Ecological Genetics and Genomics最新文献

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Advances in understanding the functional diversity of noncoding RNAs in Plants: Insights from recent studies 植物非编码rna功能多样性的研究进展
Ecological Genetics and Genomics Pub Date : 2025-04-30 DOI: 10.1016/j.egg.2025.100360
Suruchi Gupta
{"title":"Advances in understanding the functional diversity of noncoding RNAs in Plants: Insights from recent studies","authors":"Suruchi Gupta","doi":"10.1016/j.egg.2025.100360","DOIUrl":"10.1016/j.egg.2025.100360","url":null,"abstract":"<div><div>Over the past decade, accumulating evidence has shed light on the pivotal roles played by diverse classes of noncoding RNAs, including miRNAs, siRNAs, piRNAs, lncRNAs, and circRNAs, in regulating the plant growth and development. In-depth studies have revealed the regulatory functions of miRNAs and siRNAs in post-transcriptional gene regulation, highlighting their involvement in various developmental processes, stress responses, and hormone signaling pathways. Additionally, the emerging field of piRNAs has unveiled their crucial contributions to transposon silencing, genome stability maintenance, and reproductive development. The versatility of lncRNAs as regulators in chromatin remodeling, splicing regulation, and epigenetic modifications has been elucidated, alongside the functional significance of circular RNAs in alternative splicing regulation and gene expression control. Overall, this review article presents a significant advancement in our understanding of the intricate regulatory networks governing plant biology, with the potential to drive innovations in plant biotechnology, sustainable agriculture, and global food security.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100360"},"PeriodicalIF":0.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902029","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}
引用次数: 0
Characters associations and principal component analysis for quantitative traits of sesame (Sesamum indicum L.) genotypes from Ethiopia 埃塞俄比亚芝麻(Sesamum indicum L.)基因型性状关联及数量性状主成分分析
Ecological Genetics and Genomics Pub Date : 2025-04-27 DOI: 10.1016/j.egg.2025.100357
Bantayehu Bekele , Mebeaselassie Andargie , Tilahun Mekonnen , Dereje Beyene , Kassahun Tesfaye
{"title":"Characters associations and principal component analysis for quantitative traits of sesame (Sesamum indicum L.) genotypes from Ethiopia","authors":"Bantayehu Bekele ,&nbsp;Mebeaselassie Andargie ,&nbsp;Tilahun Mekonnen ,&nbsp;Dereje Beyene ,&nbsp;Kassahun Tesfaye","doi":"10.1016/j.egg.2025.100357","DOIUrl":"10.1016/j.egg.2025.100357","url":null,"abstract":"<div><div>To identify sesame genotypes with superior yield performance and related agronomic traits, a field experiment was conducted using a simple lattice design with two replications comprising of 196 accessions and released varieties. Principal component analysis (PCA) indicated that among the twelve extracted components, the first three PC1 (eigenvalue = 3.97), PC2 (eigenvalue = 1.88), and PC3 (eigenvalue = 1.03) accounted for the majority of the variability associated with yield and yield-contributing characteristics. The three principal components PC-I through PC-III with eigenvalues greater than one account for 57 % of total variance among 196 genotypes. Yield per plot showed significant and positive correlation with plant height (0.63), pod per plant (0.43), days to fifty percent flowering (0.27), and primary branch (0.39). In phenotypic path analysis diameter plant height (0.547), branch per plant (0.085), days to fifty percent flowerung (0.019), and pod per plant (0.112) showed positive direct effect on yield per plot. Traits viz., plant height, pod per plant, and height from ground to first branch exhibited a positive direct effect on yield per plant. This comprehensive study provides key insights into the intricate relationships among sesame traits, highlighting how genotype selection using a multi-trait index can effectively guide future breeding and cultivation strategies.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100357"},"PeriodicalIF":0.0,"publicationDate":"2025-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143882134","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}
引用次数: 0
Recovery of DNA signatures from historical herbarium specimens using chloroplast and nuclear barcodes 利用叶绿体和细胞核条形码从历史植物标本中恢复DNA特征
Ecological Genetics and Genomics Pub Date : 2025-04-24 DOI: 10.1016/j.egg.2025.100356
Stalin Nithaniyal, Benniamin Asir, Kaushik Sarkar
{"title":"Recovery of DNA signatures from historical herbarium specimens using chloroplast and nuclear barcodes","authors":"Stalin Nithaniyal,&nbsp;Benniamin Asir,&nbsp;Kaushik Sarkar","doi":"10.1016/j.egg.2025.100356","DOIUrl":"10.1016/j.egg.2025.100356","url":null,"abstract":"<div><div>Expert-verified curated collections of herbarium specimens are invaluable assets of plant biodiversity. Several historical specimens of rare and endangered taxa in herbaria face difficulty in identifying the morphology. The emerging DNA-based technology recovers genetic data from preserved herbarium are efficiently used for plant identification complementing taxonomy. Therefore, the current study utilized DNA barcodes from chloroplast (<em>rbcL</em>, <em>trn</em>H-<em>psb</em>A) and nuclear (ITS2) genomes to identify chronologically preserved specimens of endemic and threatened taxa. Fifteen herbarium accessions belonged to the 19th, 20th, and 21st centuries representing eight taxa studied as test samples by comparing with three control samples. Extraction of DNA from 16 to 140-year-old herbarium showed positive results using our standardised isolation protocol. The PCR amplification was successful using <em>rbcL</em> DNA barcode in all the samples but the <em>trn</em>H-<em>psb</em>A and ITS2 markers amplified only two species. The DNA sequence recovery from ∼100 old specimens yielded short fragments ranging between 100 bp and 150 bp. The DNA sequence was successfully recovered from the sixty and twenty-year-old herbarium specimens of <em>Ischaemum santapaui</em> and <em>Lepidagathis lutea,</em> respectively. The presence of mononucleotide repeats affected the sequence recoverability in <em>trn</em>H-<em>psb</em>A and ITS2 markers. Our results indicated that the increased rate of DNA degradation, fragmentation, and mixing of microbial DNA in the specimen during long-term storage significantly affected the PCR amplification in preserved herbarium specimens. This study highlighted the application of DNA barcoding in unmasking the trove of genetic diversity in the present and historical herbarium collections.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100356"},"PeriodicalIF":0.0,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891787","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}
引用次数: 0
Genetic variation and lack of hybridization in five cichlid fish species in the Malagarasi River basin, Tanzania 坦桑尼亚马拉加拉西河流域5种慈鲷的遗传变异和杂交缺失
Ecological Genetics and Genomics Pub Date : 2025-04-19 DOI: 10.1016/j.egg.2025.100355
Alex Nehemia
{"title":"Genetic variation and lack of hybridization in five cichlid fish species in the Malagarasi River basin, Tanzania","authors":"Alex Nehemia","doi":"10.1016/j.egg.2025.100355","DOIUrl":"10.1016/j.egg.2025.100355","url":null,"abstract":"<div><div>Among the most widely cultured groups of freshwater fish species are tilapiine cichlids. This has contributed to introduction of cichlid fish species in area where they were not native. Consequently, has contributed to negative ecological effects on local species and their habitats through competition, habitat alteration and loss of unique population genetic structures due to hybridization. This research study aimed to assess the genetic status of five cichlid fish species red listed by the International Union for Conservation of Nature (IUCN) as least concerned species. A mitochondrial Cytochrome Oxidase Subunit I (COI) gene fragment from 112 individuals collected from three sampling sites were used to determine the present genetic diversity of the cichlid species inhabit the Malagarasi River system which discharge water into Lake Tanganyika. The highest nucleotide diversity (0.02 ± 0.01) and haplotype diversity (0.94 ± 0.04) were recorded from <em>Haplochromis pharyngalis</em>. The lowest levels of nucleotide and haplotype diversity were recorded from <em>Oreochromis leucostictus</em>. The Analysis of Molecular Variance (AMOVA) resulted into statistically significant genetic differences (Φst: 0.96, P &lt; 0.001) among the cichlid species studied. The minimum spanning haplotype network and maximum-likelihood phylogenetic analyses support the AMOVA findings as no species is sharing any haplotype with other species. The values of neutrality tests suggested that the studied cichlid fish species are stable and not expanding. These findings highlight the necessity of conservation interventions in the area especially for the species which displayed low nucleotide and haplotype diversity.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100355"},"PeriodicalIF":0.0,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143854982","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}
引用次数: 0
Interrelationships among agro-morphological characteristics of Iranian safflower germplasm under cold and rain-fed conditions 寒、雨养条件下伊朗红花种质形态特征的相互关系
Ecological Genetics and Genomics Pub Date : 2025-04-19 DOI: 10.1016/j.egg.2025.100354
Hossein Zeinalzadeh-Tabrizi , Saba Kokab , Hamid Hatami Maleki , Mozhgan Farzamisepehr
{"title":"Interrelationships among agro-morphological characteristics of Iranian safflower germplasm under cold and rain-fed conditions","authors":"Hossein Zeinalzadeh-Tabrizi ,&nbsp;Saba Kokab ,&nbsp;Hamid Hatami Maleki ,&nbsp;Mozhgan Farzamisepehr","doi":"10.1016/j.egg.2025.100354","DOIUrl":"10.1016/j.egg.2025.100354","url":null,"abstract":"<div><div>Safflower is a promising oilseed crop for semi-arid regions like Iran, however, conventional yield analysis frequently encounters difficulties due to interrelated variables. This study utilized sequential path analysis to examine these relationships across 31 safflower genotypes under cold, rain-fed conditions in Iran during 2019–2020. Conducted at the Dryland Research Station of Maragheh, Iran using a randomized complete block design (RCBD) with three replications, the research identified significant correlations between safflower seed yield and key traits: plant height (0.65∗∗), the number of seeds per head (0.63∗∗), and capitula number (0.51∗∗). Biological yield (0.927∗∗) and harvest index (0.222∗∗) directly positively influenced seed yield, while seed weight had a negative direct effect (−0.084∗∗). Taller plants enhanced biomass production (0.718∗∗), though heavier seeds negatively affected biological yield (−0.316∗∗). Lower branching height correlated with a higher harvest index (−0.477∗), suggesting resource allocation toward seed production. Kernel weight was strongly driven by husk weight (0.846∗∗), emphasizing its role in determining seed weight. These findings highlight how different factors work together to affect crop yield suggest that optimizing husk weight could improve seed yield. The study emphasized that biologically nonsensical pathways, such as seed weight indirectly affecting biological yield via plant height, were excluded to ensure the model's validity. Sequential path analysis proved effective in unraveling these complex interactions, offering insights to enhance safflower productivity sustainably in arid and semi-arid regions, thereby supporting global food security and agricultural resilience.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100354"},"PeriodicalIF":0.0,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143850047","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}
引用次数: 0
Metagenomic analysis of rice rhizosphere in a uniquely fertile Kole wetland reveals the microbiome contributing to enhanced nutrient availability 对独特肥沃的科勒湿地水稻根瘤菌群进行元基因组分析,揭示微生物群对提高养分供应的贡献
Ecological Genetics and Genomics Pub Date : 2025-04-18 DOI: 10.1016/j.egg.2025.100353
Vivek Krishnankutty, Keerthy Vijayan, Ravisankar Valsalan, Mariya C. Francis, Sherin Mary Johnson, Deepu Mathew
{"title":"Metagenomic analysis of rice rhizosphere in a uniquely fertile Kole wetland reveals the microbiome contributing to enhanced nutrient availability","authors":"Vivek Krishnankutty,&nbsp;Keerthy Vijayan,&nbsp;Ravisankar Valsalan,&nbsp;Mariya C. Francis,&nbsp;Sherin Mary Johnson,&nbsp;Deepu Mathew","doi":"10.1016/j.egg.2025.100353","DOIUrl":"10.1016/j.egg.2025.100353","url":null,"abstract":"<div><div>The <em>Kole</em> wetlands (Kerala state, India) have deeply inundated, clayey and acidic soils rich in humic acids, tannins and mineral ions. High soil fertility coupled with the presence of microflora contributing to the fixation, solubilisation and mobilization of different nutrients is understood to contribute to high rice yields in these fields. However, the rhizosphere microflora of <em>Kole</em> land rice is yet to be profiled. Metagenomic DNA isolated through a manual Modified Improved method was sequenced on Illumina MiSeq platform, targeting the V3-V4 hypervariable region of 16 S rRNA gene. The results have shown a diverse microbial community dominated by bacteria and archaea. Taxonomic annotation highlighted major bacterial phyla Chloroflexota, Acidobacteriota and Pseudomonadota, and archaeal phyla Thermoproteota, Thermoplasmatota, and Halobacteriota. Alpha diversity indices revealed exceptional species richness, yet dominated by a few key species. The analysis has revealed the presence of bacterial and archaeal genera, the members of which are reported to have multifaceted ecological roles including plant growth promotion, nitrogen fixation, carbon-, nitrogen- and phosphorus-cycling, sulphur solubilisation and iron reduction. Bacterial genera accommodating the members with biodegradation, bioremediation and wastewater treatment capabilities, along with methanotrophs and archaeal methanogens were also found. Additionally, microbial phyla including the members having biocontrol, stress adoption, anti-microbial and herbicide degradation potential were identified. This paper provides insights on the microbial diversity and activities contributing to enhanced nutrient availability to rice plants under <em>Kole</em> wetland conditions.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100353"},"PeriodicalIF":0.0,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851454","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}
引用次数: 0
Economic importance of wattle rust (Uromycladium acaciae) disease on Acacia mearnsii in Fagita Lekoma, North-Western highlands of Ethiopia. 埃塞俄比亚西北高地Fagita Lekoma地区金合欢锈病的经济意义。
Ecological Genetics and Genomics Pub Date : 2025-04-17 DOI: 10.1016/j.egg.2025.100352
Abebaw Alene Yallew , Asmamaw Alemu Abtew
{"title":"Economic importance of wattle rust (Uromycladium acaciae) disease on Acacia mearnsii in Fagita Lekoma, North-Western highlands of Ethiopia.","authors":"Abebaw Alene Yallew ,&nbsp;Asmamaw Alemu Abtew","doi":"10.1016/j.egg.2025.100352","DOIUrl":"10.1016/j.egg.2025.100352","url":null,"abstract":"<div><div><em>Acacia mearnsii-</em>based rotational crop production system dominated North-Western highlands of Ethiopia, over the last two decades. The forest cover of Fagita Lekoma district, Ethiopia reached 68 % by 2021 because of <em>A. mearnsii</em> expansion. However, the production is now threatened by <em>Uromycladium acaciae</em> disease. This study examines the economic importance of <em>U. acaciae</em> disease in the district. Ten woodlots for two age classes were randomly selected with five replications. Two age classes were considered, as charcoal was produced from these ages, and only 4.5- and 5.5-year-old woodlots were found during data collection. To determine the growth performance and productivity of <em>A. mearnsii</em> post-disease occurrence, all trees (68–112) within 0.01-ha circular plots were recorded. Household surveys and field observation were led to comprehend inventory data. The economic loss was determined in terms of the growth loss of the trees. A T-test was used to determine the difference between the growth and productivity of <em>A. mearnsii</em> pre- and post-disease occurrence. Plantations of both age classes have significantly shown height, diameter, and volume losses following <em>Uromycladium acaciae</em> disease spread, particularly for those of younger counterparts. Financial losses were estimated at 7558.54 USD and 9514.35 USD per round for each age class. The district's overall forest cover and the area of <em>A. mearnsii</em> plantations have decreased by 3.9 % and 15.2 %, respectively, since 2020. The study urges management improvements and consideration of alternative non-target tree species to mitigate the disease's environmental impact.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100352"},"PeriodicalIF":0.0,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143882133","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}
引用次数: 0
Genomic blueprint of four soil bacteria with insights into their potential adaptation mechanisms in tropical savanna 热带稀树草原四种土壤细菌的基因组图谱及其潜在的适应机制
Ecological Genetics and Genomics Pub Date : 2025-04-16 DOI: 10.1016/j.egg.2025.100351
Osiel Silva Gonçalves , Mateus Ferreira Santana
{"title":"Genomic blueprint of four soil bacteria with insights into their potential adaptation mechanisms in tropical savanna","authors":"Osiel Silva Gonçalves ,&nbsp;Mateus Ferreira Santana","doi":"10.1016/j.egg.2025.100351","DOIUrl":"10.1016/j.egg.2025.100351","url":null,"abstract":"<div><div>Soil bacteria play a fundamental role in maintaining soil ecosystem functions, yet their genetic and metabolic adaptations to complex environments remain underexplored. To address this question, we analyzed the genomes of four soil bacteria isolated from tropical savanna soil, uncovering key insights into their metabolic potential and ecological roles. Our findings indicate that these bacteria represent novel species, including new strains of <em>Bosea</em>, <em>Nocardioides</em>, <em>Cupriavidus</em>, and <em>Enterobacter roggenkampii</em>. Their genomes encode essential genes and pathways related to central metabolism, particularly those involved in sugar and amino acid metabolism, highlighting their adaptive strategies for survival in soil environments. These strains also play important roles in biogeochemical cycles, including carbon, nitrogen, and sulfur cycling, as well as plant growth promotion. Furthermore, we identified 164 defense genes across 32 defense families, along with at least one antimicrobial resistance (AMR) gene in each strain. Additionally, twelve biosynthetic gene clusters were identified in three strains. The diverse genetic arsenal of these bacteria, including defense mechanisms, antimicrobial resistance genes, and secondary metabolite biosynthesis, may enhance their ability to survive and compete in the complex and dynamic soil environment.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100351"},"PeriodicalIF":0.0,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859451","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}
引用次数: 0
Genetic diversity analysis in finger millet through RAPD and ISSR marker 利用RAPD和ISSR标记分析手指粟的遗传多样性
Ecological Genetics and Genomics Pub Date : 2025-04-16 DOI: 10.1016/j.egg.2025.100350
Kirankumar P. Suthar , Diwakar Singh , J.V. Patel , Rehana Niyaria , Komal G. Lakhani , A.K. Pandey
{"title":"Genetic diversity analysis in finger millet through RAPD and ISSR marker","authors":"Kirankumar P. Suthar ,&nbsp;Diwakar Singh ,&nbsp;J.V. Patel ,&nbsp;Rehana Niyaria ,&nbsp;Komal G. Lakhani ,&nbsp;A.K. Pandey","doi":"10.1016/j.egg.2025.100350","DOIUrl":"10.1016/j.egg.2025.100350","url":null,"abstract":"<div><div>Finger millet (<em>Eleusine coracana</em>), also known as “Nutra-cereals” is a self-pollinated crop well versed in unfavorable environmental conditions. Despite its agronomic and nutritional importance, the genetic diversity within available germplasm resources remains underexplored. To bridge this gap, this study assessed genetic diversity among twenty-five finger millet genotypes using random amplified polymorphic deoxyribonucleic acid (RAPD) and inter-simple sequence repeat (ISSR) PCR genotyping methods. Analysis with fourteen RAPD primers produced 182 loci, 77 % of which were polymorphic, with a Polymorphic Information Content (PIC) of 0.29. ISSR analysis utilizing ten primers generated 83 bands with 74 % polymorphism. PopGene analysis revealed higher Nei's genetic diversity for ISSR than for RAPD. The RAPD primers exhibited a higher Shannon's Information Index than ISSR, indicating superior genotype differentiation. RAPD primers OPA-18, OPH-05, OPI-10, and ISSR primers UBC-841, UBC-857, and UBC-863 were determined to be the most effective in identifying genetic diversity in finger millet based on Polymorphic Information Content (PIC), Marker Index (MI), and Effective Multiplex Ratio (EMR) values. The Jaccard's similarity coefficient indicated moderate genetic diversity in finger millet based on combined RAPD and ISSR analysis, as the similarity coefficient values were arranged from 0.59 to 0.87. Combined RAPD and ISSR-based PCA and HCA grouped genotypes based on genetic relationships indicated through geographical origin, revealing the highest diversity between GN-4 and GPU-48 &amp; GPU-28. Analysis of Molecular Variance (AMOVA) indicated that genotypes from different ecological regions explained higher variation, whereas within regions showed less variation. The genetic relationship among genotypes could be explored for breeding and genetic improvement of finger millet. The comprehensive data presented here highlight the potential for utilizing these genotypes in finger millet improvement programs, enhancing productivity and resilience.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100350"},"PeriodicalIF":0.0,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143850046","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}
引用次数: 0
Machine learning-based transcriptome mining to discover key genes for density stress in sweet corn 基于机器学习的转录组挖掘发现甜玉米密度胁迫的关键基因
Ecological Genetics and Genomics Pub Date : 2025-04-14 DOI: 10.1016/j.egg.2025.100349
Hossein Zeinalzadeh-Tabrizi , Leyla Nazari
{"title":"Machine learning-based transcriptome mining to discover key genes for density stress in sweet corn","authors":"Hossein Zeinalzadeh-Tabrizi ,&nbsp;Leyla Nazari","doi":"10.1016/j.egg.2025.100349","DOIUrl":"10.1016/j.egg.2025.100349","url":null,"abstract":"<div><div>Sweet corn stands as a crucial staple in the food industry, offering consumers a nutritious and diverse option. However, understanding its response to density stress remains pivotal for enhancing its resilience and productivity. We employed Weighted Gene Co-expression Network Analysis (WGCNA), differential gene expression analysis, and Least Absolute Shrinkage and Selection Operator (LASSO) regression to dissect its molecular mechanisms. Four key genes (GRMZM2G129246, GRMZM2G143602, GRMZM2G162670, and GRMZM5G851026) and six hub genes (GRMZM2G162175, GRMZM2G155746, GRMZM2G092325, GRMZM2G328612, AC218148.2_FGT008, and GRMZM5G879127) were identified. Gene expression prediction under density stress was performed using various classifiers including Naïve Bayes, Simple Logistic, KStar, MultiClassClassifier, JRip, LMT, and RandomForest. Utilizing Simple Logistic and LMT models, we achieved an impressive overall accuracy of 100 % in predicting density stress response based on hub gene expression profiles. This highlights the robustness and reliability of our findings, paving the way for developing targeted interventions and breeding strategies to bolster sweet corn's resilience to density stress. Key genes include glycolate oxidase 1, essential for oxidative stress tolerance, and CK2 alpha subunit, involved in signaling pathways for abiotic stress adaptation. Other important proteins, like those from the phosphatidylinositolglycan synthase family, contribute to lipid metabolism and stress signaling. Additionally, uncharacterized genes, LOC103635295 and LOC100274670, are highlighted for their potential roles in stress regulation. The study emphasizes the need for continued research on these genes to enhance crop resilience and productivity.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100349"},"PeriodicalIF":0.0,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143829482","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}
引用次数: 0
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