Ecological Genetics and Genomics最新文献

{"title":"Distribution and diversity studies of endophytic and rhizospheric fungi associated with the mangrove, Acanthus ilicifolius, using amplicon sequencing-based metagenomic approach","authors":"Sagar P. Shah ,&nbsp;Jacinta Teresa George ,&nbsp;Jayaprada Rao Chunduri","doi":"10.1016/j.egg.2024.100261","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100261","url":null,"abstract":"<div><p>Fungal endophytes exhibit a broad diversity and are found universally associated with all plant species, playing a vital role in enhancing the host plant's resilience against both biotic and abiotic stressors. In this investigation conducted in Mumbai, India, the Illumina MiSeq sequencing platform was employed to study the endophytic fungal diversity of the common mangrove, <em>Acanthus ilicifolius</em> and its rhizosphere utilizing the amplification of the fungal ribosomal ITS2 region. The results revealed the creation of 307 Operational Taxonomic Units (OTUs) from a total of 663,600 sequencing reads, clustered at a 97 percent similarity level. Evaluation using Simpson and Shannon indices indicated that the highest community diversity was observed in stem tissue compared to root and leaf samples. The total OTUs were categorized into five phyla, 41 orders, 89 families, and 133 genera, with <em>Ascomycota</em> being the predominant phylum at 76.9% relative abundance, followed by <em>Basidiomycota</em> at 22.87%. The most abundant genera in the soil were <em>Malassezia</em> (35%) and <em>Aspergillus</em> (29.5%), while <em>Vishniacozyma</em> (61%) dominated in leaf samples. Unlike stem and root, no single genus dominated these tissues. The findings demonstrated significant distinctions between the fungal endophytic communities in plant tissues and the fungal microbiome in the soil. Notably, the endophyte fungi community in roots exhibited a closer resemblance to stem samples than to leaf samples. FunGuild analysis also revealed characteristic communities in different samples indicating specific functions of these genera. Overall, this study provides novel insights into the intricate composition of endophytic fungi within the tissues of <em>A. ilicifolius</em> and its rhizosphere.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140914219","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":"Precise and consistent genotype identification for essential oil yield and ursolic acid in a multi-year assessment of basil","authors":"R.K. Lal,&nbsp;C.S. Chanotiya,&nbsp;Pankhuri Gupta,&nbsp;Ashish Kumar","doi":"10.1016/j.egg.2024.100260","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100260","url":null,"abstract":"<div><p>In the current study, sixteen basil genotypes in India were analyzed over three years using the AMMI stability model. The study years explained the bulk of the variation in all nine variables. The vast amount of data required for this inquiry hinders plant breeding processes. For basil's two most critical features, ursolic acid and essential oil yield, we found that genotypes 6, 11, and 12 were the best and most consistent options for practically every analyzed property. Furthermore, there were substantial + ve and -ve correlations among the major characteristics that drove stable line selection. Trait associations and stability-related factors both influence stable genotype selection in basil. Based on the results, genotypes 6, 11, and 12 may be recommended for large-area cultivation.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900933","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":"Genealogical structure and genetic variability: A step towards conservation of white Morada Nova sheep in semi-arid region","authors":"Daniel Caetano Sales ,&nbsp;José Ernandes Rufino de Sousa ,&nbsp;Marcos Aurelio Victor de Assunção ,&nbsp;Natanael Silva Félix ,&nbsp;Bianca Ferreira do Nascimento ,&nbsp;Wanderson Lucas Alves dos Santos ,&nbsp;Antonia Gessica Beatriz de Araujo Noronha ,&nbsp;Robson Mateus Freitas Silveira ,&nbsp;Concepta McManus ,&nbsp;Débora Andréa Evangelista Façanha","doi":"10.1016/j.egg.2024.100256","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100256","url":null,"abstract":"<div><p>Morada Nova breed has a low effective herd, and its white variety is in risk of extinction in Brazilian semi-arid region. This study aimed to evaluate white Morada Nova sheep’s genetic variability and population structure in four flocks. These are the only flocks in the world. The assessed parameters of pedigree integrity and a genealogy record of 219 animals. 44.74 % did not have pedigree information on their mother or father, and 50.47 % did not have available information on their grandparents. 52.97 % had a pedigree in their first ancestry (obtained through the average of known parents), 23.74 % in the second, 13.58 % in the third, and 5.33 % in the fourth. The effective size was 10.7, considering the complete equivalent generation. The effective number of founding animals (fe) and ancestors (fa) was 10, indicating the effective participation of all founding animals in the population over the generations, reducing losses of genetic variability. Out of all the ancestors, only 3 explained 50 % of the population’s genetic variability, reflecting the low values of fa and fe. The population’s average inbreeding and kinship coefficients were 2.61 and 4.54. The F statistics of Wright, Fis, Fst, and Fit, were −0.012, 0.016, and 0.003. The genetic conservation index (GCI) had an average of 2.01 ± 1.29, with minimum and maximum values of 1.0 and 6.38, respectively. Approximately, 71 % of the population had GCI below 2.0, while only 5.9 % of sheep had an GCI bigger than 5.0. This indicates the absence of sub-structures inf the population. There is no population subdivision, considering the genealogical structure of the evaluated flocks. The inbreeding and kinship coefficient values are controlled and serve as a starting point for establishing a future management plan for the genetic variability of the flock. It is recommended to use strategies to increase the effective population size, to meet the minimum number recommended by FAO and to promote the conservation and genetic improvement of the breed.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140894267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A review on the application of genomic selection in the improvement of dairy cattle productivity","authors":"Birara Tade,&nbsp;Aberra Melesse","doi":"10.1016/j.egg.2024.100257","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100257","url":null,"abstract":"<div><p>The scope of the present review is to highlight and discuss the application of genomic selection to the improvement of dairy cattle productivity in the face of climate change. The field of genomics is conceived as the scientific study of a species' genome's structure and function using several nucleotide sequences. Genomic selection is the selection of a population based on estimated genomic breeding values. It has been applied as an invaluable tool for increasing the rate of genetic gain with reduced generation intervals while maintaining a good level of selection accuracy. Moreover, it has been widely used for the selection of superior animals with great accuracy at an early age, resulting in enhanced productivity in dairy cattle populations. Genomic selection is particularly efficient in improving low-heritability traits related to the efficiency of feed conversion, reproduction, adaptation to changing production environments, and resistance to various disease transmitting pathogens and vectors. Genomic selection implementation requires careful model selection, and one of the popular models is best linear unbiased prediction (BLUP). Most studies have shown that pure breeds' genomic evaluation can be utilized to improve productivity, efficiency, and genetics by providing a large reference population for dairy cows with high milk production. Research concentrating on the use of genomic selection on <em>Bos indicus</em> cattle is required to assess its effect on the productivity of tropical cattle breeds, as the majority of research studies have been carried out using <em>Bos taurus</em> cattle.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140914288","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":"Review on optimizing dairy sector efficiency: Integrating of genetic markers with managemental techniques","authors":"Muhammad Safdar ,&nbsp;Muhammad Kaleem ,&nbsp;Phelipe Magalhães Duarte ,&nbsp;Sina Salajegheh Tazerji ,&nbsp;Mehmet Ozaslan ,&nbsp;Shahin Hassanpour ,&nbsp;Jayadev Rath ,&nbsp;Swagatika Priyadarsini ,&nbsp;Muhammad Arif Rizwan","doi":"10.1016/j.egg.2024.100259","DOIUrl":"10.1016/j.egg.2024.100259","url":null,"abstract":"<div><p>Recently, advances in molecular genetic markers have raised significant opportunities for enhancing genetic improvement in dairy animals. Commonly used genetic markers are the DNA-based markers; RFLPs and minisatellites, and PCR-based markers like PCR-RFLP, AFLP, microsatellites, and SNP, etc. They are more direct molecular markers that survey DNA variation itself rather than relying on variations in the electrophoretic mobility of proteins that the DNA encodes. These genetic marker approaches are promising tools for improvement in desired milk production traits in dairy animals. While in some instances, the environmental fluctuations are not being considered while selecting a species for a particular geographical locality which results in productivity deterioration and impaired health conditions. These factors incur a huge financial burden on farmers especially in the developing countries. Therefore, the present study attempts to review various genetic markers in versatile aspects which will prove beneficial for scientists, government and non government organizations as well as breeders to undertake further research in animal selection in addition to promote healthy breeding habits in dairy sector.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141034429","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":"Analysis of genetic variability among regional mango varieties grown in Rajshahi district using RAPD markers","authors":"Md Abuhena ,&nbsp;Jubair Al-Rashid ,&nbsp;Abul Kalam Azad","doi":"10.1016/j.egg.2024.100258","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100258","url":null,"abstract":"<div><p>The evaluation of genetic relatedness and diversity is a crucial step in describing and utilizing germplasm for the development of new varieties. In this study, the genetic diversity of four indigenous mango varieties was investigated. Three RAPD primers were used to perform the DNA fingerprint after the DNA was extracted from the leaf sample using the modified CTAB procedure. Cluster analysis was carried out using the unweighted pair-group method of arithmetic means (UPGMA). According to the results, the highest amount of DNA was recovered from the Fazli cultivar (1142.7 ± 0.6 ng/μl). On amplification, the RAPD analysis revealed 25 scoreable bands, of which twenty (20) were monomorphic and five (5) were polymorphic. The primer OPA-03 had the highest polymorphism of 23 %, whereas OPD-04 had no band. The Amropali versus Fazli variety pair had the highest linkage distance (4.69), whilst the Ashawina versus Lengra variety pair had the lowest linkage distance (2.00). At a linkage distance of 4.25, the dendrogram revealed the segregation of the four mango cultivars into two major clusters. Amropali was placed in cluster 1 (C1) and Ashawina, Fazli, and Lengra were placed in cluster 2 (C2) demonstrates that the Amropali variety is distinct from all others. According to the findings, this research could potentially provide insight about the regional mango diversity and be helpful for future mango breeding programs.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140948064","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":"Estimation of genetic diversity utilizing gene-targeted SCoT markers and morpho-chemotypic analyses in Senna alexandrina Mill. (Senna)","authors":"Ashish Kumar ,&nbsp;Anil Kumar Gupta ,&nbsp;Saba Siddiqui ,&nbsp;Soni Gupta ,&nbsp;R.K. Lal ,&nbsp;Abhilasha Srivastava ,&nbsp;Mohammed Haris Siddiqui","doi":"10.1016/j.egg.2024.100252","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100252","url":null,"abstract":"<div><p>Senna, an industrial crop that generates foreign exchange, is planted predominantly in southern India. Senna leaves and pods grown in India are valued in international trade and the global market because they contain a high concentration of the chemical component sennosides. The current investigation was conducted in the CSIR-CIMAP experimental farm in Hyderabad, India. The experiment was designed in an RCBD and replicated three times using twenty-five senna accessions in the years 2020–21 and 2021–22. The combined ANOVA found that all fourteen of the traits studied were highly significant. The D2 analysis and λ1-λ2 values classified the 25 accessions into five clusters with 91.05 % diversity. The molecular diversity was also examined using SCoT markers. As SCoT markers target expressed portions of the genome, the variation among accessions reflects some of the morphological changes among them. For pharmaceutical applications, various lines Gen-1 and 2 (high in Sennosides A and B content) and Gen-4 can be hybridized with Gen-5 and 25 to produce generations high in pharmaceutically relevant Sennosides A and B. Considering genotypes Gen 1 and 2 rank first and second in terms of sennoside A and B contents in leaves (%) and pods, these two genotypes can be employed for large-scale cultivation and to transfer favorable traits in future breeding programs.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140813457","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":"Developments in extremophilic bacterial genomics: A post next generation sequencing era","authors":"Digvijay Verma ,&nbsp;Swati Joshi ,&nbsp;Priyanka Ghimire ,&nbsp;Archana Mishra ,&nbsp;Vinay Kumar","doi":"10.1016/j.egg.2024.100255","DOIUrl":"https://doi.org/10.1016/j.egg.2024.100255","url":null,"abstract":"<div><p>Advancements in sequencing technology, especially the emergence of next-generation sequencing (NGS), have immensely revolutionized the search for extremophilic microorganisms. The complementation of metagenomics and next-generation sequencing tools provides an unprecedented opportunity to explore hidden information about microbial diversity in extreme environments. NGS techniques allow us to understand the genomics, physiology, and evolution of extremophiles. Whole-genome/metagenome-based sequencing has revealed several mysteries of extremophiles that have enhanced our understanding of the evolution of extremophilic microbes. The present article attempts to provide extensive information on bacterial type extremophiles in the context of advanced NGS platforms.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141241769","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":"Unveiling thymosin antimicrobial peptide from pearl spot, Etroplus suratensis: Molecular characterization, phylogenetic analysis, and functional implications","authors":"Kavya Gokul,&nbsp;Raniya Samad,&nbsp;Anne Maria Thomas,&nbsp;Swapna P. Antony","doi":"10.1016/j.egg.2024.100253","DOIUrl":"10.1016/j.egg.2024.100253","url":null,"abstract":"<div><h3>Background</h3><p>Antimicrobial peptides are small, cationic, amphipathic peptides composed of 10–50 amino acids, playing a crucial role in innate immunity. While they are found in both vertebrates and invertebrates, they are particularly effective in invertebrates. This study presents the identification and molecular characterization of the potential antimicrobial peptide thymosin from Pearl spot, <em>Etroplus suratensis</em> (<em>Es-Thyβ</em>). Phylogenetic analysis and structural characterization of the identified peptide are analyzed and substantiated through the study.</p></div><div><h3>Results</h3><p>The sequence analysis of <em>Es-Thyβ</em> revealed an Open Reading Frame (ORF) of 132 nucleotides, encoding a 43-amino acid peptide. The hydrophobicity of the peptide, determined using PepDraw, was found to be +68.93 Kcal*mol⁻¹. Through <em>in silico</em> analysis the identified Thymosin was determined to be <em>Es-Thyβ</em>. The structure and characteristics of the peptide sequence were further analyzed using multiple <em>in silico</em> software tools, providing confirmation of its identity as <em>Es-Thyβ.</em></p></div><div><h3>Conclusion</h3><p>The study identified and described a potential antimicrobial peptide <em>Es-Thyβ</em>, a member of the thymosin β4 family, with conserved sequences and evolutionary links across teleost fishes.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140786975","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":"Estimation of standard heterosis and heterotic grouping of elite sorghum [Sorghum bicolor (L) Moench] inbred lines under moisture stress conditions","authors":"Temesgen Begna ,&nbsp;Techale Birhan ,&nbsp;Taye Tadesse","doi":"10.1016/j.egg.2024.100242","DOIUrl":"10.1016/j.egg.2024.100242","url":null,"abstract":"<div><p>The development and selection of appropriate parents are prerequisites for sorghum hybrid variety development. The lack of a broad genetic base is the most significant constraint to sorghum crop improvement. The assignment of sorghum germplasm lines to appropriate heterotic groups is critical for increasing sorghum productivity. The experiment was conducted to determine the amount of standard heterosis and to categorize sorghum inbred lines into distinct heterotic groups. In the 2019 main cropping season, 42 sorghum genotypes were tested using an alpha-lattice design with two replications. Combined analysis of variance showed that there was a highly significant difference (p &lt; 0.01) among the genotypes for all studied traits. The maximum grain yield was obtained from the hybrids 4x14 (6.32 tha^-1), followed by the hybrids 8x15 (5.92 tha^-1), 1x15 (5.88 tha^-1), 13x14 (5.78 tha^-1) and 6x15 (5.57 tha^-1), with an average value of 5.0 tha^-1. Similarly, the 4x14 hybrid exhibited a maximum grain yield with 30.71 % heterosis, which was greater than the standard check (ESH-4) for grain yield. The two heterotic (A and B) groups were identified based on their specific combining ability effects, whereas three heterotic groups were identified based on their general combining ability effects to develop superior hybrids from broad base and suitable parents. Finally, based on yield performance, heterotic response and combining ability estimates for grain yield and its components, the hybrid crosses 4x14, 8x15, 1x15, 11x14, 11x15, 13x14, and 6x15 were found to be the most promising and potential hybrids that could be exploited commercially after critical evaluation for their superiority and yield stability across locations over the years.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140797005","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}