{"title":"Plant-derived saponins and their prospective for cosmetic and personal care products.","authors":"Mayuree Kanlayavattanakul, Donia Mersni, Nattaya Lourith","doi":"10.1186/s40529-024-00438-8","DOIUrl":"https://doi.org/10.1186/s40529-024-00438-8","url":null,"abstract":"<p><p>Plants are industrially cultivated and processed serving for specified sectors for human consumptions including cosmetic and personal care products. Where, the consumers' awareness towards sustainability are increasing year by year. Among which, those of the materials derived from the plants produced with good agricultural and manufacturing practices abided with bio-circular-green economy theme, are of eminence. This perspective is in line with the researchers' bioprospective onto natural products. Special attention sheds on saponins, the biosurfactants that will not cause detrimental effects on the environment. Which, plants are regarded as the sustainable sources of these cosmetic substances. However, among tremendous plants that have been continuously explored upon their potential applications. Most of the studies focus on preparation of the saponins and biological activities. Surprisingly, those that are abided with the list published in the European Commission (CosIng) that are of crucially for cosmetic regulation are insufficiently demonstrated, which burden their applications in the sector. This context summarizes the industrial crops that are registered as plant saponin in the CosIng database. Those that are insufficiently exploited on the information required for cosmetic formulations are therefore encouraged to be examined. In addition, multidirectional cosmetic beneficials of the filled plants saponin would be encouraged to be explored. These plants will be properly knowledge managed for their sustainable utilizations as the bio-based materials promising for cosmetic and personal care industrial perspectives.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142603111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identification of powdery mildew resistance quantitative trait loci in melon and development of resistant near-isogenic lines through marker-assisted backcrossing.","authors":"Chun-San Wang, Ssu-Yu Lin, Jin-Hsing Huang, Hsin-Yi Chang, Di-Kuan Lew, Yu-Hua Wang, Kae-Kang Hwu, Yung-Fen Huang","doi":"10.1186/s40529-024-00435-x","DOIUrl":"10.1186/s40529-024-00435-x","url":null,"abstract":"<p><strong>Background: </strong>Melon (Cucumis melo L.), an important cucurbit crop, faces production limitations due to powdery mildew (PM). Developing resistant varieties offers a sustainable, genetics-based alternative to chemical treatments. Therefore, identifying PM resistance quantitative trait loci (QTL) and creating trait-associated markers are essential for efficient melon PM resistance improvement through marker-assisted backcrossing (MABC).</p><p><strong>Results: </strong>Three F<sub>2</sub> populations, A6, B2, and C4, were generated for QTL mapping of PM resistance. Major QTL were identified on chromosome 2 in A6, chromosome 5 in B2, and chromosomes 5 and 12 in C4. A series of TaqMan® assays targeting regions on chromosomes 2, 5, and 12 were developed and validated for foreground and recombinant selection, complemented by the double digest restriction-site associated DNA genotyping system to evaluate the recurrent parent genome recovery. Three MABC programs using resistant donor parents from A6 and C4 crossed with elite susceptible recurrent parents with green and orange fruit flesh were implemented. After two to three cycles of MABC, individual QTL was successfully introgressed into elite genetic backgrounds, giving six PM resistance lines in each green- and orange-fleshed background. PM inoculation on the twelve near-isogenic lines confirmed their resistance to PM.</p><p><strong>Conclusions: </strong>We have identified major PM resistance QTL for melon on chromosomes 2, 5, and 12 and have introgressed individual QTL to elite genetic backgrounds using MABC in three and a half years. This study demonstrates the power of combining high-throughput genotyping with breeding efforts and showcases the efficiency of molecular breeding.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11534953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Botanical StudiesPub Date : 2024-10-08DOI: 10.1186/s40529-024-00436-w
Pradeepkumara N, Chander Parkash, Reeta Bhatia, Anilabha Das Munshi, Mahesh Rao, Subhashree Subhasmita, Tusar Kanti Behera, Shyam Sundar Dey
{"title":"An efficient and easy-to-use protocol for induction of haploids in cucumber through parthenogenic embryo development.","authors":"Pradeepkumara N, Chander Parkash, Reeta Bhatia, Anilabha Das Munshi, Mahesh Rao, Subhashree Subhasmita, Tusar Kanti Behera, Shyam Sundar Dey","doi":"10.1186/s40529-024-00436-w","DOIUrl":"10.1186/s40529-024-00436-w","url":null,"abstract":"<p><strong>Background: </strong>Cucumber (Cucumis sativus L.) is a model crop to study cell biology, including the development of haploids and doubled haploids in vegetable crops. In plant breeding, haploid and doubled haploids are valuable tools for developing pure homozygous inbred lines and accelerating genetic progress by reducing the time required for breeding cycles. Besides, the haploids are also valuable in genomic studies. We are reporting the induction of haploids in cucumber involving gynoecious and parthenocarpic genotypes for the first time. This study aimed to assess the efficient induction of haploids through pollination with gamma-irradiated pollen in cucumber. The effect of gamma irradiation dose on pollen viability and germination, fruit setting percentage, seed development, and haploid embryo development in cucumber hybrid genotypes were studied in detail. The goal was to utilize this information to produce haploid plants for genomics and transformation works in this model vegetable crop.</p><p><strong>Results: </strong>Pollination was done on six cucumber genotypes using varying doses of gamma rays (100, 200, 300, 400, and 500 Gy). Genotypes, doses of irradiation, and embryo developmental stage influenced the successful generation of in-vitro haploid plants. The optimal timeframe for embryo rescue was found to be 25 to 30 days after pollination. Haploid embryos were effectively induced using irradiated pollen at 400 to 500 Gy doses. Parthenogenetic plantlets were analyzed, and their ploidy level was confirmed through stomatal physiology, cytology (mitosis), and flow cytometry methods.</p><p><strong>Conclusion: </strong>Through parthenogenic embryo development, it is possible to induce a large number of haploids in cucumber. This technique's power lies in its ability to streamline the breeding process, enhance genetic gain, and produce superior cultivars that contribute to sustainable agriculture and food security.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11461365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142388043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Botanical StudiesPub Date : 2024-09-29DOI: 10.1186/s40529-024-00437-9
Pavol Prokop, Kristián Tučník, Zuzana Provazník, Zuzana Čiamporová-Zaťovičová, Fedor Čiampor
{"title":"Pollinator behaviour and prevalence of the anther smut Antherospora vindobonensis in its host, the Hungarian two-leaf squill (Scilla vindobonensis).","authors":"Pavol Prokop, Kristián Tučník, Zuzana Provazník, Zuzana Čiamporová-Zaťovičová, Fedor Čiampor","doi":"10.1186/s40529-024-00437-9","DOIUrl":"10.1186/s40529-024-00437-9","url":null,"abstract":"<p><p>Anther smuts are fungal diseases that have detrimental effects on the biology of their host plants. We investigated the transmission of Anther smut Antherospora vindobonensis to its host, Scilla vindobonensis under natural and laboratory conditions. Plants flowering early in spring were less vulnerable to disease (∼ 20-30% of plants which appeared early in the season were diseased) than flowers that bloom at the end of the season (∼ 60% of plants which appeared late in the season were diseased) which contradicts the patterns observed for other anther smuts species. Diseased plants showed thicker stems, lower nectar production and smaller flower radius than healthy plants. The disease prevalence in S. vindobonensis was not influenced by plant density. The production of spores in diseased flowers was 125 times higher than the production of pollen in healthy flowers. The number of pollen grains attached to pollinator bodies from healthy plants under controlled conditions was similar to the number of spores attached from diseased plants. Experienced honeybees in the field showed almost identical preferences for healthy plants (65%) over diseased ones, as did naïve bumblebees under controlled laboratory conditions (69%). eDNA metabarcoding revealed that healthy flowers attracted a significantly higher number of arthropod species (M = 6.23, SE = 1.48) than diseased flowers (M = 2.32, SE = 0.31). Strong seasonal differences in the risk of infection suggest that S. vindobonensis solves the trade-off between low pollinator availability and low risk of infection at the beginning of the season and high risk of infection and high pollinator availability at the end of season. By reproducing early in the season, plants can reduce the risk of disease.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11439859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142341810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Botanical StudiesPub Date : 2024-09-23DOI: 10.1186/s40529-024-00434-y
Salma N Eladl, Aya M Elnabawy, Eladl G Eltanahy
{"title":"Recent biotechnological applications of value-added bioactive compounds from microalgae and seaweeds.","authors":"Salma N Eladl, Aya M Elnabawy, Eladl G Eltanahy","doi":"10.1186/s40529-024-00434-y","DOIUrl":"10.1186/s40529-024-00434-y","url":null,"abstract":"<p><p>Microalgae and seaweed have been consumed as food for several decades to combat starvation and food shortages worldwide. The most famous edible microalgae species are Nostoc, Spirulina, and Aphanizomenon, in addition to seaweeds, which are used in traditional medicine and food, such as Nori, which is one of the most popular foods containing Pyropia alga as a major ingredient. Recently, many applications use algae-derived polysaccharides such as agar, alginate, carrageenan, cellulose, fucoidan, mannan, laminarin, ulvan, and xylan as gelling agents in food, pharmaceuticals, and cosmetics industries. Moreover, pigments (carotenoids particularly astaxanthins, chlorophylls, and phycobilins), minerals, vitamins, polyunsaturated fatty acids, peptides, proteins, polyphenols, and diterpenes compounds are accumulated under specific cultivation and stress conditions in the algal cells to be harvested and their biomass used as a feedstock for the relevant industries and applications. No less critical is the use of algae in bioremediation, thus contributing significantly to environmental sustainability.This review will explore and discuss the various applications of microalgae and seaweeds, emphasising their role in bioremediation, recent products with algal added-value compounds that are now on the market, and novel under-developing applications such as bioplastics and nanoparticle production. Nonetheless, special attention is also drawn towards the limitations of these applications and the technologies applied, and how they may be overcome.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11420431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Botanical StudiesPub Date : 2024-09-03DOI: 10.1186/s40529-024-00432-0
Latifa AlHusnain, Muneera D F AlKahtani, Kotb A Attia, Tayyaba Sanaullah, Dalia E Elsharnoby
{"title":"Application of CRISPR/Cas9 system to knock out GluB gene for developing low glutelin rice mutant.","authors":"Latifa AlHusnain, Muneera D F AlKahtani, Kotb A Attia, Tayyaba Sanaullah, Dalia E Elsharnoby","doi":"10.1186/s40529-024-00432-0","DOIUrl":"10.1186/s40529-024-00432-0","url":null,"abstract":"<p><p>The nutritional quality improvement is among the most integral objective for any rice molecular breeding programs. The seed storage proteins (SSPs) have greater role to determine the nutritional quality of any cereal grains. Rice contains relatively balanced amino acid composition and the SSPs are fractioned into albumins (ALB), globulins (GLO), prolamins (PRO) and glutelins (GLU) according to differences in solubility. GLUs are further divided into subfamilies: GluA, GluB, GluC, and GluD depending on resemblance in amino acid. The GLU protein accounts for 60-80% of total protein contents, encoded by 15 genes located on different chromosomes of rice genome. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system was employed to knockout Glu-B (LOC-Os02g15070) gene in non-basmati rice PK386 cultivar. The mutant displayed two base pair and three base pair mutation in the targeted regions. The homozygous mutant plant displayed reduction for both in total protein contents and GLU contents whereas, elevation in GLO, ALB and PRO. Moreover, the mutant plant also displayed reduction in physio-chemical properties e.g., total starch, amylose and gel consistency. The agronomic characteristics of both mutant and wild type displayed non-significant differences along with increase in higher percentage of chalkiness in mutant plants. The results obtained from scanning electron microscopy showed the loosely packed starch granules compared to wild type. The gene expression analysis displayed the lower expression of gene at 5 days after flowering (DAF), 10 DAF, 15 DAF and 20 DAF compared to wild type. GUS sub-cellular localization showed the staining in seed which further validated the results obtained from gene expression. Based on these findings it can be concluded Glu-B gene have significant role in controlling GLU contents and can be utilized in breeding programs to enhance the nutritional quality of rice, and may serve as healthy diet for patient allergic with high GLU contents.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Association mapping of important agronomic traits in Mucuna pruriens (L.) DC.","authors":"Patrush Lepcha, Mahesh Shekhar, Leelambika Murugesan, Mahammad Jaheer, Ratan Chopra, Vikas Belamkar, Narayana Sathyanarayana","doi":"10.1186/s40529-024-00421-3","DOIUrl":"10.1186/s40529-024-00421-3","url":null,"abstract":"<p><strong>Background: </strong>The tropical legume Mucuna pruriens (L.) DC. can meet three agricultural needs: low-cost protein, high-value medicines, and green manure or cover crops. But like other underutilized crops, it needs more modern breeding resources. Identifying marker-trait associations (MTAs) can facilitate marker-assisted breeding and crop improvement. Recent studies have demonstrated the feasibility of identifying MTAs using a small number of accessions (< 100). We have characterized a panel of 70 M. pruriens accessions across two consecutive years and performed association analysis for 16 phenotypic traits related to seed (seed length, seed width, seed thickness, seed yield per plant, hundred seed weight); pod (pod length, pod width, number of pods per cluster, number of pods per plant); inflorescence (inflorescence length, flower buds per inflorescence, flower length, pedicel length), and biochemical attributes (L-DOPA, total protein, total carbohydrate), using 66 genic-microsatellite markers following mixed linear model.</p><p><strong>Results: </strong>The results showed significant phenotypic (P < 0.05) and genetic diversity (Shannon's information index, I = 0.62) in our germplasm collection. Many tested traits were highly heritable (broad-sense heritability ranging from 42.86 to 99.93%). A total of 15 MTAs was detected at an adjusted significance level of P < 5.55 × 10<sup>- 3</sup> for nine traits (seed length, seed thickness, seed width, hundred seed weight, seed yield per plant, inflorescence length, flower buds per inflorescence, flower length, and petiole length), contributed by 10 SSR markers (MPU_19, MPU_42, MPU_54, MPU_57, MPU_58, MPU_83, MPU_89, MPU_108, MPU_111, and MPU_122.) with phenotypic variance explained (PVE) ranging from 14.7 to 31.1%. Out of the ten trait-associated markers, the BLAST analysis revealed putative functions of seven markers, except MPU_57, MPU_58, and MPU_83.</p><p><strong>Conclusion: </strong>Fifteen MTAs identified for important traits with phenotypic variance explained > 10% from mixed linear model offer a solid resource base for improving this crop. This is the first report on association mapping in M. pruriens and our results are expected to assist with marker-assisted breeding and identifying candidate genes in this promising legume.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11333416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Botanical StudiesPub Date : 2024-08-14DOI: 10.1186/s40529-024-00423-1
Mykyta Peregrym, Ingrid Turisová, Peter Turis
{"title":"A new insight on the genus Pteridium (Dennstaedtiaceae) in Europe based on a revision in the flora of Slovakia.","authors":"Mykyta Peregrym, Ingrid Turisová, Peter Turis","doi":"10.1186/s40529-024-00423-1","DOIUrl":"10.1186/s40529-024-00423-1","url":null,"abstract":"<p><strong>Background: </strong>The genus Pteridium Gled. ex Scop. was thought to be monotypic with the cosmopolitan species P. aquilinum (L.) Kuhn. for many years. However, morphological variations among these plants in different regions have been noted since the 1940's, leading to the description of new taxa later. Molecular investigations, while not resolving all taxonomical questions within the genus, have highlighted its rich genetic diversity globally, confirming the status of several previously described species and subspecies. This wealth of data has prompted revisions of the Pteridium genus in regional floras, with Northern Eurasia serving as a central arena for such studies in the last 30 years. Recent data suggest that the European flora comprises a single species, P. aquilinum, with two subspecies, P. a. subsp. aquilinum and P. a. subsp. pinetorum (C.N. Page & R.R. Mill) J.A. Thomson. However, their distribution within the continent remains unclear. Therefore, this study aims to elucidate the representation and distribution of Pteridium taxa in Slovakia with an attempt to describe natural ranges of P. aquilinum subspecies based on herbarium materials and citizen science data within Europe for a whole.</p><p><strong>Results: </strong>It is confirmed that the genus Pteridium is represented by the single species with two mentioned subspecies in the flora of Europe, as well as in the flora of Slovakia. The distribution of these subspecies is mapped in the country. Additionally, we discuss the ranges of these subspecies for a whole, and we evidence the growth of P. aquilinum subsp. pinetorum within the Netherlands, Czechia, Austria, Hungary and Romania for the first time. Also, two new combinations of taxa from the Asian part of Russia are offered.</p><p><strong>Conclusion: </strong>Our study is a significant contribution in the present knowledge about the distribution and taxonomy of P. aquilinum, however it also shows that many questions concerning this taxon and its infraspecific taxa remain open. Additional field investigations and herbarium processing should be carried out for detailed explorations of biological and ecological peculiarities of the mentioned subspecies, and for the clear understanding of their regional distribution. Such explorations also might become a basis for new syntaxonomic revisions.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11324619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Botanical StudiesPub Date : 2024-08-14DOI: 10.1186/s40529-024-00433-z
Zahra Zinati, Leyla Nazari, Ali Niazi
{"title":"Uncovering waterlogging-responsive genes in cucumber through machine learning and differential gene correlation analysis.","authors":"Zahra Zinati, Leyla Nazari, Ali Niazi","doi":"10.1186/s40529-024-00433-z","DOIUrl":"10.1186/s40529-024-00433-z","url":null,"abstract":"<p><p>As climate change intensifies, the frequency and severity of waterlogging are expected to increase, necessitating a deeper understanding of the cucumber response to this stress. In this study, three public RNA-seq datasets (PRJNA799460, PRJNA844418, and PRJNA678740) comprising 36 samples were analyzed. Various feature selection algorithms including Uncertainty, Relief, SVM (Support Vector Machine), Correlation, and logistic least absolute shrinkage, and selection operator (LASSO) were performed to identify the most significant genes related to the waterlogging stress response. These feature selection techniques, which have different characteristics, were used to reduce the complexity of the data and thereby identify the most significant genes related to the waterlogging stress response. Uncertainty, Relief, SVM, Correlation, and LASSO identified 4, 4, 10, 21, and 13 genes, respectively. Differential gene correlation analysis (DGCA) focusing on the 36 selected genes identified changes in correlation patterns between the selected genes under waterlogged versus control conditions, providing deeper insights into the regulatory networks and interactions among the selected genes. DGCA revealed significant changes in the correlation of 13 genes between control and waterlogging conditions. Finally, we validated 13 genes using the Random Forest (RF) classifier, which achieved 100% accuracy and a 1.0 Area Under the Curve (AUC) score. The SHapley Additive exPlanations (SHAP) values clearly showed the significant impact of LOC101209599, LOC101217277, and LOC101216320 on the model's predictive power. In addition, we employed the Boruta as a wrapper feature selection method to further validate our gene selection strategy. Eight of the 13 genes were common across the four feature weighting algorithms, LASSO, DGCA, and Boruta, underscoring the robustness and reliability of our gene selection strategy. Notably, the genes LOC101209599, LOC101217277, and LOC101216320 were among genes identified by multiple feature selection methods from different categories (filtering, wrapper, and embedded). Pathways associated with these specific genes play a pivotal role in regulating stress tolerance, root development, nutrient absorption, sugar metabolism, gene expression, protein degradation, and calcium signaling. These intricate regulatory mechanisms are crucial for cucumbers to adapt effectively to waterlogging conditions. These findings provide valuable insights for uncovering targets in breeding new cucumber varieties with enhanced stress tolerance.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11324642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Botanical StudiesPub Date : 2024-07-23DOI: 10.1186/s40529-024-00430-2
Zhaohui Ran, Zhi Li, Xu Xiao, Ming Tang
{"title":"Camellia neriifolia and Camellia ilicifolia (Theaceae) as separate species: evidence from morphology, anatomy, palynology, molecular systematics.","authors":"Zhaohui Ran, Zhi Li, Xu Xiao, Ming Tang","doi":"10.1186/s40529-024-00430-2","DOIUrl":"10.1186/s40529-024-00430-2","url":null,"abstract":"<p><strong>Background: </strong>The systematic status of sect. Tuberculata and its taxonomy have recently attracted considerable attention. However, the different bases for defining the characteristics of sect. Tuberculata has led to many disagreements among the plants in this group. Camellia neriifolia and Camellia ilicifolia have been the subject of taxonomic controversy and have been treated as different species or varieties of the same species. Therefore, it is important to use multiple methods, i.e., integrative taxonomy, to determine the taxonomic status of C. neriifolia and C. ilicifolia. This is the first study to systematically explore the taxonomic position of these two plants on the basis of Morphology, Anatomy, Palynology and Molecular Systematics.</p><p><strong>Results: </strong>Extensive specimen reviews and field surveys showed that many differences exist in C. neriifolia and C. ilicifolia, such as the number of trunk (heavily debarked vs. slightly peeling), leaf type (smooth thin leathery, shiny vs. smooth leathery, obscure or slightly shiny), leaf margin (entire vs. serrate), flower type (subsessile vs. sessile), number of styles (3-4 vs. 3), and sepal (ovate vs. round). Moreover, C. neriifolia has a more distinctive faint yellow flower color, and trunk molting was more severe in C. neriifolia than that in C. ilicifolia. In addition, micromorphological analysis of the leaf epidermis showed that the two species differed in the anticlinal wall, stomatal apparatus, and stomatal cluster, and pollen morphology analyses based on pollen size, germination furrow, and polar and equatorial axes showed that they are both distinct from each other. The results of the phylogenetic tree constructed based on the whole chloroplast genome, protein-coding genes, and ITS2 showed that both C. ilicifolia and C. neriifolia were clustered in different branches and gained high support.</p><p><strong>Conclusions: </strong>The results combine morphology, anatomy, palynology, and molecular systematics to treat both C. neriifolia and C. ilicifolia as separate species in the sect. Tuberculata, and the species names continue to be used as they were previously. In conclusion, clarifying the taxonomic status of C. neriifolia and C. ilicifolia deepens our understanding of the systematic classification of sect. Tuberculata.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11266325/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}