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An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)

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dc.contributor.author Adugna Abdi Woldesemayat
dc.contributor.author Van Heusden, Peter
dc.contributor.author Ndimba, Bongani K.
dc.contributor.author Christoffels, Alan
dc.date.accessioned 2018-01-01T09:00:20Z
dc.date.available 2018-01-01T09:00:20Z
dc.date.issued 2017-12-22
dc.identifier.citation Woldesemayat, A.A., Van Heusden, P., Ndimba, B.K. et al. An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench). BMC Genet 18, 119 (2017)
dc.identifier.uri http://dx.doi.org/10.1186/s12863-017-0584-5
dc.identifier.uri http://hdl.handle.net/10500/23482
dc.description.abstract Background: Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth characterization of genetic determinants using model organisms and high-throughput technologies. However, studies on drought tolerance have generally been limited to traditional candidate gene approach that targets only a single gene in a pathway that is related to a trait. In this study, we used sorghum, one of the model crops that is well adapted to arid regions, to mine genes and define determinants for drought tolerance using drought expression libraries and RNA-seq data. Results: We provide an integrated and comparative in silico candidate gene identification, characterization and annotation approach, with an emphasis on genes playing a prominent role in conferring drought tolerance in sorghum. A total of 470 non-redundant functionally annotated drought responsive genes (DRGs) were identified using experimental data from drought responses by employing pairwise sequence similarity searches, pathway and interprodomain analysis, expression profiling and orthology relation. Comparison of the genomic locations between these genes and sorghum quantitative trait loci (QTLs) showed that 40% of these genes were co-localized with QTLs known for drought tolerance. The genome reannotation conducted using the Program to Assemble Spliced Alignment (PASA), resulted in 9.6% of existing single gene models being updated. In addition, 210 putative novel genes were identified using AUGUSTUS and PASA based analysis on expression dataset. Among these, 50% were single exonic, 69.5% represented drought responsive and 5.7% were complete gene structure models. Analysis of biochemical metabolism revealed 14 metabolic pathways that are related to drought tolerance and also had a strong biological network, among categories of genes involved. Identification of these pathways, signifies the interplay of biochemical reactions that make up the metabolic network, constituting fundamental interface for sorghum defence mechanism against drought stress. Conclusions: This study suggests untapped natural variability in sorghum that could be used for developing drought tolerance. The data presented here, may be regarded as an initial reference point in functional and comparative genomics in the Gramineae family.
dc.format.extent 1 online resource (24 pages) : illustrations (chiefly color) + 15 additional PDFs
dc.language.iso en
dc.rights © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated en
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject Candidate gene identification en
dc.subject Drought tolerance
dc.subject Functional genomics en
dc.subject Integrated in silico approach en
dc.subject Genome annotation en
dc.subject Sorghum bicolor (L.) Moench en
dc.subject.ddc 633.17423
dc.subject.lcsh Sorghum -- Breeding en
dc.subject.lcsh Sorghum -- Drought tolerance en
dc.subject.lcsh Sorghum -- Genetics en
dc.subject.lcsh Sorghum -- Varieties en
dc.subject.lcsh Sorghum -- Yields en
dc.title An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)
dc.type Article
dc.description.department Environmental Sciences
dc.date.updated 2018-01-01T09:00:20Z
dc.rights.holder The Author(s).


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© The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated Except where otherwise noted, this item's license is described as © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated

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