%). Incubation occurred over 16 weeks, divided into two phases of 8 weeks each. The results showed that the application of organic materials in the form of compost could reduce water loss caused by environmental heat and sugarcane growing process. Furthermore, compost application improved soil chemical and biological properties by increasing soil pH, total nitrogen (N), total phosphate (P), total potassium (K), and the total microbial population, although differences were not significant compared to the control. Additionally, applying organic matter in the form of compost or litter helped suppress or reduce emissions, with compost treatment proving more effective than litter in reducing CO₂ emissions.

Shallot (Allium ascalonicum L.) is one of leading vegetable commodities intensively cultivated by farmers for a long time, including farmers in East Nusa Tenggara (ENT). The purpose of this study was to produce water hyacinth compost with ability to interact with Trichoderma sp. in order to improve the shallot bulb quality cultivated in dry land. This factorial experimental research was arranged in a Split Plot Design with 10 treatments and 3 replications. There were 10 treatment combinations with 30 experimental plots. Two factors were tested in this research. The first factor was the water hyacinth compost as the main plot, namely: 15 ton ha⁻¹ water hyacinth compost (K1) and without water hyacinth compost (K2), while the second factor as a sub-plot was the concentration of Trichoderma sp., consisting of watering with plain water (as control) of 100 mL(P0), watering with a concentration of Trichoderma sp. 5 mL.L⁻¹ (P1), watering with a concentration of Trichoderma sp. 10 mL.L⁻¹ (P2), watering with Trichoderma sp. concentration 15 mL.L⁻¹ (P3) and watering with Trichoderma sp. 20 mL.L⁻¹ (P4). The treatment of water hyacinth compost fertilizer at 15 tons ha⁻¹ with a concentration of Trichoderma sp 20 mL.L⁻¹ resulted in the highest number of shallot leaves (84.27 strands) and tillers (10.82). The shallot bulb weight per plot was 2455.33 g, and the number of bulbs per plot was 350.40 bulbs.

Tomatoes are climacteric fruits that experience a surge in respiration rate and ethylene production. This condition affects the fruits’ physiological deterioration, shortens their shelf-life, and degrades the quality of tomatoes. The study aimed to enhance the shelf-life of commercial tomatoes with different genetic backgrounds by utilizing the Sletr1-2 mutant, which has a lower sensitivity to ethylene. A randomized block design (RBD) was applied to achieve this goal, where 12 different plant genotypes were considered as treatments, and each treatment was replicated four times. The results showed that fruit shelf-life was extended by crossing commercial tomatoes with Sletr1-2 mutant tomatoes. Genetic variability for all shelf-life characteristics were narrow. In contrast, there were broad phenotypic variability for fruit hardness and weight loss characteristics.

Nutrient uptake efficiency in sugarcane (Saccharum officinarum L.) must be increased using organic matter to restore soil fertility, resulting in greater productivity. The humic substance is a complex organic material that is excellent for overcoming this challenge. This study aimed to determine the effect of the humic acid enriched by liquid urea by-product (PSUC) and liquid NPK by-product (PSNC) application on the growth and productivity of sugarcane. The experiment was conducted from October 2021 to September 2022 on PT RNI plantation land, Jatitujuh, Majalengka. The research was arranged in a completely randomized (CRD) using two different humic acid product prototypes (PSUC and PSNC) with two evaluation times, a screening and a semi-pilot scale. Solid humic at a dose of 15 Kg ha⁻¹ was applied by mixing it with inorganic fertilizers, while liquid humic at a total dose of 15 L ha⁻¹ was applied by foliar spray technique at 1, 2, and 3 months after planting (MAP). The results showed that applying humic acid PSUC and PSNC enhanced sugarcane shoot growth, segmented stem number, and diameter. In addition, it could consistently promote sugarcane yields on the semi-pilot scale up to 19.18% and 24.26% under humic acid PSUC and PSNC treatments, respectively. Therefore, both in the screening and semi-pilot evaluation, the solid and liquid humic acid PSUC and PSNC applied simultaneously are potential organic materials to enhance sugarcane growth and yield.

In Indonesia, corn is an important commodity that serves as the second source of carbohydrates after rice, whose productivity is influenced by management practices applied during cultivation. This research aimed to determine the effects of different management practices on the growth and yield of corn. This research was arranged in a single-factor Randomized Complete Block Design, with different agriculture management practices as treatments, consisting of TI1 = Best Practices (Drip Irrigation + Rice Husk + Mycorrhiza), TI2 = Farmers’ Practices (Furrow Irrigation) + Mycorrhiza, and TI3 = Farmers’ practices (Furrow Irrigation). The data observed were analyzed using Analysis of Variance and followed by the Post Hoc Tukey’s HSD at α= 5%. The results showed that the TI1 produced significantly higher plant height, stem diameter, leaf dry weight, weight of cob with cornhusk and kernel dry weight, and effectively suppressed weed growth compared to TI2 and TI3. TI1 produced a significantly higher number of leaves, root dry weight, and total dry weight compared to TI3, but not significantly different compared to TI2. TI1 produced not significantly different stem dry weight and harvest index compared to TI2 and TI3. The kernel dry weight per plant observed in TI1 was 157.63 g, which was 14.22% and 22.91% higher than in TI2 and TI3, respectively. Based on the coefficient correlation and path analysis, the number of leaves, plant height, and total dry weight should be considered as important plant growth variables to produce high kernel dry weight.

Peatland serves as a crucial natural resource with hydrological and other environmental functions essential for all living organisms. In some regions, peat soil isn't limited to lowland areas, it is also found in highland areas. This study is a survey research aiming to examine the characteristics of the highland peatlands of Toba North Sumatera, namely in the Village of Matiti II, Humbang Hasundutan Regency, North Sumatera and lowland peatlands as control of peatlands in general in Sidomulyo Village, Bilah Hilir Subdistrict, Labuhan Batu. The study employed a survey research approach with a descriptive method to determine the differences in the characteristics of highland Toba peat soils. In each area, a representative profile was made, and the soil morphology, characteristics and classification were observed according to the 2014 soil taxonomic classification. Soil samples were taken from each layer in the soil profile for soil analysis in the laboratory. Soil analysis included bulk density, pH H₂O, pH NaF, CEC, base saturation, organic C, total N, C/N, electrical conductivity (EC) and ash content. The results showed that the difference in altitude directly affected the microclimate and the hydrologic conditions, which in turn affected the characteristics of the peat soil. In the context of the Toba highland, the main source of peat soils comes from rainfall. In contrast with the peatland of the lowlands, where the impact of tides is a significant factor, the peat of the Toba highland is affected by the surrounding hills.

Arabica coffee cultivation is limited by altitude, which affects its production. Some farmers in Jember Regency are innovating to grow arabica coffee in the lowland, but the potential for leaf rust disease is quite high. Plant natural resistance can be enhanced by adding minerals formulation (containing silica, iodine, and calcium). This research aimed to determine which phase is more effective for applying mineral formulation that induces plant resistance. The formulation was tested on arabica coffee plants grown at the lowland (460 masl) in Jember Regency on 12 years old (y.o) mature and 1 y.o immature plants. One formulation was dissolved in 14 L of water and applied by foliar feeding. The effect was analyzed using two-way T-test of two samples assuming unequal variances at 95% confidence level to determine the differences. The analysis showed that the plants supplemented with the formulation could increase the variables that supported the natural resistance of plants (both mechanically and through the production of chemical compounds), such as polyphenol content, flavonoids, antioxidant activity, total dissolved protein, vitamin C, reducing sugar, lignin, cellulose, hemicellulose, and iodine content in the plant. The response of the formulation application showed that the most resistance variables was better in 1 y.o immature plants than in 12 y.o mature plants. The application of mineral formulation in immature phase will have a better impact on increasing natural resistance, and it has the potential to be used as a supplement for arabica coffee plants cultivated in the lowland.

The success of controlling basal stem rot (BSR) disease caused by Ganoderma sp. is mostly determined by the early detection of the fungi. Hence, when the signs of infection begin to appear, plants are generally difficult to rescue since the pathogen infection has spread widely to all parts of the plant. Therefore, early detection through the application of biosensors for Ganoderma sp. infection is absolutely necessary. This study aim was to identify biomarker compounds of Ganoderma sp. infection in oil palm plants with GC-MS for volatile compounds, and LC-MS for non-volatile compounds. The results showed that Ganoderma sp. mycelium produced pyrimidinamine compounds. Meanwhile in early infected nursery plants, were found benzo[h]quinoline, hexaoxa-7,9,11-trisilaheptad, tris-(trimethyl-silyl ester and methyl-tris(trimethyl-siloxy)-silane). Whereas in Bekri, Rejosari, and Adolina plantation, the compound methyl-tris(trimethyl-siloxy)-silane was also found in healthy mature plants. GC-MS test results showed that for early, moderate and severe plants produced several benzene derivative compounds such as ethylbenzene, xylene, and benzaldehyde. These compounds were assumed to be resulted from the breakdown of the lignin structure which build plant cell walls, and have potency to be used as marker compounds for early infected Ganoderma sp. detection. The result of the produced gas quantification concluded that in the produced oil palm plants released less CO2 compared to healthy plants. On the other hand, the NH3 produced was higher than the healthy plants. Meanwhile, two non-volatile compounds were found that they were only produced by infected trunk and root tissue, namely pseudobrucine and picrasidine.

Kopyor coconut is one of Indonesia's origin germplasms that has a high economic value. The flesh of the kopyor coconuts is quickly damaged characterized by rancidity due to the presence of microorganisms. This study aimed to investigate the effect of blanching and freeze-drying processes, considering the factors of drying duration and pressure, on the quality of kopyor coconut Flesh. The kopyor coconuts used in this studywere obtained from Ciomas Plantation IOPRI Bogor Unit, Bogor, West Java. The kopyor coconut flesh was grouped into two categories: one treated with steam blanching at 100 °C for 10 min and the other without blanching treatment. Freeze-drying processes were carried out for 12, 24, 48, and 72 h and at absolute pressures of 0.01 and 0.05 mbar. The characteristics observed were the moisture content, pH, whiteness index,and free fatty acids content (FFA).The combining of steam blanching and freeze-drying process for 48 h and a pressure of 0.01 mbar was the best treatment. The dried product had uniform texture with moisture content of 5.31%, whiteness index of 89.67%, pH of 7,04 and free fatty acid of 0,51%. These values indicated that the quality of dried fruit complied with the Indonesian standard of dried fruit quality (SNI 3710:2018).

Fungal entomopathogens are suggested to be used as a bioinsecticide due to their biological persistence and ecological friendliness. Beauveria bassiana is an entomopathogenic fungus that can effectively control insect pests, including cocoa pod borer. This study aims to determine the level of effectivity of the B. bassiana (Bb) formulation product from Palu against cocoa pod borer pupae in vitro . This research used a completely randomized design (CRD) consisting of two factors: conidia concentrations and chitin treatments, which were repeated thrice. The conidia concentrations consisted of two levels, that were 106 and 107 conidia/mL. The chitin treatment included seven treatments: isolate from Kediri without formulation with chitin (Bb-K), isolate from Palu without formulation with chitin (Bb-P0), four formulations of isolates from Palu with the addition of chitin to various growth media (Bb-P1, Bb-P2, Bb-P3, and Bb-P4), and control (without Bb suspension). Bb-P0 and Bb-P2 treatments at a concentration of 107conidia/mL began to colonize CPB on the third day after the treatment application, while the other formulations started on the fifth day. However, Bb-P0 showed the lowest infection rate at the end of the observation. Contrarily, the data on the pupa-infected ratio showed that the Bb-P2 treatment was the highest compared to other treatments. It conformed to the adult emergence ratio that Bb-P2 exhibited the lowest, which means Bb-P2 has the most virulence of other formula. The result showed that PDA and PDB media-supplemented chitin was the most effective for culturing B. bassiana origin Palu before mass production.

Phytic acid is a chemical compound consisting of inositol and phosphoric acid and is an antinutrient compound found in monogastric poultry feed ingredients made from cereal crops. Phytase hydrolyzes phosphoester bonds in phytic acid, releasing inorganic phosphate and phosphate esters. Aspergillus is a genus of molds that produce phytase and has been widely used in phytase production because they are easy to culture. This study aims to compare the structures, physicochemical characteristics, and phylogenetic relationships of phytases from several species of Aspergillus in silico as an initial screening step in obtaining the most suitable phytase to be used in poultry feed. Phylogenetic trees were constructed using MEGA 11 and physicochemical characteristics were analyzed using ProtParam. Protein structures were modeled with AlphaFold. The phytase structures were then docked with phytic acid using the YASARA Structure. The results showed that phytase 1QFX from Aspergillus niger, P34755 from A. awamori, and D5HQ11 from A. ficuum have very high similarity in terms of phylogenetics, sequences, physicochemical characteristics, and protein structures. The docking results from the three phytase structures showed that phytase 1QFX has the most negative ΔG value and the lowest Kd, which indicated the highest affinity to the phytic acid substrate. This research concludes that among the three phytase structures that have been compared and docked with phytic acid, phytase 1QFX from A. niger is the most suitable to be applied to poultry feed.

Banana peel is one of the wastes that can be explored for various applications. Cavendish is among the most highly consumed bananas in the world, which implies a high amount of banana peel waste. Our study evaluated the potential of Cavendish banana peels as the source of antioxidant and anti-aging agents. Antioxidant was extracted using three different solvents, i.e., water, ethyl acetate, and methanol. Each extract was then assayed for antioxidant activity in vitro using a 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay. The antioxidant and anti-aging activity of the extracts were further evaluated at the cellular level using the yeast Schizosaccharomyces pombe as a model. Our data indicated that the methanol extract of banana peel showed the highest antioxidant activity with an IC50 value of 253.8 µg mL-1 compared to ethyl acetate and water, yet it was considered weak. Interestingly, the methanol extract (600 ppm) showed antioxidant and anti-aging activities at cellular levels in yeast S. pombe. Therefore, this research reveals the potential for developing banana peel methanol extract as a component of pharmaceutical or cosmetic products with antioxidant and anti-aging properties.

Bioflavor is a type of natural flavor that is obtained from microbial metabolites during the process of fermentation. Most of the bacteria involved in food fermentation are lactic acid bacteria, including Lactobacillus sp. The optimal medium for Lactobacillus sp. growth is de Man Rogosa and Sharpe (MRS), but it is considered to be less economical. Therefore, alternative carbon and nitrogen sources are needed. This study aimed to determine the bioflavor produced in de Man Rogosa dan Sharpe Broth (MRSB) media that was substituted with Oil Palm Empty Fruit Bunch (OPEFB) hydrolysate and Crude Palm Oil (CPO) at concentrations of 5, 15, and 30%, respectively by using gas chromatography-mass spectrometry. The results showed that substituting MRSB with 15% CPO produced the best results for the growth of Lactobacillus sp. However, each medium produced different bioflavor compounds. In the control media (MRSB), the highest amount of bioflavor compound was 2,3-dihydro-3,5-dihydroxy-6-methyl -4H-Pyran-4-one (rose tea). In the OPEFB hydrolysate-substituted medium, it was benzene-acetaldehyde (sweet, bread, rose), in the CPO-substituted medium, it was furaneol (pineapple and strawberry) and pyrazine (nutty, roasted coffee).

Infection by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) triggers COVID-19 disease of the respiratory tract similar to pneumonia. The virus encodes four structural proteins and 16 non-structural proteins (nsp), one of which includes nsp15 or endoribonuclease (NendoU). NendoU plays an important role in viral replication and transcription and reduces the stimulation of immune cell responses. Active compounds in Gmelina arborea Roxb. bark have antioxidant properties that can inhibit the NendoU activity of SARS-CoV-2. This study aims to analyze the potential of compounds from Gmelina arborea Roxb. bark in inhibiting SARS-CoV-2 NendoU within in silico using the YASARA structure application. Balnophonin is the best test ligand based on binding ΔG value, dissociation constant (Kd), prediction of physicochemical characteristics, pharmacokinetics, and toxicity. Therefore, balanophonin can be developed as an effective alternative drug to inhibit SARS CoV-2 NendoU.

Oil palm empty fruit bunches (OPEFB) are lignocellulosic biomass that can be used to produce a biocomposite as an alternative to substitute non-renewable materials, such as plastic. Generally, the production of biocomposites uses OPEFB, which has been processed into cellulose, microcrystalline cellulose, or nanocellulose and is mixed with starch. However, the OPEFB pretreatment into various types of cellulose requires a long process and many chemicals. The OPEFB pretreatment with less process, such as cutting to shorter fibers and without chemicals, was expected to shorten the process. This study aims to produce and evaluate the characteristics of biocomposite pellets from a combination of cassava starch and OPEFB fibers. Short OPEFB fibers (3-5 mm) with varying concentrations of 0, 5, 10, 15, and 20% were added to the cassava starch before mixing with other materials. The twin screw extruder used to produce biocomposite pellets was set at six temperature zones ranging from 85-140 °C and the screw speed in the range of 160-190 rpm. The results show that higher concentrations of OPEFB fibers produced darker pellets, which tended to be greyish. The biocomposite pellets had densities of 1.322-1.417 g cm-3. SEM results show some agglomerations on the surface of starch-OPEFB fibers biocomposite pellets. The water solubility of biocomposite pellets ranged from 32.97 – 36.44%. In conclusion, biocomposite pellets could be produced from a mixture of cassava starch and OPEFB fibers up to 20%. In its application for rigid packaging production, the biocomposite pellets’ performance could be improved by mixing them with recycled polypropylene.

Knowledge of the function of growth-regulating factors (GRFs) in sugarcane (Saccharum officinarum and S. spontaneum) growth and development could assist breeders in selecting desirable plant architectures. However, limited information about GRFs is available in Saccharum due to their polyploidy. In this study, 22 GRFs were identified in the two species and their conserved domains, gene structures, chromosome location, and synteny were characterized. GRF7 expression varied among tissues and responded to diurnal rhythm. SsGRF7-YFP was localized preferentially in the nucleus and appears to act as a transcriptional cofactor. SsGRF7 positively regulated the size and length of rice leaves, possibly by regulating cell size and plant hormones. Of seven potential transcription factors binding to the SsGRF7 promoter in S. spontaneum, four showed positive expression patterns, and two showed negative expression patterns relative to SsGRF7.

Drought poses a significant challenge, restricting the productivity of medicinal and aromatic plants. The strain induced by drought can impede vital processes like respiration and photosynthesis, affecting various aspects of plants’ growth and metabolism. In response to this adversity, medicinal plants employ mechanisms such as morphological and structural adjustments, modulation of drought-resistant genes, and augmented synthesis of secondary metabolites and osmotic regulatory substances to alleviate the stress. Extreme water scarcity can lead to leaf wilting and may ultimately result in plant death. The cultivation and management of medicinal plants under stress conditions often differ from those of other crops. This is because the main goal with medicinal plants is not only to increase the yield of the above-ground parts but also to enhance the production of active ingredients such as essential oils. To elucidate these mechanisms of drought resistance in medicinal and aromatic plants, the current review provides a summary of recent literature encompassing studies on the morphology, physiology, and biochemistry of medicinal and aromatic plants under drought conditions.

Bulked-segregant analysis by deep sequencing (BSA-seq) is a widely used method for mapping QTL (quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2 populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F3 populations offering notable advantages over F2 populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading (DTH) in a 7200-plant rice F3 population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near 41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F3 populations and multi-environment experiments can achieve high power, resolution, and reliability.

To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrimination, it is desirable to identify the optimal marker combinations. We describe a marker combination screening model based on the genetic algorithm (GA) and implemented in a software tool, LociScan. Ratio-based variety discrimination power provided the largest optimization space among multiple fitness functions. Among GA parameters, an increase in population size and generation number enlarged optimization depth but also calculation workload. Exhaustive algorithm afforded the same optimization depth as GA but vastly increased calculation time. In comparison with two other software tools, LociScan accommodated missing data, reduced calculation time, and offered more fitness functions. In large datasets, the sample size of training data exerted the strongest influence on calculation time, whereas the marker size of training data showed no effect, and target marker number had limited effect on analysis speed.

“Synthetic” allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement. Such synthetic allopolyploids often undergo rapid genomic structural variation (SV). However, how such SV arises, is inherited and fixed, and how it affects important traits, has rarely been comprehensively and quantitively studied in advanced generation synthetic lines. A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs. Here, we analyzed three genetic mapping populations (735 DH lines) derived from crosses between advanced synthetic and conventional Brassica napus (rapeseed) lines, using whole-genome sequencing to determine genome composition. We observed high tolerance of large structural variants, particularly toward the telomeres, and preferential selection for balanced homoeologous exchanges (duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs), including stable events involving whole chromosomes (“pseudoeuploidy”). Given the experimental design (all three populations shared a common parent), we were able to observe that parental SV was regularly inherited, showed genetic hitchhiking effects on segregation, and was one of the major factors inducing adjacent novel and larger SV. Surprisingly, novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines. However, incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits. Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs, and support the use of synthetic parents as an important source of novel trait variation.

Diverse bacterial and fungal pathogens attack plants, causing biotic stress and severe yield losses globally. These losses are expected to become more serious as climate change improves conditions for many pathogens. Therefore, identifying genes conferring broad-spectrum disease resistance and elucidating their underlying mechanisms provides important resources for plant breeding. WRKY transcription factors affect plant growth and stress responses. However, the functions of many WRKY proteins remain to be elucidated. Here, we demonstrated the role of rice (Oryza sativa) WRKY group III transcription factor OsWRKY65 in immunity. OsWRKY65 localized to the nucleus and acted as transcriptional repressor. Genetic and molecular functional analyses showed that OsWRKY65 increases resistance to the fungal pathogen Fusarium fujikuroi through downregulation of GA signaling and upregulation of JA signaling. Moreover, OsWRKY65 modulated the expression of the key genes that confer susceptibility or resistance to Xanthomonas oryzae pv. oryzae to enhance immunity against the pathogen. In particular, OsWRKY65 directly bound to the promoter region of OsSWEET13 and repressed its expression. Taken together, our findings demonstrate that the OsWRKY65 enhances resistance to fungal and bacterial pathogens in rice.

In crop plants, various environmental stresses affect the balance of carbon, nitrogen, and phosphorus (C:N:P), leading to biochemical and physiological alterations and reductions in yield. Silicon (Si) is a beneficial element that alleviates plant stress. Most studies involving silicon have focused on physiological responses, such as improvements in photosynthetic processes, water use efficiency, and antioxidant defense systems. But recent research suggests that stressed plants facing either limited or excessive resources (water, light, nutrients, and toxic elements), strategically employ Si to maintain C:N:P homeostasis, thereby minimizing biomass losses. Understanding the role of Si in mitigating the impact of abiotic stresses on plants by regulating C:N:P homeostasis holds great potential for advancing sustainable agricultural practices in crop production. This review presents recent advances in characterizing the influence of environmental stresses on C:N:P homeostasis, as well as the role of Si in preserving C:N:P equilibrium and attenuating biological damage associated with abiotic stress. It underscores the beneficial effects of Si in sustaining C:N:P homeostasis and increasing yield via improved nutritional efficiency and stress mitigation.

Subclass III sucrose nonfermenting1-related protein kinase 2s (SnRK2s) function in ABA and abiotic stress responses by unknown mechanisms. We found that osmotic stress/ABA-activated protein kinase 10 (SAPK10), a member of rice SnRK2s, physically interacted with CBL-interacting protein kinase 1 (OsCIPK1). OsCIPK1 expression was up-regulated by ABA and PEG treatment, and overexpression increased the ABA sensitivity of seed germination and root growth and plant osmotic stress tolerance. Osmotic stress or ABA-induced activation of OsCIPK1 is dependent on SAPK10. SAPK10 phosphorylates Thr-24 of OsCIPK1 in vitro, and this phosphorylation increases the activity of OsCIPK1 and positively regulates the function of OsCIPK1 in ABA responses and plant osmotic stress tolerance. This study suggests that OsCIPK1 is a direct phosphorylated substrate of SAPK10, and SAPK10-mediated phosphorylation of OsCIPK1 functions in ABA signaling and increases rice osmotic stress tolerance.

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement. To investigate its molecular mechanisms in rice, we performed map-based cloning and characterization of OPEN PANICLE 1 (OP1), a gain-of-function allele of LIGULELESS 1 (LG1), controlling the spread-panicle phenotype. This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch. Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1 (sp1). Knocking out BRASSINOSTEROID UPREGULATED1 (BU1) gene in the background of OP1 complementary plants resulted in compact panicles, suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway. We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

Agrobacterium tumefaciens mediated plant transformation is a versatile tool for plant genetic engineering following its discovery nearly half a century ago. Numerous modifications were made in its application to increase efficiency, especially in the recalcitrant major cereals plants. Recent breakthroughs in transformation efficiency continue its role as a mainstream technique in CRISPR/Cas-based genome editing and gene stacking. These modifications led to higher transformation frequency and lower but more stable transgene copies with the capability to revolutionize modern agriculture. In this review, we provide a brief overview of the history of Agrobacterium-mediated plant transformation and focus on the most recent progress to improve the system in both the Agrobacterium and the host recipient. A promising future for transformation in biotechnology and agriculture is predicted.