The Nemacheilidae family of cypriniform fishes comprises more than 700 species inhabiting the rivers and streams throughout Eurasia. This family is considered one of the most taxonomically ambiguous, and recent research has shed light on its complexity. The Nemacheilid loaches collected during the survey of fish species in Kaptai Lake exhibited morphological ambiguity. The voucher specimens have incomplete lateral lines, including 10–12 round blotches. Molecular and morphological techniques were employed to identify and resolve the taxonomic confusion. The molecular study confirmed the species level of the specimens, showing an average similarity of 99.17 % with GenBank data of Acanthocobitis zonalternans. The highest level of genetic divergence recorded was 19.32 % between Paracanthocobitis botia, while proximity was noted with Paracanthocobitis abutwebi at 1 %. The phylogenetic tree based on maximum likelihood and maximum parsimony, constructed from the COI gene sequences of voucher specimens, reveals a monophyletic clade that includes the reference sequence of A. zonalternans. This analysis may also suggest incomplete lineage sorting with P. abutwebi. The Cytb gene sequences formed a distinct clade for the voucher specimens, indicating that they belong to the same species. Regarding molecular relatedness and morphological similarity voucher specimens conferred as A. zonalternans.
{"title":"Identification of a Nemacheilid loach from Kaptai Lake, Bangladesh using morphology and two molecular markers","authors":"Jonaira Rashid , Md Amdadul Haque , Md Khaled Rahman , Md Lipon Mia , Rabina Akther Lima , Md Harunor Rashid , Anuradha Bhadra","doi":"10.1016/j.egg.2024.100318","DOIUrl":"10.1016/j.egg.2024.100318","url":null,"abstract":"<div><div>The Nemacheilidae family of cypriniform fishes comprises more than 700 species inhabiting the rivers and streams throughout Eurasia. This family is considered one of the most taxonomically ambiguous, and recent research has shed light on its complexity. The Nemacheilid loaches collected during the survey of fish species in Kaptai Lake exhibited morphological ambiguity. The voucher specimens have incomplete lateral lines, including 10–12 round blotches. Molecular and morphological techniques were employed to identify and resolve the taxonomic confusion. The molecular study confirmed the species level of the specimens, showing an average similarity of 99.17 % with GenBank data of <em>Acanthocobitis zonalternans</em>. The highest level of genetic divergence recorded was 19.32 % between <em>Paracanthocobitis botia</em>, while proximity was noted with <em>Paracanthocobitis abutwebi</em> at 1 %. The phylogenetic tree based on maximum likelihood and maximum parsimony, constructed from the COI gene sequences of voucher specimens, reveals a monophyletic clade that includes the reference sequence of <em>A. zonalternans</em>. This analysis may also suggest incomplete lineage sorting with <em>P. abutwebi</em>. The Cytb gene sequences formed a distinct clade for the voucher specimens, indicating that they belong to the same species. Regarding molecular relatedness and morphological similarity voucher specimens conferred as <em>A. zonalternans.</em></div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100318"},"PeriodicalIF":0.0,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133344","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}
Pub Date : 2024-12-09DOI: 10.1016/j.egg.2024.100316
Phumzile Mkhize , Hussein Shimelis , Jacob Mashilo
Bottle gourd (Lagenaria siceraria (Molina) Standl.) genetic resources cultivated in sub-Saharan Africa (SSA) are relatively tolerant to heat and drought stress, presenting opportunities for developing climate-smart and drought-resilient cultivars adapted to dry environments. Therefore, the objective of this study was to determine drought tolerance and stability among newly-developed F1 bottle gourd hybrids to recommend best-performers for production and commercialization in South Africa. Fifty-three F1 families were developed and field evaluated with 12 parental accessions under non-stressed (NS) and drought-stressed (DS) conditions in two growing seasons using a 5 × 13 α-lattice design with three replicates. Data were collected on fruit yield per plant (FYPP) and drought tolerance indices computed. Genotype-by-environment interaction (GEI) patterns were inferred using the additive main effects and multiplicative interaction (AMMI) and genotype and genotype-by-environment (GGE) biplot analyses. Significant interactions were detected among test genotypes and water regimes for FYPP. The mean FYPP were 0.3 and 1.0 kg under DS and NS conditions. Based on the AMMI analysis, the proportions of the genotypic (G), environment (E) and GEI effects were computed at 6.49, 23.04 and 22.24 %, respectively. The GGE-biplot analysis explained 76.51 % of the total variation for FYPP. Based on tolerance indices, AMMI and GGE-biplot analyses the following hybrids were identified as drought tolerant and stable: BG-31 × BG-67, BG-27 × BG-31, BG-31 × BG-70, BG-31 × BG-78, BG-67 × BG-70, BG-58 × BG-79 and BG-58 × BG-80. The newly-developed bottle gourd hybris are recommended for cultivation in drought-prone agro-ecologies in South Africa and similar environments in SSA after multi-environment testing.
{"title":"Hybrid performance of bottle gourd [Lagenaria siceraria] under drought stress and non-stress conditions","authors":"Phumzile Mkhize , Hussein Shimelis , Jacob Mashilo","doi":"10.1016/j.egg.2024.100316","DOIUrl":"10.1016/j.egg.2024.100316","url":null,"abstract":"<div><div>Bottle gourd (<em>Lagenaria siceraria</em> (Molina) Standl.) genetic resources cultivated in sub-Saharan Africa (SSA) are relatively tolerant to heat and drought stress, presenting opportunities for developing climate-smart and drought-resilient cultivars adapted to dry environments. Therefore, the objective of this study was to determine drought tolerance and stability among newly-developed F<sub>1</sub> bottle gourd hybrids to recommend best-performers for production and commercialization in South Africa. Fifty-three F<sub>1</sub> families were developed and field evaluated with 12 parental accessions under non-stressed (NS) and drought-stressed (DS) conditions in two growing seasons using a 5 × 13 α-lattice design with three replicates. Data were collected on fruit yield per plant (FYPP) and drought tolerance indices computed. Genotype-by-environment interaction (GEI) patterns were inferred using the additive main effects and multiplicative interaction (AMMI) and genotype and genotype-by-environment (GGE) biplot analyses. Significant interactions were detected among test genotypes and water regimes for FYPP. The mean FYPP were 0.3 and 1.0 kg under DS and NS conditions. Based on the AMMI analysis, the proportions of the genotypic (G), environment (E) and GEI effects were computed at 6.49, 23.04 and 22.24 %, respectively. The GGE-biplot analysis explained 76.51 % of the total variation for FYPP. Based on tolerance indices, AMMI and GGE-biplot analyses the following hybrids were identified as drought tolerant and stable: BG-31 × BG-67, BG-27 × BG-31, BG-31 × BG-70, BG-31 × BG-78, BG-67 × BG-70, BG-58 × BG-79 and BG-58 × BG-80. The newly-developed bottle gourd hybris are recommended for cultivation in drought-prone agro-ecologies in South Africa and similar environments in SSA after multi-environment testing.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100316"},"PeriodicalIF":0.0,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133413","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}
Pub Date : 2024-12-06DOI: 10.1016/j.egg.2024.100314
Mojtaba Najafi
Motivations and aim
Currently, coat color scoring is of significant interest to researchers due to its effect on a sheep's ability to adapt to environmental heat stress, as well as its implications for the marketability of sheep products, such as wool and skin, which are vital to the textile industry. Additionally, coat color can indicate its breed and genetic characteristics. Former studies have demonstrated that some genetic variants are directly associated with coat color. The MC1R gene is one of the major genes associated with coat color in sheep. This study aimed to investigate the comparative analysis of MC1R gene among some Iranian sheep breeds for the first time.
Materials and methods
Ten blood samples were collected from each of the following sheep breeds: Zel, Romanov, Iran-Black, Naeini, Baluchi, and Kurdi. Following DNA isolation using the modified salting-out method, the 5-flanking region of the MC1R gene was amplified and subsequently analyzed using sanger sequencing. Then, the resulting sequences were assessed by bioinformatics software.
Results
Sequencing analysis of the 5′-UTR region of the gene revealed various motifs and transcription factor binding sites. A 26-nucleotide deletion/insertion mutation in this region was found in some breeds, such as Romanov, Zel, and Iran-Black. Additionally, a nucleotide substitution of −206G > A was observed in these breeds. Overall, the identified polymorphisms resulted in the loss and alteration of the number and type of motifs and transcription factor binding sites, such as MOK2 and Gamma_IRE_CS, which may influence the mechanism of gene expression.
Conclusion
The presence of A 26-nucleotide deletion/insertion mutation and a nucleotide substitution (−206G > A) among different sheep breeds and its effect on the coat color scoring confirm the 5′-UTR region of the MC1R gene as a functional candidate locus. The findings reveal significant mutations resulted in alterations to motifs and transcription factor binding sites, potentially affecting gene expression mechanisms and, consequently, coat color phenotypes.
{"title":"Comparative analysis of gene structure in 5-flanking region of MC1R gene in indigenous sheep breeds","authors":"Mojtaba Najafi","doi":"10.1016/j.egg.2024.100314","DOIUrl":"10.1016/j.egg.2024.100314","url":null,"abstract":"<div><h3>Motivations and aim</h3><div>Currently, coat color scoring is of significant interest to researchers due to its effect on a sheep's ability to adapt to environmental heat stress, as well as its implications for the marketability of sheep products, such as wool and skin, which are vital to the textile industry. Additionally, coat color can indicate its breed and genetic characteristics. Former studies have demonstrated that some genetic variants are directly associated with coat color. The <em>MC1R</em> gene is one of the major genes associated with coat color in sheep. This study aimed to investigate the comparative analysis of <em>MC1R</em> gene among some Iranian sheep breeds for the first time.</div></div><div><h3>Materials and methods</h3><div>Ten blood samples were collected from each of the following sheep breeds: Zel, Romanov, Iran-Black, Naeini, Baluchi, and Kurdi. Following DNA isolation using the modified salting-out method, the 5-flanking region of the <em>MC1R</em> gene was amplified and subsequently analyzed using sanger sequencing. Then, the resulting sequences were assessed by bioinformatics software.</div></div><div><h3>Results</h3><div>Sequencing analysis of the 5′-UTR region of the gene revealed various motifs and transcription factor binding sites. A 26-nucleotide deletion/insertion mutation in this region was found in some breeds, such as Romanov, Zel, and Iran-Black. Additionally, a nucleotide substitution of −206G > A was observed in these breeds. Overall, the identified polymorphisms resulted in the loss and alteration of the number and type of motifs and transcription factor binding sites, such as <em>MOK2</em> and <em>Gamma_IRE_CS</em>, which may influence the mechanism of gene expression.</div></div><div><h3>Conclusion</h3><div>The presence of A 26-nucleotide deletion/insertion mutation and a nucleotide substitution (−206G > A) among different sheep breeds and its effect on the coat color scoring confirm the 5′-UTR region of the <em>MC1R</em> gene as a functional candidate locus. The findings reveal significant mutations resulted in alterations to motifs and transcription factor binding sites, potentially affecting gene expression mechanisms and, consequently, coat color phenotypes.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100314"},"PeriodicalIF":0.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133341","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}
Pub Date : 2024-12-05DOI: 10.1016/j.egg.2024.100315
Sudarshna, Nivedita Sharma
Intercropping is a crucial soil management strategy for boosting orchard productivity. This study explores the cultivation of Trillium govanianum within an integrated apple farming system in the Indian Himalayan region. Three plant growth-promoting endophytic bacterial strains—Pantoea spp. Ar13, Microbacterium spp. Ar17, and Pseudomonas spp. Ms5—were isolated and identified from the rhizomes of T. govanianum. These strains were used individually and in consortia to create a charcoal-based bioformulation. A field experiment was conducted in a 10-year-old apple orchard to evaluate the effectiveness of the bacterial bioformulation. The bioformulations were applied alongside a reduced dose of chemical fertilizer (NPK) to assess their impact on apple growth characteristics, while no chemical fertilizer was used with T. govanianum. Results indicated that the bioformulation containing a consortium of Pantoea spp. Ar13, Microbacterium spp. Ar17, and Pseudomonas spp. Ms5 significantly increased the plant height (4.04 ± 0.06 cm), leaf length (2.86 ± 0.03 cm), rhizome size, rhizome weight, and root length of T. govanianum compared to the uninoculated control. Additionally, the height (448.52 ± 0.63 cm), girth (24.58 ± 0.12 cm), shoot length (86.63 ± 0.77 cm), canopy (18.92 ± 0.05 m³), and yield efficiency of the apple trees were significantly improved with the inoculation of the consortium combined with 80 % NPK. Overall, the findings of this study suggest that inoculating with these endophytic bacterial bioformulations benefits the cultivation of T. govanianum and apples in an intercropping system. This has significant implications for producing bioformulations, especially in low-temperature environments.
{"title":"Bioprospecting of endophytic bacterial inoculation in intercropped Trillium govanianum (Wall. Ex. Royle) and Apple cv. Royal delicious","authors":"Sudarshna, Nivedita Sharma","doi":"10.1016/j.egg.2024.100315","DOIUrl":"10.1016/j.egg.2024.100315","url":null,"abstract":"<div><div>Intercropping is a crucial soil management strategy for boosting orchard productivity. This study explores the cultivation of <em>Trillium govanianum</em> within an integrated apple farming system in the Indian Himalayan region. Three plant growth-promoting endophytic bacterial strains—<em>Pantoea</em> spp. Ar13, <em>Microbacterium</em> spp. Ar17, and <em>Pseudomonas</em> spp. Ms5—were isolated and identified from the rhizomes of <em>T. govanianum</em>. These strains were used individually and in consortia to create a charcoal-based bioformulation. A field experiment was conducted in a 10-year-old apple orchard to evaluate the effectiveness of the bacterial bioformulation. The bioformulations were applied alongside a reduced dose of chemical fertilizer (NPK) to assess their impact on apple growth characteristics, while no chemical fertilizer was used with <em>T. govanianum</em>. Results indicated that the bioformulation containing a consortium of <em>Pantoea</em> spp. Ar13, <em>Microbacterium</em> spp. Ar17, and <em>Pseudomonas</em> spp. Ms5 significantly increased the plant height (4.04 ± 0.06 cm), leaf length (2.86 ± 0.03 cm), rhizome size, rhizome weight, and root length of <em>T. govanianum</em> compared to the uninoculated control. Additionally, the height (448.52 ± 0.63 cm), girth (24.58 ± 0.12 cm), shoot length (86.63 ± 0.77 cm), canopy (18.92 ± 0.05 m³), and yield efficiency of the apple trees were significantly improved with the inoculation of the consortium combined with 80 % NPK. Overall, the findings of this study suggest that inoculating with these endophytic bacterial bioformulations benefits the cultivation of <em>T. govanianum</em> and apples in an intercropping system. This has significant implications for producing bioformulations, especially in low-temperature environments.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100315"},"PeriodicalIF":0.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133342","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}
Pub Date : 2024-11-30DOI: 10.1016/j.egg.2024.100313
Albert Thembinkosi Modi
Crop response to environment is determined by genetic characteristics of developed cultivars. Phenotypic markers have been shown to be directly linked to genotypic markers. The objective of this study was to use local cowpea (Vigna unguiculata L.) germplasm to determine relationship between intercepted photosynthetically active radiation (PAR), a microenvironment factor, with chlorophyll content index (CCI), stomal conductance and crop growth under field conditions. These physiological factors are useful for enhancing the value of phenotypic and genetic markers. Multivariate analysis confirmed the significant differences between three cowpea genotypes (p ≤ 0.05) in terms of response to microenvironment and grain yield. The patterns of change in temperature, rainfall and evapotranspiration were related to those of PAR, CCI and stomatal conductance during crop growth. Despite the consistent pattern of change in PAR, CCI and stomatal conductance in relation to plant growth during the season, regression analysis indicated weak correlation between plant growth PAR, microclimate-related variables across genotypes. However, the positive relationship between PAR and early plant growth could be explained in the context of a highly significant correlation between CCI and stomatal conductance. Consequently, the study was able to provide evidence of linkage between a cowpea morphological trait and productivity in a manner that also differentiated the three cowpea varieties for future pedigree determination research.
{"title":"Using Vigna unguiculata genotypes to relate photosynthetically active radiation, chlorophyll content index and stomatal conductance","authors":"Albert Thembinkosi Modi","doi":"10.1016/j.egg.2024.100313","DOIUrl":"10.1016/j.egg.2024.100313","url":null,"abstract":"<div><div>Crop response to environment is determined by genetic characteristics of developed cultivars. Phenotypic markers have been shown to be directly linked to genotypic markers. The objective of this study was to use local cowpea (<em>Vigna unguiculata</em> L.) germplasm to determine relationship between intercepted photosynthetically active radiation (PAR), a microenvironment factor, with chlorophyll content index (CCI), stomal conductance and crop growth under field conditions. These physiological factors are useful for enhancing the value of phenotypic and genetic markers. Multivariate analysis confirmed the significant differences between three cowpea genotypes (p ≤ 0.05) in terms of response to microenvironment and grain yield. The patterns of change in temperature, rainfall and evapotranspiration were related to those of PAR, CCI and stomatal conductance during crop growth. Despite the consistent pattern of change in PAR, CCI and stomatal conductance in relation to plant growth during the season, regression analysis indicated weak correlation between plant growth PAR, microclimate-related variables across genotypes. However, the positive relationship between PAR and early plant growth could be explained in the context of a highly significant correlation between CCI and stomatal conductance. Consequently, the study was able to provide evidence of linkage between a cowpea morphological trait and productivity in a manner that also differentiated the three cowpea varieties for future pedigree determination research.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100313"},"PeriodicalIF":0.0,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133340","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}
Pub Date : 2024-11-30DOI: 10.1016/j.egg.2024.100310
Rakshitha H M. Jain, Y.L. Krishnamurty, K. Manjunath, Shashwathi H S
Cocculus hirsutus (L.) Diels (Menispermaceae) is a perennial liana found mainly in tropical and subtropical regions of the Western Ghats, India. This study investigates the variation in leaf morphology within this species. Five samples were selected based on differences in leaf structure, and morphological analysis of foliar traits (Petiole length, Leaf length and Leaf width) revealed significant variation (p < 0.0001) through one-way ANOVA (F-values for PL = 1247.46, LL = 1303.51, and LW = 1413.46). Principal component analysis (PCA) was used to further explore this diversity. Morphoanatomical features, including leaf epidermis, were examined for accurate species identification. DNA barcoding using matK, rbcL, and combined sequences showed superior results with rbcL and the combined sequence. Maximum likelihood (ML) and Bayesian Inference (BI) were applied to assess species relationships, and the analysis suggested all samples belong to the same species. Nevertheless, discrepancies in the bootstrap and posterior probability values revealed by the rbcL and combined sequences may be attributed to microbial influence or mimicry from the host plant.
{"title":"Divergent leaf traits of medicinally important Cocculus hirsutus (L.) Diels- morphoanatomical and molecular authentication","authors":"Rakshitha H M. Jain, Y.L. Krishnamurty, K. Manjunath, Shashwathi H S","doi":"10.1016/j.egg.2024.100310","DOIUrl":"10.1016/j.egg.2024.100310","url":null,"abstract":"<div><div>Cocculus hirsutus (L.) Diels (Menispermaceae) is a perennial liana found mainly in tropical and subtropical regions of the Western Ghats, India. This study investigates the variation in leaf morphology within this species. Five samples were selected based on differences in leaf structure, and morphological analysis of foliar traits (Petiole length, Leaf length and Leaf width) revealed significant variation (p < 0.0001) through one-way ANOVA (F-values for PL = 1247.46, LL = 1303.51, and LW = 1413.46). Principal component analysis (PCA) was used to further explore this diversity. Morphoanatomical features, including leaf epidermis, were examined for accurate species identification. DNA barcoding using matK, rbcL, and combined sequences showed superior results with rbcL and the combined sequence. Maximum likelihood (ML) and Bayesian Inference (BI) were applied to assess species relationships, and the analysis suggested all samples belong to the same species. Nevertheless, discrepancies in the bootstrap and posterior probability values revealed by the <em>rbcL</em> and combined sequences may be attributed to microbial influence or mimicry from the host plant.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100310"},"PeriodicalIF":0.0,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133343","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}
The present study aimed to evaluate the genetic diversity among vetiver accessions obtained from diverse geographic locations worldwide using two molecular markers, namely Inter-Simple Sequences Repeat (ISSR) and Start Codon Targeted Polymorphism (SCoT). The objective of this analysis was to enhance the taxonomic accuracy and to ascertain the evolutionary relationships among the studied accessions. The study population comprised three groups, i.e., North Indian, South Indian, and Abroad Population. The effective multiplex ratio (EMR), marker index (MI), resolving power (Rp), and polymorphic information content (PIC) were determined. The SCoT system exhibited higher values for all parameters examined except for resolving power (Rp), which was lower than ISSR. The Mantel test showed a weak correlation between ISSR and SCoT, indicating that these marker systems have limited genetic background similarities in vetiver. Analysis of molecular variance (AMOVA) shows a significant differentiation among the investigated populations, with the majority of the variation observed within the populations. The South Indian accessions were the most heterogenic to others. The fixation index and population analysis indicate a close relatedness among the accessions. This study used SCoT-based molecular markers as a novel approach to evaluate the genetic diversity and relationships among different vetiver accessions. These studies will assist in the molecular ecology, genetic mapping, and identification of elite varieties and the efficiency of the breeding methodology in fulfilling worldwide industrial demand.
{"title":"Analysis of genetic divergence and heterogeneity in vetiver (Chrysopogon zizanioides (L.) Roberty) using SCoT and ISSR molecular markers","authors":"Anand Mishra , R.K. Lal , Pankhuri Gupta , Sunita Singh Dhawan","doi":"10.1016/j.egg.2024.100312","DOIUrl":"10.1016/j.egg.2024.100312","url":null,"abstract":"<div><div>The present study aimed to evaluate the genetic diversity among vetiver accessions obtained from diverse geographic locations worldwide using two molecular markers, namely Inter-Simple Sequences Repeat (ISSR) and Start Codon Targeted Polymorphism (SCoT). The objective of this analysis was to enhance the taxonomic accuracy and to ascertain the evolutionary relationships among the studied accessions. The study population comprised three groups, i.e., North Indian, South Indian, and Abroad Population. The effective multiplex ratio (EMR), marker index (MI), resolving power (Rp), and polymorphic information content (PIC) were determined. The SCoT system exhibited higher values for all parameters examined except for resolving power (Rp), which was lower than ISSR. The Mantel test showed a weak correlation between ISSR and SCoT, indicating that these marker systems have limited genetic background similarities in vetiver. Analysis of molecular variance (AMOVA) shows a significant differentiation among the investigated populations, with the majority of the variation observed within the populations. The South Indian accessions were the most heterogenic to others. The fixation index and population analysis indicate a close relatedness among the accessions. This study used SCoT-based molecular markers as a novel approach to evaluate the genetic diversity and relationships among different vetiver accessions. These studies will assist in the molecular ecology, genetic mapping, and identification of elite varieties and the efficiency of the breeding methodology in fulfilling worldwide industrial demand.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100312"},"PeriodicalIF":0.0,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133339","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}
Pub Date : 2024-11-28DOI: 10.1016/j.egg.2024.100311
Gebeyaw Achenef Haile , Muluken Banteayehu
Increasing faba bean production is indispensable to supply the growing demand for plant-based protein on a global scale. A thorough understanding of genotype-environment interaction patterns is critical to developing high-yielding varieties with wider adaptation. Twelve faba bean genotypes were evaluated in 10 environments during 2018–2019 in Ethiopia to estimate the effect of genotype by environment interaction on grain yield and identify stable genotypes. The results revealed significant differences among the genotypes, indicating that certain varieties consistently performed better across diverse conditions. This stability underscores the potential for these selected genotypes to contribute effectively to sustainable agriculture and food security in the region. The study found substantial differences (P < 0.001) between genotypes, environments, and G × E interactions. This suggests that genotypes respond differently across environments, allowing for stability analysis. Environmental variance was larger (83 % of overall variation), with genotype and genotype-by-environment interaction accounting for 6 % and 11 %, respectively. The average grain yield of the faba bean genotypes varied by environment, from 2791.22 kg/ha for genotype G7 to 3300.43 kg/ha for the standard checks variety Tumsa (G12). A genotype plus genotype by environment interaction biplot is created by plotting the first principal component (PC1 = 38.25) scores of the genotypes and environments against their respective second principal component (PC2 = 21.95) scores, which explained 60.2 % of the total variation. According to the polygon view analysis, genotypes G6, G9, and G10 are the best fit for the test conditions. Notably, genotypes G12 and G8 have demonstrated great yield and stability, making them ideal candidates for production in diverse environments.
{"title":"Analysis of genotype by environment interaction effect on faba bean (Vicia faba) elite genotype yield performance and stability in Ethiopia","authors":"Gebeyaw Achenef Haile , Muluken Banteayehu","doi":"10.1016/j.egg.2024.100311","DOIUrl":"10.1016/j.egg.2024.100311","url":null,"abstract":"<div><div>Increasing faba bean production is indispensable to supply the growing demand for plant-based protein on a global scale. A thorough understanding of genotype-environment interaction patterns is critical to developing high-yielding varieties with wider adaptation. Twelve faba bean genotypes were evaluated in 10 environments during 2018–2019 in Ethiopia to estimate the effect of genotype by environment interaction on grain yield and identify stable genotypes. The results revealed significant differences among the genotypes, indicating that certain varieties consistently performed better across diverse conditions. This stability underscores the potential for these selected genotypes to contribute effectively to sustainable agriculture and food security in the region. The study found substantial differences (P < 0.001) between genotypes, environments, and G × E interactions. This suggests that genotypes respond differently across environments, allowing for stability analysis. Environmental variance was larger (83 % of overall variation), with genotype and genotype-by-environment interaction accounting for 6 % and 11 %, respectively. The average grain yield of the faba bean genotypes varied by environment, from 2791.22 kg/ha for genotype G7 to 3300.43 kg/ha for the standard checks variety Tumsa (G12). A genotype plus genotype by environment interaction biplot is created by plotting the first principal component (PC1 = 38.25) scores of the genotypes and environments against their respective second principal component (PC2 = 21.95) scores, which explained 60.2 % of the total variation. According to the polygon view analysis, genotypes G6, G9, and G10 are the best fit for the test conditions. Notably, genotypes G12 and G8 have demonstrated great yield and stability, making them ideal candidates for production in diverse environments.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100311"},"PeriodicalIF":0.0,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133414","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}
Pub Date : 2024-11-23DOI: 10.1016/j.egg.2024.100309
Mohammadhadi Najafi , Mehdi Nasr Esfahani , Arman Nasr Esfahani , Kowsar Shirazii , Ava Nasr Esfahani , Hamid Akbarzadeh
Pumpkin (Cucurbita pepo), a versatile-member of the Cucurbitaceae-family, holds significant commercial-value in numerous countries, both as a cultivated-field-crop and a home-garden-staple. As with all crops, pumpkins are subject to diseases that can limit crop quality and yield. Considering the importance of the subject, in this research, SSR-markers were employed to investigate genetic-diversity and population-structure within a collection of 41 pumpkin-genotypes for the first time. At the same time, the screening for resistance to Phytophthora melonis, one of the important diseases of pumpkin globally, was carried out at greenhouse-conditions. In addition, defense-genes were analyzed against P. melonis, accordingly. The results showed that the pumpkin-genotypes have a high genetic-diversity. The 13-primers produced a total of 73-amplicons, of which 72 displayed polymorphic-patterns. Based on the dendrogram generated, the genotypes could be clustered into five distinct groups. Variance-analysis, showed that the related-genotypes had significant-reaction to the P. melonis. The genotypes were stratified into four groups based on their varying degrees of infection. (resistant, tolerant, sensitive and very sensitive) on the cut-off line found on the dendrogram. Comparison between the classification of genotypes in terms of disease-resistance and their grouping based on SSR-marker, there was a high agreement between the disease-severity and the dendrogram of the molecular-marker comprised their accordance with the disease-severity-percentage of the related pumpkin-genotyped accordingly. Moreover, the related defense-genes overexpressed following inoculation with to P. melonis, of which MYB, bHLH87 and ERF014 were more predominant significantly. The findings of this investigation elucidate the underlying mechanisms governing pumpkin resistance to Phytophthora root and crown rot. The data generated from this study can be leveraged to identify resistant pumpkin genotypes, promising SSR-marker and candidate genes for genetic enhancement of susceptible pumpkin cultivars and the subsequent development of P. melonis-resistant pumpkin varieties.
南瓜（Cucurbita pepo）是葫芦科植物中用途广泛的一种，在许多国家都具有重要的商业价值，既是田间栽培作物，也是家庭园艺主菜。与所有作物一样，南瓜也会受到病害的影响，从而限制作物的质量和产量。考虑到这一课题的重要性，本研究首次采用 SSR 标记研究 41 个南瓜基因型的遗传多样性和种群结构。同时，还在温室条件下筛选了南瓜对全球南瓜重要病害之一瓜疫霉（Phytophthora melonis）的抗性。此外，还相应地分析了南瓜的防御基因。结果表明，南瓜基因型具有很高的遗传多样性。13 个引物共产生 73 个扩增子，其中 72 个显示多态性模式。根据生成的树枝图，基因型可分为五个不同的组。方差分析显示，相关基因型对瓜皮病菌有显著的反应。根据不同的感染程度，基因型被分为四组。(根据树枝图上的分界线，基因型被分为四组（抗性组、耐受组、敏感组和极敏感组）。比较基因型的抗病性分类和基于 SSR 标记的分组，发现抗病性和分子标记的树枝状图与相关南瓜基因型的抗病性百分比高度一致。此外，接种甜瓜病菌后，相关的防御基因过度表达，其中 MYB、bHLH87 和 ERF014 的表达更为显著。本研究结果阐明了南瓜抗根腐病和冠腐病的内在机制。本研究产生的数据可用于鉴定抗性南瓜基因型、有希望的 SSR 标记和候选基因，以对易感南瓜栽培品种进行遗传改良，进而开发抗瓜皮病的南瓜品种。
{"title":"Genetic diversity and population structure associated with resistance to Phytophthora melonis-Pumpkin interaction pathosystem","authors":"Mohammadhadi Najafi , Mehdi Nasr Esfahani , Arman Nasr Esfahani , Kowsar Shirazii , Ava Nasr Esfahani , Hamid Akbarzadeh","doi":"10.1016/j.egg.2024.100309","DOIUrl":"10.1016/j.egg.2024.100309","url":null,"abstract":"<div><div>Pumpkin (<em>Cucurbita pepo</em>), a versatile-member of the Cucurbitaceae-family, holds significant commercial-value in numerous countries, both as a cultivated-field-crop and a home-garden-staple. As with all crops, pumpkins are subject to diseases that can limit crop quality and yield. Considering the importance of the subject, in this research, SSR-markers were employed to investigate genetic-diversity and population-structure within a collection of 41 pumpkin-genotypes for the first time. At the same time, the screening for resistance to <em>Phytophthora melonis</em>, one of the important diseases of pumpkin globally, was carried out at greenhouse-conditions. In addition, defense-genes were analyzed against <em>P. melonis</em>, accordingly. The results showed that the pumpkin-genotypes have a high genetic-diversity. The 13-primers produced a total of 73-amplicons, of which 72 displayed polymorphic-patterns. Based on the dendrogram generated, the genotypes could be clustered into five distinct groups. Variance-analysis, showed that the related-genotypes had significant-reaction to the <em>P. melonis.</em> The genotypes were stratified into four groups based on their varying degrees of infection. (resistant, tolerant, sensitive and very sensitive) on the cut-off line found on the dendrogram. Comparison between the classification of genotypes in terms of disease-resistance and their grouping based on SSR-marker, there was a high agreement between the disease-severity and the dendrogram of the molecular-marker comprised their accordance with the disease-severity-percentage of the related pumpkin-genotyped accordingly. Moreover, the related defense-genes overexpressed following inoculation with to <em>P. melonis</em>, of which <em>MYB</em>, <em>bHLH87</em> and <em>ERF014</em> were more predominant significantly. The findings of this investigation elucidate the underlying mechanisms governing pumpkin resistance to <em>Phytophthora</em> root and crown rot. The data generated from this study can be leveraged to identify resistant pumpkin genotypes, promising SSR-marker and candidate genes for genetic enhancement of susceptible pumpkin cultivars and the subsequent development of <em>P. melonis</em>-resistant pumpkin varieties.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100309"},"PeriodicalIF":0.0,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142721671","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}
Pub Date : 2024-11-18DOI: 10.1016/j.egg.2024.100308
K.L. Dhanya Lenin, Swapna P. Antony
Background
Antimicrobial peptides (AMPs) are molecules of the innate immune defense mechanism, which play a vital role in maintaining the healthy state of organisms thriving in varied and diverse habitats.
Methods and results
The present study investigated the expression profile of ten AMP genes, such as β-defensin, hepcidin, histone H2A-derived AMP, piscidin-1 to -5, thymosin β1, and thymosin β4, in tissues like gill, blood, skin, muscle, stomach, intestine, pancreas, gonad, brain, heart, and liver of healthy adult Oreochromis niloticus. Quantitative PCR analysis affirmed the constitutive expression of all AMP genes, albeit at varying levels across tissues. The constitutive expression pattern of β-defensin, hepcidin, and histone H2A-derived AMP in mucosal and systemic tissues indicates its active involvement in the innate immune responses. The expression profile of piscidin isoforms also reinstates the functional diversity within the piscidin AMP family and the transcriptomic profiling of thymosin isoforms suggests its involvement in various physiological functions.
Conclusions
The findings suggest tissue-specific roles for AMPs in the innate immune defense system of Oreochromis niloticus. The expression of thymosin β in non-immune related tissues highlights its involvement in broader physiological processes. These results contribute to the understanding of AMP expression patterns and their functional disposition in the fish tissues. Further studies are needed to elucidate the functional significance of tissue-specific AMP expression and its role in fish health and disease resistance.
{"title":"Constitutive expression and tissue-specific variations of antimicrobial peptide genes in healthy adult Oreochromis niloticus","authors":"K.L. Dhanya Lenin, Swapna P. Antony","doi":"10.1016/j.egg.2024.100308","DOIUrl":"10.1016/j.egg.2024.100308","url":null,"abstract":"<div><h3>Background</h3><div>Antimicrobial peptides (AMPs) are molecules of the innate immune defense mechanism, which play a vital role in maintaining the healthy state of organisms thriving in varied and diverse habitats.</div></div><div><h3>Methods and results</h3><div>The present study investigated the expression profile of ten AMP genes, such as β-defensin, hepcidin, histone H2A-derived AMP, piscidin-1 to -5, thymosin β1, and thymosin β4, in tissues like gill, blood, skin, muscle, stomach, intestine, pancreas, gonad, brain, heart, and liver of healthy adult <em>Oreochromis niloticus</em>. Quantitative PCR analysis affirmed the constitutive expression of all AMP genes, albeit at varying levels across tissues. The constitutive expression pattern of β-defensin, hepcidin, and histone H2A-derived AMP in mucosal and systemic tissues indicates its active involvement in the innate immune responses. The expression profile of piscidin isoforms also reinstates the functional diversity within the piscidin AMP family and the transcriptomic profiling of thymosin isoforms suggests its involvement in various physiological functions.</div></div><div><h3>Conclusions</h3><div>The findings suggest tissue-specific roles for AMPs in the innate immune defense system of <em>Oreochromis niloticus</em>. The expression of thymosin β in non-immune related tissues highlights its involvement in broader physiological processes. These results contribute to the understanding of AMP expression patterns and their functional disposition in the fish tissues. Further studies are needed to elucidate the functional significance of tissue-specific AMP expression and its role in fish health and disease resistance.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100308"},"PeriodicalIF":0.0,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142705028","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}
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