1,069 results on '"diversity analysis"'
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2. Chia (Salvia hispanica L.) flour modulates the intestinal microbiota in Wistar rats fed a high-fat and high-fructose diet
- Author
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Morais, Violeta Nunes de, Gomes, Mariana Juste Contin, Grancieri, Mariana, Moreira, Luiza de Paula Dias, Toledo, Renata Celi Lopes, Costa, Neuza Maria Brunoro, da Silva, Bárbara Pereira, and Martino, Hércia Stampini Duarte
- Published
- 2023
- Full Text
- View/download PDF
3. Caffeic acid-grafted chitosan/polylactic acid packaging affects bacterial infestation and volatile flavor of postharvest Agaricus bisporus
- Author
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Bai, Shiqi, Han, Ping, Zhou, Zhicheng, Ma, Ning, Fang, Donglu, Yang, Wenjian, Hu, Qiuhui, and Pei, Fei
- Published
- 2023
- Full Text
- View/download PDF
4. Assessment of bacterial communities of Coptotermes gestroi termite workers attacking Ironwood trees (Casuarina equisetifolia) in Guam for the presence of Ironwood tree decline-associated pathogens.
- Author
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Setia, Garima, Chen, Junyan, Schlub, Robert, and Husseneder, Claudia
- Subjects
KLEBSIELLA oxytoca ,RALSTONIA solanacearum ,BACTERIA classification ,BACTERIAL communities ,TERMITES - Abstract
The Ironwood tree (Casuarina equisetifolia) holds a significant ecological role in Guam where a decline in Ironwood trees was first documented in 2002. Studies have linked the Ironwood tree decline (IWTD) to bacteria from the Ralstonia solanacearum complex and wetwood bacteria, specifically Klebsiella oxytoca and Klebsiella variicola. Presence of termites was first found to be associated with IWTD in 2010; however, the role of termites in IWTD is still not clear. The Asian subterranean termite, Coptotermes gestroi (Wasmann) (Blattodea: Rhinotermitidae) frequently attacks Ironwood trees. As workers of this soil-dwelling species of the lower termites harbor a diverse microbial community in their bodies, we examined whether C. gestroi workers carry IWTD-associated bacteria and could, therefore, act as vectors. We described the bacterial community in C. gestroi workers using 16S rRNA gene sequencing and tested the impact of factors related to the location and health of the Ironwood tree the termites were collected from on termite bacterial diversity. Feeding assays were performed to assess if workers show preference in consumption depending on the amount of Ralstonia and wetwood bacteria in the food source. Health of Ironwood trees and level of site management impacted the bacterial composition of C. gestroi termite workers attacking the trees. Although C. gestroi workers equally consumed food sources with high and low Ralstonia and wetwood bacteria load in lab experiments, Ralstonia and other IWTD-related bacteria were not detected in considerable amounts in termite workers collected from trees. Thus, C. gestroi workers are not a vector for bacteria associated with IWTD in Guam. [ABSTRACT FROM AUTHOR]
- Published
- 2025
- Full Text
- View/download PDF
5. 不同富营养培养基对人肠道菌群的体外培养效果比较分析.
- Author
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路婧, 夏雪娟, 黄骏楠, 陈泫羽, 周璐, and 董庆利
- Abstract
Copyright of Food & Fermentation Industries is the property of Food & Fermentation Industries and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2024
- Full Text
- View/download PDF
6. Analysis of intestinal bacterial diversity and its gene function prediction in black-capped capuchin (Sapajus apella).
- Author
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Yu, Jinghe, Bai, Gaowa, He, Yuxing, Liu, Mingchao, Yang, Xiaofeng, Li, Jiao, Shen, Yue, Lu, Shoufeng, and Bao, Wuyundalai
- Subjects
- *
CAPUCHIN monkeys , *BACTERIAL diversity , *FECAL analysis , *NUCLEOTIDE sequencing , *INTESTINES - Abstract
In this study, we used high-throughput sequencing technology to analyze the diversity and predict gene function of intestinal bacteria from captive black-capped capuchin in two wildlife parks. The results showed that the composition of intestinal gut bacterial diversity was significantly higher in black-capped capuchins monkeys from ES than HT. Moreover, high similarity of intestinal bacteria of black-capped capuchins at the same site was found by sample stratum clustering. Black-capped capuchins intestinal bacteria can be clustered into 2296 ASVs, belonging to 16 phyla, 99 families and 210 genera, respectively. The dominant phyla were Bacteroidota and Firmicutes in the intestinal bacteria of black-capped capuchins, but there were differences in the dominant bacterial families and dominant bacterial genera between ES and HT, and the bacterial families with significant differences had correspondence with bacterial genera. The results provide a basis for the study of intestinal bacteria in black-capped capuchins and the isolation and purification of dominant bacteria. The results of this study fill the gap in the study of intestinal bacterial diversity and its gene functions in black-capped capuchins, and provide a reference for the isolation of dominant bacteria in black-capped capuchins' intestinal microbes and the discovery and study of novel functional genes. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
7. Characterization of rice landraces of Lamjung and Tanahun districts.
- Author
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Shrestha, Prajwal, Kandel, Bishnu Prasad, Shrestha, Prabin, Karanjit, Ritika, Dhakal, Merina, and Poudel, Ankur
- Abstract
Agro-morphological characterization of rice is vital for rice breeding programs, which help to document phenotypical differences. The research was conducted in Sundarbazar, Lamjung, during the spring season from February to August 2023, where the design was completely randomized with two replications. Twenty-five quantitative and thirty-nine qualitative traits were recorded according to the characterization descriptors of the International Rice Research Institute, Sixteen quantitative traits were observed for 16 landraces, and 11 showed high coefficient of variance (CV) values. In comparison, for the remaining nine traits, two traits showed a high CV value for all 20 landraces. Three principal components with an eigenvalue greater than one accounted for 88.2% variation. Furthermore, principal component analysis bolsters our results by clustering rice landraces into four clusters. The intra-cluster distance was most significant in cluster I (4.25) and the lowest in cluster IV (2.16), thereby indicating that genotype diversity was the greatest in cluster I and least diverse in cluster IV. Three of the four clusters did not follow geographic distribution, possibly indicating free exchange of landraces among the farmers and adaption of the landraces in both districts. Monomorphism was observed for leaf blade: lemma: anthocyanin in keel and lemma: anthocyanin of the area below apiculus, while high polymorphism was observed for lemma: the colour of apiculus (early observation) (1.542) according to Shannon-Weiner diversity index (H′). Even distribution was observed for traits ligule: colour (0.971), lemma: colour of apiculus: (late observation) (0.920), and sterile lemma: shape (0.908). The Simpson evenness index was maximum for lemma: colour of apiculus (0.783), indicating a higher probability of obtaining two characters for a trait under random selection. Thus, the present study is the preliminary depiction for characterization and diversity analysis in cultivated rice landraces with potential for further rice improvement programs. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
8. Comparative root phenotyping unveils key insights into the root system architecture of buckwheat (Fagopyrum sp.) species, a valuable crop of western Himalayan Kashmir.
- Author
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Singh, Diksha, Sudan, Jebi, Zaffar, Aaqif, Naik, Zafir, Bhat, M. Ashraf, Shikari, Asif B., Dhekale, Bhagyashree, Sofi, Parvaze Ahmad, and Zargar, Sajad Majeed
- Subjects
- *
AGRICULTURE , *CROP yields , *POLYVINYL chloride , *DROUGHT tolerance , *ABIOTIC stress , *BUCKWHEAT - Abstract
Buckwheat is an important nutritional and nutraceutical crop; however, owing to its low yield and productivity, its potential has not been harnessed on account of its cultivation in low-input marginal farming systems, where its productivity is limited by various abiotic stresses, including water stress. Roots play a critical role in plant growth, development, and tolerance to drought stress. The present study was the first comprehensive attempt to understand the root system architecture (RSA) of buckwheat using root morphology and in-depth features of RSA through root scanning. A total of 117 diverse genotypes of buckwheat, comprising both common and Tartary buckwheat, were cultivated in polyvinyl chloride columns in the greenhouse. The study revealed substantial variability for all the root and shoot traits of buckwheat. Comparative analysis indicated that Tartary buckwheat has better root features compared to common buckwheat. The correlation analysis showed the surface area, medium root length, and medium root volume were positively correlated and branching frequency and root shoot ratio were negatively correlated. The study identified potential genotypes with robust RSA that can be used for the development of climate-resilient buckwheat varieties. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
9. Pathogenicity and multigene sequence analysis reveal the widespread distribution of Alternaria alternata causing early blight in tomato.
- Author
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Abassy, Omer, Balamurugan, Alexander, Sahu, Kuleshwar Prasad, Patel, Asharani, Sheoran, Neelam, Reddy, Bhaskar, Gogoi, Robin, Singh, Krishna Kumar, and Kumar, Aundy
- Subjects
ALTERNARIA alternata ,ALTERNARIA ,MYCOSES ,SEQUENCE analysis ,DATABASES ,TUBULINS - Abstract
The study investigated early blight, a major fungal disease affecting tomatoes, across two distinct agroclimatic zones in India, resulting in a collection of 90 Alternaria isolates. Morpho-cultural characterization grouped these isolates into 11 putative clusters, which were subjected to further analysis. Pathogenicity tests revealed that all 11 isolates were pathogenic on the Pusa-Ruby tomato cultivar. Molecular analysis, specifically comparing nucleotide sequences of the ß-tubulin (ß-tub), cytochrome-B (cyt-B) and Alternaria major allergen gene (Alt a1) using the MycoCosm and NCBI databases, identified these isolates as Alternaria alternata. The phylogenetic tree, constructed via the Maximum-Likelihood method using the Alt a1 gene, demonstrated that all 11 isolates clustered with A. alternata, Sector—Alternaria, alongside reference strains from the NCBI database. Additionally, Alt a1 showed the capability to differentiate sub-groups within Sect.—Alternaria, indicating its intraspecific discriminatory potential. In conclusion, the study confirms the widespread presence of pathogenic A. alternata on tomatoes and highlights the importance of marker gene, Alt a1 in discerning the identity of Alternaria species. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
10. Diversity analysis, nutrition, and flavor evaluation of amino acids in Chinese native geese germplasms
- Author
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Haiyue Cao, Zhenfei Yang, Ligang Wang, Xin Li, Yuanyuan Bian, Hongchang Zhao, Mengli Zhao, Xiaoming Li, Jun Wang, Guobo Sun, Shanmao Ren, Jun Yu, Huizhen Gao, Xuan Huang, and Jian Wang
- Subjects
amino acids ,diversity analysis ,flavor ,geese germplasms evaluation ,nutrition ,Animal culture ,SF1-1100 ,Veterinary medicine ,SF600-1100 - Abstract
Background and Aim: As living standards improve and consumption patterns shift, the market for goose meat continues to grow because of its exceptional dietary quality and distinctive flavor. The composition and content of amino acids are critical for determining the nutritional value and flavor of meat. This study aimed to evaluate the nutritional value and flavor of 10 Chinese native geese germplasms based on their amino acid content and composition. Materials and Methods: A total of 568 geese from 10 Chinese native geese germplasms reared under identical conditions were slaughtered at 10 weeks of age. The pectoralis and thigh muscles (thighs) were collected to determine the amino acid content using an amino acid analyzer. Subsequently, diversity, variance, cluster, and principal component analyses were performed to identify superior germplasm with improved nutrition and flavor. Results: The results revealed 17 amino acids in goose meat, with Glutamate and Aspartate being the most abundant. The amino acid scores of goose meat exceeded the values recommended by the Food and Agriculture Organization/World Health Organization. The Shannon–Wiener Diversity Index (1.72–2.07) indicated a high degree of diversity in amino acid content among geese germplasms. The pectoralis exhibited significantly higher amino acid content (p < 0.05 or p < 0.01) than the thigh, except for the essential amino acids to total amino acids ratio (p < 0.05 or p < 0.01). The 10 germplasms were categorized into four clusters, with Wanxi (WX) and Taizhou (TZ) geese grouped in Cluster I, displaying significantly higher nutritional value and flavor (p < 0.05 or p < 0.01) than other germplasms. Conclusion: Germplasms with superior nutritional value and flavor (WX and TZ) were identified among 10 Chinese native geese germplasms, providing valuable insights for the conservation of existing germplasms and the cultivation of new goose breeds with improved meat quality.
- Published
- 2024
- Full Text
- View/download PDF
11. Comparative root phenotyping unveils key insights into the root system architecture of buckwheat (Fagopyrum sp.) species, a valuable crop of western Himalayan Kashmir
- Author
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Diksha Singh, Jebi Sudan, Aaqif Zaffar, Zafir Naik, M. Ashraf Bhat, Asif B. Shikari, Bhagyashree Dhekale, Parvaze Ahmad Sofi, and Sajad Majeed Zargar
- Subjects
Buckwheat ,Root phenotyping ,Diversity analysis ,Root biomass ,Crop yield ,Agriculture (General) ,S1-972 ,Environmental sciences ,GE1-350 - Abstract
Abstract Buckwheat is an important nutritional and nutraceutical crop; however, owing to its low yield and productivity, its potential has not been harnessed on account of its cultivation in low-input marginal farming systems, where its productivity is limited by various abiotic stresses, including water stress. Roots play a critical role in plant growth, development, and tolerance to drought stress. The present study was the first comprehensive attempt to understand the root system architecture (RSA) of buckwheat using root morphology and in-depth features of RSA through root scanning. A total of 117 diverse genotypes of buckwheat, comprising both common and Tartary buckwheat, were cultivated in polyvinyl chloride columns in the greenhouse. The study revealed substantial variability for all the root and shoot traits of buckwheat. Comparative analysis indicated that Tartary buckwheat has better root features compared to common buckwheat. The correlation analysis showed the surface area, medium root length, and medium root volume were positively correlated and branching frequency and root shoot ratio were negatively correlated. The study identified potential genotypes with robust RSA that can be used for the development of climate-resilient buckwheat varieties.
- Published
- 2024
- Full Text
- View/download PDF
12. GENETIC VARIABILITY, ASSOCIATION AND GENETIC DIVERSITY STUDIES OF GERMPLASM LINES IN RICE (Oryza Sativa L.) BASED ON YIELD COMPONENTS, YIELD AND BRAN OIL CHARACTERISTICS.
- Author
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Stephen, Tessy Snega, Palaniappan, Shanthi, Ramasamy, Venkatachalam, Padmanaban, Geetha, Kaliappan, Sathiya Bama, and Swaminathan, Manonmani
- Abstract
Genetic variability is crucial in improving crops like rice (Oryza sativa L.), focusing on enhancing yield and nutritional quality. In this study 54 rice genotypes were evaluated for phenotypic and genetic variability, heritability, genetic advance, correlations, direct and indirect effects, and genetic diversity on yield attributing traits, yield, and bran oil character. Results showed that traits like flag leaf length, flag leaf width, total number of spikelets, total number of fertile spikelets, test weight, rice bran oil (RBO) percentage, and single plant yield exhibited high values for PCV,GCV, h2,GAM exhibiting its potential for selection in breeding programmes. Correlation studies indicated negative correlation of rice bran oil % with flag leaf length (r = -0.34) which was further confirmed in path analysis where flag leaf length(-0.15) and rice bran oil %(-0.12) had a negative direct effect on single plant yield. Diversity analysis using Mahalanobis's D² categorized the genotypes into 22 distinct groups, highlighting significant genetic diversity. According to the analysis, rice bran oil percentage contributed the most to genetic divergence (37.09%), followed by grain length (22.42%) and test weight (20.07%). This study offers crucial insights for future breeding strategies targeting improved yield and nutritional quality, particularly emphasizing bran oil content and other essential traits. [ABSTRACT FROM AUTHOR]
- Published
- 2024
13. Duck swarm algorithm: theory, numerical optimization, and applications.
- Author
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Zhang, Mengjian and Wen, Guihua
- Subjects
- *
PARTICLE swarm optimization , *OPTIMIZATION algorithms , *GREY Wolf Optimizer algorithm , *SWARM intelligence , *WIRELESS sensor networks , *BEES algorithm - Abstract
A swarm intelligence-based optimization algorithm, named Duck Swarm Algorithm (DSA), is proposed in this study, which is inspired by the searching for food sources and foraging behaviors of the duck swarm. Two rules are modeled from the finding food and foraging of the duck, which corresponds to the exploration and exploitation phases of the proposed DSA, respectively. The performance of the DSA is verified by using multiple CEC benchmark functions, where its statistical (best, mean, standard deviation, and average running-time) results are compared with seven well-known algorithms like Particle swarm optimization (PSO), Firefly algorithm (FA), Chicken swarm optimization (CSO), Grey wolf optimizer (GWO), Sine cosine algorithm (SCA), and Marine-predators algorithm (MPA), and Archimedes optimization algorithm (AOA). Moreover, the Wilcoxon rank-sum test, Friedman test, and convergence curves of the comparison results are utilized to prove the superiority of the DSA against other algorithms. The results demonstrate that DSA is a high-performance optimization method in terms of convergence speed and exploration–exploitation balance for solving the numerical optimization problems. Also, DSA is applied for the optimal design of six engineering constrained optimization problems and the node optimization deployment task of the Wireless Sensor Network (WSN). Overall, the comparison results revealed that the DSA is a promising and very competitive algorithm for solving different optimization problems. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
14. Assessment and phenotypic identification of millet germplasm (Setaria italica L.) in Liaoning, China.
- Author
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Li, Xintong, He, Weifeng, Wang, Honghao, and Xu, Min
- Subjects
GREY relational analysis ,GERMPLASM ,FOXTAIL millet ,CLUSTER analysis (Statistics) ,PRINCIPAL components analysis - Abstract
Aims: This study evaluated millet germplasms in Liaoning Province to support the collection, preservation and innovation of millet germplasm resources. Methods: The study was conducted from 2018 to 2020, involved the selection of 105 millet germplasm resources from the Germplasm Bank of the Liaoning Academy of Agricultural Sciences (LAAS), the observation and recording of 31 traits, and the application of multivariate analysis methods to assess phenotypic diversity. Results: From the diversity analysis and correlation analysis, it was found that the tested traits had abundant diversity and complex correlations among them. Principal component analysis (PCA) comprehensively analyzed all quantitative traits and extracted seven principal components. Grey relational analysis (GRA) highlighted the varied contributions of different traits to yield. Through systematic cluster analysis (SCA), the resources were categorized into six groups at Euclidean distance of 17.09. K-mean cluster analysis determined the distribution interval and central value of each trait, then identified resources with desirable traits. Conclusion: The results revealed resources that possess characteristics such as upthrow seedling leaves, more tillers and branches, larger and well-formed ears, and lodging resistance prefer to higher grain yield. It was also discovered that the subear internode length (SIL) could be an indicator for maturity selection. Four specific resources, namely, Dungu No. 1, Xiao-li-xiang, Basen Shengu, and Yuhuanggu No. 1, were identified for further breeding and practical applications. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
15. Comparative Analysis of Bacterial Community Structures in Earthworm Skin, Gut, and Habitat Soil across Typical Temperate Forests.
- Author
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Wang, Kang, Yuan, Ning, Zhou, Jia, and Ni, Hongwei
- Subjects
TEMPERATE forests ,TEMPERATE forest ecology ,CONIFEROUS forests ,DECIDUOUS forests ,MICROBIAL communities - Abstract
Earthworms are essential components in temperate forest ecosystems, yet the patterns of change in earthworm-associated microbial communities across different temperate forests remain unclear. This study employed high-throughput sequencing technology to compare bacterial community composition and structure in three earthworm-associated microhabitats (skin, gut, and habitat soil) across three typical temperate forests in China, and investigated the influence of environmental factors on these differential patterns. The results indicate that: (1) From warm temperate forests to cold temperate forests, the soil pH of the habitat decreased significantly. In contrast, the physicochemical properties of earthworm skin mucus exhibited different trends compared to those of the habitat soil. (2) Alpha diversity analysis revealed a declining trend in Shannon indices across all three microhabitats. (3) Beta diversity analysis revealed that the transition from warm temperate deciduous broad-leaved forest to cold temperate coniferous forest exerted the most significant impact on the gut bacterial communities of earthworms, while its influence on the skin bacterial communities was comparatively less pronounced. (4) Actinobacteria and Proteobacteria were the predominant phyla in earthworm skin, gut, and habitat soil, but the trends in bacterial community composition differed among the three microhabitats. (5) Mantel tests revealed significant correlations between bacterial community structures and climatic factors, physicochemical properties of earthworm habitat soil, and physicochemical properties of earthworm skin mucus. The findings of this study offer novel perspectives on the interplay between earthworms, microorganisms, and the environment within forest ecosystems. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
16. 三江源地区野生多枝黄耆资源表型性状 多样性及与环境因子的相关性分析.
- Author
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刘青青, 蔡宗程, 吕亮雨, 雷莎清, 张海蓉, 马 芳, and 施建军
- Subjects
ASTRAGALUS (Plants) ,PRINCIPAL components analysis ,POPULATION differentiation ,CITIES & towns ,CALYX - Abstract
Copyright of Journal of Henan Agricultural Sciences is the property of Editorial Board of Journal of Henan Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2024
- Full Text
- View/download PDF
17. Metagenome-based diversity and functional analysis of culturable microbes in sugarcane
- Author
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Haidong Lin, Liang Wu, Lijun Zhang, Quang Kiet Ta, Peng Liu, Jinkang Song, and Xiping Yang
- Subjects
sugarcane ,culturable microbes ,metagenome ,diversity analysis ,functional analysis ,Microbiology ,QR1-502 - Abstract
ABSTRACT Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane’s tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields.IMPORTANCEThis work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.
- Published
- 2025
- Full Text
- View/download PDF
18. Assessment of bacterial communities of Coptotermes gestroi termite workers attacking Ironwood trees (Casuarina equisetifolia) in Guam for the presence of Ironwood tree decline-associated pathogens
- Author
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Garima Setia, Junyan Chen, Robert Schlub, and Claudia Husseneder
- Subjects
termite ,bacterial taxonomy ,diversity analysis ,metataxonomics ,amplicon sequencing ,16S ,Microbiology ,QR1-502 - Abstract
The Ironwood tree (Casuarina equisetifolia) holds a significant ecological role in Guam where a decline in Ironwood trees was first documented in 2002. Studies have linked the Ironwood tree decline (IWTD) to bacteria from the Ralstonia solanacearum complex and wetwood bacteria, specifically Klebsiella oxytoca and Klebsiella variicola. Presence of termites was first found to be associated with IWTD in 2010; however, the role of termites in IWTD is still not clear. The Asian subterranean termite, Coptotermes gestroi (Wasmann) (Blattodea: Rhinotermitidae) frequently attacks Ironwood trees. As workers of this soil-dwelling species of the lower termites harbor a diverse microbial community in their bodies, we examined whether C. gestroi workers carry IWTD-associated bacteria and could, therefore, act as vectors. We described the bacterial community in C. gestroi workers using 16S rRNA gene sequencing and tested the impact of factors related to the location and health of the Ironwood tree the termites were collected from on termite bacterial diversity. Feeding assays were performed to assess if workers show preference in consumption depending on the amount of Ralstonia and wetwood bacteria in the food source. Health of Ironwood trees and level of site management impacted the bacterial composition of C. gestroi termite workers attacking the trees. Although C. gestroi workers equally consumed food sources with high and low Ralstonia and wetwood bacteria load in lab experiments, Ralstonia and other IWTD-related bacteria were not detected in considerable amounts in termite workers collected from trees. Thus, C. gestroi workers are not a vector for bacteria associated with IWTD in Guam.
- Published
- 2024
- Full Text
- View/download PDF
19. Analysis of intestinal bacterial diversity and its gene function prediction in black-capped capuchin (Sapajus apella)
- Author
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Jinghe Yu, Gaowa Bai, Yuxing He, Mingchao Liu, Xiaofeng Yang, Jiao Li, Yue Shen, Shoufeng Lu, and Wuyundalai Bao
- Subjects
Black-capped capuchin ,feces ,bacteria ,diversity analysis ,gene function ,Veterinary medicine ,SF600-1100 - Abstract
In this study, we used high-throughput sequencing technology to analyze the diversity and predict gene function of intestinal bacteria from captive black-capped capuchin in two wildlife parks. The results showed that the composition of intestinal gut bacterial diversity was significantly higher in black-capped capuchins monkeys from ES than HT. Moreover, high similarity of intestinal bacteria of black-capped capuchins at the same site was found by sample stratum clustering. Black-capped capuchins intestinal bacteria can be clustered into 2296 ASVs, belonging to 16 phyla, 99 families and 210 genera, respectively. The dominant phyla were Bacteroidota and Firmicutes in the intestinal bacteria of black-capped capuchins, but there were differences in the dominant bacterial families and dominant bacterial genera between ES and HT, and the bacterial families with significant differences had correspondence with bacterial genera. The results provide a basis for the study of intestinal bacteria in black-capped capuchins and the isolation and purification of dominant bacteria. The results of this study fill the gap in the study of intestinal bacterial diversity and its gene functions in black-capped capuchins, and provide a reference for the isolation of dominant bacteria in black-capped capuchins’ intestinal microbes and the discovery and study of novel functional genes.
- Published
- 2024
- Full Text
- View/download PDF
20. Unveiling the genetic potential of Terminalia chebula Retz. accessions from North-East and South India: A morphometric analysis
- Author
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Shobith Murthy Mahadeva, Umesh Kanna Subramani, Parthiban Kalappan Thangamuthu, Devanand Pachanoor Subbian, Radha Palaniswamy, Senthilraja Kandasamy, and Venkatesan Subramanian
- Subjects
Association studies ,Genetic variability ,Path co-efficient analysis ,Diversity analysis ,Cluster analysis ,Forestry ,SD1-669.5 ,Plant ecology ,QK900-989 - Abstract
This study examined genetic diversity and growth performance of thirty Terminalia chebula genotypes from various regions of India. Seedlings were evaluated for growth attributes over 180 days after transplanting (DAT). Significant variations were observed across accessions for traits like shoot length, root length, collar diameter and volume. MHTC 04 showed superior performance, with maximum shoot length (36.23 cm) and root length (38.47 cm) at 180 DAT. KETC 05 exhibited the highest collar diameter (1.08 cm) and volume index (39.35) at 180 DAT. The genetic analysis revealed low to moderate PCV and GCV for most traits. Volume index showed the highest PCV (47.31 %) and GCV (47.23 %). High heritability (>95 %) was observed for several traits viz., root length, collar diameter and volume index. Path coefficient analysis identified collar diameter and shoot fresh weight as having the strongest positive direct effects on quality index. Cluster analysis grouped 30 genotypes into 10 clusters with cluster II being the largest (8 progenies). Quality index contributed the maximum (59.30 %) towards divergence followed by shoot dry weight (13.94 %) and volume index (8.28 %). This study identified promising genotypes and important traits for T. chebula improvement programmes, highlighting the potential for selective breeding to enhance the seedling quality and growth performance.
- Published
- 2024
- Full Text
- View/download PDF
21. Analysis of the Microbial Communities and Populations in Soils with Continuous Cropping of Curcuma wenyujin and Fumigation
- Author
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Yanhui GUAN, Zixue JIN, Lang XU, Bo WANG, and Qiongguang LIU
- Subjects
curcuma wenyujin ,continuous cropping ,dazomet ,fumigation ,soil microorganism ,diversity analysis ,Agriculture - Abstract
【Objective】The study was conducted to clarify the microbial community structure in soil with continuous cropping of Curcuma wenyujin and fumigation treatment, aiming to lay a foundation for alleviating continuous cropping obstacles in C. wenyujin cultivation.【Method】The soil under a continuous cropping of C. wenyujin for 3 years was selected and fumigated with dazomet one month before planting C. wenyujin. After 7-month cultivation of C. wenyujin, we collected soil samples from three types of plots: continuous cropping, fumigated and uncultivated. Total soil DNA was extracted, and the population and diversity of microbial communities (fungi and bacteria) were analyzed by using PacBio Sequel thirdgeneration sequencing.【Result】The results showed that C. wenyujin plants in the fumigated soil exhibited good growth and minimal disease incidence, while those in the continuous cropping soil had poor growth and severe seedling death. Analysis of bacterial communities at the phylum level revealed that the abundance of AD3, TK10 and WPS-2 decreased in rhizosphere soil after continuous cropping compared with those in uncultivated soil. Fumigation of continuous cropping soil increased the abundance of beneficial bacteria with biocontrol functions such as Bacillus and Sphingomonas. Among the three soil types, 5 fungal phyla were abundant, including Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, and unclassified_k_ Fungi. Ascomycota had the lowest abundance in uncultivated C. wenyujin soil, but continuous cropping significantly increased its abundance, while Basidiomycota showed a significant decrease. Several beneficial fungal genera, including Chaetomium, Penicillium, Aspergillus, Myrothecium, Thielavia, Humicola, Rhizophlyctis, Microdochium, Ramicandelaber, Albifi mbria, Curvularia, Gigaspora, Nigrospora, Neocosmospora, Talaromyces, Roussoella, Rhytidhysteron, Boothiomyces, Apiotrichum, Ochroconis, Saitozyma, Trichosporon and Phoma, had higher abundance in fumigated soil than that in continuous cropping soil. In contrast, continuous cropping soil had a higher accumulation of pathogenic microorganisms.【Conclusion】Continuous cropping of C. wenyujin leads to the accumulation of harmful soil microorganism, resulting in continuous cropping obstacles. Fumigation with dazomet can reduce the number of soil-borne pathogens and increase the abundance of beneficial microbial populations, thereby mitigating continuous cropping obstacles in C. wenyujin cultivation.
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- 2024
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22. Karakterisasi sifat kuantitatif dan sifat kualitatif dua puluh satu genotipe melon (Cucumis melo L.)
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Rova Endang Kuhesa, Parwito Parwito, and Dia Novita Sari
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cluster analysis ,diversity analysis ,fruit characterization ,quantitative ,qualitative. ,Education (General) ,L7-991 ,Science (General) ,Q1-390 - Abstract
Dalam tiga tahun terakhir produksi melon mengalami penurunan. Oleh sebab itu, perlu dilakukan peningkatan produksi dengan melakukan pengembangan varietas unggul berdaya hasil tinggi. Karakterisasi merupakan langkah awal dalam perakitan varietas tanaman. Penelitian ini bertujuan untuk mengetahui karakteristik 21 genotipe buah melon. Penelitian telah dilakukan pada Januari hingga Maret 2024. Penelitian dilakukan di kebun percobaan di Desa Lubuk Saung Kabupaten Bengkulu Utara Provinsi Bengkulu. Penelitian menggunakan rancangan kelompok lengkap teracak (RKLT) faktor tunggul dan diulang sebanyak tiga kali. Faktor yang digunakan adalah 21 genotipe melon. Hasil penelitian menujukkan bahwa analisis cluster dengan kemiripian 33,33 menghasilkan 5 kelompok melon dan G15 adalah genotipe paling berbeda diantara genotipe lainnya. Ukuran daun sedang dan warna daun hijau sedang adalah ukuran dan warna paling dominan. Panjang cuping daun kategori sedang dan perkembangan cuping daun kategori lemah adalah yang paling dominan. Bentuk dasar buah berbentuk bulat adalah bentuk dasar buah yang paling banyak. Kulit buah sebelum matang paling banyak adalah berwarna hijau dan warna daging buah saat matang paling banyak adalah warna putih. Buah tidak memiliki alur adalah paling dominan dan keriputan permukaan buah kategori sangat lemah adalah paling dominan.
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- 2024
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23. Development of MetaXplore: An Interactive Tool for Targeted Metagenomic Analysis
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Naima Bel Mokhtar, Elias Asimakis, Ioannis Galiatsatos, Amal Maurady, Panagiota Stathopoulou, and George Tsiamis
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microbial profiling ,shiny framework ,amplicon data analysis ,data visualization ,taxonomic composition ,diversity analysis ,Biology (General) ,QH301-705.5 - Abstract
Over the last decades, the analysis of complex microbial communities by high-throughput sequencing of marker gene amplicons has become routine work for many research groups. However, the main challenges faced by scientists who want to make use of the generated sequencing datasets are the lack of expertise to select a suitable pipeline and the need for bioinformatics or programming skills to apply it. Here, we present MetaXplore, an interactive, user-friendly platform that enables the discovery and visualization of amplicon sequencing data. Currently, it provides a set of well-documented choices for downstream analysis, including alpha and beta diversity analysis, taxonomic composition, differential abundance analysis, identification of the core microbiome within a population, and biomarker analysis. These features are presented in a user-friendly format that facilitates easy customization and the generation of publication-quality graphics. MetaXplore is implemented entirely in the R language using the Shiny framework. It can be easily used locally on any system with R installed, including Windows, Mac OS, and most Linux distributions, or remotely via a web server without bioinformatic expertise. It can also be used as a framework for advanced users who can modify and expand the tool.
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- 2024
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24. Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection.
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Anglin, Noelle L., Chavez, Oswaldo, Soto-Torres, Julian, Gomez, Rene, Panta, Ana, Vollmer, Rainer, Durand, Marisol, Meza, Charo, Azevedo, Vania, Manrique-Carpintero, Norma C., Kauth, Philip, Coombs, Joesph J., Douches, David S., and Ellis, David
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INTROGRESSION (Genetics) ,SEED potatoes ,GERMPLASM ,GENE flow ,GENETIC variation ,BAYESIAN analysis ,POTATOES - Abstract
A total of 3,860 accessions from the global in trust clonal potato germplasm collection w3ere genotyped with the Illumina Infinium SolCAP V2 12K potato SNP array to evaluate genetic diversity and population structure within the potato germplasm collection. Diploid, triploid, tetraploid, and pentaploid accessions were included representing the cultivated potato taxa. Heterozygosity ranged from 9.7% to 66.6% increasing with ploidy level with an average heterozygosity of 33.5%. Identity, relatedness, and ancestry were evaluated using hierarchal clustering and model-based Bayesian admixture analyses. Errors in genetic identity were revealed in a side-by-side comparison of in vitro clonal material with the original mother plants revealing mistakes putatively occurring during decades of processing and handling. A phylogeny was constructed to evaluate inter- and intraspecific relationships which together with a STRUCTURE analysis supported both commonly used treatments of potato taxonomy. Accessions generally clustered based on taxonomic and ploidy classifications with some exceptions but did not consistently cluster by geographic origin. STRUCTURE analysis identified putative hybrids and suggested six genetic clusters in the cultivated potato collection with extensive gene flow occurring among the potato populations, implying most populations readily shared alleles and that introgression is common in potato. Solanum tuberosum subsp. andigena (ADG) and S. curtilobum (CUR) displayed significant admixture. ADG likely has extensive admixture due to its broad geographic distribution. Solanum phureja (PHU), Solanum chaucha (CHA)/Solanum stenotomum subsp. stenotomum (STN), and Solanum tuberosum subsp. tuberosum (TBR) populations had less admixture from an accession/population perspective relative to the species evaluated. A core and mini core subset from the genebank material was also constructed. SNP genotyping was also carried out on 745 accessions from the Seed Savers potato collection which confirmed no genetic duplication between the two potato collections, suggesting that the collections hold very different genetic resources of potato. The Infinium SNP Potato Array is a powerful tool that can provide diversity assessments, fingerprint genebank accessions for quality management programs, use in research and breeding, and provide insights into the complex genetic structure and hybrid origin of the diversity present in potato genetic resource collections. [ABSTRACT FROM AUTHOR]
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- 2024
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25. 典型河流岸线利用空间特征及驱动因子研究.
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李子远, 顾希俊, and 张辰旸
- Abstract
Copyright of China Rural Water & Hydropower is the property of China Rural Water & Hydropower Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2024
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- View/download PDF
26. 四百八十七份玉米地方种质资源穗部性状的表型多样性.
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李清超, 杨珊, 张登峰, 刘建新, 孙开利, and 吴迅
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GERMPLASM ,PRINCIPAL components analysis ,CLUSTER analysis (Statistics) ,REFERENCE sources ,CORN ,STATISTICAL correlation - Abstract
Copyright of Acta Agriculturae Zhejiangensis is the property of Acta Agriculturae Zhejiangensis Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2024
- Full Text
- View/download PDF
27. 不同種類高溫大曲真菌群落多樣性與結構分析.
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李彥濤, 梁紅東, 尉軍強, 郭永昌, 趙新民, 林一心, 陶寅亮, 王海, and 唐云
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FUNGAL communities ,NUCLEOTIDE sequencing ,CLUSTER analysis (Statistics) ,MONASCUS ,BOTANY - Abstract
Copyright of China Brewing is the property of China Brewing Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2024
- Full Text
- View/download PDF
28. Spatial and temporal variations of zooplankton assemblage in Chiffa Wadi (North Algeria).
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Hamil, Somia, Arab, Siham, Baha, Mounia, and Arab, Abdeslem
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ZOOPLANKTON ,SPATIAL variation ,WATER quality ,AUTUMN ,CLADOCERA ,ROTIFERA - Abstract
The spatial and temporal variations in the distribution, abundance, and assemblage structure of zooplankton were examined in the Chiffa Wadi River, north central Algeria. Samples were taken seasonally from autumn 2020 to summer 2022. Nine physical and chemical variables were recorded, and their relationship with the density of 39 zooplankton species was established using canonical correspondence analysis. In order to study the structure of the zooplankton, Shannon–Wiener diversity indices (H′), Margalef richness index (Dmg), Pielou evenness (E), and abundance were calculated. During the analysis, rotifera was the dominant group in the zooplankton community, represented by 27 taxa, followed by Cladocera (9 taxa) and Copepoda (3 taxa). The diversity index indicated the higher richness, abundance, and evenness of zooplankton at a eutrophic site (S2) compared with other sites. The canonical correspondence analysis (CCA) showed that the structure of zooplankton is influenced by local environmental factors. The present study demonstrates that anthropogenic activities including urban discharge and the construction of Algeria's Medea-Chiffa highway, which increased the nutrient load in the aquatic system, disrupted water quality. Consequently, the distribution and quantity of zooplankton were dramatically impacted by these changes in water quality. [ABSTRACT FROM AUTHOR]
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- 2024
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29. 温郁金连作和熏蒸处理土壤微生物种群数量分析.
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管艳辉, 金自学, 徐朗, 王 波, and 刘琼光
- Subjects
- *
SOIL microbiology , *MICROBIAL diversity , *MICROORGANISM populations , *BACTERIAL communities , *SOIL classification - Abstract
[Objective] The study was conducted to clarify the microbial community structure in soil with continuous cropping of Curcuma wenyujin and fumigation treatment, aiming to lay a foundation for alleviating continuous cropping obstacles in C. wenyujin cultivation. [Method] The soil under a continuous cropping of C. wenyujin for 3 years was selected and fumigated with dazomet one month before planting C. wenyujin. After 7-month cultivation of C. wenyujin, we collected soil samples from three types of plots: continuous cropping, fumigated and uncultivated. Total soil DNA was extracted, and the population and diversity of microbial communities (fungi and bacteria) were analyzed by using PacBio Sequel third-generation sequencing. [Result] The results showed that C. wenyujin plants in the fumigated soil exhibited good growth and minimal disease incidence, while those in the continuous cropping soil had poor growth and severe seedling death. Analysis of bacterial communities at the phylum level revealed that the abundance of AD3, TK10 and WPS-2 decreased in rhizosphere soil after continuous cropping compared with those in uncultivated soil. Fumigation of continuous cropping soil increased the abundance of beneficial bacteria with biocontrol functions such as Bacillus and Sphingomonas. Among the three soil types, 5 fungal phyla were abundant, including Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, and unclassified_k_ Fungi. Ascomycota had the lowest abundance in uncultivated C. wenyujin soil, but continuous cropping significantly increased its abundance, while Basidiomycota showed a significant decrease. Several beneficial fungal genera, including Chaetomium, Penicillium, Aspergillus, Myrothecium, Thielavia, Humicola, Rhizophlyctis, Microdochium, Ramicandelaber, Albifi mbria, Curvularia, Gigaspora, Nigrospora, Neocosmospora, Talaromyces, Roussoella, Rhytidhysteron, Boothiomyces, Apiotrichum, Ochroconis, Saitozyma, Trichosporon and Phoma, had higher abundance in fumigated soil than that in continuous cropping soil. In contrast, continuous cropping soil had a higher accumulation of pathogenic microorganisms. [Conclusion] Continuous cropping of C. wenyujin leads to the accumulation of harmful soil microorganism, resulting in continuous cropping obstacles. Fumigation with dazomet can reduce the number of soil-borne pathogens and increase the abundance of beneficial microbial populations, thereby mitigating continuous cropping obstacles in C. wenyujin cultivation. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
- View/download PDF
30. The Object Identification & Classification Methods in a Class of Objects using AI Based Supervised and Unsupervised Training Algorithms.
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Shekhar, Nilesh Kumar, Ajay, Shashishekhar, Kumar, Abhishek, Kumar, Sumit, Mandal, Jay, G., Pavithra, and Manjunath, T. C.
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ARTIFICIAL intelligence ,CONVOLUTIONAL neural networks ,SUPPORT vector machines ,ALGORITHMS ,K-means clustering ,SUPERVISED learning ,IDENTIFICATION - Abstract
In this paper, the object identification & classification methods in a class of objects using AI based supervised and unsupervised training algorithms is presented. This paper explores object identification and classification methods within a specific class of objects using a combination of AI-based supervised and unsupervised training algorithms. The design involves a path that integrates both approaches to identify distinct patterns within the object class. In supervised learning, a labeled dataset is utilized, employing algorithms such as Support Vector Machines, Random Forests, or Convolutional Neural Networks. The model trained on this dataset learns to recognize patterns associated with different classes, enabling accurate identification of new, unlabeled data. In contrast, unsupervised learning, using algorithms like K-Means or Hierarchical Clustering, clusters objects based on inherent similarities, revealing patterns without predefined labels. The synergistic application of both methods offers a comprehensive understanding of intricate patterns within the object class, facilitating a nuanced analysis. [ABSTRACT FROM AUTHOR]
- Published
- 2024
31. Molecular Identification, Multigenic Characterization and Phylogenetic Analysis of Ctenocephalides Canis Fleas from Humans and Domestic Animals in Iran.
- Author
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Seidi, Shahin, Tavassoli, Mousa, Malekifard, Farnaz, and Ben Said, Mourad
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DOMESTIC animals ,CANIS ,CYTOCHROME oxidase ,DISEASE vectors ,FLEAS ,HUMAN beings - Abstract
Background: Fleas belonging to the Pulicidae are prevalent ectoparasites infesting mammals and birds in Iran. This study focused on genetically identifying and characterizing Ctenocephalides canis collected both off-host and infesting humans and various domestic animals in the country. Methods: A total of 918 adult flea samples were collected from 10 sites in western and northwestern Iran between April 2018 and May 2019. Out of these, 71 specimens were found off-host, while the remaining fleas were collected from humans (121), sheep (126), goats (184), and dogs (416). Morphological identification at the genus level was performed on all fleas, and ten selected specimens selected based on the sampling sites and hosts were subjected to molecular detection at the species level by using partial amplification and sequencing of the internal transcribed spacer 1 and 2, as well as the cytochrome oxidase I (COXI) markers. Results: The morphological identification confirmed all fleas as Ctenocephalides spp. Alignment and phylogenetic analysis of nuclear and mitochondrial partial sequences confirmed the presence of C. canis. However, molecular divergence was observed among the ten isolates based on the ITS1 and ITS2 with diversity rates estimated at 0.15% and 3.36%, respectively. Notably, the analysis of the COXI marker revealed no molecular divergence among the partial sequences representing the ten studied isolates from C. canis. Conclusions: This study explores the diversity of C. canis in the western and northwestern regions of Iran, providing insights into their molecular taxonomy and potential role as disease vectors in these areas. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
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32. Morpho-molecular characterization based diversity analysis of Bipolaris isolates infecting graminaceous hosts.
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Kaur, Amrinder, Sharma, Vineet K., Rani, Ritu, and Hunjan, Mandeep Singh
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BIPOLARIS ,ROOT rots ,LEAF spots ,FIELD crops ,SOCIOCULTURAL factors ,GENETIC variation ,SYMPTOMS - Abstract
The genus Bipolaris is found to be commonly associated with leaf spots, leaf blights, root rots, foot rots and other disease symptoms mainly in high value field crops in the family Poaceae. Spot blotch caused by Bipolaris sorokiniana (Sacc.) Shoemaker is one of the most important diseases of wheat and barley. The fungus causes germination failure, seed mortality and spot blotch development with small, dark brown lesions without chlorotic margin. Therefore, in the present study, attempts were made to investigate the morphological variations among different Bipolaris isolates collected from the different graminaceous hosts in north-western regions of India and to assess the genetic diversity of the fungus using SSR markers. The results revealed that all the 50 isolates exhibited various levels of morphological and cultural variations. Colony colour varied from dark ash to white with raised and irregular margins in most of the isolates. The size of the conidia varied from 31–75 µm × 15–27 µm, slightly curved, elliptical or oblong, mostly tapering towards ends, light to dark brown in colour, 3–12 distoseptate, having bipolar germination. The molecular identification of the pathogen associated with all the test isolates carried out using B. sorokiniana-specific primer pair, i.e. COSA_F/R, also cross-identified the pathogen to be B. sorokiniana by producing one sharp band (519 bp) in all the test isolates. All the ten SSR primers exhibited different levels of polymorphism among the different isolates. The PIC values revealing allelic diversity and frequency among all the isolates varied from 0.153 in the case of primer pair BS051 to 0.493 in primer pair BS065 and this variation in PIC values among the ten primer pairs indicated variability in amplified product and allelic frequency among the isolates. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
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33. Modulation of the rat intestinal microbiota in the course of Anisakis pegreffii infection.
- Author
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Min-hao Zeng, Shan Li, Qing-bo Lv, Xiao-xu Wang, Qadeer, Abdul, and Mahmoud, Mohamed H.
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GUT microbiome ,HELMINTHS ,ANISAKIS ,MOLECULAR biology ,MARINE fishes ,IMMUNOREGULATION - Abstract
Background: Anisakis are globally distributed, marine parasitic nematodes that can cause human health problems, including symptoms such as vomiting, acute diarrhea, and allergic reactions. As parasitic nematodes that primarily affect the patient's digestive tract, intestinal helminths can interact directly with the host microbiota through physical contact, chemicals, or nutrient competition. It is widely accepted that the host microbiota plays a crucial role in the regulation of immunity. Materials and methods: Nematodes collected from the abdominal cavity of marine fish were identified by molecular biology and live worms were artificially infected in rats. Infection was determined by indirect ELISA based on rat serum and worm extraction. Feces were collected for 16S rDNA-based analysis of microbiota diversity. Results: Molecular biology identification based on ITS sequences identified the collected nematodes as A. pegreffii. The success of the artificial infection was determined by indirect ELISA based on serum and worm extraction from artificially infected rats. Microbiota diversity analysis showed that a total of 773 ASVs were generated, and PCoA showed that the infected group was differentiated from the control group. The control group contained five characterized genera (Prevotellaceae NK3B31 group, Turicibacter, Clostridium sensu stricto 1, Candidatus Stoquefichus, Lachnospira) and the infected group contained nine characterized genera (Rodentibacter, Christensenella, Dubosiella, Streptococcus, Anaeroplasma, Lactococcus, Papillibacter, Desulfovibrio, Roseburia). Based on the Wilcoxon test, four processes were found to be significant: bacterial secretion system, bacterial invasion of epithelial cells, bacterial chemotaxis, and ABC transporters. Conclusion: This study is the first to analyze the diversity of the intestinal microbiota of rats infected with A. pegreffii and to determine the damage and regulation of metabolism and immunity caused by the infection in the rat gut. The findings provide a basis for further research on host-helminth-microbe correlationships. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
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34. Assessment and phenotypic identification of millet germplasm (Setaria italica L.) in Liaoning, China
- Author
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Xintong Li, Weifeng He, Honghao Wang, and Min Xu
- Subjects
Millet ,Germplasm resources ,Agronomy trait ,Phenotypic identification ,Diversity analysis ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Aims This study evaluated millet germplasms in Liaoning Province to support the collection, preservation and innovation of millet germplasm resources. Methods The study was conducted from 2018 to 2020, involved the selection of 105 millet germplasm resources from the Germplasm Bank of the Liaoning Academy of Agricultural Sciences (LAAS), the observation and recording of 31 traits, and the application of multivariate analysis methods to assess phenotypic diversity. Results From the diversity analysis and correlation analysis, it was found that the tested traits had abundant diversity and complex correlations among them. Principal component analysis (PCA) comprehensively analyzed all quantitative traits and extracted seven principal components. Grey relational analysis (GRA) highlighted the varied contributions of different traits to yield. Through systematic cluster analysis (SCA), the resources were categorized into six groups at Euclidean distance of 17.09. K-mean cluster analysis determined the distribution interval and central value of each trait, then identified resources with desirable traits. Conclusion The results revealed resources that possess characteristics such as upthrow seedling leaves, more tillers and branches, larger and well-formed ears, and lodging resistance prefer to higher grain yield. It was also discovered that the subear internode length (SIL) could be an indicator for maturity selection. Four specific resources, namely, Dungu No. 1, Xiao-li-xiang, Basen Shengu, and Yuhuanggu No. 1, were identified for further breeding and practical applications.
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- 2024
- Full Text
- View/download PDF
35. Sorghum [Sorghum bicolor (L.) Moench] breeding enrichment potential through genetic comparison of Hungarian and East African lines
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Chege, Paul, Kamau, Stephen, Kitti, Tóth-Lencsés, Andrea, Palágyi, Odeny, Damaris, and Erzsébet, Kiss
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- 2024
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36. Agro-morphological characterization and digitization of job's tears (Coix lacryma-jobi L.) germplasm: A minor cereal crop of northeastern India
- Author
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Laxmisha, KM, Bhatt, Kailash C., Arya, Mamta, Bhardwaj, Rakesh, Semwal, Dinesh P., and Gupta, Veena
- Published
- 2023
37. Gut metagenomic analysis of gastric cancer patients reveals Akkermansia, Gammaproteobacteria, and Veillonella microbiota as potential non-invasive biomarkers
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Nath, Anju R. and Natarajan, Jeyakumar
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- 2024
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38. Diversity of soil fungi from sacred groves of Kerala, India revealed by comparative metagenomics analysis using illumina sequencing.
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Nandakumar, Keerthana, Anto, P. V., and Antony, Ignatius
- Subjects
- *
SOIL fungi , *COMPARATIVE studies , *TALAROMYCES , *METAGENOMICS , *BASIDIOMYCOTA - Abstract
The diversity, composition, and abundance of soil fungi from three sacred groves in Kerala, namely Iringole kavu of Ernakulam District, Kollakal Thapovanam of Alappuzha District, and Poyilkavu of Kozhikode District were analysed using Metagenomics analysis and Illumina sequencing. A total of 30,584, 78,323, and 55,640 reads were obtained from these groves, respectively. Ascomycota constitutes over 96% of the total fungi, making it the most abundant phylum, followed by Mortierellomycota, Basidiomycota, Chytridiomycota, and Rozellomycota. These phyla were subdivided into 20 classes, 40 orders, 83 families, 119 genera, and 135 species, while 1269 OTUs remained unidentified at the species level. Eurotiomycetes predominates the class, while the genus Talaromyces from the family Trichomaceae dominates the genera. Neocarmospora falciformis, Trichoderma lixii, and Candida ethanolic are the most abundant fungal species. Diversity analysis shows that Kollakal Thapovanam is rich in fungal species, while Poyilkavu is rich in biodiversity, with a high degree of dominance. Several species were found only in a particular grove and were absent in others and vice-versa, indicating high fungal specificity. Therefore, fungi have to be preserved in their original habitat. The Principal Coordinate Analysis revealed that each grove is distinct highlighting the importance of preserving the unique diversity of each sacred grove. In conclusion, this research provides valuable information about the soil fungal genera in their natural habitat. It emphasizes the need for more systematic research to understand the actual diversity and ecological role of fungi in sacred groves. This study is the first of its kind to analyse and compare soil fungal diversity in sacred groves using the metagenomics approach. [ABSTRACT FROM AUTHOR]
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- 2024
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39. 基于多样性指标的病虫害系统聚类防治区划研究 ——以主要碳汇森林类型楠竹林为例.
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顾卿先, 潘志舟, 贺 琦, 支 华, and 刘德波
- Abstract
Copyright of Journal of Shenyang Agricultural University is the property of Journal of Shenyang Agricultural University Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2024
- Full Text
- View/download PDF
40. Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection
- Author
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Noelle L. Anglin, Oswaldo Chavez, Julian Soto - Torres, Rene Gomez, Ana Panta, Rainer Vollmer, Marisol Durand, Charo Meza, Vania Azevedo, Norma C. Manrique - Carpintero, Philip Kauth, Joesph J. Coombs, David S. Douches, and David Ellis
- Subjects
SolCAP SNP array ,in vitro ,diversity analysis ,introgression ,Solanaceae ,genetic analysis ,Plant culture ,SB1-1110 - Abstract
A total of 3,860 accessions from the global in trust clonal potato germplasm collection w3ere genotyped with the Illumina Infinium SolCAP V2 12K potato SNP array to evaluate genetic diversity and population structure within the potato germplasm collection. Diploid, triploid, tetraploid, and pentaploid accessions were included representing the cultivated potato taxa. Heterozygosity ranged from 9.7% to 66.6% increasing with ploidy level with an average heterozygosity of 33.5%. Identity, relatedness, and ancestry were evaluated using hierarchal clustering and model-based Bayesian admixture analyses. Errors in genetic identity were revealed in a side-by-side comparison of in vitro clonal material with the original mother plants revealing mistakes putatively occurring during decades of processing and handling. A phylogeny was constructed to evaluate inter- and intraspecific relationships which together with a STRUCTURE analysis supported both commonly used treatments of potato taxonomy. Accessions generally clustered based on taxonomic and ploidy classifications with some exceptions but did not consistently cluster by geographic origin. STRUCTURE analysis identified putative hybrids and suggested six genetic clusters in the cultivated potato collection with extensive gene flow occurring among the potato populations, implying most populations readily shared alleles and that introgression is common in potato. Solanum tuberosum subsp. andigena (ADG) and S. curtilobum (CUR) displayed significant admixture. ADG likely has extensive admixture due to its broad geographic distribution. Solanum phureja (PHU), Solanum chaucha (CHA)/Solanum stenotomum subsp. stenotomum (STN), and Solanum tuberosum subsp. tuberosum (TBR) populations had less admixture from an accession/population perspective relative to the species evaluated. A core and mini core subset from the genebank material was also constructed. SNP genotyping was also carried out on 745 accessions from the Seed Savers potato collection which confirmed no genetic duplication between the two potato collections, suggesting that the collections hold very different genetic resources of potato. The Infinium SNP Potato Array is a powerful tool that can provide diversity assessments, fingerprint genebank accessions for quality management programs, use in research and breeding, and provide insights into the complex genetic structure and hybrid origin of the diversity present in potato genetic resource collections.
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- 2024
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41. Characterization of exotic tomato germplasm from ICAR-NBPGR gene bank
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Yerasu, Suresh R., Tiwari, Shailesh K., Pandey, Chithra D., and Pandey, Sushil
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- 2023
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42. Eco-geographic survey, In-situ characterization and spatial analysis of phenotypic traits diversity among the maize landraces collected from Chhattisgarh
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Bishnoi, Santosh K., Malav, Pavan K., Singh, Kartar, Phuke, Rahul M., Choudhary, S.B., Sharma, Hariom K., and Ahlawat, S.P.
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- 2023
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43. Diversity studies in Assam rice genotypes for ratooning ability and perennation.
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Chakrawarti, Neha, Borgohain, Rupam, and Verma, Rajshree
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- *
GENETIC variation , *GENOTYPES , *RICE - Abstract
The objective of the research was to assess diversity among 50 rice genotypes for ratooning and perennation which refers to ability of a plant to regrow from stubble remaining after harvesting. Results showed that 30 genotypes exhibited different degree of ratoon production and ratoon yield. Diversity analysis revealed that all the ratooning genotypes could be assigned to ten clusters. Clusters III (Binadhan-11 and Sayjihari) and VI (IR-64, DRR-44) were the best performing for ratoon yield. Maximum inter-cluster distance was observed between genotypes falling under clusters III and X followed by genotypes under clusters III and II indicating wider genetic diversity between these genotypes. Thus, these genotypes may be useful for future breeding to develop superior varieties with respect to ratooning ability and ratoon yield. [ABSTRACT FROM AUTHOR]
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- 2024
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44. Comparative Analysis of Bacterial Community Structures in Earthworm Skin, Gut, and Habitat Soil across Typical Temperate Forests
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Kang Wang, Ning Yuan, Jia Zhou, and Hongwei Ni
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earthworm ,bacteria ,diversity analysis ,mantel test ,environmental factors ,Biology (General) ,QH301-705.5 - Abstract
Earthworms are essential components in temperate forest ecosystems, yet the patterns of change in earthworm-associated microbial communities across different temperate forests remain unclear. This study employed high-throughput sequencing technology to compare bacterial community composition and structure in three earthworm-associated microhabitats (skin, gut, and habitat soil) across three typical temperate forests in China, and investigated the influence of environmental factors on these differential patterns. The results indicate that: (1) From warm temperate forests to cold temperate forests, the soil pH of the habitat decreased significantly. In contrast, the physicochemical properties of earthworm skin mucus exhibited different trends compared to those of the habitat soil. (2) Alpha diversity analysis revealed a declining trend in Shannon indices across all three microhabitats. (3) Beta diversity analysis revealed that the transition from warm temperate deciduous broad-leaved forest to cold temperate coniferous forest exerted the most significant impact on the gut bacterial communities of earthworms, while its influence on the skin bacterial communities was comparatively less pronounced. (4) Actinobacteria and Proteobacteria were the predominant phyla in earthworm skin, gut, and habitat soil, but the trends in bacterial community composition differed among the three microhabitats. (5) Mantel tests revealed significant correlations between bacterial community structures and climatic factors, physicochemical properties of earthworm habitat soil, and physicochemical properties of earthworm skin mucus. The findings of this study offer novel perspectives on the interplay between earthworms, microorganisms, and the environment within forest ecosystems.
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- 2024
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45. Autoantibody Diversity Is Augmented in Women with Breast Cancer and Is Related to the Stage of the Disease
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Jesús Pérez-Hernández, Rosalba León-Díaz, Alejandro Zentella, Edmundo Lamoyi, Marcela Esquivel-Velázquez, Antonia Barranca-Enríquez, and Tania Romo-González
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breast cancer progression ,serological data ,diversity analysis ,Mexican women ,autoantibodies ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Breast cancer (BC) is the most frequent malignant neoplasia and leading cause of cancer mortality for women. A timely diagnosis of BC is crucial to ensure the best chances of survival. Among the various screening tools for BC, antibodies directed towards self-antigens or tumor-associated antigens (autoantibodies) have emerged as an alternative to image-based screening modalities. However, little attention has been paid to the global diversity of autoantibodies. This work aimed to analyze the diversity of autoantibodies reactive to antigens expressed by the BC cell line T47D in the sera of Mexican women with BC, benign breast pathology (BBP), or without breast pathology (WBP). We found that the diversity of antibodies in the sera was higher in the BC and BBP groups than in the WBP group. Likewise, the diversity changed with the progression of BC. Our results show and measure the complexity of the antibody response in breast health and disease.
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- 2023
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46. Reliability-based multi-objective optimization of trusses with greylag goose algorithm
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Mashru, Nikunj, Tejani, Ghanshyam G., and Patel, Pinank
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- 2025
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47. Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process
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Liqun Jiang, Da Ke, Bingrui Sun, Jing Zhang, Shuwei Lyu, Hang Yu, Pingli Chen, Xingxue Mao, Qing Liu, Wenfeng Chen, Zhilan Fan, Li Huang, Sanjun Yin, Yizhen Deng, and Chen Li
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root-associated microbiota ,Oryza rufipogon ,Oryza sativa ,ITS and 16S rRNA ,diversity analysis ,Microbiology ,QR1-502 - Abstract
ABSTRACTThe root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.
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- 2024
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48. 长江口南部水域春、秋季鱼类群落结构比较.
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李诗佳, 施利燕, 钟俊生, and 赵路路
- Abstract
In order to ascertain the fish community structure in the southern waters of the Yangtze River Estuary, 12 stations were set up in the North Port, the North Channel and the South Channel of the Yangtze River Estuary in April (spring) and September (autumn) of 2020, and two voyages of fishery resource surveys were conducted using single bag trawls (minimum mesh size 25 mm). By calculating individual, weight resource density, relative importance index, α-diversity index, combined with multiple factor regression analysis and canonical correspondence analysis (CCA), we could determine the spatio-temporal change rule of the community and the impact of environmental factors on the distribution. In this study, 49 species of fish were collected, belonging to 16 orders, 25 families and 41 genera. All of them are warm temperature and warm water fish. The majority of them are estuarine fish, while the narrow salt fish are less and distributed regionally. The resource density in spring is higher than that in autumn, while the weight resource density in autumn is higher than that in spring. Coilia mystus, Coilia nasus, Collichthys lucidus and Miichthys miiuy were dominant species in both seasons. In spring, Miichthys miiuy's individual resource density has the highest contribution rate to the total density and the most significant impact. In autumn, the contribution rate of the individual resource density of Harpadon nehereus is the highest, but the influence of the individual resource density of Coilia nasus is the most significant. The results of individual and weight diversity index showed that H', J' and D' in autumn were higher than those in spring, while the average value of C' in spring was higher. The surface salt temperature of the water surface in the study area is affected by many dynamic factors and there is a large seasonal change. The resource density plane distribution map and the ranking map reveal that certain groups have a life habit of tending to temperature and salt. [ABSTRACT FROM AUTHOR]
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- 2024
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49. Unraveling Diversity and Character Association in Sesame (Sesamum indicum L.) using Different Agro-Morphological Traits.
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Patel, Manoj Kumar, Tiwari, Deepti, Sharma, Versha, Singh, Dhirendra, and Kumar, Shahil
- Abstract
The article "Unraveling Diversity and Character Association in Sesame (Sesamum indicum L.) using Different Agro-Morphological Traits" examines the genetic diversity and character associations of twenty sesame genotypes. The study identifies two distinct clusters among the genotypes and finds positive associations between seed yield per plant and other traits such as capsules per plant, biological yield per plant, and harvest index. Negative associations are observed with days to flowering and maturity. The findings can be useful for selecting parent plants for hybrid breeding and improving sesame seed yield. The article "Hierarchical grouping to optimize an objective function" discusses the concept of hierarchical grouping and its application in optimizing an objective function. The author provides a mathematical approach to hierarchical clustering and highlights its potential benefits in various fields. This research is valuable for those interested in statistical analysis and data clustering techniques. [Extracted from the article]
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- 2024
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50. Association mapping of plant structure and yield traits in faba bean (Vicia faba L.).
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Abuzayed, Mazen A., Baytar, Asena A., Yanar, Ertuğrul G., Doğanlar, Sami, and Frary, Anne
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- *
FAVA bean , *PLANT anatomy , *LINEAR models (Communication) , *SEED yield , *INFLORESCENCES - Abstract
Background: Faba bean (Vicia faba L.) is an important crop with high protein content. Tens of thousands of faba bean accessions are available in germplasm collections throughout the world. Morphological characterization of these materials can enrich these collections and aid in the selection of genotypes for use in breeding programs. Results: In this study, 26 morphological characters were analyzed for 61 faba bean landraces and 53 cultivars over two seasons in Izmir, Turkey. The genotypes had high diversity for several yield traits including number of pods per plant, dry seed yield, and 100‐seed weight. Association mapping was conducted for the morphological characters using 651 alleles from 100 simple sequence repeat (SSR) markers and a general linear model based on the Q matrix. A false discovery rate of 0.20 was used to test the significance of marker–trait associations resulting in 75 loci detected for 20 of the morphological characters (p ≤ 0.001). Conclusion: Overall, 44% of the quantitative trait loci (QTLs) were for seed traits, with 24%, 15%, and 17% of QTL identified for vegetative, inflorescence, and pod traits, respectively. The phenotypic data and marker–trait associations generated by this work can help breeding programs in the selection and improvement of faba bean. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
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