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<jats:sec><jats:title>Objectives</jats:title><jats:p>Bamboo is a globally significant plant with ecological, environmental, and economic bene-fits. Choosing suitable native tree species for mixed planting in bamboo forests is an effective measure for achieving both ecological and economic benefits of bamboo forests. However, little is currently known about the impact of bamboo forests on nitrogen cycling and utilization efficiency after mixing with other tree species. Therefore, our study aims to compare the nitrogen cycling in pure bamboo forests with that in mixed forests.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Through field experiments, we investigated pure <jats:italic>Qiongzhuea tumidinoda</jats:italic> forests and <jats:italic>Q. tumidinoda-Phellodendron chinense</jats:italic> mixed forests, and utilized <jats:sup>15</jats:sup>N tracing technology to explore the fertilization effects and fate of urea-<jats:sup>15</jats:sup>N in different forest stands.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The results demonstrated the following: 1) in both forest stands, bamboo culms account for the highest biomass percentage (42.99%-51.86%), while the leaves exhibited the highest nitrogen concentration and total nitrogen uptake (39.25%-44.52%/29.51%-33.21%, respectively) Additionally, the average nitrogen uptake rate of one-year-old bamboo is higher (0.25 mg kg<jats:sup>-1</jats:sup> a<jats:sup>-1</jats:sup>) compared to other age groups. 2) the urea-<jats:sup>15</jats:sup>N absorption in mixed forests (1066.51–1141.61 g ha<jats:sup>-1</jats:sup>, including 949.65–1000.07 g ha<jats:sup>-1</jats:sup> for bamboo and 116.86–141.54 g ha<jats:sup>-1</jats:sup> for trees) was significantly higher than that in pure forests (663.93–727.62 g ha<jats:sup>-1</jats:sup>, <jats:italic>P&amp;lt;0.05</jats:italic>). Additionally, the <jats:sup>15</jats:sup>N recovery efficiency of culms, branches, leaves, stumps, and stump roots in mixed forests was significantly higher than that in pure forests, with increases of 43.14%, 69.09%, 36.84%, 51.63%, 69.18%, 34.60%, and 26.89%, respectively. 3) the recovery efficiency of urea-<jats:sup>15</jats:sup>N in mixed forests (45.81%, comprising 40.43% for bamboo and 5.38% for trees) and the residual urea-<jats:sup>15</jats:sup>N recovery rate in the 0–60 cm soil layer (23.46%) are significantly higher compared to those in pure forests (28.61%/18.89%). This could be attributed to the nitrogen losses in mixed forests (30.73%, including losses from ammonia volatilization, runoff, leaching, and nitrification-denitrification) being significantly lower than those in pure forests (52.50%).</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>These findings suggest that compared to pure bamboo forests, bamboo in mixed forests exhibits higher nitrogen recovery efficiency, particularly with one-year-old bamboo playing a crucial role.</jats:p></jats:sec>

<jats:p>Currently, the control of rhizosphere selection on farms has been applied to achieve enhancements in phenotype, extending from improvements in single root characteristics to the dynamic nature of entire crop systems. Several specific signals, regulatory elements, and mechanisms that regulate the initiation, morphogenesis, and growth of new lateral or adventitious root species have been identified, but much more work remains. Today, phenotyping technology drives the development of root traits. Available models for simulation can support all phenotyping decisions (root trait improvement). The detection and use of markers for quantitative trait loci (QTLs) are effective for enhancing selection efficiency and increasing reproductive genetic gains. Furthermore, QTLs may help wheat breeders select the appropriate roots for efficient nutrient acquisition. Single-nucleotide polymorphisms (SNPs) or alignment of sequences can only be helpful when they are associated with phenotypic variation for root development and elongation. Here, we focus on major root development processes and detail important new insights recently generated regarding the wheat genome. The first part of this review paper discusses the root morphology, apical meristem, transcriptional control, auxin distribution, phenotyping of the root system, and simulation models. In the second part, the molecular genetics of the wheat root system, SNPs, TFs, and QTLs related to root development as well as genome editing (GE) techniques for the improvement of root traits in wheat are discussed. Finally, we address the effect of omics strategies on root biomass production and summarize existing knowledge of the main molecular mechanisms involved in wheat root development and elongation.</jats:p>

<jats:p>The spines of Chinese red chestnut are red and the depth of their color gradually increases with maturity. To identify the anthocyanin types and synthesis pathways in red chestnut and to identify the key genes regulating the anthocyanin biosynthesis pathway, we obtained and analyzed the transcriptome and anthocyanin metabolism of red chestnut and its control variety with green spines at 3 different periods. GO and KEGG analyses revealed that photosynthesis was more highly enriched in green spines compared with red spines, while processes related to defense and metabolism regulation were more highly enriched in red spines. The analysis showed that the change in spine color promoted photoprotection in red chestnut, especially at the early growth stage, which resulted in the accumulation of differentially expressed genes involved in the defense metabolic pathway. The metabolome results revealed 6 anthocyanins in red spines. Moreover, red spines exhibited high levels of cyanidin, peonidin and pelargonidin and low levels of delphinidin, petunidin and malvidin. Compared with those in the control group, the levels of cyanidin, peonidin, pelargonidin and malvidin in red spines were significantly increased, indicating that the cyanidin and pelargonidin pathways were enriched in the synthesis of anthocyanins in red spines, whereas the delphinidin pathways were inhibited and mostly transformed into malvidin. During the process of flower pigment synthesis, the expression of the <jats:italic>CHS</jats:italic>, <jats:italic>CHI</jats:italic>, <jats:italic>F3H</jats:italic>, <jats:italic>CYP75A</jats:italic>, <jats:italic>CYP75B1</jats:italic>, <jats:italic>DFR</jats:italic> and <jats:italic>ANS</jats:italic> genes clearly increased, that of <jats:italic>CYP73A</jats:italic> decreased obviously, and that of <jats:italic>PAL</jats:italic>, <jats:italic>4CL</jats:italic> and <jats:italic>LAR</jats:italic> both increased and decreased. Notably, the findings revealed that the synthesized anthocyanin can be converted into anthocyanidin or epicatechin. In red spines, the upregulation of <jats:italic>BZ1</jats:italic> gene expression increases the corresponding anthocyanidin content, and the upregulation of the <jats:italic>ANR</jats:italic> gene also promotes the conversion of anthocyanin to epicatechin. The transcription factors involved in color formation included 4 <jats:italic>WRKYs</jats:italic>.</jats:p>

<jats:p>Abscisic acid (ABA) is a key phytohormone involved in wound healing in fruits and vegetables, while fluridone (FLD) is its synthetic inhibitor. However, it is unknown whether ABA signaling and downstream transcription factors are involved in the synthesis of phenolic acids and lignin monomers in muskmelon wounds, and the underlying mechanisms. In our study, exogenous ABA promoted endogenous ABA synthesis by increasing the levels of β-carotenoid and zeaxanthin, activating 9-cis-epoxycarotenoid dioxygenase (NCED) and zeaxanthin epoxidase (ZEP), facilitated ABA signaling by increasing the expression levels of protein phosphatases type 2C (<jats:italic>CmPP2C</jats:italic>) and ABA-responsive element binding factors (<jats:italic>CmABF</jats:italic>), upregulated the expression levels of <jats:italic>CmMYB1</jats:italic> and <jats:italic>CmWRKY1</jats:italic>, and ABA induced phenylpropanoid metabolism by activating phenylalanine ammonia-lyase (PAL), 4-coenzyme A ligase (4CL), and cinnamyl alcohol dehydrogenase (CAD), which further increased the synthesis of phenolic acids and lignin monomers in muskmelon wounds during healing. Taken together, exogenous ABA induced phenylpropanoid metabolism and increased the synthesis of phenolic acid and lignin monomer in muskmelon wounds during healing, and may be involved in endogenous ABA synthesis and signaling and related transcription factors.</jats:p>

<jats:p>Controlled environment agriculture (CEA) is critical for achieving year-round food security in many regions of the world. CEA is a resource-intensive endeavor, with lighting consuming a large fraction of the energy. To lessen the burden on the grid and save costs, an extended photoperiod strategy can take advantage of off-peak time-of-day options from utility suppliers. However, extending the photoperiod limits crop production morphologically and physiologically if pushed too long. Here, we present a continuous-light dynamic light-emitting diode (LED) strategy (involving changes in spectra, intensity, and timing), that overcomes these limitations. We focused on tomato, a well described photoperiodic injury–sensitive species, and mini-cucumber, a photoperiodic injury-tolerant species to first assess morphological responses under control (16-h photoperiod, unchanging spectrum), constant (24-h photoperiod, unchanging spectrum), and two variations of a dynamic LED strategy, dynamic 1 (16-h “day”, 3-h “peak”, 8-h “night” spectra) and dynamic 2 (20-h “day”, 5-h “peak”, 4-h “night” spectra). Next, we tested the hypothesis of photorespiration’s involvement in photoperiodic injury by using a leaf gas exchange coupled with chlorophyll fluorescence protocol. We further explored Adenosine triphosphate (ATP): Nicotinamide adenine dinucleotide phosphate (NADPH) ratio supply/demand responses by probing photosynthetic electron flow and proton flow with the MultispeQ instrument. We found canopy architecture can be tuned by minor variations of the same dynamic LED strategy, and we highlight dynamic 1 as the optimal choice for both tomato and mini-cucumber as it improved biomass/architecture and first-yield, respectively. A central discovery was that dynamic 1 had a significantly higher level of photorespiration than control, for both species. Unexpectedly, photorespiration was comparable between species under the same treatments, except under constant. However, preliminary data on a fully tolerant tomato genotype grown under constant treatment upregulated photorespiration similar to mini-cucumber. These results suggest that photoperiodic injury tolerance involves a sustained higher level of photorespiration under extended photoperiods. Interestingly, diurnal MultispeQ measurements point to the importance of cyclic electron flow at subjective nighttime that may also partially explain why dynamic LED strategies mitigate photoperiodic injury. We propose an ontology of photoperiodic injury involving photorespiration, triose phosphate utilization, peroxisomal H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub>-catalase balance, and a circadian external coincidence model of sensitivity that initiates programmed cell death.</jats:p>

<jats:p>Microsatellites, known as simple sequence repeats (SSRs), are short tandem repeats of 1 to 6 nucleotide motifs found in all genomes, particularly eukaryotes. They are widely used as co-dominant markers in genetic analyses and molecular breeding. <jats:italic>Triticeae</jats:italic>, a tribe of grasses, includes major cereal crops such as bread wheat, barley, and rye, as well as abundant forage and lawn grasses, playing a crucial role in global food production and agriculture. To enhance genetic work and expedite the improvement of <jats:italic>Triticeae</jats:italic> crops, we have developed TriticeaeSSRdb, an integrated and user-friendly database. It contains 3,891,705 SSRs from 21 species and offers browsing options based on genomic regions, chromosomes, motif types, and repeat motif sequences. Advanced search functions allow personalized searches based on chromosome location and length of SSR. Users can also explore the genes associated with SSRs, design customized primer pairs for PCR validation, and utilize practical tools for whole-genome browsing, sequence alignment, and <jats:italic>in silico</jats:italic> SSR prediction from local sequences. We continually update TriticeaeSSRdb with additional species and practical utilities. We anticipate that this database will greatly facilitate trait genetic analyses and enhance molecular breeding strategies for <jats:italic>Triticeae</jats:italic> crops. Researchers can freely access the database at <jats:ext-link>http://triticeaessrdb.com/</jats:ext-link>.</jats:p>

<jats:p>Accurate identification the species composition in mixtures poses a significant challenge, especially in processed mixtures comprising multiple species, such as those found in food and pharmaceuticals. Therefore, we have attempted to utilize shotgun metabarcoding technology to tackle this issue. In this study, the method was initially established using two mock samples of the Mongolian compound preparation Gurigumu-7 (G-7), which was then applied to three pharmaceutical products and 12 hospital-made preparations. A total of 119.72 Gb of raw data sets were obtained through shotgun metagenomic sequencing. By combining ITS2, <jats:italic>matK</jats:italic>, and <jats:italic>rbcL</jats:italic>, all the labeled bio-ingredients specified in the G-7 prescription can be detected, although some species may not be detectable in all samples. The prevalent substitution of <jats:italic>Akebia quinata</jats:italic> can be found in all the pharmaceutical and hospital samples, except for YN02 and YN12. The toxic alternative to <jats:italic>Akebia quinata</jats:italic>, <jats:italic>Aristolochia manshuriensis</jats:italic>, was exclusively identified in the YN02 sample. To further confirm this result, we validated it in YN02 using HPLC and real-time PCR with TaqMan probes. The results showed that aristolochic acid A (AAA) was detected in YN02 using HPLC, and the ITS2 sequence of <jats:italic>Aristolochia manshuriensis</jats:italic> has been validated in YN02 through qPCR and the use of a TaqMan probe. This study confirms that shotgun metabarcoding can effectively identify the biological components in Mongolian medicine compound preparation G-7. It also demonstrates the method’s potential to be utilized as a general identification technique for mixtures containing a variety of plants.</jats:p>