Ecological Genetics and Genomics最新文献

{"title":"Computational analysis of haplotype diversity, phylogenetic variation, and population structure of Candidatus Phytoplasma aurantifolia using tuf gene sequences","authors":"Varucha Misra ,&nbsp;Himanshu Pandey ,&nbsp;Santeshwari Srivastava ,&nbsp;Avinash Sharma ,&nbsp;Rajnish Kumar ,&nbsp;Avnish Kumar Pandey ,&nbsp;Sushil Kumar Singh ,&nbsp;Vivek Singh","doi":"10.1016/j.egg.2024.100229","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100229","url":null,"abstract":"<div><p>The study investigated the genetic diversity and population structure of <em>Candidatus</em> P. aurantifolia using <em>tuf</em> gene sequences sourced from GenBank™. A total of 29 sequences were analyzed based on location availability, unveiling 8 distinct haplotypes. Haplotype 5, encompassing sequences from Egypt, Australia, and Thailand, emerged as the most prevalent. Phylogenetic analysis revealed two different major clades with a significant genetic divergence within species. Notably, calculated haplotype diversity ranged from 0.0 to 0.5909, with India exhibiting the highest diversity. Moreover, haplotype diversity (Hd) was absent in several regions, including Egypt, Australia, and Burkina Faso. Furthermore, nucleotide diversity varied across regions, with Oman displaying the highest value (0.78182) and Thailand showing the lowest (0.09422). A high raggedness index value in the populations of Oman, and Thailand and a low value in India. Substantial genetic divergence in the populations between India-Egypt with limited gene flow was evident by high values of DeltaSt, GammaSt and Fst. Fu Fs values, indicative of demographic expansions or selection events, were notably high in India (34.035). Significant Tajima D values (2.035) in India further support deviations from neutral evolution. Our findings provide unprecedented insights into the population genetics and haplotype network of <em>Candidatus</em> P. aurantifolia, shedding light on its genetic diversity and geographic distribution in different countries. The study results will aid in the prediction of bacterium transmission and the implementation of effective quarantine measures. Moreover, the identification of regions having high genetic divergence and unique haplotypes may help in developing disease management strategies for targeted areas.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139749279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Grain yield stability analysis for oat (Avena sativa L.) genotypes using additive main effects and multiplicative interactions model under different environments in Ethiopia","authors":"Gezahagn Kebede ,&nbsp;Walelign Worku ,&nbsp;Fekede Feyissa ,&nbsp;Habte Jifar","doi":"10.1016/j.egg.2024.100228","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100228","url":null,"abstract":"<div><p>The performance of oat genotypes usually varies across environments due to variations in growing environments and the existence of genotype by environment interaction (GEI) complicates the selection process. In this study, twenty-four oat genotypes were assessed for grain yield and yield components in nine environments using randomized complete bock design (RCBD) with three replications in 2020/2021 cropping season. Hence, a GEI study was performed using additive main effects and multiplicative interactions (AMMI) analysis model to identify high grain yielding and stable genotypes. The AMMI analysis of variance for grain yield showed significant variation for genotype, environment and GEI effects and the environment's main effect was a predominant source of variation (44.62%) followed by genotype (28.84%) and their interactions (26.54%). The first two interaction principal component axes of AMMI were significant and cumulatively explained 63.96% of the total GEI variance. The environments located far from the biplot origin based on the AMMI-1 and AMMI-2 analyses were E2, E6, E5, E3, and E7 indicating these environments had high discriminating power and more contribution to GEI compared to other environments. Among the studied genotypes, G8, G17, G12, G19, G5, G14, G11, G22, G16, and G4 had mean grain yield above the grand mean. The result of stability analysis obtained from the AMMI-2 analysis was more accurate than the AMMI-1. Accordingly, genotypes which had mean grain yield above the grand mean and relatively stable performance were G4, G11, G12, G22, G14, G8, and G17. However, G4, G11, G12, and G14 were released varieties while G8, G17, and G22 have not been yet released. Therefore, G8 and G17 were selected for verification and commercial production in oat growing areas of Ethiopia.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139700309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic dissection of Hessian fly resistance in bread wheat (Triticum aestivum L.) using genome-wide association study in Morocco","authors":"Imane Imseg ,&nbsp;Zakaria El Gataa ,&nbsp;Karima Samir ,&nbsp;Mustapha El Bouhssini ,&nbsp;Wuletaw Tadesse","doi":"10.1016/j.egg.2024.100226","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100226","url":null,"abstract":"<div><p>Hessian fly (HF), <em>Mayetiola destructor (Say</em>), is an important wheat insect pest that annually results in significant production losses. In Morocco, this insect reduces wheat yields by 32–36 % during drought years. The purpose of the current study is to identify the genomic region, marker-trait associations (MTAs), and putative genes associated with the trait of hessian fly resistance in 210 bread wheat (<em>Triticum aestivum</em> L.<em>)</em> genotypes from the International Center for Agricultural Research in Dry Areas (ICARDA). The screening was carried out in the growth chamber using the Hessian fly Mayetiola destructor (Say) populations collected from the Chaouia Ouardigha region in Morocco. The 210 genotypes tested showed various degrees of resistance to the Hessian fly, with eighty-six accessions showing high levels of resistance. The HF severity ranged from 0 to 100 %, whereas the coefficient of variance (CV) was recorded at 84.15 %. Genome-wide association studies (GWAS) using a mixed linear model (MLM) identified 20 significant MTAs at P &lt; 0.001 associated with Hessian fly resistance. The highest number of MTA (10) was recorded in the A sub-genome, followed by 9 MTAs in the B genome. The highest significant marker is <em>AX-95143016</em> which is located on chromosome 3B with a -Log10(p) of 10.23. After mapping the 20 significant markers associated with Hessian fly resistance, there were 12 potential candidate genes found. This study identified highly resistant genotypes and significant markers that could be used in future wheat breeding programs.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139700310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of genotype x environment interaction for Hordeum vulgare L. ssp. vulgare recombinant inbred lines in multi-environments of Tigray, Ethiopia","authors":"Hailekiros Tadesse Tekle, Y. Tsehaye, Genet Atsbeha, F. Abera, Rogério Marcos Chiulele","doi":"10.1016/j.egg.2024.100231","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100231","url":null,"abstract":"","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139880891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variability and evaluation of water-deficit stress tolerant of spring bread wheat genotypes using drought tolerance indices","authors":"Ahmad MajidiMehr ,&nbsp;Zakaria El Gataa ,&nbsp;Sima Abyar ,&nbsp;Hassan Nourinejad","doi":"10.1016/j.egg.2024.100227","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100227","url":null,"abstract":"<div><p><span><span>Water deficit stress is one of the most important environmental factors that reduce grain yield in bread wheat. Despite the recent progress in breeding this plant, there is still a need to improve bread wheat cultivars that tolerate water stress in the country. In the current research, 100 genotypes of spring bread wheat during the years 2020–2021 and 2021–2022 in two conditions of non-stress and water deficit stress in the form of a simple 10x10 lattice square design at the beginning of flowering in Gachsaran Research Center located in the south of Iran. Eight quantitative indices of tolerance to water deficit were calculated. Principal component analysis (PCA), hierarchical cluster analysis (HCA), analysis of variance, and Pearson correlation were carried out in this study. According to the data, significant </span>genotypic variation was seen among genotypes for both individual yield and drought indices. Geometric Mean Productivity (GMP) recorded the lowest coefficient of variation (CV) value with 10.6 %, while Tolerance Index (TOL) recorded the highest CV value with 45.4 %. The </span>heritability of several of the indices is moderate to high; the Stress Susceptibility Index (SSI) has the greatest heritability at 0.96. Four distinct clusters were formed from the 100 genotypes. PC1 and PC2 make up 98.4 % of the total variance. Specifically, PC1 covers 68.9 %, while PC2 accounts for the remaining 29.5 %. These chosen genotypes will act as parent plants in breeding initiatives to create novel varieties resistant to drought.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139675671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide versus transcriptome-wide association studies: Prospects and limitations","authors":"Jemal Mohammed Abdela","doi":"10.1016/j.egg.2024.100221","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100221","url":null,"abstract":"<div><p><span><span>Genome-wide Association Studies (GWAS) and Transcriptome-wide Association Studies (TWAS) are pivotal tools in genetics<span> research. GWAS, with its comprehensive genome coverage, reveals insights into complex trait variations among different populations. It finds applications beyond gene identification, including historical population studies and linkage disequilibrium<span> pattern assessments. However, GWAS faces challenges like multiple testing corrections and difficulties in pinpointing causal variants. Conversely, TWAS offers higher gene resolution and the potential for deeper insights into genetic mechanisms. Yet, TWAS prediction accuracy is contingent on gene </span></span></span>heritability, and its complexity lies in navigating </span>gene regulatory networks<span> and epigenetic factors. Understanding the strengths and limitations of both GWAS and TWAS is crucial for harnessing their full potential in genetic research endeavours.</span></p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139473387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A study on molecular taxonomy of South Indian species Selaginella sweared by DNA barcoding using rbcL","authors":"M. Narayani ,&nbsp;M. Johnson ,&nbsp;Sunil Tulshiram Hajare ,&nbsp;Shrikant B. Bhosale ,&nbsp;Vijay Upadhye ,&nbsp;Sathe Ganesh Sadashiv ,&nbsp;Babsaheb Surwase","doi":"10.1016/j.egg.2024.100224","DOIUrl":"10.1016/j.egg.2024.100224","url":null,"abstract":"<div><p><span><span><span>In this study, genetic polymorphisms using </span>DNA barcoding has been performed on selected ten species of </span>Selaginella<span> collected form Tamil Nadu and the Hills of Kerala. The main aim of this study was to estimate a phylogenetic<span> and evolutionary relationship between selected species of Selaginella using DNA barcoding. The genomic DNA of selected species of </span></span></span><em>Selaginella</em><span> was isolated and were examined for DNA polymorphisms. The method described by Sanger has been used to sequence the PCR rbcL products. The phylogenetic analysis was carried out using four methods </span><em>viz.,</em><span> minimum evolution, neighbor joining, UPGMA and maximum parsimony. For the studied species, the PCR amplification result was good, the molecular weight<span> range from 500 to 600 base pairs and the amplicons were sequenced. The obtained sequences were aligned, annotated and submitted in GenBank. The phylogenetic analysis of studied </span></span><em>Selaginella</em><span> species using minimum evolution, NJ and UPGMA methods showed similar trees whether maximum parsimony tree displayed varied tree. The sequence alignment results illustrated that the sequence of </span><em>S. involvens</em>, <em>S. intermedia</em>, <em>S. inaequalifolia</em>, <em>S. wightii</em> and <em>S. tenera</em> were distinct from the other studied <em>Selaginella</em> species <em>viz., S. brachystachya, S. repanda, S. radicata, S. bryopteris</em> and <em>S. delicatula</em>. The cladistics tree also explains the relationship between <em>S. delicatula</em> with and without cones. This concludes that <em>rbcL</em> data is most valuable for inferring phylogenetic relationship between closely related species. DNA barcoding using <em>rbcL</em> gene was applied to distinguish the inter-specific variation among the selected <em>Selaginella</em> species.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139635823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic analysis of bacterial diversity in the surface water, top soil and sediment from the Mangrove ecosystem of Panangad, India","authors":"Elza John ,&nbsp;Nivya Mariam Paul ,&nbsp;S. Selven","doi":"10.1016/j.egg.2024.100225","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100225","url":null,"abstract":"<div><p><span>Mangrove ecosystem contains diverse group of microorganisms<span> that have not been studied extensively. The present study used metagenomic<span> approach for understanding the diversity of bacteria in a mangrove ecosystem from South India. Water, top soil and sediment samples were analyzed and the dominant Phyla were </span></span></span><span><em>Firmicutes</em></span>(75–81 %) followed by <span><em>Proteobacteria</em></span>(12–15 %). <em>Oenococcusoeni</em>(33–35 %) was the most abundant bacterial species, followed by <em>Bacillus(18–22 %)</em> in all the samples. But the remaining species showed variedabundanceamong the samples. <span><em>Lysinibacillus</em><span><em> </em><em>halotolerance</em><em> (9–17 %), Loktanella cinnabarina</em></span></span> (11–13 %), <em>Cohnella hongkongensis</em> (2–7%), <em>Parcubacteria</em>(1–2.5 %) and <em>Oreniasivashensis</em><span> (0.7–2%). Top soil sample had the most abundance of bacteria, but sediment sample had the most species diversity. Water samplefrom Mangrove contained bacteria of more diverse evolutionary lineage, which showed significant diversity among other samples.</span></p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139467774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the genetic tapestry of Indian chicken: A comprehensive study of molecular variations and diversity","authors":"Rangasai Chandra Goli ,&nbsp;Nidhi Sukhija ,&nbsp;Pallavi Rathi ,&nbsp;Kiyevi G. Chishi ,&nbsp;Subrata Koloi ,&nbsp;Anoop Anand Malik ,&nbsp;Chandana Sree C ,&nbsp;P.B. Purohit ,&nbsp;Mahantesh Shetkar ,&nbsp;Kanaka K K","doi":"10.1016/j.egg.2024.100220","DOIUrl":"10.1016/j.egg.2024.100220","url":null,"abstract":"<div><p><span>The genetic<span><span> composition and diversity of chicken breeds/populations have been shaped through selective breeding and management practices. Understanding the </span>genetic diversity<span> of chicken breeds can inform breeding strategies and conservation priorities as well as improve desirable traits in </span></span></span>offspring<span><span>. Assessing genetic diversity between indigenous and exotic breeds provides insights into the benefits of selective breeding and/or crossbreeding. Various studies have investigated genetic diversity indicators in indigenous chicken breeds. Markers are central to study diversity, among them DNA-based markers have proven to be more effective than protein-based markers due to their polymorphism, codominance, and ease of genotyping. Among the 19 diverse chicken breeds currently registered in India, the indigenous Aseel and Kadaknath breeds have more peculiar distinctive characteristics. Synthetic chicken breeds developed by various research organizations exhibit variations in physical features and closely resemble native breeds in terms of eggshell color and meat quality. Overall, chicken is a significant species, because of its economic importance, short </span>reproductive cycle and high fertility. This review shall deal with various aspects of genetic diversity explored in chicken breeds in Indian context.</span></p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139454740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variety × Environment interactions for essential oil yield and cultivar recommendations of lemongrass in drought-prone areas","authors":"Kishan Kumar Singh ,&nbsp;Raj Kishori Lal ,&nbsp;Bhise Rushikesh Nanasaheb ,&nbsp;C.S. Chanotiya ,&nbsp;Yatish Pant ,&nbsp;Somi Ahmed ,&nbsp;Alok Kumar Krishna","doi":"10.1016/j.egg.2024.100222","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100222","url":null,"abstract":"<div><p><span>Lemongrass (</span><span><em>Cymbopogon</em></span><span><span><span> spp.), is a well-known aromatic grass distinguished by its unique lemon scent. The importance of lemongrass in gastronomic, pharmacological, and cosmetic uses is examined in this research paper. The chemical makeup of lemongrass is discussed, emphasizing the presence of citral and other bioactive chemicals that give the herb its flavor, aroma, and medicinal qualities. The study highlights the possible advantages of growing lemongrass in semi-arid areas like Lalitpur (U.P.) and Datia (M.P.) in the Indian state of Bundelkhand, since it may flourish there with little water and improve soil fertility. Five lemongrass varieties—Nima, Praman, CIMAP-Suwarna, Krishna, and CIM-Shikhar—are compared in the study according to their </span>morphological traits, oil yield, herb yield, and citral content. Results demonstrate that the total citral content and essential oil output of the two kinds, LG1 and LG4, are constant between the two genotypes, LG3 and LG5, respectively, across the locations. Regarding the stable types, the location-specific recommendations for essential oil yield were LG1 and LG3, while LG2 and LG4 were suggested for the total citral content. With a few exceptions in the first and second locations, where some traits showed low to medium </span>heritability<span>, most traits in the different sites had broad-sense heritability that was generally high. In all three locations, there were substantial percentages of genetic advance over mean (GAM) for specific features. The retention of genotype stability depends on these characteristics. These cultivars possess advantageous characteristics for growing in the Bundelkhand area, potentially providing farmers with financial gains and improving land in semi-arid regions. The findings highlight the importance of lemongrass as a useful plant with a wide range of applications and aid in the selection of cultivars that are appropriate for a certain area.</span></span></p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139434178","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}