|dc.contributor.author||Woldesemayat, Adugna Abdi||
|dc.contributor.author||Modise, David M.||
|dc.contributor.author||Ndimba, Bongani K.||
|dc.identifier.citation||Woldesemayat, A.A. (2018). Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PLoS ONE, 13(3): e0192678.||en_US
Crop response to the changing climate and unpredictable effects of global warming with
adverse conditions such as drought stress has brought concerns about food security to the
fore; crop yield loss is a major cause of concern in this regard. Identification of genes with
multiple responses across environmental stresses is the genetic foundation that leads to
crop adaptation to environmental perturbations.
In this paper, we introduce an integrated approach to assess candidate genes for multiple
stress responses across-species. The approach combines ontology based semantic data
integration with expression profiling, comparative genomics, phylogenomics, functional
gene enrichment and gene enrichment network analysis to identify genes associated with
plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO), Trait Ontology
(TO), Plant Ontology (PO), Growth Ontology (GRO) and Environment Ontology (EO) were
used to semantically integrate drought related information.
Target genes linked to Quantitative Trait Loci (QTLs) controlling yield and stress tolerance
in sorghum (Sorghum bicolor (L.) Moench) and closely related species were identified.
Based on the enriched GO terms of the biological processes, 1116 sorghum genes with
potential responses to 5 different stresses, such as drought (18%), salt (32%), cold (20%), heat (8%) and oxidative stress (25%) were identified to be over-expressed. Out of 169 sorghum
drought responsive QTLs associated genes that were identified based on expression
datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168
additional genes that have been evaluated for orthologous pairs, 90% were conserved
across species for drought tolerance. Over 50% of identified maize and rice genes were
responsive to drought and salt stresses and were co-located within multifunctional QTLs.
Among the total identified multi-stress responsive genes, 272 targets were shown to be colocalized
within QTLs associated with different traits that are responsive to multiple stresses.
Ontology mapping was used to validate the identified genes, while reconstruction of the phylogenetic
tree was instrumental to infer the evolutionary relationship of the sorghum orthologs.
The results also show specific genes responsible for various interrelated components
of drought response mechanism such as drought tolerance, drought avoidance and drought
We submit that this approach is novel and to our knowledge, has not been used previously
in any other research; it enables us to perform cross-species queries for genes that are likely
to be associated with multiple stress tolerance, as a means to identify novel targets for engineering
stress resistance in sorghum and possibly, in other crop species.||en_US
|dc.publisher||Public Library of Science||en_US
|dc.rights||© 2018 Woldesemayat et al. This is an
open access article distributed under the terms of
the Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited.||
|dc.title||Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species||en_US