Ecological Genetics and Genomics最新文献

{"title":"Phytochemical profile and allelopathic activity of eight Eucalyptus species on the performance of initial growth stage of four local species in the southern Tunisia","authors":"","doi":"10.1016/j.egg.2024.100291","DOIUrl":"10.1016/j.egg.2024.100291","url":null,"abstract":"<div><p>We aimed thought this survey 1) to investigate and compare the phytotoxicity features of eight <em>Eucalyptus</em> species frequently planted in southern Tunisia (<em>Eucalyptus camaldulensis</em> Dehn<em>., Eucalyptus gomphocephala</em> DC., <em>Eucalyptus torquata</em> Luehm., <em>Eucalyptus microtheca</em> F.Muell., <em>Eucalyptus occidentalis</em> Endl., <em>Eucalyptus diversifolia</em> Bonpl.<em>, Eucalyptus sargentii</em> Maiden., and <em>Eucalyptus torwood</em>) on seed germination and radicle growth of <em>Medicago sativa</em> L., <em>Corchorus olitorius</em> L., <em>Cenchrus ciliaris</em> L., <em>Peganum harmala</em> L., and 2) to classify those species according to their allelopathic efficiency. The laboratory experiment was conducted using aqueous extracts made from dried and ground plant leaves to obtain concentrations of 5 % and 10 %. These were prepared alongside control treatments for comparison. Afterward, methanol extracts were utilized in the chemical composition identification procedure via HPLC-DAD-ESI-MS. Different responses were obtained for the species studied for germination and extraction. Results highlighted that <em>C. ciliaris</em> and <em>P. harmala</em> were the most susceptible to eucalypt extracts, while, <em>M. sativa</em> and <em>C. olitorius</em> were more resistant. Statistically, lower concentrations were less effective, but higher ones had noticeable inhibitory effects on seedling growth parameters. We assumed that <em>E. occidentalis</em>, <em>E. gomphocephala</em>, <em>E. torquata</em> and <em>E. camaldulensis</em> were recognized as the most noxious species, <em>E. sargentii</em> and <em>E. microtheca</em> produced moderate effects, while <em>E. torwood</em> and <em>E. diversifolia</em> were regarded as benign species. Phytochemicals especially ellagitannins and flavonols derivatives were the major compounds identified accounted for 21–78 % and 8–59 %, but hydroxycinnamic acids derivatives, gallic acid derivatives, total flavonols content and non-phenolic acids were acknowledged as the major causes for the observed outcomes.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142117563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotype and environmental interactions determine the root digging time and essential oil production in vetiver (Chrysopogon zizanioides (L.) Roberty)","authors":"","doi":"10.1016/j.egg.2024.100290","DOIUrl":"10.1016/j.egg.2024.100290","url":null,"abstract":"<div><p>Thirty different vetiver genotypes were grown for evaluation in the experiments at CSIR- Central Institute for Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, U.P. 226015, India, to assess the impact of genotype × environment interactions (GEI) on essential oil yield and chemical composition in vetiver lines grown in north India, as well as identifying appropriate genotypes and representative root digging times throughout the year for essential oil production. The interplay of genotype and environment is a significant constraint in crop development. The additive main effects and multiplicative interaction (AMMI) and the analysis of variance (ANOVA) revealed significant effects for genotype (G), environment (E), and genotype × environment (GE) (p &lt; 0.01). The primary root transverse section confirmed the changes in cortical sclerenchyma thickness and variety observed in the dug-out roots from different vetiver genotypes after six and twelve months. The quantity and number of sclerenchyma rows in the peripheral cortical region vary throughout vetiver genotypes. Following root digging, one component (Khusol content) had 40 %, while Khusilal content had 20 % for genotype VTR-23. However, after twelve months, Khusol content had 19 %, whereas Khusilal content had 41 %. The shift in essential oil makeup was apparent. The level of essential oil did not alter considerably. Based on the GGE biplot analysis, VTR-1, 11, and 14 were identified as the most stable genotypes with high essential yields; therefore, it is recommended to use these genotypes in India's enormous agriculture.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142087917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variability and characters association for lodging, yield and related traits of field pea (Pisum sativum L.) genotypes in contrasting plant types","authors":"","doi":"10.1016/j.egg.2024.100289","DOIUrl":"10.1016/j.egg.2024.100289","url":null,"abstract":"<div><p>A total of 49 field pea genotypes, belonging to two different plant types were evaluated for 13 traits at Bekoji and Kofele in 2020 to assess the extent of genetic variability and association among morpho-agronomic traits. Analysis of variance revealed a highly significant difference between plant types and among the tested genotypes within each plant type for most of traits. Relatively, genotypes within prostrate type are more variable in thousand seed weight and genotypes within semi-leaf less type are more diverse in plant height, ascochyta blight and lodging severity score. Moderate to high genotypic coefficient of variation (GCV), heritability in broad sense (H2b) and genetic advance as a percent of mean (GAM) combination were recorded from seed yield, thousand seed weight, plant height and number of seeds per plant in both plant types. The path and correlation analysis showed that lodging score had significant negative association and negative direct effect on seed yield in prostrate type. Number of seeds per plant and plant height had both positive direct effects and significant positive association with seed yield consistently in both plant types. Thousand seed weight also showed both positive direct effects and significant positive association with seed yield in semi-leaf less type. Therefore, great emphasis should be given for those traits while making selection of field pea genotypes for high seed yield. However, for the improvement of yield and lodging simultaneously there should be balance between yield and lodging related traits especially in prostrate type. The principal component analysis (PCA) indicated that the first five principal component axes accounted for 71.67 % of the total variability. Generally, the results suggested the possibility of further improvement of seed yield and associated desired traits through selection in both plant types.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ingestion of microplastics affects the diversity of the gut microbiome and testicular development in Japanese quail","authors":"","doi":"10.1016/j.egg.2024.100288","DOIUrl":"10.1016/j.egg.2024.100288","url":null,"abstract":"<div><p>Five Japanese quail <em>Coturnix japonica</em> were administered with powdered microplastics (MPs, test group) while five quail did not receive MPs (control group) to investigate the effect of MPs on gut microbiota. In the MP administration, a powdered form of commercially available polystyrene was mixed with sterile water and orally delivered to the quail's proventriculus using a syringe. After the experiments, all 10 quail were euthanized and dissected to measure the weight of each organ and collect samples. A next-generation sequencing analysis based on the 16S rRNA gene was conducted using DNA extracted from pellets of gut fluid samples to investigate gut microbe diversity. A canonical correspondence analysis using the next-generation sequencing data was conducted to examine the correlation between visceral weight changes induced by MP exposure and alterations in the gut microbiome diversity. The dominant bacterial families showed no significant correlation with gut and testis weights in the test group. However, a correlation was inferred between distinct dominant bacterial families and gut and testis weights in the control group, which differed from those observed in the experimental group. Although the underlying cause of gut microbiota changes due to MP ingestion remains to be elucidated, MP ingestion was demonstrated to have some effect on quail gut microbiota and testis.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405985424000727/pdfft?md5=ef8932586e4f71076afe5d9b7c98422d&pid=1-s2.0-S2405985424000727-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142077447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic characterization of white onion genotypes (Allium cepa L.) using ISSR markers","authors":"","doi":"10.1016/j.egg.2024.100287","DOIUrl":"10.1016/j.egg.2024.100287","url":null,"abstract":"<div><p>Understanding the genetic characteristics is crucial for preserving and developing Moroccan's white onion genotypes, with increased yield and quality as well as improved tolerance to biotic and abiotic stresses. In the present paper, inter simple sequence repeat (ISSR) markers were used to assess the genetic diversity and characteristics of white onion genotypes (<em>Allium cepa</em> L.) of Morocco. Based on the ISSR markers bands, 28 white onion genotypes were divided into four distinguished subgroups, with a genetic similarity value of 0.46 based on Jaccard index. Molecular markers analysis revealed that all ISSR markers were 100 % polymorphic with the white onions genotypes. Concerning markers performance, polymorphic information content (PIC) ranges from 0.051 to 0.39 with a mean of 0.301; however, the effective multiplex ratio (EMR) and marker index (MI) vary between 3–17 and 0.35–5.04, respectively. Based on resolving power (RP), it appears that the marker UBC825 has an efficient discriminatory power with an RP = 15.67. In contrast, the lowest RP value was detected with the marker UBC815 (RP = 1.58). Based on their high performance, markers UBC825, UBC835, UBC826, UBC840, and UBC811 ISSR seem to be specific and efficient for the identification of Moroccan white onion genotypes. Thus, given the genetic diversity shown by ISSR markers, the abundant resources of white onion genotypes in Morocco could be exploited in more valuable ways.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142040840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular evidence of novel Begomoviruses and associated Betasatellite complexes linked to Papaya Leaf Curl Disease in Indian Provinces","authors":"","doi":"10.1016/j.egg.2024.100286","DOIUrl":"10.1016/j.egg.2024.100286","url":null,"abstract":"<div><p>Papaya leaf curl disease (PLCD) is caused by distinct begomoviruses affecting papaya globally. This study aims to identify and dissect the genetic complexities of begomoviruses-betasatellites associated with PLCD. Surveys in various Indian provinces to collect symptomatic papaya leaf samples. Molecular characterization of 15 DNA-A positives isolates revealed that PSB 8 and PSB 14 from Lucknow shared 89.69 % and 87.25 % nucleotide sequence identity with other reported begomoviruses and 85.36 % with each other. Based on ICTV's species demarcation threshold, these isolates are proposed as novel begomoviruses, named papaya leaf curl Lucknow virus-1 (PaLCLV-1) and papaya leaf curl Lucknow virus-2 (PaLCLV-2). This study also reports a novel strain (PSB 63) of duranta leaf curl virus (DLCV) on papaya, with a 93.48 % sequence identity with known DLCV. The samples did not amplify for DNA-B but did for betasatellites. Nine of the 15 DNA-A positive samples were associated with betasatellites, revealing a novel betasatellite (PSBB 34) from Gujarat, sharing 88.46 % similarity with ludwigia leaf distortion betasatellite (LuLDB), named papaya leaf curl Lucknow betasatellite (PaLCLB). Another new strain, tomato leaf curl betasatellite (ToLCLB), shared 91.96 % identity with other betasatellites. These begomoviruses are monopartite and likely originated in the Old World. This study is the first to show an association between LuLDB and PaLCV (PSB 34). Recombination analysis revealed that major viral genome regions were obtained from previously reported begomoviruses. The study identified eight papaya-infecting begomoviruses and seven associated betasatellites as prominent in the sampled regions.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142011238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatic characterization and functional evaluation of Ph-Def: A novel marine antimicrobial peptide from Panulirus homarus","authors":"","doi":"10.1016/j.egg.2024.100285","DOIUrl":"10.1016/j.egg.2024.100285","url":null,"abstract":"<div><p>The present study describes the discovery of Ph-Def, the first marine antimicrobial peptide (AMP) isolated from <em>Panulirus homarus</em>, the Indian spiny lobster. Ph-Def is a 65-amino acid β-defensin (including signal peptide) with potential antimicrobial properties. Phylogenetic analysis revealed its close relationship to β-defensins in other <em>Panulirus</em> lobsters and suggested an evolutionary connection with vertebrate β-defensins. <em>In silico</em> analysis identified hot spot areas and a hydrophobic face, supporting its potential as a marine AMP with antimicrobial activity. A predicted bactericidal stretch spanning from Cys⁵³–Tyr⁶⁴ was notably identified, covering the mature peptide. Ph-Def demonstrated similarity to β-defensins in other lobster species and fish β-defensins, suggesting a shared functional role against microorganisms. Predicted biological processes associated with Ph-Def include metabolic regulation, cellular biosynthesis, transport, cation transmembrane transport, and immune system processes. These findings underscore the potential of Ph-Def as a marine AMP and expand our understanding of immune responses and defense mechanisms in <em>P. homarus</em>.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141993098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic polymorphism amongst moth bean (Vigna aconitifolia (Jacq.) Marechal) accessions evaluated using various molecular markers","authors":"","doi":"10.1016/j.egg.2024.100284","DOIUrl":"10.1016/j.egg.2024.100284","url":null,"abstract":"<div><p>This study presents genetic level diversity of 50 moth bean legume accessions (<em>Vigna aconotifolia</em> (Jacq.) Marechal). Despite seeds being a rich source of soluble nutritional proteins, it still remains an underutilized crop commercially. To assess the molecular diversity amongst accessions, RAPD, ISSR, DAMD, SCoT and SSR were employed as PCR markers. Of the total 5064 polymorphic bands shown with these makers, DAMD1 and SCoT1 presented higher levels of polymorphism with 407 and 262 polymorphic bands respectively. These genotypes revealed logical similarity and variation under UPGMA clustering. The PCA analysis of IC-258167, IC-415167, and IC-402286 present three highest eigen values, hence seem fit to be considered as parents for moth bean breeding programme. The polymorphic bands as produced by SCoT and DAMD primers can serve unique genotypic identifiers. This study seems to present a maiden report in labelling genetic marker based polymorphism amongst the accessions of moth bean.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142011237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic structure and gene flow among populations of willow (Salix species)","authors":"","doi":"10.1016/j.egg.2024.100283","DOIUrl":"10.1016/j.egg.2024.100283","url":null,"abstract":"<div><p>The newly developed <em>Salix</em> hybrids were assessed for genetic diversity using ISSR (Inter Simple Sequence Repeats) molecular markers. The results revealed 88.08 polymorphism, 0.53 polymorphism information content, 4.70 effective multiplex ratio, 2.54 marker index, and 7.18 resolving power from the amplified primers. Clones of the <em>Salix matsudana</em> (MAT) population recorded a maximum mean number of effective alleles (1.42), Shannon information index (0.38), gene diversity (0.25), and percentage of polymorphic loci (82.24 %). The AMOVA (Analysis of molecular variance) results revealed a moderate genetic divergence with a genetic variation of 88 per cent within populations and 12 per cent among the populations. The highest value of total diversity (0.28) and gene diversity (0.24) was recorded between <em>S. matsudana</em> (MAT) and <em>S. tetrasperma</em> (TETRA) populations, while there was more gene flow between <em>S. matsudana</em> (MAT) and <em>S. tetrasperma</em> (TETRA) populations (5.86). The clustering pattern obtained through STRUCTURE software showed two main gene pools and a mixture of 6–7 gene pools to confirm the hybrids based on ISSR marker data. <em>S. matsudana</em> and <em>S. tetrasperma</em> clones showed the highest gene diversity due to their proximity from their original locations, resulting in the least amount of gene exchange among populations. Molecular characterization using ISSR markers was extremely useful for studying the genetic diversity among the willow hybrids and high genetic variability should be utilized for breeding purposes in the future.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141952896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A review of the mangrove ecosystem in Indonesia: Biodiversity, conservation, and challenges in sustainable management","authors":"","doi":"10.1016/j.egg.2024.100282","DOIUrl":"10.1016/j.egg.2024.100282","url":null,"abstract":"<div><p>Mangrove ecosystem in Indonesia, representing almost 1/5 of the world's mangroves, plays a pivotal role in biodiversity conservation, coastal protection, and the provision of ecosystem services. The diverse geographic landscapes of the country contribute to one of the largest mangrove forests in the world. However, the mangrove ecosystem in the country was damaged and reduced greatly in the past decades due to anthropogenic activities. To take a further step in the conservation of the ecosystem, it is important to understand the current status of the population distribution, species diversity, and conservation strategies. This article presents a comprehensive assessment of the status of Indonesia's mangrove ecosystems with a specific focus on biodiversity, ongoing conservation endeavors, and prevailing management practices. The principal objective of this review is to gain an in-depth understanding of the significance of these unique ecosystems and the challenges associated with sustaining their health.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141853809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}