Resultados de búsqueda - "ontology"

Morphological and metabolic profiling of a tropical‐adapted potato association panel subjected to water recovery treatment reveals new insights into plant vigor por Toubiana, D., Cabrera, R., Salas, E., Maccera, C., Franco dos Santos, G., Cevallos, D., Lindqvist-Kreuze, H., López, J., Maruenda, H.

“…Eleven single nucleotide polymorphism (SNP) markers were associated with fumarate. Gene Ontology analysis of quantitative trait loci regions associated with fumarate revealed an enrichment of genes regulating metabolic processes. …”
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Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations por Barria, Agustin, Penaloza, Carolina, Papadopoulou, Athina, Mahmuddin, Mahirah, Benzie, John, Houston, Ross, Wiener, Pamela

“…The Poolseq data identified genomic regions with high levels of differentiation (FST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. …”
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Identification of genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis por Kitavi, M., Gemenet, Dorcus C., Wood, J.C., Hamilton, J., Wu, S., Fei, Z., Khan, A., Buell, C.R.

“…Analysis revealed both common (35 up regulated, 259 down regulated genes in the three stress conditions) and unique sets of up regulated (1337 genes by drought, 516 genes by heat, and 97 genes by salt stress) and down regulated (2445 genes by drought, 678 genes by heat, and 204 genes by salt stress) differentially expressed genes (DEGs) suggesting common, yet stress-specific transcriptional responses to these three abiotic stressors. Gene Ontology analysis of down regulated DEGs common to both heat and salt stress revealed enrichment of terms associated with “cell population proliferation” suggestive of an impact on the cell cycle by the two stress conditions. …”
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Transcriptional alterations of the resistant potato genotype 'Cruza 148' in response to Ralstonia solanacearum infection por Okiro, L.A., Mulwa, R.M., Oyoo, M.E., Mendes, T.

“…A total of 54.2% of the DEGs were upregulated and 45.8% were downregulated in the roots of the ‘Cruza 148’ potato genotype, while 45.5% and 54.5% of DEGs were upregulated and downregulated in the roots of the susceptible potato genotype ‘Shangi’ respectively. The gene ontology (GO) enrichment analysis indicated that the ‘Cruza 148’ genotype consistently displayed the ‘defence response’ category throughout every stage of infection. …”
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Identification of potential zinc deficiency responsive genes and regulatory pathways in rice by weighted gene co-expression network analysis por Muvunyi, Blaise Pascal, Xiang, Lu, Zhan, Junhui, He, Sang, Ye, Guoyou

“…Functional enrichment analysis showed that 24 of the 28 conserved modular DEGs from leaf and crown tissues significantly up-regulated 2 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 15 Gene Ontology (GO) terms, including the substrate- specific transmembrane transporter and the small molecule metabolic process. …”
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Novel sources of pre-harvest sprouting resistance for japonica rice improvement por Lee, Jae-Sung, Chebotarov, Dmytro, McNally, Kenneth L., Pede, Valerien, Setiyono, Tri Deri, Raquid, Rency, Hyun, Woong-Jo, Jeung, Ji-Ung, Kohli, Ajay, Mo, Youngjun

“…A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways.…”
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Molecular programming of drought-challenged Trichoderma harzianum-bioprimed rice (Oryza sativa L.) por Bashyal, Bishnu Maya, Parmar, Pooja, Zaidi, Najam Waris, Aggarwal, Rashmi

“…Furthermore, to establish host–T. harzianum interaction, transcriptome analysis of Trichoderma was also carried out. The Gene Ontology (GO) analysis of T. harzianum transcriptome suggested that the annotated genes are functionally related to carbohydrate binding module, glycoside hydrolase, GMC oxidoreductase, and trehalase and were mainly upregulated, playing an important role in establishing the mycelia colonization of rice roots and its growth. …”
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Novel Genomic Regions Linked to Ascochyta Blight Resistance in Two Differentially Resistant Cultivars of Chickpea por Alo, Fida, Ran, Anupalli, Baum, Michael, Singh, Sarvjeet, Kehel, Zakaria, Rani, Upasana, Udupa, Sripada M., Al-Shamaa, Khaled, Alsamman, Alsamman M., Istanbuli, Tawffiq, Attar, Basem, Hamwieh, Aladdin, Amri, Ahmed

“…The proposed physical map narrows down AB resistance to consistent genomic regions identified across different environments. Gene ontology (GO) assigned these QTLs to 319 genes, many of which were associated with stress and disease resistance, and with most important genes belonging to resistance gene families such as leucine-rich repeat (LRR) and transcription factor families. …”
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Connecting Data for Consumer Preferences, Food Quality and Breeding in support of Market-oriented Breeding of Root, Tuber, and Banana Crops por Arnaud, E., Menda, N., Tran, T., Asiimwe, A., Kanaabi, M., Meghar, K., Forsythe, L., Kawuki, R.S., Ellebrock, B., Siraj Kayondo, I., Agbona, A., Zhang, X., Mendes, T., Laporte, Marie-Angélique, Nakitto, M., Ssali, R.T., Asfaw, F., Uwimana, Brigitte, Ogbete, C.E., Makunde, G.S., Maraval, I., Mueller, L.A., Bouniol, A., Fauvelle, E., Dufour, D.

“…Names and descriptions of food quality traits were added into the Crop Ontology, along with the various methods of measurement used by the project, for labelling data in the databases. …”
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Variation in seed longevity among diverse Indica rice varieties por Lee, Jae-Sung, Velasco-Punzalan, Marlina, Pacleb, Myrish, Valdez, Rocel, Kretzschmar, Tobias, McNally, Kenneth L., Ismail, Abdel M., Sta. Cruz, Pompe C., Hamilton, Ruaraidh Sackville, Hay, Fiona R.

“…A priori candidate genes selected based on rice genome annotation and gene network ontology databases suggested that the mechanisms conferring high seed longevity might be related to DNA repair and transcription, sugar metabolism, reactive oxygen species scavenging and embryonic/root development.…”
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Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL por Dixit, Shalabh, Kumar Biswal, Akshaya, Min, Aye, Henry, Amelia, Oane, Rowena H., Raorane, Manish L., Longkumer, Toshisangba, Pabuayon, Isaiah M., Mutte, Sumanth K., Vardarajan, Adithi R., Miro, Berta, Govindan, Ganesan, Albano-Enriquez, Blesilda, Pueffeld, Mandy, Sreenivasulu, Nese, Slamet-Loedin, Inez, Sundarvelpandian, Kalaipandian, Tsai, Yuan-Ching, Raghuvanshi, Saurabh, Hsing, Yue-Ie C., Kumar, Arvind, Kohli, Ajay

“…Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. …”
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Defining the genome structure of ‘tongil’ rice, an important cultivar in the korean “green revolution por Kim, Backki, Kim, Dong-Gwan, Lee, Gileung, Seo, Jeonghwan, Choi, Ik-Young, Choi, Beom-Soon, Yang, Tae-Jin, Kim, Kwang Soo, Lee, Joohyun, Chin, Joong Hyoun, Koh, Hee-Jong

“…Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. …”
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Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.) por Blair, Matthew W., Fernández, A.C., Ishitani, Manabu, Moreta Mejia, DE, Seki, M., Ayling, S., Shinozaki, Kazuo

“…These were functionally annotated with gene ontology terms and placed into KEGG pathways. Compared to other EST sequencing efforts in common bean, about half of the sequences were novel or represented the 5' ends of known genes. …”
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Deciphering signature of selection affecting beef quality traits in Angus cattle por Taye, M., Joon Yoon, Dessie, Tadelle, Seoae Cho, Sung Jong Oh, Hak-Kyo Lee, Heebal Kim

“…The WebGestalt gene ontology analysis resulted in sixteen (A–H) and five (A–J) significantly enriched KEGG pathways. …”
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AgroFIMS: A tool to enable digital collection of standards-compliant FAIR data por Devare, Medha, Aubert, Céline, Benites Alfaro, Omar Eduardo, Pérez Masias, Ivan Omar, Laporte, Marie-Angélique

“…The tool enables the creation of fieldbooks through a user-friendly interface that allows the entry of metadata tied to the Dublin Core standard schema, and trial details via picklists or autocomplete that are based on semantic standards like the Agronomy Ontology (AgrO). Choices are organized by field operations or measurements of relevance to an agronomist, with specific terms drawn from ontologies. …”
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Summary: creating systems innovation platforms for transformative pathways in circular economy por Sobratee‑Fajurally, Nafiisa, Nhamo, L., Mabhaudhi, Tafadzwanashe

“…These are organised as (i) realising that the current equilibrium is outdated and skewed towards linearity such that impacts are additive but non-systemic, (ii) creating a new culture for enabling transformative patterns by connecting actors who share a new set of values, (iii) enabling Community of Practice (CoP) that share a common identity, (iv) connecting resources in novel ways by repurposing existing capacities, that is, extending the ontology of the CE, (v) institutionalising and supporting new networked configurations till normalisation, and (vi) impacts become systemic through synergies, trade-offs and comprise are negotiated and new patterns co-exist and are visible. …”
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Unraveling the genetic basis of general combining ability in CIMMYT elite bread wheat germplasm: implications for breeding strategies optimization por Saavedra-Avila, José Ignacio, Gerard, Guillermo Sebastián, Esposito, Salvatore, Velu, Govindan, Huerta-Espino, Julio, Tarekegn, Zerihun Tadesse, Dreisigacker, Susanne, Saint Pierre, Carolina, Pacheco Gil, Rosa Angela, Toledo, Fernando Henrique, Gardner, Keith, Crespo Herrera, Leonardo Abdiel, Crossa, Jose, Vitale, Paolo

“…Using a genome-wide association study (GWAS), gene ontology (GO) analysis, and genomic prediction (GP), our objectives were to i) identify marker-trait associates (MTAs) and candidate genes, ii) assess temporal allele frequency dynamics of identified MTAs, and iii) estimate prediction accuracy (PA) for key traits: Progeny Number per-Cross (PNC), grain yield (GY), and a combined index incorporating these traits ("index"). …”
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De novo assembly of red clover transcriptome based on RNASeq data provides insight into drought response, gene discovery and marker identification por Yates, S., Swain, M., Hegarty, M., Chernukin, I., Lowe, M., Allison, G., Ruttink, T., Abberton, Michael T., Jenkins, G., Skot, L.

“…These transcript tags were annotated with gene ontology (GO) terms. One of the most striking results from the expression analysis was that the drought sensitive plants were characterised by having approximately twice the number of differentially expressed transcript tags than the tolerant plants after drought. …”
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ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data por Gonzalez, Sergio Alberto, Clavijo, Bernardo, Rivarola, Maximo Lisandro, Moreno, Patricio, Fernández, Paula, Dopazo, Joaquín, Paniego, Norma Beatriz

“…Results: We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results. …”
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Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice por Shanks, Carly M., Huang, Ji, Cheng, Chia-Yi, Shih, Hung-Jui S., Brooks, Matthew D., Álvarez, José M., Araus, Viviana, Swift, Joseph, Henry, Amelia, Coruzzi, Gloria M.

“…We validated the direct regulated targets of two of these candidate NUEg TFs in a plant cell-based TF assay called TARGET, for which we also had in planta data for comparison. Gene ontology analysis revealed that 6/18 NUEg TFs - OsbZIP23 (LOC_Os02g52780), Oshox22 (LOC_Os04g45810), LOB39 (LOC_Os03g41330), Oshox13 (LOC_Os03g08960), LOC_Os11g38870, and LOC_Os06g14670 - regulate genes annotated for N and/or W signaling. …”
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