Ecological Genetics and Genomics最新文献

Genetic variation and lack of hybridization in five cichlid fish species in the Malagarasi River basin, Tanzania

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-04-19 DOI: 10.1016/j.egg.2025.100355

Alex Nehemia

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 Haplochromis pharyngalis. The lowest levels of nucleotide and haplotype diversity were recorded from Oreochromis leucostictus. The Analysis of Molecular Variance (AMOVA) resulted into statistically significant genetic differences (Φst: 0.96, P < 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.

{"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 < 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

Q3 Agricultural and Biological Sciences

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

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.

{"title":"Interrelationships among agro-morphological characteristics of Iranian safflower germplasm under cold and rain-fed conditions","authors":"Hossein Zeinalzadeh-Tabrizi , Saba Kokab , Hamid Hatami Maleki , 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

Q3 Agricultural and Biological Sciences

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

The Kole 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 Kole 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 Kole wetland conditions.

{"title":"Metagenomic analysis of rice rhizosphere in a uniquely fertile Kole wetland reveals the microbiome contributing to enhanced nutrient availability","authors":"Vivek Krishnankutty, Keerthy Vijayan, Ravisankar Valsalan, Mariya C. Francis, Sherin Mary Johnson, 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

Genomic blueprint of four soil bacteria with insights into their potential adaptation mechanisms in tropical savanna

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-04-16 DOI: 10.1016/j.egg.2025.100351

Osiel Silva Gonçalves , Mateus Ferreira Santana

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 Bosea, Nocardioides, Cupriavidus, and Enterobacter roggenkampii. 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.

{"title":"Genomic blueprint of four soil bacteria with insights into their potential adaptation mechanisms in tropical savanna","authors":"Osiel Silva Gonçalves , 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

Q3 Agricultural and Biological Sciences

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

Finger millet (Eleusine coracana), 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 & 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.

{"title":"Genetic diversity analysis in finger millet through RAPD and ISSR marker","authors":"Kirankumar P. Suthar , Diwakar Singh , J.V. Patel , Rehana Niyaria , Komal G. Lakhani , 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 & 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

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-04-14 DOI: 10.1016/j.egg.2025.100349

Hossein Zeinalzadeh-Tabrizi , Leyla Nazari

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.

{"title":"Machine learning-based transcriptome mining to discover key genes for density stress in sweet corn","authors":"Hossein Zeinalzadeh-Tabrizi , 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

Phylogenetic systematics of genus Holigarna Buch.-Ham. ex Roxb. An endemic tree plant species of Western Ghats

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-04-07 DOI: 10.1016/j.egg.2025.100348

Kumbar Mudakappa Manjunath , Y.L. Krishnamurthy , K.S. Shreeharsha

The genus Holigarna Buch.-Ham. ex Roxb. (Family: Anacardiaceae) contributes significantly to the Western Ghats forest flora, with seven species, five indigenous to the area. The genus is classified as taxonomically challenging owing to its diverse and complex floral features. In this context, we took the molecular phylogenetics of the genus Holigarna as the main objective of this study. Molecular tools are becoming more widely accepted as a useful tool in phylogenetic investigations of taxonomically challenging taxa. Molecular markers can depict the genetic link across plant groupings, and DNA-based molecular taxonomic techniques provide an accurate and quick way to differentiate specimens based on interspecies variance. The genetic profiles of five Holigarna species, Holigarna arnottiana Hook. f., Holigarna beddomei Hook. f., Holigarna ferruginea Marchand, Holigarna grahamii Wight, and Holigarna nigra Bourd. Phylogenetic results confirmed that the genus Holigarna is a monophyletic group with best-supporting bootstrap values and unresolved relationships and a polytomy within the group suggest rapid evolution or limited resolution from the current markers. The unresolved connections and polytomy within the group indicate either fast evolution or insufficient resolution from the existing markers. These results provide a foundation for further taxonomic and evolutionary research on Holigarna.

{"title":"Phylogenetic systematics of genus Holigarna Buch.-Ham. ex Roxb. An endemic tree plant species of Western Ghats","authors":"Kumbar Mudakappa Manjunath , Y.L. Krishnamurthy , K.S. Shreeharsha","doi":"10.1016/j.egg.2025.100348","DOIUrl":"10.1016/j.egg.2025.100348","url":null,"abstract":"<div><div>The genus <em>Holigarna</em> Buch.-Ham. ex Roxb. (Family: Anacardiaceae) contributes significantly to the Western Ghats forest flora, with seven species, five indigenous to the area. The genus is classified as taxonomically challenging owing to its diverse and complex floral features. In this context, we took the molecular phylogenetics of the genus <em>Holigarna</em> as the main objective of this study. Molecular tools are becoming more widely accepted as a useful tool in phylogenetic investigations of taxonomically challenging taxa. Molecular markers can depict the genetic link across plant groupings, and DNA-based molecular taxonomic techniques provide an accurate and quick way to differentiate specimens based on interspecies variance. The genetic profiles of five <em>Holigarna</em> species, <em>Holigarna arnottiana</em> Hook. f., <em>Holigarna beddomei</em> Hook. f., <em>Holigarna ferruginea</em> Marchand, <em>Holigarna grahamii</em> Wight, and <em>Holigarna nigra</em> Bourd. Phylogenetic results confirmed that the genus <em>Holigarna</em> is a monophyletic group with best-supporting bootstrap values and unresolved relationships and a polytomy within the group suggest rapid evolution or limited resolution from the current markers. The unresolved connections and polytomy within the group indicate either fast evolution or insufficient resolution from the existing markers. These results provide a foundation for further taxonomic and evolutionary research on <em>Holigarna</em>.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100348"},"PeriodicalIF":0.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143823320","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 among Ghanaian Okra (Abelmoschus esculentus L.) Germplasm using Morphological and Molecular markers

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-04-05 DOI: 10.1016/j.egg.2025.100347

Andrews Appiah , Richard Akromah , Alexander Wireko Kena , Benjamin Annor , Stephen Amoah , Emmanuel Yaw Owusu , Benjamin Karikari

Knowledge of genetic diversity among germplasm is a prerequisite in any crop improvement programme. The present study, therefore, aimed to determine the extent of genetic variability and relationship in Ghanaian okra genotypes using morphological and simple sequence repeats (SSR) markers. A total of 40 okra accessions were collected from all agro-ecological zones of Ghana and evaluated under optimal conditions in Ghana in 2020 using alpha lattice design. Analysis of variance revealed significant (p < 0.01) variations among the genotypes for all traits studied, indicating high variability among the genotypes studied which could be exploited to develop improved okra varieties. Genotypes: Avata, Ayigbe, Baabo, Sunyani aba and Ponana ponana were identified as the superior genotypes which could further be tested and promoted among farmers. The 40 okra accessions were classified into four (4) major clusters based on the morphological traits as well as the SSR markers. The most discriminating traits identified by the principal component analysis were days to first flowering, days to first fruiting, first flowering node, fruit width, fruit yield, plant height at first flowering, leaf breadth, leaf length and the number of internodes. The findings from this study provide valuable information for okra conservation, breeding, and utilization.

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引用次数: 0

Molecular and agro-morphological evaluations of interspecific hybridisation in two wild yams (Dioscorea spp.) for genetic improvement

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-03-26 DOI: 10.1016/j.egg.2025.100345

F.P. Oyedoyin , O.J. Olawuyi , P.A. Agre , Asrat Asfaw

Yam (Dioscorea spp.) is an essential food crop particularly in Sub-Saharan Africa. As breeders struggle to meet the rising demand for high-yielding and quality yam, hybridising underutilised wild species presents a promising solution. This study therefore investigated the potentials of hybridising two wild yam species, Dioscorea abyssinica and Dioscorea praehensilis known for their resilience and genetic potential as ancestors of the cultivated West African yam, Dioscorea rotundata, using hand-pollination method. Hybridity was assessed with eight sub-sets of Kompetitive allele-specific markers, and the progenies were evaluated morphologically using standard descriptors. Markers detected heterozygosity in 65 (92.9 %) of 70 progenies, confirming successful hybridisation. Significant (p < 0.05) variation was observed in growth and yield traits, with TDabp2101048, TDabp2101010, and TDabp2101068 excelling in stem length (348.91 cm), internode length (23.36 cm), and vigour (5.85) respectively. The highest tuber length (42.91 cm), tuber weight (1.14 kg) and number of tubers (4) were produced by TDabp2101052, TDabp2101046 and TDabp2101054, respectively. Progenies showed comparable traits to D. rotundata, indicating high genetic compatibility. These findings suggest putative potential for selecting superior genotypes, improving yam breeding programs through genetic diversity, enhancing crop resilience and productivity.

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引用次数: 0

Agronomic evaluation and genetic variability studies among fenugreek (trigonella foenum-graecum L.) genotypes at Kulumsa, southeastern Ethiopia

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-03-26 DOI: 10.1016/j.egg.2025.100343

Gizaw Wegayehu Tilahun , Awoke Ali Zeleke , Demis Fikre Limeneh

To develop fenugreek varieties through selection or hybridization, evidence of accession variability is compulsory. This study aimed to evaluate the agronomic performance and get insights on the variability of 28 fenugreek genotypes based on 15 morpho-agronomic traits in Kulumsa, during the 2021 and 2022 cropping years with 5 × 5 alpha lattice design in three replications. The analysis of variance revealed the presence of highly significant (P < 0.01) differences between genotypes for all traits. The top three accessions, namely fg-53072 (2243.70 kg ha-1), fg-201609 (2180.41 kg ha⁻¹), and fg-201604 (2049.95 kg ha⁻¹), were the high yielders compared to standard checks in a range of 666.69–2395.76 kg ha⁻¹ seed yield. The majority of traits demonstrated high heritability (≥60) coupled with high genetic advance as the percentage of the mean (>20) and genotypic coefficient of variation (>20). The study found strong positive associations between seed yield and yield-related traits. The first three main components accounted for 83.1 % of the variance in the genotype and five variables contributed the most. The result suggests that to boost the seed yield, selection and improvement could be focused on those traits to enhance progenies' performance. Furthermore, the seed yield of fenugreek could be enhanced by selecting the associated traits with seed yield. The findings have practical implications for breeders and farmers.

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引用次数: 0