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<jats:p>Estimating the crop leaf area index (LAI) accurately is very critical in agricultural remote sensing, especially in monitoring crop growth and yield prediction. The development of unmanned aerial vehicles (UAVs) has been significant in recent years and has been extensively applied in agricultural remote sensing (RS). The vegetation index (VI), which reflects spectral information, is a commonly used RS method for estimating LAI. Texture features can reflect the differences in the canopy structure of rice at different growth stages. In this research, a method was developed to improve the accuracy of rice LAI estimation during the whole growing season by combining texture information based on wavelet transform and spectral information derived from the VI. During the whole growth period, we obtained UAV images of two study areas using a 12-band Mini-MCA system and performed corresponding ground measurements. Several VI values were calculated, and the texture analysis was carried out. New indices were constructed by mathematically combining the wavelet texture and spectral information. Compared with the corresponding VIs, the new indices reduced the saturation effect and were less sensitive to the emergence of panicles. The determination coefficient (R<jats:sup>2</jats:sup>) increased for most VIs used in this study throughout the whole growth period. The results indicated that the estimation accuracy of LAI by combining spectral information and texture information was higher than that of VIs. The method proposed in this study used the spectral and wavelet texture features extracted from UAV images to establish a model of the whole growth period of rice, which was easy to operate and had great potential for large-scale auxiliary rice breeding and field management research.</jats:p>

<jats:p>Muscadine berries display enhanced nutraceutical value due to the accumulation of distinctive phytochemical constituents with great potential antioxidant activity. Such nutritional and health merits are not only restricted to muscadine, but muscadine berries accumulate higher amounts of bioactive polyphenolics compared with other grape species. For the genetic study of the antioxidant trait in muscadine, a multi-locus genome-wide association study (GWAS) with 350 muscadine genotypes and 1,283 RNase H2 enzyme-dependent amplicon sequencing (rhAmpSeq) markers was performed. Phenotyping was conducted with several antioxidant-related traits, including total phenolic content (TPC), total flavonoid content (TFC), 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity, and FRAP antioxidant assay in muscadine berry skin. The correlation coefficient analysis revealed that the TPC, and DPPH/FRAP activities were significantly correlated. Through the GWAS analysis, 12 QTNs were identified from the four traits, of which six were pleiotropic QTNs. Two pleiotropic QTNs, chr2_14464718 and chr4_16491374, were commonly identified from the TPC and DPPH/FRAP activities. Co-located genes with the two pleiotropic QTNs were isolated, and two candidate genes were identified with transcriptome analysis. UDP-glycosyltransferase and 4-hydroxy-4-methyl-2-oxoglutarate aldolase were the candidate genes that are positively and negatively correlated to the quantitative property of traits, respectively. These results are the first genetic evidence of the quantitative property of antioxidants in muscadine and provide genetic resources for breeding antioxidant-rich cultivars for both <jats:italic>Muscadinia</jats:italic> and <jats:italic>Euvitis</jats:italic> species.</jats:p>

<jats:p>Jasmonate (JA) signaling plays a pivotal role in plant stress responses and secondary metabolism. Many studies have demonstrated that JA effectively induce the expressions of alkaloid biosynthetic genes in various plants, which rendered to the accumulation of alkaloid to counteract stresses. Despite the multiple roles of JA in the regulation of plant growth and different stresses, less studied involved in the regulatory role of JA in <jats:italic>Dendrobium officinale</jats:italic> alkaloids. A strategy for the rapid identification of alkaloid and the intermediates of <jats:italic>D. officinale</jats:italic> was established based on a solid-phase extraction coupled with high-performance liquid chromatography tandem mass spectrometry method. By using SPE-LC-MS/MS method, the potential compounds were tentatively identified by aligning the accurate molecular weight with the METLIN and Dictionary of Natural Products databases. The chemical structures and main characteristic fragments of the potential compounds were further confirmed by retrieving the multistage mass spectra from the MassBank and METLIN databases. The Mass Frontier software was used to speculate the fragmentation pathway of the identified compounds. Seven alkaloids were separated and identified from <jats:italic>D. officinale</jats:italic>, which were mainly classified into five types (tropane alkaloids, tetrahydroisoquinoline alkaloids, quinolizidine alkaloids, piperidine alkaloids, and spermidine alkaloids). Besides the alkaloids, forty-nine chemical substances, including guanidines, nucleotides, dipeptides, sphingolipids and nitrogen-containing glucosides, were concurrently identified. These findings gives the composition of chemicals currently found in <jats:italic>D. officinale</jats:italic>, which could provide the scientific method for the identification of alkaloids in other <jats:italic>Dendrobium</jats:italic> plants.</jats:p>

<jats:p>Aluminum (Al) toxicity poses a significant challenge for the yield improvement of chickpea, which is an economically important legume crop with high nutritional value in human diets. The genetic basis of Al-tolerance in chickpea remains unclear. Here, we assessed the Al-tolerance of 8 wild <jats:italic>Cicer</jats:italic> and one cultivated chickpea (PBA Pistol) accessions by measuring the root elongation in solution culture under control (0 μM Al<jats:sup>3+</jats:sup>) and Al treatments (15, 30 μM Al<jats:sup>3+</jats:sup>). Compared to PBA Pistol, the wild <jats:italic>Cicer</jats:italic> accessions displayed both tolerant and sensitive phenotypes, supporting wild <jats:italic>Cicer</jats:italic> as a potential genetic pool for Al-tolerance improvement. To identify potential genes related to Al-tolerance in chickpea, genome-wide screening of multidrug and toxic compound extrusion (MATE) encoding genes was performed. Fifty-six <jats:italic>MATE</jats:italic> genes were identified in total, which can be divided into 4 major phylogenetic groups. Four chickpea <jats:italic>MATE</jats:italic> genes (<jats:italic>CaMATE1-4</jats:italic>) were clustered with the previously characterized citrate transporters <jats:italic>MtMATE66</jats:italic> and <jats:italic>MtMATE69</jats:italic> in <jats:italic>Medicago truncatula</jats:italic>. Transcriptome data showed that <jats:italic>CaMATE1-4</jats:italic> have diverse expression profiles, with <jats:italic>CaMATE2</jats:italic> being root-specific. qRT-PCR analyses confirmed that <jats:italic>CaMATE2</jats:italic> and <jats:italic>CaMATE4</jats:italic> were highly expressed in root tips and were up-regulated upon Al treatment in all chickpea lines. Further measurement of carboxylic acids showed that malonic acid, instead of malate or citrate, is the major extruded acid by <jats:italic>Cicer</jats:italic> spp. root. Protein structural modeling analyses revealed that CaMATE2 has a divergent substrate-binding cavity from <jats:italic>Arabidopsis</jats:italic> AtFRD3, which may explain the different acid-secretion profile for chickpea. Pangenome survey showed that <jats:italic>CaMATE1-4</jats:italic> have much higher genetic diversity in wild <jats:italic>Cicer</jats:italic> than that in cultivated chickpea. This first identification of <jats:italic>CaMATE2</jats:italic> and <jats:italic>CaMATE4</jats:italic> responsive to Al<jats:sup>3+</jats:sup> treatment in <jats:italic>Cicer</jats:italic> paves the way for future functional characterization of MATE genes in <jats:italic>Cicer</jats:italic> spp., and to facilitate future design of gene-specific markers for Al-tolerant line selection in chickpea breeding programs.</jats:p>

<jats:p>While plants are an abundant source of valuable natural products, it is often challenging to produce those products for commercial application. Often organic synthesis is too expensive for a viable commercial product and the biosynthetic pathways are often so complex that transferring them to a microorganism is not trivial or feasible. For plants not suited to agricultural production of natural products, hairy root cultures offer an attractive option for a production platform which offers genetic and biochemical stability, fast growth, and a hormone free culture media. Advances in metabolic engineering and synthetic biology tools to engineer hairy roots along with bioreactor technology is to a point where commercial application of the technology will soon be realized. We discuss different applications of hairy roots. We also use a case study of the advancements in understanding of the terpenoid indole alkaloid pathway in <jats:italic>Catharanthus roseus</jats:italic> hairy roots to illustrate the advancements and challenges in pathway discovery and in pathway engineering.</jats:p>

<jats:p>Comparative mitogenomics of <jats:italic>Ulva</jats:italic> species have revealed remarkable variations in genome size due to the integration of exogenous DNA fragments, the proliferation of group I/II introns, and the change of repeat sequences. The genus <jats:italic>Ulva</jats:italic> is a species-rich taxonomic group, containing a variety of green-tide forming algae. In this study, five complete mitogenomes of the green-tide forming macroalga, <jats:italic>Ulva meridionalis</jats:italic> R. Horimoto and S. Shimada, were assembled and compared with the available ulvophyceae mtDNAs. The main circular mitogenomes of <jats:italic>U. meridionalis</jats:italic> ranged from 82.94 to 111.49 kb in size, and its 111.49-kb mitogenome was the largest <jats:italic>Ulva</jats:italic> mitogenome sequenced so far. The expansion of <jats:italic>U. meridionalis</jats:italic> mitogenomes is mainly due to the tandem integration of a 5.36-kb mitochondrial circular plasmid (pUme), as well as the proliferation of introns. An intact DNA-directed RNA polymerase gene (<jats:italic>rpo</jats:italic>) was present in pUme of <jats:italic>U. meridionalis</jats:italic> and was then detected in two putative plasmids (pUmu1 and pUmu2) found in <jats:italic>Ulva mutabilis</jats:italic>. The observed integration of the circular plasmid into <jats:italic>U. meridionalis</jats:italic> mitogenomes seems to occur <jats:italic>via</jats:italic> homologous recombination, and is a more recent evolutionary event. Many highly homologous sequences of these three putative plasmids can be detected in the other <jats:italic>Ulva</jats:italic> mtDNAs sequenced thus far, indicating the integration of different mitochondrial plasmid DNA into the mitogenomes is a common phenomenon in the evolution of <jats:italic>Ulva</jats:italic> mitogenomes. The random incidence of destruction of plasmid-derived <jats:italic>rpo</jats:italic>s and open reading frames (<jats:italic>orf</jats:italic>s) suggests that their existence is not the original characteristic of <jats:italic>Ulva</jats:italic> mitogenomes and there is no selective pressure to maintain their integrity. The frequent integration and rapid divergence of plasmid-derived sequences is one of the most important evolutionary forces to shape the diversity of <jats:italic>Ulva</jats:italic> mitogenomes.</jats:p>

<jats:p><jats:italic>Cyclocarya paliurus</jats:italic> is mainly distributed in subtropical areas of China. Its leaves are rich in beneficial triterpenoids that have bioactivities against human diseases, including hyperlipemia, diabetes, and hypertension. In this study, data on the genetic diversity, distributing environment, and triterpenoids of <jats:italic>C. paliurus</jats:italic> samples were collected from a wide area in China. The data covered 316 <jats:italic>C. paliurus</jats:italic> germplasms collected from 26 distinct populations. Association analysis between genotype and triterpenoids was carried out to describe triterpenoids accumulation pattern. Based on our analyses, we identified the important trend that genotypes with higher triterpenoid contents belonged to a unique genotype subgroup. The results showed that pterocaryoside B and pterocaryoside A significantly vary among the genotypic subgroups. In addition, the different genotypic subgroups showed distinct geographical distributing areas. These findings provide information about the relationship between genetic and environmental factors and how this affects triterpenoids accumulation. This information will be valuable for targeted breeding and for further germplasm selection of <jats:italic>C. paliurus</jats:italic> resources.</jats:p>

<jats:p><jats:italic>Brittle Culm 15</jats:italic> (<jats:italic>BC15</jats:italic>) gene encodes a membrane-associated chitinase-like protein that participates in cellulose synthesis, and <jats:italic>BC15</jats:italic> gene mutation affects cell wall composition in plant, such as cellulose or hemicellulose. The present study was designed to investigate the changes of carbohydrates composition in <jats:italic>bc15</jats:italic> mutant straw, and the resulting consequence on rumen fermentation, methanogenesis, and microbial populations (qPCR) during <jats:italic>in vitro</jats:italic> ruminal fermentation process. Two substrates, <jats:italic>bc15</jats:italic> mutant and wild-type (WT) rice straws, were selected for <jats:italic>in vitro</jats:italic> rumen batch culture. The first experiment was designed to investigate the kinetics of total gas and CH<jats:sub>4</jats:sub> production through 48-h <jats:italic>in vitro</jats:italic> ruminal fermentation, while the second experiment selected incubation time of 12 and 48 h to represent the early and late stage of <jats:italic>in vitro</jats:italic> ruminal incubation, respectively, and then investigated changes in biodegradation, fermentation end products, and selected representative microbial populations. The <jats:italic>bc15</jats:italic> mutant straw had lower contents of cellulose, neutral detergent fiber (NDF) and acid detergent fiber (ADF), and higher contents of water-soluble carbohydrates, neutral detergent solubles (NDS) and monosaccharides. The <jats:italic>bc15</jats:italic> mutant straw exhibited a distinct kinetics of 48-h total gas and CH<jats:sub>4</jats:sub> production with faster increases in early incubation when compared with WT straw. The <jats:italic>bc15</jats:italic> mutant straw had higher DM degradation, NDF degradation and total volatile fatty acid concentration at 12 h of incubation, and lower NDF degradation and CH<jats:sub>4</jats:sub> production at 48 h of incubation, together with lower acetate to propionate ratio and ADF degradation and higher butyrate molar percentage and NDS degradation at both incubation times. Furthermore, the <jats:italic>bc15</jats:italic> mutant straw resulted in greater 16S gene copies of <jats:italic>F. succinogenes</jats:italic>, with lower 18S gene copies of fungi at both incubation times. These results indicated that the <jats:italic>BC15</jats:italic> gene mutation decreased fibrosis of cell wall of rice straw, enhanced degradation at the early stage of rumen fermentation, and shifts fermentation pattern from acetate to propionate and butyrate production, leading to the decreased volume and fractional rate of CH<jats:sub>4</jats:sub> production. However, <jats:italic>BC15</jats:italic> gene mutation may enhance hardenability of cell wall structure of rice straw, which is more resistant for microbial colonization with decreased fiber degradation. Thus, this study modified rice straw by manipulating a cell wall biosynthesis gene and provides a potential strategy to alter degradation and CH<jats:sub>4</jats:sub> production during <jats:italic>in vitro</jats:italic> ruminal fermentation process.</jats:p>

<jats:p>Alfalfa sprouts are among the most nutritionally rich foods, and light exposure is a critical factor in determining their biomass and quality. However, detailed metabolic and molecular differences between yellow and green alfalfa sprouts remain unclear. In this study, comprehensive metabolomic and transcriptomic analyses were integrated to evaluate the nutrient composition of alfalfa sprouts during germination with or without light exposure. Differentially expressed genes and differentially accumulated metabolites in green and yellow alfalfa sprouts were significantly enriched in secondary metabolic pathways, such as the isoflavonoid biosynthesis pathway. Green alfalfa sprouts contained a wide variety of lipids, flavonoids, phenolic acids, and terpenoids, among which the top three upregulated were calycosin, methyl gallate, and epicatechin 3-gallate, whereas yellow alfalfa sprouts contained relatively more isoquercitrin. These results provide new insights into the nutritional value and composition of alfalfa sprouts under different germination regimes.</jats:p>

<jats:p>Changes in global climate and precipitation patterns have exacerbated the existing uneven distribution of water, causing many plants to face the alternate situation of drought and water flooding. We studied the growth and physiological response of the wetland plant <jats:italic>Artemisia selengensis</jats:italic> to drought and rehydration. In this study, <jats:italic>Artemisia selengensis</jats:italic> seedlings were subjected to 32.89% (SD), 47.36 % (MD), 60.97% (MID), and 87.18 % (CK) field water holding capacity for 70 days, followed by 14 days of rehydration. The results showed that drought inhibited the increase of plant height, basal diameter, and biomass accumulation under SD and MD, but the root shoot ratio (R/S) increased. Drought stress also decreased the content of total chlorophyll (Chl), chlorophyll a (Chl-a), chlorophyll b (Chl-b), and carotenoid (Car). Soluble sugar (SS) and proline (Pro) were accumulated rapidly under drought, and the relative water content (RWC) of leaves was kept at a high level of 80%. After rehydration, the plant height, basal diameter, biomass, and R/S ratio could not be recovered under SD and MD, but these indicators were completely recovered under MID. The RWC, Chl, Chl-a, Chl-b, Car, and osmotic substances were partially or completely recovered. In conclusion, <jats:italic>Artemisia selengensis</jats:italic> not only can improve drought resistance by increasing the R/S ratio and osmotic substances but also adopt the compensatory mechanism during rehydration. It is predictable that <jats:italic>A. selengensis</jats:italic> may benefit from possible future aridification of wetlands and expand population distribution.</jats:p>