South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Belleville, South Africa.
Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Science Campus, Florida, Johannesburg, South Africa.
PLoS One. 2018 Mar 28;13(3):e0192678. doi: 10.1371/journal.pone.0192678. eCollection 2018.
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 co-localized 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 escape.
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.
作物对气候变化的反应以及全球变暖带来的干旱等不利条件的不可预测影响，使人们对粮食安全产生了担忧；作物产量损失是这方面的主要关注点。具有多种环境胁迫反应的基因的鉴定是导致作物适应环境波动的遗传基础。
本文提出了一种综合方法来评估跨物种多种胁迫反应的候选基因。该方法结合了基于本体论的语义数据集成、表达谱分析、比较基因组学、系统发生基因组学、功能基因富集和基因富集网络分析，以鉴定与植物胁迫表型相关的基因。使用了五个不同的本体论，即基因本体论 (GO)、性状本体论 (TO)、植物本体论 (PO)、生长本体论 (GRO) 和环境本体论 (EO)，对与干旱相关的信息进行语义集成。
鉴定出与高粱 (Sorghum bicolor (L.) Moench) 和相关物种中控制产量和胁迫耐受性的数量性状位点 (QTL) 相关的目标基因。根据生物过程的富集 GO 术语，鉴定出 1116 个高粱基因，它们可能对 5 种不同的胁迫有潜在反应，如干旱 (18%)、盐 (32%)、冷 (20%)、热 (8%) 和氧化应激 (25%)。基于表达数据集鉴定出的 169 个高粱干旱响应 QTL 相关基因中，有 56% 表现出多种胁迫响应。另一方面，在评估的 168 个具有同源对的额外基因中，90% 在物种间具有耐旱性。鉴定出的玉米和水稻基因中有 50%以上对干旱和盐胁迫有反应，并在多功能 QTL 中共同定位。在鉴定出的多胁迫反应基因中，有 272 个靶标被鉴定为与不同性状相关的 QTL 内共同定位，这些性状对多种胁迫有反应。本体论映射用于验证鉴定出的基因，而系统发生树的重建有助于推断高粱同源物的进化关系。结果还显示了负责各种与干旱反应机制相关的特定基因，如耐旱性、避旱性和抗旱性。
我们认为这种方法是新颖的，据我们所知，以前在任何其他研究中都没有使用过；它使我们能够进行跨物种查询，以寻找可能与多种胁迫耐受性相关的基因，从而鉴定高粱和可能其他作物物种中工程抗胁迫的新靶标。
