Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance.
Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance.
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DOI：
10.1186/s12870-015-0422-8
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发表时间：
2015-02-03
影响因子：
5.3
通讯作者：
Li Z
中科院分区：
文献类型：
--
作者：
Shin JH;Vaughn JN;Abdel-Haleem H;Chavarro C;Abernathy B;Kim KD;Jackson SA;Li Z
在非生物胁迫中，干旱是最常见的作物减产因素。慢萎蔫大豆基因型PI 416937对水分亏缺有一定的抵抗力，以前已用于在双亲本群体中绘制该性状。由于干旱胁迫响应是一个复杂的生物学过程，为了更深入地了解大豆的干旱响应，我们进行了全基因组转录组分析。通过比较PI 416937和本宁的数据，我们建立了一个分类系统，以确定在两种基因型中对水分亏缺作出反应的基因或对基因型x环境（GxE）作出反应的基因。尽管萎蔫表型差异很大，但90%的可分类基因在两种基因型中都有恒定的表达（33%）或非常相似的反应谱（E基因，57%）。通过进一步根据表达谱对E基因进行分类，我们能够辨别出缺水特定阶段转录反应的功能特异性，注意到众所周知的光合作用基因的减少以及鲜为人知的蛋白质转运途径的上调。2%的可分类基因具有明确的GxE反应，其中许多位于慢萎蔫qtl中。我们认为这些强有力的候选基因可能是PI 416937独特的干旱避免策略的潜在原因。对水分缺乏有一个普遍且功能显著的转录反应，不仅涉及已知的途径，如光合作用的下调，还涉及蛋白质转运和染色质重塑的上调。表现出基因型差异的基因比基因型之间不变的基因更有可能表现出环境反应。在这项研究中，至少有5个基因明确表现出基因型x环境反应，属于已知的QTL，是进一步研究缓慢萎蔫的很好的候选者。本文的在线版本（doi:10.1186/s12870-015-0422-8）包含补充材料，仅供授权用户使用。
Among abiotic stresses, drought is the most common reducer of crop yields. The slow-wilting soybean genotype PI 416937 is somewhat robust to water deficit and has been used previously to map the trait in a bi-parental population. Since drought stress response is a complex biological process, whole genome transcriptome analysis was performed to obtain a deeper understanding of the drought response in soybean. Contrasting data from PI 416937 and the cultivar ‘Benning’, we developed a classification system to identify genes that were either responding to water-deficit in both genotypes or that had a genotype x environment (GxE) response. In spite of very different wilting phenotypes, 90% of classifiable genes had either constant expression in both genotypes (33%) or very similar response profiles (E genes, 57%). By further classifying E genes based on expression profiles, we were able to discern the functional specificity of transcriptional responses at particular stages of water-deficit, noting both the well-known reduction in photosynthesis genes as well as the less understood up-regulation of the protein transport pathway. Two percent of classifiable genes had a well-defined GxE response, many of which are located within slow-wilting QTLs. We consider these strong candidates for possible causal genes underlying PI 416937’s unique drought avoidance strategy. There is a general and functionally significant transcriptional response to water deficit that involves not only known pathways, such as down-regulation of photosynthesis, but also up-regulation of protein transport and chromatin remodeling. Genes that show a genotypic difference are more likely to show an environmental response than genes that are constant between genotypes. In this study, at least five genes that clearly exhibited a genotype x environment response fell within known QTL and are very good candidates for further research into slow-wilting. The online version of this article (doi:10.1186/s12870-015-0422-8) contains supplementary material, which is available to authorized users.
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影响因子：
2.3
作者：
Ries, Landon L.;Purcell, Larry C.;King, C. Andy
通讯作者：
King, C. Andy
影响因子：
5.4
作者：
Abdel-Haleem, Hussein;Carter, Thomas E., Jr.;Boerma, H. Roger
通讯作者：
Boerma, H. Roger
DOI：
10.1073/pnas.0604421103
发表时间：
2006-11-21
影响因子：
11.1
作者：
Leshem, Yehoram;Melamed-Book, Naomi;Levine, Alex
通讯作者：
Levine, Alex
影响因子：
3.7
作者：
Le DT;Nishiyama R;Watanabe Y;Tanaka M;Seki M;Ham le H;Yamaguchi-Shinozaki K;Shinozaki K;Tran LS
通讯作者：
Tran LS
影响因子：
12.3
作者：
Covington, Michael F.;Maloof, Julin N.;Straume, Marty;Kay, Steve A.;Harmer, Stacey L.
通讯作者：
Harmer, Stacey L.