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<jats:p>The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 <jats:italic>Japonica</jats:italic> cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.</jats:p>

<jats:p>Accurate predictions of wheat yields are essential to farmers’production plans and to the international trade in wheat. However, only poor approximations of the productivity of wheat crops in China can be obtained using traditional linear regression models based on vegetation indices and observations of the yield. In this study, Sentinel-2 (multispectral data) and ZY-1 02D (hyperspectral data) were used together with 15709 gridded yield data (with a resolution of 5 m × 5 m) to predict the winter wheat yield. These estimates were based on four mainstream data-driven approaches: Long Short-Term Memory (LSTM), Random Forest (RF), Gradient Boosting Decision Tree (GBDT), and Support Vector Regression (SVR). The method that gave the best estimate of the winter wheat yield was determined, and the accuracy of the estimates based on multispectral and hyperspectral data were compared. The results showed that the LSTM model, for which the RMSE of the estimates was 0.201 t/ha, performed better than the RF (RMSE = 0.260 t/ha), GBDT (RMSE = 0.306 t/ha), and SVR (RMSE = 0.489 t/ha) methods. The estimates based on the ZY-1 02D hyperspectral data were more accurate than those based on the 30-m Sentinel-2 data: RMSE = 0.237 t/ha for the ZY-1 02D data, which is about a 5% improvement on the RSME of 0.307 t/ha for the 30-m Sentinel-2 data. However, the 10-m Sentinel-2 data performed even better, giving an RMSE of 0.219 t/ha. In addition, it was found that the greenness vegetation index SR (simple ratio index) outperformed the traditional vegetation indices. The results highlight the potential of the shortwave infrared bands to replace the visible and near-infrared bands for predicting crop yields Our study demonstrates the advantages of the deep learning method LSTM over machine learning methods in terms of its ability to make accurate estimates of the winter wheat yield.</jats:p>

<jats:p>Abiotic stresses causing extensive yield loss in various crops globally. Over the past few decades, the application of silicon nanoparticles (nSi) has emerged as one of the abiotic stress mitigators. The initial responses of plants are shown by the biogenesis of reactive oxygen species (ROS) to sustain cellular/organellar integrity to ensure <jats:italic>in vivo</jats:italic> operation of metabolic functions by regulating physiological and biochemical pathways during stress conditions. Plants have evolved various antioxidative systems to balance/maintain the process of homeostasis <jats:italic>via</jats:italic> enzymatic and non-enzymatic activities to repair the losses. In the adverse environment, supplementation of Si mitigates the stress condition and improved the growth and development of plants. Its ameliorative effects were correlated with the enhanced antioxidant enzymes activities to maintain the equilibrium between the ROS generation and reduction. However, there are limited studies covered the role of nSi in the abiotic stress condition. This review addresses the accumulation and/or uptake of nSi in several crops and its mode of action linked with improved plants’ growth and tolerance capabilities to confer sustainable agriculture.</jats:p>

<jats:p>Acute and early symptoms of forest dieback linked to climate warming and drought episodes have been reported for relict <jats:italic>Abies pinsapo</jats:italic> Boiss. fir forests from Southern Spain, particularly at their lower ecotone. Satellite, orthoimages, and field data were used to assess forest decline, tree mortality, and gap formation and recolonization in the lower half of the altitudinal range of <jats:italic>A. pinsapo</jats:italic> forests (850-1550 m) for the last 36 years (1985-2020). Field surveys were carried out in 2003 and in 2020 to characterize changes in stand canopy structure and mortality rates across the altitudinal range. Time series of the Normalized Difference Vegetation Index (NDVI) at the end of the dry season (derived from Landsat 5 and 7 imagery) were used for a Dynamic Factor Analysis to detect common trends across altitudinal bands and topographic solar incidence gradients (SI). Historical canopy cover changes were analyzed through aerial orthoimages classification. Here we show that extensive decline and mortality contrast to the almost steady alive basal area for 17 years, as well as the rising photosynthetic activity derived from NDVI since the mid-2000s and an increase in the forest canopy cover in the late years at mid and high altitudes. We hypothesized that these results suggest an unexpected resilience in <jats:italic>A. pinsapo</jats:italic> forests to climate change-induced dieback, that might be promoted by compensation mechanisms such as (i) recruitment of new <jats:italic>A. pinsapo</jats:italic> individuals; (ii) facilitative effects on such recruitment mediated by revegetation with other species; and (iii) a ‘release effect’ in which surviving trees can thrive with fewer resource competition. Future research is needed to understand these compensation mechanisms and their scope in future climate change scenarios.</jats:p>

<jats:p>In this work we compiled information on current and emerging microbial-based fertilization practices, especially the use of cell-free microbial culture filtrates (CFs), to promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identified limitations to bring microbial CFs to the market as biostimulants. In nature, plants act as metaorganisms, hosting microorganisms that communicate with the plants by exchanging semiochemicals through the phytosphere. Such symbiotic interactions are of high importance not only for plant yield and quality, but also for functioning of the soil microbiota. One environmentally sustainable practice to increasing crop productivity and/or protecting plants from (a)biotic stresses while reducing the excessive and inappropriate application of agrochemicals is based on the use of inoculants of beneficial microorganisms. However, this technology has a number of limitations, including inconsistencies in the field, specific growth requirements and host compatibility. Beneficial microorganisms release diffusible substances that promote plant growth and enhance yield and stress tolerance. Recently, evidence has been provided that this capacity also extends to phytopathogens. Consistently, soil application of microbial cell-free culture filtrates (CFs) has been found to promote growth and enhance the yield of horticultural crops. Recent studies have shown that the response of plants to soil application of microbial CFs is associated with strong proliferation of the resident beneficial soil microbiota. Therefore, the use of microbial CFs to enhance both crop yield and stress tolerance, and to activate beneficial soil microbiota could be a safe, efficient and environmentally friendly approach to minimize shortfalls related to the technology of microbial inoculation. In this review, we compile information on microbial CFs and the main constituents (especially volatile compounds) that promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identify challenges and limitations for their use as biostimulants to bring them to the market and we propose remedial actions and give suggestions for future work.</jats:p>

<jats:sec><jats:title>Background</jats:title><jats:p>Understanding the spatial distribution of active compounds can effectively evaluate the quality of decoction pieces of traditional Chinese medicine (TCM). Traditional methods are economical and practical but lack chemical information on the original distribution. Time-of-flight secondary ion mass spectrometry (TOF-SIMS), with the advantage of non-destructive detection of samples, can directly analyze the distribution of chemical compounds on the surface of various samples.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>In this study, TOF-SIMS image analysis technology was used to detect TCM for the first time. Taking Coptis rhizome (CR) as an example, a commonly used TCM, the distribution of the compounds in the cross-section of CR was studied. Meanwhile, ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLCQQQ-MS/MS) was used to verify the results of TOF-SIMS.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The distribution of nine active compounds: berberine, epiberberine, coptisine, palmatine, columbamine, jatrorrhizine, tetrahydricheilanthifolinium, and oxyberberine, was well imaged in the cross-section of CR by TOF-SIMS. The content of berberine and epiberberine was the highest; Palmatine distribution in the pith was more than that in other parts; Oxyberberine was mainly concentrated in the cork and xylem rays. Normalization analysis showed contents of these compounds increased along with the growth years. The result was consistent with UPLC-QQQ-MS/MS.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>The TOF-SIMS method can display the spatial distribution status of the active compounds of herbs, providing a basis for selecting the medicine site with non-destructive and fast detection.</jats:p></jats:sec>

<jats:p><jats:italic>WRKY</jats:italic> transcription factors (TFs), one of the largest TF families, serve critical roles in the regulation of secondary metabolite production. However, little is known about the expression pattern of <jats:italic>WRKY</jats:italic> genes during the germination and maturation processes of <jats:italic>Toona sinensis</jats:italic> buds. In the present study, the new assembly of the <jats:italic>T. sinensis</jats:italic> genome was used for the identification of 78 <jats:italic>TsWRKY</jats:italic> genes, including gene structures, phylogenetic features, chromosomal locations, conserved protein domains, cis-regulatory elements, synteny, and expression profiles. Gene duplication analysis revealed that gene tandem and segmental duplication events drove the expansion of the <jats:italic>TsWRKYs</jats:italic> family, with the latter playing a key role in the creation of new <jats:italic>TsWRKY</jats:italic> genes. The synteny and evolutionary constraint analyses of the <jats:italic>WRKY</jats:italic> proteins among <jats:italic>T. sinensis</jats:italic> and several distinct species provided more detailed evidence of gene evolution for <jats:italic>TsWRKYs</jats:italic>. Besides, the expression patterns and co-expression network analysis show <jats:italic>TsWRKYs</jats:italic> may multi-genes co-participate in regulating terpenoid biosynthesis. The findings revealed that <jats:italic>TsWRKYs</jats:italic> potentially play a regulatory role in secondary metabolite synthesis, forming the basis for further functional characterization of <jats:italic>WRKY</jats:italic> genes with the intention of improving <jats:italic>T. sinensis</jats:italic>.</jats:p>

<jats:p>The goal of this research is to determine the mechanism of action of two <jats:italic>Bacillus</jats:italic> spp. that can manage <jats:italic>Meloidogyne incognita</jats:italic> population density in cotton. The overall objectives are 1) determine the efficacy and direct antagonistic capabilities of the <jats:italic>Bacillus</jats:italic> spp. and 2) determine the systemic capabilities of the <jats:italic>Bacillus</jats:italic> spp. The greenhouse <jats:italic>in planta</jats:italic> assay indicated <jats:italic>B. amyloliquefaciens</jats:italic> QST713 and <jats:italic>B. firmus</jats:italic> I-1582 could manage <jats:italic>M. incognita</jats:italic> similarly to the chemical standard fluopyram. An <jats:italic>in vitro</jats:italic> assay determined that <jats:italic>B. firmus</jats:italic> I-1582 and its extracted metabolites were able to directly manage <jats:italic>M. incognita</jats:italic> second stage juveniles by increasing mortality rate above 75%. A split root assay, used to determine systemic capabilities of the bacteria, indicated <jats:italic>B. amyloliquefaciens</jats:italic> QST713 and <jats:italic>B. firmus</jats:italic> I-1582 could indirectly decrease the nematode population density. Another species, <jats:italic>B. mojavensis</jats:italic> strain 2, also demonstrated systemic capabilities but was not a successful biological control agent because it supported a high population density in greenhouse <jats:italic>in planta</jats:italic> assay and in the split root assay. A RT-qPCR assay was used to confirm any systemic activity observed in the split root assay. At 24 hours both <jats:italic>B. amyloliquefaciens</jats:italic> QST713 and <jats:italic>B. firmus</jats:italic> I-1582 upregulated one gene involved in the initial stages of JA synthesis pathway but not another gene involved in the later stages of JA synthesis. These results point to a JA intermediate molecule, most likely OPDA, stimulated by the bacteria rather than JA in a short-term systemic response. After 1 week, the <jats:italic>Bacillus</jats:italic> spp. stimulated a SA-responsive defense related gene. The long-term systemic response to the <jats:italic>Bacillus</jats:italic> spp. indicates salicylic acid also plays a role in defense conferred by these bacteria. The final assay was a qPCR to determine the concentration of the bacteria on the cotton roots after 24 days. <jats:italic>Bacillus amyloliquefaciens</jats:italic> QST713 and <jats:italic>B. firmus</jats:italic> I-43 1582 were able to colonize the root successfully, with the concentration after 24 days not significantly differing from the concentration at inoculation. This study identifies two bacteria that work <jats:italic>via</jats:italic> systemic resistance and will help aid in implementing these species in an integrated management system.</jats:p>