Hossain Mohammad R, Bassel George W, Pritchard Jeremy, Sharma Garima P, Ford-Lloyd Brian V
Department of Genetics and Plant Breeding, Bangladesh Agricultural UniversityMymensingh, Bangladesh; School of Biosciences, University of BirminghamBirmingham, UK.
School of Biosciences, University of Birmingham Birmingham, UK.
Front Plant Sci. 2016 May 3;7:567. doi: 10.3389/fpls.2016.00567. eCollection 2016.
Stress responsive gene expression is commonly profiled in a comparative manner involving different stress conditions or genotypes with contrasting reputation of tolerance/resistance. In contrast, this research exploited a wide natural variation in terms of taxonomy, origin and salt sensitivity in eight genotypes of rice to identify the trait specific patterns of gene expression under salt stress. Genome wide transcptomic responses were interrogated by the weighted continuous morpho-physiological trait responses using modified Significance Analysis of Microarrays. More number of genes was found to be differentially expressed under salt stressed compared to that of under unstressed conditions. Higher numbers of genes were observed to be differentially expressed for the traits shoot Na(+)/K(+), shoot Na(+), root K(+), biomass and shoot Cl(-), respectively. The results identified around 60 genes to be involved in Na(+), K(+), and anion homeostasis, transport, and transmembrane activity under stressed conditions. Gene Ontology (GO) enrichment analysis identified 1.36% (578 genes) of the entire transcriptome to be involved in the major molecular functions such as signal transduction (>150 genes), transcription factor (81 genes), and translation factor activity (62 genes) etc., under salt stress. Chromosomal mapping of the genes suggests that majority of the genes are located on chromosomes 1, 2, 3, 6, and 7. The gene network analysis showed that the transcription factors and translation initiation factors formed the major gene networks and are mostly active in nucleus, cytoplasm and mitochondria whereas the membrane and vesicle bound proteins formed a secondary network active in plasma membrane and vacuoles. The novel genes and the genes with unknown functions thus identified provide picture of a synergistic salinity response representing the potentially fundamental mechanisms that are active in the wide natural genetic background of rice and will be of greater use once their roles are functionally verified.
应激反应基因表达通常以比较的方式进行分析，涉及不同的应激条件或具有不同耐受/抗性声誉的基因型。相比之下，本研究利用了8个水稻基因型在分类学、起源和盐敏感性方面的广泛自然变异，以确定盐胁迫下基因表达的性状特异性模式。通过使用改良的微阵列显著性分析，对全基因组转录组反应与加权连续形态生理性状反应进行了比对。与非胁迫条件相比，发现盐胁迫下有更多基因差异表达。分别观察到更多基因在地上部Na(+)/K(+)、地上部Na(+)、根部K(+)、生物量和地上部Cl(-)等性状上差异表达。结果确定约60个基因参与胁迫条件下的Na(+)、K(+)和阴离子稳态、运输及跨膜活性。基因本体（GO）富集分析确定在盐胁迫下，整个转录组的1.36%（578个基因）参与主要分子功能，如信号转导（>150个基因）、转录因子（81个基因）和翻译因子活性（62个基因）等。基因的染色体定位表明，大多数基因位于第1、2、3、6和7号染色体上。基因网络分析表明，转录因子和翻译起始因子形成主要基因网络，主要在细胞核、细胞质和线粒体中活跃，而膜和囊泡结合蛋白形成在质膜和液泡中活跃的次要网络。由此鉴定出的新基因和功能未知的基因提供了协同盐度反应的图景，代表了在水稻广泛自然遗传背景中活跃的潜在基本机制，一旦其作用得到功能验证，将具有更大的用途。
