In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum)
Common wheat (Triticum aestivum) is the most widely grown cereal crop and is cultivated extensively in dry regions. Water shortage, resulting from either drought or salinity, leads to slow growth and loss of wheat yield. In order to predict new genes responsive to the drought and salt stresses in wh...
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| description | Common wheat (Triticum aestivum) is the most widely grown cereal crop and is cultivated extensively in dry regions. Water shortage, resulting from either drought or salinity, leads to slow growth and loss of wheat yield. In order to predict new genes responsive to the drought and salt stresses in wheat, 6,717 expressed sequence tags (ESTs), expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI). The downloaded ESTs were clustered and assembled into 354 contigs; 14 transcription factor families in 29 contigs were identified. In addition, 119 contigs were organized in five enzyme classes. Biological functions were obtained for only 324 of the 354 contigs using gene ontology. In addition, using Kyoto Encyclopedia of Genes and Genomes database, 191 metabolic pathways were identified. The remaining contigs were used for further analysis and the search for new genes responsive to drought and salt stresses. These contigs were mapped on the International Wheat Genome Sequencing Consortium RefSeq v1.0 assembly, the most complete version of the reference sequence of the bread wheat variety Chinese Spring. They were found to have from one to three locations on the subgenomes A, B, and D. Full-length gene sequences were designed for these contigs, which were further validated using promoter analysis. These predicted genes may have applications in molecular breeding programs and wheat drought and salinity research. |
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Water shortage, resulting from either drought or salinity, leads to slow growth and loss of wheat yield. In order to predict new genes responsive to the drought and salt stresses in wheat, 6,717 expressed sequence tags (ESTs), expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI). The downloaded ESTs were clustered and assembled into 354 contigs; 14 transcription factor families in 29 contigs were identified. In addition, 119 contigs were organized in five enzyme classes. Biological functions were obtained for only 324 of the 354 contigs using gene ontology. In addition, using Kyoto Encyclopedia of Genes and Genomes database, 191 metabolic pathways were identified. The remaining contigs were used for further analysis and the search for new genes responsive to drought and salt stresses. These contigs were mapped on the International Wheat Genome Sequencing Consortium RefSeq v1.0 assembly, the most complete version of the reference sequence of the bread wheat variety Chinese Spring. They were found to have from one to three locations on the subgenomes A, B, and D. Full-length gene sequences were designed for these contigs, which were further validated using promoter analysis. These predicted genes may have applications in molecular breeding programs and wheat drought and salinity research.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0223962</identifier><identifier>PMID: 31671113</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abiotic stress ; Abscisic acid ; Agricultural research ; Applications programs ; Binding sites ; Biology and Life Sciences ; Biotechnology ; Bread ; Cereal crops ; Computer Simulation ; Consortia ; Crop yield ; Crop yields ; Cultivation ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Drought ; Droughts ; Ecology and Environmental Sciences ; Encyclopedias ; Enzymes ; Expressed sequence tags ; Expressed Sequence Tags - metabolism ; Gene expression ; Gene sequencing ; Genes ; Genes, Plant - genetics ; Genetic engineering ; Genomes ; Genomics ; Grain cultivation ; Metabolic pathways ; Metabolism ; Physical Sciences ; Physiology ; Plant breeding ; Plant sciences ; Predictions ; Promoter Regions, Genetic - genetics ; Proteins ; Research and Analysis Methods ; RNA polymerase ; Salinity ; Salinity effects ; Salt ; Salt Tolerance - genetics ; Stress, Physiological ; Stresses ; Transcription factors ; Transcription Factors - metabolism ; Triticum - genetics ; Triticum - physiology ; Triticum aestivum ; Water shortages ; Water supply ; Wheat ; Wheat yield</subject><ispartof>PloS one, 2019-10, Vol.14 (10), p.e0223962-e0223962</ispartof><rights>COPYRIGHT 2019 Public Library of Science</rights><rights>2019 Dabab Nahas et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Water shortage, resulting from either drought or salinity, leads to slow growth and loss of wheat yield. In order to predict new genes responsive to the drought and salt stresses in wheat, 6,717 expressed sequence tags (ESTs), expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI). The downloaded ESTs were clustered and assembled into 354 contigs; 14 transcription factor families in 29 contigs were identified. In addition, 119 contigs were organized in five enzyme classes. Biological functions were obtained for only 324 of the 354 contigs using gene ontology. In addition, using Kyoto Encyclopedia of Genes and Genomes database, 191 metabolic pathways were identified. The remaining contigs were used for further analysis and the search for new genes responsive to drought and salt stresses. 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These predicted genes may have applications in molecular breeding programs and wheat drought and salinity research.</description><subject>Abiotic stress</subject><subject>Abscisic acid</subject><subject>Agricultural research</subject><subject>Applications programs</subject><subject>Binding sites</subject><subject>Biology and Life Sciences</subject><subject>Biotechnology</subject><subject>Bread</subject><subject>Cereal crops</subject><subject>Computer Simulation</subject><subject>Consortia</subject><subject>Crop yield</subject><subject>Crop yields</subject><subject>Cultivation</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Drought</subject><subject>Droughts</subject><subject>Ecology and Environmental Sciences</subject><subject>Encyclopedias</subject><subject>Enzymes</subject><subject>Expressed sequence tags</subject><subject>Expressed Sequence Tags - metabolism</subject><subject>Gene expression</subject><subject>Gene 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aestivum</subject><subject>Water shortages</subject><subject>Water supply</subject><subject>Wheat</subject><subject>Wheat 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prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum)</title><author>Dabab Nahas, Laila ; Al-Husein, Naim ; Lababidi, Ghinwa ; Hamwieh, Aladdin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-6337a0c52aa55452b8926e98d78fe26396cf97bb6deaa646cd8e5b97bed932713</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Abiotic stress</topic><topic>Abscisic acid</topic><topic>Agricultural research</topic><topic>Applications programs</topic><topic>Binding sites</topic><topic>Biology and Life Sciences</topic><topic>Biotechnology</topic><topic>Bread</topic><topic>Cereal crops</topic><topic>Computer Simulation</topic><topic>Consortia</topic><topic>Crop yield</topic><topic>Crop yields</topic><topic>Cultivation</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>Drought</topic><topic>Droughts</topic><topic>Ecology and Environmental Sciences</topic><topic>Encyclopedias</topic><topic>Enzymes</topic><topic>Expressed sequence tags</topic><topic>Expressed Sequence Tags - metabolism</topic><topic>Gene expression</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genes, Plant - genetics</topic><topic>Genetic engineering</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Grain cultivation</topic><topic>Metabolic pathways</topic><topic>Metabolism</topic><topic>Physical Sciences</topic><topic>Physiology</topic><topic>Plant breeding</topic><topic>Plant sciences</topic><topic>Predictions</topic><topic>Promoter Regions, Genetic - genetics</topic><topic>Proteins</topic><topic>Research and Analysis Methods</topic><topic>RNA polymerase</topic><topic>Salinity</topic><topic>Salinity effects</topic><topic>Salt</topic><topic>Salt Tolerance - genetics</topic><topic>Stress, 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(Triticum aestivum) is the most widely grown cereal crop and is cultivated extensively in dry regions. Water shortage, resulting from either drought or salinity, leads to slow growth and loss of wheat yield. In order to predict new genes responsive to the drought and salt stresses in wheat, 6,717 expressed sequence tags (ESTs), expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI). The downloaded ESTs were clustered and assembled into 354 contigs; 14 transcription factor families in 29 contigs were identified. In addition, 119 contigs were organized in five enzyme classes. Biological functions were obtained for only 324 of the 354 contigs using gene ontology. In addition, using Kyoto Encyclopedia of Genes and Genomes database, 191 metabolic pathways were identified. The remaining contigs were used for further analysis and the search for new genes responsive to drought and salt stresses. These contigs were mapped on the International Wheat Genome Sequencing Consortium RefSeq v1.0 assembly, the most complete version of the reference sequence of the bread wheat variety Chinese Spring. They were found to have from one to three locations on the subgenomes A, B, and D. Full-length gene sequences were designed for these contigs, which were further validated using promoter analysis. These predicted genes may have applications in molecular breeding programs and wheat drought and salinity research.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>31671113</pmid><doi>10.1371/journal.pone.0223962</doi><tpages>e0223962</tpages><orcidid>https://orcid.org/0000-0002-6809-554X</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Abiotic stress Abscisic acid Agricultural research Applications programs Binding sites Biology and Life Sciences Biotechnology Bread Cereal crops Computer Simulation Consortia Crop yield Crop yields Cultivation Deoxyribonucleic acid DNA DNA sequencing Drought Droughts Ecology and Environmental Sciences Encyclopedias Enzymes Expressed sequence tags Expressed Sequence Tags - metabolism Gene expression Gene sequencing Genes Genes, Plant - genetics Genetic engineering Genomes Genomics Grain cultivation Metabolic pathways Metabolism Physical Sciences Physiology Plant breeding Plant sciences Predictions Promoter Regions, Genetic - genetics Proteins Research and Analysis Methods RNA polymerase Salinity Salinity effects Salt Salt Tolerance - genetics Stress, Physiological Stresses Transcription factors Transcription Factors - metabolism Triticum - genetics Triticum - physiology Triticum aestivum Water shortages Water supply Wheat Wheat yield |
| title | In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-23T10%3A52%3A29IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=In-silico%20prediction%20of%20novel%20genes%20responsive%20to%20drought%20and%20salinity%20stress%20tolerance%20in%20bread%20wheat%20(Triticum%20aestivum)&rft.jtitle=PloS%20one&rft.au=Dabab%20Nahas,%20Laila&rft.date=2019-10-31&rft.volume=14&rft.issue=10&rft.spage=e0223962&rft.epage=e0223962&rft.pages=e0223962-e0223962&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0223962&rft_dat=%3Cgale_plos_%3EA604389942%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2310994125&rft_id=info:pmid/31671113&rft_galeid=A604389942&rft_doaj_id=oai_doaj_org_article_7ad203d2bfa141dd84cda2fdfb37ae50&rfr_iscdi=true |