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<jats:p><jats:italic>Casuarina equisetifolia</jats:italic> is an important tree of the forest, cultivated in tropical and subtropical regions, providing fuelwood, land reclamation, dune stabilization, paper production, and nitrogen fixation. We have developed a systematic <jats:italic>in vitro</jats:italic> propagation protocol in <jats:italic>C. equisetifolia</jats:italic> using nodal segments (NS). Murashige and Skoog (MS) medium augmented with BA (5.0 μM) and NAA (0.5 μM) gave rise to a maximum of 32.00 ± 0.31 shoots per explant (S/E) with shoot length (SL) of 3.94 ± 0.02 cm, and a maximum of 70% regeneration potential (RP) was recorded after 8 weeks of post inoculation. For root induction, <jats:italic>in vitro</jats:italic> derived shoots were transferred to the nutrient medium consisting of a half-strength (½) MS medium augmented with 2.5 μM NAA, which produced a maximum of 12.68 ± 0.33 roots/shoot (R/S) with 3.04 ± 0.50 cm root length (RL) in 60% of culture after 6 weeks. Micropropagated plants with healthy shoots and roots were successfully acclimatized in vermicompost + garden soil + sand (1:2:1) and a maximum survival percentage of 95.1% was recorded. NS was taken from a 6-weeks-old <jats:italic>in vitro</jats:italic> derived plant of <jats:italic>C. equisetifolia</jats:italic> for synthetic seed production, and it was reported that CaCl<jats:sub>2</jats:sub> · 2H<jats:sub>2</jats:sub>O (100 mM) + Na<jats:sub>2</jats:sub>-alginate (4%) resulted in clear and uniform beads. Furthermore, the maximum conversion of synthetic seeds into plantlets occurred over a period of 4 weeks of storage at 4°C. Scanning Electron Microscopy (SEM) revealed the formation of direct shoot buds without any intermediate callus formation. In addition, the chlorophyll and carotenoid contents of the direct regenerated and mother plant were compared. Similarly, RAPD and ISSR primers were used for genetic homogeneity assessment of the direct regenerated plants, where a total of 18 and 19, respectively, clear and reproducible bands with 100% monomorphism were recorded. The developed micropropagation protocol can certainly be used for large-scale multiplication and germplasm preservation of <jats:italic>C. equisetifolia</jats:italic>. It will also help in meeting the growing demands of <jats:italic>C. equisetifolia</jats:italic> in the forest industry.</jats:p>

<jats:p>Tryptophan decarboxylases (TDCs) are a group of pyridoxal 5′-phosphate-dependent enzymes involved in the enzymatic conversion of tryptophan into tryptamine, a critical biogenic amine. We herein mined and cloned a TDC-encoding gene, <jats:italic>CaTDC3</jats:italic>, from camptothecin-producing plant <jats:italic>Camptotheca acuminata</jats:italic>. The intact <jats:italic>CaTDC3</jats:italic> was heterologously overexpressed in <jats:italic>Escherichia coli</jats:italic> and the recombinant CaTDC3 was purified to homogeneity. High-performance liquid chromatography (HPLC)-diode array detector (DAD) and high resolution mass spectrometry (HRMS) data analyses of the CaTDC3-catalyzed reaction mixture confirmed the catalytically decarboxylative activity of CaTDC3. CaTDC3 shows strict stereoselectivity for L-tryptophan. Homology modeling and molecular docking implied CaTDC3’s recognition of L-tryptophan derivatives and analogs. Substrate scope investigations revealed that the appropriate substituent groups on the indole ring, i.e., hydroxylated and halogenated L-tryptophans, could be recognized by CaTDC3 and the decarboxylation reactions generated the corresponding tryptamines. The C<jats:sup>β</jats:sup> -methyl-L-tryptophans were decarboxylated by CaTDC3 efficiently. 1-Thio-L-tryptophan, the NH group of the indole ring replaced by an S atom, could be decarboxylated by CaTDC3. CaTDC3 catalyzed the decarboxylation of 7-aza-L-tryptophan, an N displacement of the C on the aromatic ring, to afford 7-aza-tryptamine. L-Kynurenine, an L-tryptophan degradation product, could be decarboxylated by CaTDC3. The present works uncover a catalytically promiscuous TDC and the TDC is a versatile decarboxylase in synthetic biology for specialized pharmaceutically important substances.</jats:p>

<jats:p>The nucleotide-binding site (NBS)-encoding gene is a major type of resistance (R) gene, and its diverse evolutionary patterns were analyzed in different angiosperm lineages. Until now, no comparative studies have been done on the NBS encoding genes in <jats:italic>Ipomoea</jats:italic> species. In this study, various numbers of NBS-encoding genes were identified across the whole genome of sweet potato (<jats:italic>Ipomoea batatas</jats:italic>) (#889), <jats:italic>Ipomoea trifida</jats:italic> (#554), <jats:italic>Ipomoea triloba</jats:italic> (#571), and <jats:italic>Ipomoea nil</jats:italic> (#757). Gene analysis showed that the CN-type and N-type were more common than the other types of NBS-encoding genes. The phylogenetic analysis revealed that the NBS-encoding genes formed three monophyletic clades: CNL, TNL, and RNL, which were distinguished by amino acid motifs. The distribution of the NBS-encoding genes among the chromosomes was non-random and uneven; 83.13, 76.71, 90.37, and 86.39% of the genes occurred in clusters in sweet potato, <jats:italic>I. trifida</jats:italic>, <jats:italic>I. triloba</jats:italic>, and <jats:italic>I. nil</jats:italic>, respectively. The duplication pattern analysis reveals the presence of higher segmentally duplicated genes in sweet potatoes than tandemly duplicated ones. The opposite trend was found for the other three species. A total of 201 NBS-encoding orthologous genes were found to form synteny gene pairs between any two of the four <jats:italic>Ipomea</jats:italic> species, suggesting that each of the synteny gene pairs was derived from a common ancestor. The gene expression patterns were acquired by analyzing using the published datasets. To explore the candidate resistant genes in sweet potato, transcriptome analysis has been carried out using two resistant (JK20 and JK274) and susceptible cultivars (Tengfei and Santiandao) of sweet potato for stem nematodes and <jats:italic>Ceratocystis fimbriata</jats:italic> pathogen, respectively. A total of 11 differentially expressed genes (DEGs) were found in Tengfei and JK20 for stem nematodes and 19 DEGs in Santiandao and JK274 for <jats:italic>C. fimbriata</jats:italic>. Moreover, six DEGs were further selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis. The results may provide new insights into the evolution of NBS-encoding genes in the <jats:italic>Ipomoea</jats:italic> genome and contribute to the future molecular breeding of sweet potatoes.</jats:p>

<jats:p>Canopy photosynthesis integrates leaf functional and structural traits in space and time and correlates positively with yield formation. Many models with different levels of architectural details ranging from zero-dimensional (0D) to three-dimensional (3D) have been developed to simulate canopy light interception and photosynthesis. Based on these models, a crop growth model can be used to assess crop yield in response to genetic improvement, optimized practices, and environmental change. However, to what extent do architectural details influence light interception, photosynthetic production, and grain yield remains unknown. Here, we show that a crop growth model with high-resolution upscaling approach in space reduces the departure of predicted yield from actual yield and refines the simulation of canopy photosynthetic production. We found crop yield predictions decreased by 12.0–48.5% with increasing the resolution of light simulation, suggesting that a crop growth model without architectural details may result in a considerable departure from the actual photosynthetic production. A dramatic difference in light interception and photosynthetic production of canopy between cultivars was captured by the proposed 3D model rather than the 0D, 1D, and 2D models. Furthermore, we found that the overestimation of crop yield by the 0D model is caused by the overestimation of canopy photosynthetically active radiation (PAR) interception and the RUE and that by the 1D and 2D model is caused by the overestimated canopy photosynthesis rate that is possibly related to higher predicted PAR and fraction of sunlit leaves. Overall, this study confirms the necessity of taking detailed architecture traits into consideration when evaluating the strategies of genetic improvement and canopy configuration in improving crop yield by crop modeling.</jats:p>

<jats:p>Accurate and timely disease detection plays a critical role in achieving sustainable crop protection. Globally, rice has been a staple crop for centuries plagued by the diseases that greatly hamper its productivity. Sheath rot, an emerging disease of rice caused by the seed-borne pathogen <jats:italic>Sarocladium oryzae</jats:italic>, has reportedly caused heavy losses to agricultural produce in recent years. Our study has led to the development and validation of a LAMP assay for early detection of <jats:italic>S. oryzae</jats:italic>, the causal agent of sheath rot from the live-infected tissues, seeds, weeds, and environmental samples. The assay could detect as low as 1.6 fg/μl of the pathogen in 15 min. The assay was implemented to bio-surveil the presence of this pathogen by testing it on three weed species (<jats:italic>Echinochloa colona</jats:italic>, <jats:italic>Echinochloa crus-galli</jats:italic>, and <jats:italic>Cyperus teneriffae</jats:italic>) growing around the rice fields. The results showed the presence of the pathogen in two of the weed species <jats:italic>viz</jats:italic>. <jats:italic>E. colona</jats:italic> and <jats:italic>E. crus-galli</jats:italic>. The assay was used to test 13 different rice varieties for the presence of <jats:italic>S. oryzae</jats:italic> in seeds. In total, three of the varieties did not show the presence of <jats:italic>S. oryzae</jats:italic> in their seeds while the rest were found to harbor the pathogen. The developed assay can effectively be used to detect and screen the presence of <jats:italic>S. oryzae</jats:italic> in live samples including seeds and field soil.</jats:p>

<jats:p>Insects and animals are attracted to, and feed on ripe fruit, thereby promoting seed dispersal. As a vital vitamin and nutrient source, fruit make up an indispensable and enjoyable component of the human diet. Fruit ripening involves a series of physiological and biochemical changes in, among others, pigmentation, chlorophyll (Chl) degradation, texture, sugar accumulation, and flavor. Growing evidence indicates that the coordinated and ordered trait changes during fruit ripening depend on a complex regulatory network consisting of transcription factors, co-regulators, hormonal signals, and epigenetic modifications. As one of the predominant transcription factor families in plants and a downstream component of ethylene signaling, more and more studies are showing that APETALA2/ethylene responsive factor (AP2/ERF) family transcription factors act as critical regulators in fruit ripening. In this review, we focus on the regulatory mechanisms of AP2/ERFs in fruit ripening, and in particular the recent results on their target genes and co-regulators. We summarize and discuss the role of AP2/ERFs in the formation of key fruit-ripening attributes, the enactment of their regulatory mechanisms by interaction with other proteins, their role in the orchestration of phytohormone-signaling networks, and the epigenetic modifications associated with their gene expression. Our aim is to provide a multidimensional perspective on the regulatory mechanisms of AP2/ERFs in fruit ripening, and a reference for understanding and furthering research on the roles of AP2/ERF in fruit ripening.</jats:p>

<jats:p>Isoflavones are major secondary metabolites that are exclusively produced by legumes, including soybean. Soy isoflavones play important roles in human health as well as in the plant defense system. The isoflavone content is influenced by minor-effect quantitative trait loci, which interact with polygenetic and environmental factors. It has been difficult to clarify the regulation of isoflavone biosynthesis because of its complex heritability and the influence of external factors. Here, using a genotype-by-sequencing-based genome-wide association mapping study, 189 mutant soybean genotypes (the mutant diversity pool, MDP) were genotyped on the basis of 25,646 high-quality single nucleotide polymorphisms (SNPs) with minor allele frequency of &amp;gt;0.01 except for missing data. All the accessions were phenotyped by determining the contents of 12 isoflavones in the soybean seeds in two consecutive years (2020 and 2021). Then, quantitative trait nucleotides (QTNs) related to isoflavone contents were identified and validated using multi-locus GWAS models. A total of 112 and 46 QTNs related to isoflavone contents were detected by multiple MLM-based models in 2020 and 2021, respectively. Of these, 12 and 5 QTNs were related to more than two types of isoflavones in 2020 and 2021, respectively. Forty-four QTNs were detected within the 441-Kb physical interval surrounding Gm05:38940662. Of them, four QTNs (Gm05:38936166, Gm05:38936167, Gm05:38940662, and Gm05:38940717) were located at Glyma.05g206900 and Glyma.05g207000, which encode glutathione S-transferase THETA 1 (<jats:italic>GmGSTT1</jats:italic>), as determined from previous quantitative trait loci annotations and the literature. We detected substantial differences in the transcript levels of <jats:italic>GmGSTT1</jats:italic> and two other core genes (<jats:italic>IFS1</jats:italic> and <jats:italic>IFS2</jats:italic>) in the isoflavone biosynthetic pathway between the original cultivar and its mutant. The results of this study provide new information about the factors affecting isoflavone contents in soybean seeds and will be useful for breeding soybean lines with high and stable concentrations of isoflavones.</jats:p>

<jats:p>Cotton is an important source of fiber. The precise and intelligent management of cotton fields is the top priority of cotton production. Many intelligent management methods of cotton fields are inseparable from cotton boll localization, such as automated cotton picking, sustainable boll pest control, boll maturity analysis, and yield estimation. At present, object detection methods are widely used for crop localization. However, object detection methods require relatively expensive bounding box annotations for supervised learning, and some non-object regions are inevitably included in the annotated bounding boxes. The features of these non-object regions may cause misjudgment by the network model. Unlike bounding box annotations, point annotations are less expensive to label and the annotated points are only likely to belong to the object. Considering these advantages of point annotation, a point annotation-based multi-scale cotton boll localization method is proposed, called MCBLNet. It is mainly composed of scene encoding for feature extraction, location decoding for localization prediction and localization map fusion for multi-scale information association. To evaluate the robustness and accuracy of MCBLNet, we conduct experiments on our constructed cotton boll localization (CBL) dataset (300 in-field cotton boll images). Experimental results demonstrate that MCBLNet method improves by 49.4% average precision on CBL dataset compared with typically point-based localization state-of-the-arts. Additionally, MCBLNet method outperforms or at least comparable with common object detection methods.</jats:p>

<jats:p>Male sterility is an ideal character for the female parent in commercial hybrid seed production in Chinese cabbages. We identified three allele male sterile mutants <jats:italic>msm2-1</jats:italic>/2/3 in progenies of ethyl methane sulfonate mutagenized Chinese cabbage. It was proved that their male sterilities were controlled by a same recessive nuclear gene. Cytological observation showed that the delayed tapetal programmed cell death (PCD) as well as the abnormal pollen exine and intine led to pollen abortion in these mutants. MutMap combined with KASP analyses showed that <jats:italic>BraA10g019050.3C</jats:italic>, a homologous gene of <jats:italic>AtMS1</jats:italic> encoding a PHD-finger transcription factor and regulated pollen development, was the causal gene. A single-nucleotide mutation from G to A occurred at the 2443th base of <jats:italic>BrMS1</jats:italic> in <jats:italic>msm2-1</jats:italic> which results in premature termination of the PHD-finger protein translation; a single-nucleotide mutation from G to A existed at 1372th base in <jats:italic>msm2-2</jats:italic> that makes for frameshift mutation; a single-nucleotide mutation from G to A distributed at 1887th base in <jats:italic>msm2-3</jats:italic> which issues in the amino acid changed from Asp to Asn. The three allelic mutations in <jats:italic>BrMS1</jats:italic> all led to the male sterile phenotype, which revealed its function in stamen development. Quantitative reverse transcription polymerase chain reaction analysis indicated that <jats:italic>BrMS1</jats:italic> specially expressed in the anther at the early stage of pollen development and its expression level was higher in <jats:italic>msm2-1/2/3</jats:italic> than that in the wild-type “FT.” BrMS1 was located at the nucleus and a length of 12 amino acid residues at the C-terminus had transcriptional activation activity. RNA-seq indicated that the mutation in <jats:italic>BrMS1</jats:italic> affected the transcript level of genes related to the tapetum PCD and pollen wall formation, which brought out the pollen abortion. These male sterile mutants we developed provided a novel gene resource for hybrid breeding in Chinese cabbage.</jats:p>

<jats:p><jats:italic>Agropyron mongolicum</jats:italic> (<jats:italic>A. mongolicum</jats:italic>) is an excellent gramineous forage with extreme drought tolerance, which lives in arid and semiarid desert areas. However, the mechanism that underlies the response of microRNAs (miRNAs) and their targets in <jats:italic>A. mongolicum</jats:italic> to drought stress is not well understood. In this study, we analyzed the transcriptome, small RNAome (specifically the miRNAome) and degradome to generate a comprehensive resource that focused on identifying key regulatory miRNA-target circuits under drought stress. The most extended transcript in each collection is known as the UniGene, and a total of 41,792 UniGenes and 1,104 miRNAs were identified, and 99 differentially expressed miRNAs negatively regulated 1,474 differentially expressed target genes. Among them, eight miRNAs were unique to <jats:italic>A. mongolicum</jats:italic>, and there were 36 target genes. A weighted gene co-expression network analysis identified five hub genes. The miRNAs of five hub genes were screened with an integration analysis of the degradome and sRNAs, such as osa-miR444a-3p.2<jats:italic>-MADS47</jats:italic>, bdi-miR408-5p_1ss19TA-<jats:italic>CCX1</jats:italic>, tae-miR9774_L-2R-1_1ss11GT<jats:italic>-carC</jats:italic>, ata-miR169a-3p<jats:italic>-PAO2</jats:italic>, and bdi-miR528-p3_2ss15TG20CA<jats:italic>-HOX24</jats:italic>. The functional annotations revealed that they were involved in mediating the brassinosteroid signal pathway, transporting and exchanging sodium and potassium ions and regulating the oxidation–reduction process, hydrolase activity, plant response to water deprivation, abscisic acid (ABA) and the ABA-activated signaling pathway to regulate drought stress. Five hub genes were discovered, which could play central roles in the regulation of drought-responsive genes. These results show that the combined analysis of miRNA, the transcriptome and degradation group provides a useful platform to investigate the molecular mechanism of drought resistance in <jats:italic>A. mongolicum</jats:italic> and could provide new insights into the genetic engineering of Poaceae crops in the future.</jats:p>