Ecological Genetics and Genomics最新文献

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

Ecological Genetics and Genomics Pub Date : 2025-03-26 DOI: 10.1016/j.egg.2025.100345

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

{"title":"Molecular and agro-morphological evaluations of interspecific hybridisation in two wild yams (Dioscorea spp.) for genetic improvement","authors":"F.P. Oyedoyin , O.J. Olawuyi , P.A. Agre , Asrat Asfaw","doi":"10.1016/j.egg.2025.100345","DOIUrl":"10.1016/j.egg.2025.100345","url":null,"abstract":"<div><div>Yam (<em>Dioscorea</em> spp.) is an essential food crop particularly in Sub-Saharan Africa. As breeders struggle to meet the rising demand for high-yielding and quality yam, hybridising underutilised wild species presents a promising solution. This study therefore investigated the potentials of hybridising two wild yam species, <em>Dioscorea abyssinica</em> and <em>Dioscorea praehensilis</em> known for their resilience and genetic potential as ancestors of the cultivated West African yam, <em>Dioscorea rotundata</em>, using hand-pollination method. Hybridity was assessed with eight sub-sets of Kompetitive allele-specific markers, and the progenies were evaluated morphologically using standard descriptors. Markers detected heterozygosity in 65 (92.9 %) of 70 progenies, confirming successful hybridisation. Significant (p < 0.05) variation was observed in growth and yield traits, with TDabp2101048, TDabp2101010, and TDabp2101068 excelling in stem length (348.91 cm), internode length (23.36 cm), and vigour (5.85) respectively. The highest tuber length (42.91 cm), tuber weight (1.14 kg) and number of tubers (4) were produced by TDabp2101052, TDabp2101046 and TDabp2101054, respectively. Progenies showed comparable traits to <em>D. rotundata</em>, indicating high genetic compatibility. These findings suggest putative potential for selecting superior genotypes, improving yam breeding programs through genetic diversity, enhancing crop resilience and productivity.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100345"},"PeriodicalIF":0.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143724529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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

Ecological Genetics and Genomics Pub Date : 2025-03-26 DOI: 10.1016/j.egg.2025.100343

Gizaw Wegayehu Tilahun , Awoke Ali Zeleke , Demis Fikre Limeneh

{"title":"Agronomic evaluation and genetic variability studies among fenugreek (trigonella foenum-graecum L.) genotypes at Kulumsa, southeastern Ethiopia","authors":"Gizaw Wegayehu Tilahun , Awoke Ali Zeleke , Demis Fikre Limeneh","doi":"10.1016/j.egg.2025.100343","DOIUrl":"10.1016/j.egg.2025.100343","url":null,"abstract":"<div><div>To develop fenugreek varieties through selection or hybridization, evidence of accession variability is compulsory. This study aimed to evaluate the agronomic performance and get insights on the variability of 28 fenugreek genotypes based on 15 morpho-agronomic traits in Kulumsa, during the 2021 and 2022 cropping years with 5 × 5 alpha lattice design in three replications. The analysis of variance revealed the presence of highly significant (<em>P</em> < 0.01) differences between genotypes for all traits. The top three accessions, namely fg-53072 (2243.70 kg ha-1), fg-201609 (2180.41 kg ha<sup>−1</sup>), and fg-201604 (2049.95 kg ha<sup>−1</sup>), were the high yielders compared to standard checks in a range of 666.69–2395.76 kg ha<sup>−1</sup> seed yield. The majority of traits demonstrated high heritability (≥60) coupled with high genetic advance as the percentage of the mean (>20) and genotypic coefficient of variation (>20). The study found strong positive associations between seed yield and yield-related traits. The first three main components accounted for 83.1 % of the variance in the genotype and five variables contributed the most. The result suggests that to boost the seed yield, selection and improvement could be focused on those traits to enhance progenies' performance. Furthermore, the seed yield of fenugreek could be enhanced by selecting the associated traits with seed yield. The findings have practical implications for breeders and farmers.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100343"},"PeriodicalIF":0.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CRISPR/Cas: A precise and advanced tool for quality trait improvement in crops

Ecological Genetics and Genomics Pub Date : 2025-03-26 DOI: 10.1016/j.egg.2025.100346

Raj Kumar , Supriya Singh , Lokesh Kumar Gangwar , Vivek Kumar , Anjali Ojre , Aditi Singh , Neelam Yadav , Narinderpal Kaur , Paridhi Puri , Rajeshwari Negi , Ajar Nath Yadav

{"title":"CRISPR/Cas: A precise and advanced tool for quality trait improvement in crops","authors":"Raj Kumar , Supriya Singh , Lokesh Kumar Gangwar , Vivek Kumar , Anjali Ojre , Aditi Singh , Neelam Yadav , Narinderpal Kaur , Paridhi Puri , Rajeshwari Negi , Ajar Nath Yadav","doi":"10.1016/j.egg.2025.100346","DOIUrl":"10.1016/j.egg.2025.100346","url":null,"abstract":"<div><div>A new era of agricultural biotechnology has been brought about by the development of CRISPR technology, which presents previously unheard-of possibilities for targeted genome editing and crop modification. This system enables targeted modifications in plant genomes, enhancing traits such as crop productivity, nutritional value, stress tolerance and resistance to disease and pests. Unlike conventional breeding or transgenic approaches, CRISPR/Cas allows for precise gene modification without introducing exogenous DNA, making it more sustainable method for crop improvement. It improving nutritional value by enhancing the biosynthesis of essential vitamins, minerals and proteins and also employed to reduce antinutritional factors in crops, making them healthier for consumption. Additionally, this technology facilitate the development of drought and salt tolerant crop by modifying gene associated with stress response pathways, ensuring stable production under adverse environmental conditions. Furthermore, disease resistance crop verities have generated by editing susceptibility gene or introducing resistance associated mutations, diminishing the demand of chemical pesticides. This technology also enhances post harvest quality by delaying fruit ripening, preventing spoilage and improving shelf life. Despite its potential, challenges such as regulatory hurdles, ethical concern and off target effect remain. However, continue advancement in genome technology are addressing these limitations, paying the way for CRISPR/Cas based crop improvement to play a crucial role in ensuring global food security. As this technology progresses, it offers a promising solution to meet the demand of a growing population while reducing environmental impact associated with traditional agricultural practices.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100346"},"PeriodicalIF":0.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome resource of chitinolytic Brevibacillus formosus YSY-2.2

Ecological Genetics and Genomics Pub Date : 2025-03-19 DOI: 10.1016/j.egg.2025.100344

Dinh Sy Nguyen , Le Nguyen Tieu Ngoc , Bich Thuy Vu , Phuong Thi Pham , Iuliia Pentekhina , Dinh Minh Tran

引用次数: 0

Stability assessment for selection of elite chickpea genotypes across multi-environment based on AMMI and GGE biplots

Ecological Genetics and Genomics Pub Date : 2025-03-15 DOI: 10.1016/j.egg.2025.100342

Manish Sharma, Prakashkumar R. Patel, Mukeshbhai S. Patel, Manubhai P. Patel

{"title":"Stability assessment for selection of elite chickpea genotypes across multi-environment based on AMMI and GGE biplots","authors":"Manish Sharma, Prakashkumar R. Patel, Mukeshbhai S. Patel, Manubhai P. Patel","doi":"10.1016/j.egg.2025.100342","DOIUrl":"10.1016/j.egg.2025.100342","url":null,"abstract":"<div><div>Chickpea (<em>Cicer arietinum</em> L.) is an important cool season food legume but an array of environmental conditions limits its production; therefore, introducing compatible cultivars to a range of environments is an important goal in breeding programs. The present research focused on investigating the impact of genotype-environment interaction on the yield stability and performance of chickpea genotypes across four different locations by deploying the AMMI and GGE biplot method. Over multiple harvests, yield component parameters such as the total number of pods per plant (PP) and Seed index (SI) were assessed as these factors directly contribute to yield enhancement. The AMMI analysis of variance for grain yield revealed significant genotype, environment and G × E interaction indicating the presence of variability among the genotypes and environments. AMMI model exposed the genotypes G5 and G6, as best performer and environment E1 and E2 as most favourable ones for seed yield. GGE biplots revealed that the most desirable genotypes exhibiting high levels of stability along with high yield potential were G6 and G4, both of which are adaptable to a variety of environments. This study also identified the genotypes that adapted well and uniquely to each environment. With its high representativeness and discriminative capacity, environment E1 (Sardarkrushinagar) was determined to be the optimum test environment for choosing genotypes that are typically acclimated. According to our findings, genotypes that are stable and high performing across conditions may be advocated for commercial cultivation or use in crop breeding programmes for enhanced performance.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100342"},"PeriodicalIF":0.0,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143686719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbial taxonomic profiling of textile industry effluent from Tiruppur, Tamil Nadu for water recycling using Kaiju metagenome classifier

Ecological Genetics and Genomics Pub Date : 2025-03-06 DOI: 10.1016/j.egg.2025.100341

Aswetha Iyer, S. Murugan

{"title":"Microbial taxonomic profiling of textile industry effluent from Tiruppur, Tamil Nadu for water recycling using Kaiju metagenome classifier","authors":"Aswetha Iyer, S. Murugan","doi":"10.1016/j.egg.2025.100341","DOIUrl":"10.1016/j.egg.2025.100341","url":null,"abstract":"<div><div>The textile industry in Tiruppur, Tamil Nadu, is a key economic sector, but its wastewater discharge—laden with dyes, chemicals, and heavy metals—poses significant environmental concerns. Effective treatment and recycling of this effluent are essential for sustainability and public health. This study employs the Kaiju metagenome classifier to profile microbial communities in untreated textile effluent, focusing on species-level diversity and its implications for agricultural irrigation and water reuse. Wastewater sample WWS-O was collected from a textile industry discharge point in Tiruppur, and DNA was extracted and sequenced using high-throughput methods. Shotgun metagenomic analysis provided a species-level taxonomic profile, identifying the top 50 microbial species in the effluent. The microbial community was dominated by Sulfur-Reducing Bacteria (SRBs) such as <em>Pleomorphomonas</em> sp. <em>NRK KF1</em> (5739 genes), <em>Desulfomicrobium apsheronum</em> (3942 genes), and <em>Pseudodesulfovibrio indicus</em> (3564 genes), reflecting strong industrial influence. Notably, some of these SRBs have been previously associated with the rhizosphere of agriculturally important plants, suggesting a potential but underexplored role in soil health and plant-microbe interactions. Unlike previous wastewater studies that focus on genus-level microbial diversity in treatment plants, this study achieves species-level resolution, offering deeper insights into microbial adaptation in industrial effluents. The findings emphasize the need for microbial profiling in wastewater management, particularly in evaluating industrial impact, guiding bioremediation efforts, and ensuring the safe reuse of treated water in agriculture. Understanding the taxonomic distribution of native microbial communities can support sustainable wastewater treatment strategies and long-term environmental protection.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100341"},"PeriodicalIF":0.0,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143579728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

First record of Mystus cavasius (Hamilton, 1822) with DNA barcoding confirmation from the upper reaches of the Beas River

Ecological Genetics and Genomics Pub Date : 2025-03-06 DOI: 10.1016/j.egg.2025.100340

Kushal Thakur, Amit Kumar Sharma, Sandeep Kumar, Dixit Sharma, Sunil Kumar, Rakesh Kumar

引用次数: 0

Gains in genetic enhancement of early maturing advanced breeding lines of cowpea [Vigna unguiculata (L.) Walp]

Ecological Genetics and Genomics Pub Date : 2025-03-04 DOI: 10.1016/j.egg.2025.100339

Emmanuel Yaw Owusu , Francis Kusi , Alexander Wireko Kena , Yussif Baba Kassim , Benjamin Annor , Frederick Justice Awuku , Patrick Attamah , Andrews Appiah , Salim Lamini , Felix Kuor , Richard Akromah

{"title":"Gains in genetic enhancement of early maturing advanced breeding lines of cowpea [Vigna unguiculata (L.) Walp]","authors":"Emmanuel Yaw Owusu , Francis Kusi , Alexander Wireko Kena , Yussif Baba Kassim , Benjamin Annor , Frederick Justice Awuku , Patrick Attamah , Andrews Appiah , Salim Lamini , Felix Kuor , Richard Akromah","doi":"10.1016/j.egg.2025.100339","DOIUrl":"10.1016/j.egg.2025.100339","url":null,"abstract":"<div><div>The objective of this study was to determine genetic potentials in extra-early maturing lines of cowpea. Sixteen early and extra-early maturing lines and their recurrent parents were evaluated at Nyankpala and Manga in the Guinea and Sudan savannah ecologies of Ghana, respectively during the rainy season of 2021 main cropping season. Data were collected on the key earliness-related traits, yield, and yield components. The results showed significant differences for genotypes (G) and locations (L). A hierarchical cluster on principal component analysis grouped the genotypes into super-early (≤55 days after sowing<em>,</em> DAS), extra-early (55–60, DAS) and early maturing (61–70, DAS). Within the extra-early maturing cluster, box plot analysis revealed that 75 % of the lines had high grain yield (≥2 t/ha) at Nyankpala, whilst 50 % of them had ≥1.8 t/ha at Manga. The study identified breeding lines which have key farmer preferred traits such as extra-early maturing, high grain yield, and large seed size. Five genotypes (SAC-20KTE-5, SAC-20KTE-3, SAC-20KTE-29, SAC-20KTE-6, and SAC-20KTE-7) were statistically higher than the parental lines, in terms of grain yield, number of days to maturity (≤60 DAS) and hundred seed weight (≥20 g). There was no trade-off for grain yield, biomass yield, and seed size in the selected early maturing lines. Potential lines identified from the study should be extensively evaluated at multi-locations and superior ones released to mitigate the effects of terminal drought and other stresses for cowpea production in the sub-region.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100339"},"PeriodicalIF":0.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143579727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The early immune foundation: Tracking the expression patterns of Crustin and Penaeidin antimicrobial peptide genes in the giant tiger shrimp, Penaeus monodon

Ecological Genetics and Genomics Pub Date : 2025-02-28 DOI: 10.1016/j.egg.2025.100338

K.K. Noorjahan, Anne Maria Thomas, K.L. Dhanya Lenin, Menon T. Athira, T.J. Greeshma, Swapna P. Antony

{"title":"The early immune foundation: Tracking the expression patterns of Crustin and Penaeidin antimicrobial peptide genes in the giant tiger shrimp, Penaeus monodon","authors":"K.K. Noorjahan, Anne Maria Thomas, K.L. Dhanya Lenin, Menon T. Athira, T.J. Greeshma, Swapna P. Antony","doi":"10.1016/j.egg.2025.100338","DOIUrl":"10.1016/j.egg.2025.100338","url":null,"abstract":"<div><div>Shrimp aquaculture is a rapidly growing vital industry prone to disease outbreaks impacting both shrimp health and industry sustainability. Antimicrobial peptides (AMPs), which are small but mighty proteins play a crucial role as part of the shrimp innate immune defence system. This study investigates the expression dynamics of two important Antimicrobial Peptide (AMP) families, Crustin and Penaeidin, in <em>Penaeus monodon,</em> during its developmental stages, coupled with insights into tissue-specific expressions. Two isoforms from each family were subjected to semi-quantitative RT-PCR analysis spanning from early larval stages (Nauplius V, Zoea II, Mysis I) to post-larval stages (3, 10, 13, 19, and 25) and in adult shrimp across gill, haemolymph, and muscle tissues. Our findings unveil an intriguing trajectory: the Penaeidin gene exhibits a consistent upsurge in expression from early larval stages to adulthood, whereas the Crustin gene displays an initial increase during early larval stages followed by diverse expression patterns in later stages. Notably, both genes exhibit high expression in gill tissue, emphasizing its significance as an immune hub. The critical role of AMPs in safeguarding these invertebrates against diseases underscores their potential as a cornerstone of shrimp health management. A better understanding of immunophysiological mechanisms at play along life stages can contribute to the sustainability and growth of the global shrimp aquaculture industry.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100338"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The heat shock matters with specific attention to the expression of Hsp60 under thermal stress in fish: A critical review

Ecological Genetics and Genomics Pub Date : 2025-02-24 DOI: 10.1016/j.egg.2025.100337

Md Toasin Hossain Aunkor , Mohammad Mehedi Hasan Khan , Muhammad Anamul Kabir , Md Topu Raihan , Md Faruque Miah

{"title":"The heat shock matters with specific attention to the expression of Hsp60 under thermal stress in fish: A critical review","authors":"Md Toasin Hossain Aunkor , Mohammad Mehedi Hasan Khan , Muhammad Anamul Kabir , Md Topu Raihan , Md Faruque Miah","doi":"10.1016/j.egg.2025.100337","DOIUrl":"10.1016/j.egg.2025.100337","url":null,"abstract":"<div><div>Thermal stress caused by global climate change can create major challenges in the life of fish, as they are strongly affected by deviations in environmental temperatures. Heat shock proteins (HSPs) are generally synthesized when cells are subjected to temperatures above their normal requirements for survival. In particular, Hsp60 plays a vital role in managing this stress by assisting protein folding, preventing aggregation, and maintaining cellular integrity. This review primarily highlights the different effects of heat stress on the life of fish. However, special emphasis is placed on compiling and analyzing current knowledge of Hsp60 expression in various fish species under different temperatures. This paper also investigates the physiological impacts of thermal stress on various organs, such as the liver, heart, spleen, gills, kidney, brain, muscle, ovary, and testis to enhance the broader understanding of fish response to temperature fluctuations, with a focus on Hsp60 expression. In addition, the contribution of Hsp60 to embryonic development is also accentuated to some extent. Furthermore, the paper outlines several research gaps in the study of Hsp60 expression, which will be imperative for future efforts to improve our understanding of this essential chaperon in fish species.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100337"},"PeriodicalIF":0.0,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143509751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0