The identification of candidate radio marker genes using a coexpression network analysis in gamma‐irradiated rice

Plant physiological and biochemical processes are significantly affected by gamma irradiation stress. In addition, gamma‐ray (GA) differentially affects gene expression across the whole genome. In this study, we identified radio marker genes (RMGs) responding only to GA stress compared with six abiotic stresses (chilling, cold, anoxia, heat, drought and salt) in rice. To analyze the expression patterns of differentially expressed genes (DEGs) in gamma‐irradiated rice plants against six abiotic stresses, we conducted a hierarchical clustering analysis by using a complete linkage algorithm. The up‐ and downregulated DEGs were observed against six abiotic stresses in three and four clusters among a total of 31 clusters, respectively. The common gene ontology functions of upregulated DEGs in clusters 9 and 19 are associated with oxidative stress. In a Pearson's correlation coefficient analysis, GA stress showed highly negative correlation with salt stress. On the basis of specific data about the upregulated DEGs, we identified the 40 candidate RMGs that are induced by gamma irradiation. These candidate RMGs, except two genes, were more highly induced in rice roots than in other tissues. In addition, we obtained other 38 root‐induced genes by using a coexpression network analysis of the specific upregulated candidate RMGs in an ARACNE algorithm. Among these genes, we selected 16 RMGs and 11 genes coexpressed with three RMGs to validate coexpression network results. RT‐PCR assay confirmed that these genes were highly upregulated in GA treatment. All 76 genes (38 root‐induced genes and 38 candidate RMGs) might be useful for the detection of GA sensitivity in rice roots.     

Comprehensive expression analysis of rice phospholipase D gene family during abiotic stresses and development

Phospholipase D is one of the crucial enzymes involved in lipid mediated signaling, triggered during various developmental and physiological processes. Different members of PLD gene family have been known to be induced under different abiotic stresses and during developmental processes in various plant species. In this report, we are presenting a detailed microarray based expression analysis and expression profiles of entire set of PLD genes in rice genome, under three abiotic stresses (salt, cold and drought) and different developmental stages (3-vegetative stages and 11-reproductive stages). Seven and nine PLD genes were identified, which were expressed differentially under abiotic stresses and during reproductive developmental stages, respectively. PLD genes, which were expressed significantly under abiotic stresses exhibited an overlapping expression pattern and were also differentially expressed during developmental stages. Moreover, expression pattern for a set of stress induced genes was validated by real time PCR and it supported the microarray expression data. These findings emphasize the role of PLDs in abiotic stress signaling and development in rice. In addition, expression profiling for duplicated PLD genes revealed a functional divergence between the duplicated genes and signify the role of gene duplication in the evolution of this gene family in rice. This expressional study will provide an important platform in future for the functional characterization of PLDs in crop plants.     

短期盐胁迫下盐穗木的转录组分析

盐穗木（Halostachys caspica）是荒漠盐碱地广泛分布的盐生植物,具有极强的耐盐性。为揭示盐胁迫下盐穗木基因组层面的基因表达变化特性,通过对300和500mmol·L^-1 NaCl胁迫3h的盐穗木同化枝进行了转录组测序。有效序列组装共得到153298条平均长度为643bp的unigenes,进行GO和KEGG功能聚类,分别获得47个GO功能小类和118个KEGG通路。差异表达基因分析显示,短期低盐（300mmol·L^-1）响应基因有4432个,高盐（500mmol·L^-1）响应基因有2580个,两个胁迫的共差异基因有1245个,主要富集在细胞过程、代谢过程和响应刺激等类别中。从短期盐胁迫下盐穗木转录组筛选出渗透调节和活性氧清除的相关基因,大多为上调基因。说明盐穗木能够通过促进渗透调节和增强活性氧清除提高短期的盐胁迫适应能力。     

水稻NAM基因家族的全基因组鉴定及表达分析

植物特异性转录因子NAM家族从属于NAC转录因子超家族,在植株生长发育、生理代谢以及应对各种胁迫反应中均发挥重要作用。该研究采用生物信息学方法鉴定水稻基因组中的NAM基因,分析其时空表达模式、亚细胞定位以及蛋白相互作用,并采用实时定量qRT PCR方法分析不同外源激素(如SA、ABA和MeJA)以及非生物胁迫(包括干旱、盐和冷)处理下各NAM基因的表达特征,为进一步探索NAM基因在非生物胁迫中的功能和应激机制以及激素调控途径奠定基础。结果显示：(1)从水稻基因组中共鉴定出48个NAM基因,进化分析将其分为5个亚家族;NAM基因在水稻基因组中存在9对片段复制事件。(2)组织表达分析显示,NAM基因在水稻不同组织及发育时期表现特异性表达,特别是叶鞘、茎和节的生长过程中高表达,且大多数是核定位,并存在多种蛋白互作。(3)实时定量qRT PCR表达分析显示,10个NAM基因在不同组织中均特异表达;大部分NAM基因在盐和干旱胁迫下表达上调,而在冷胁迫下表达降低;SA、ABA和MeJA处理均可显著改变各NAM基因的表达水平。研究表明,NAM基因在水稻生长发育、激素应答和非生物胁迫响应中具有重要作用。     

Functional Characterization of Maize C<Subscript>2</Subscript>H<Subscript>2</Subscript> Zinc-Finger Gene Family

Plant C2H2-type zinc finger proteins (ZFPs) play essential roles in developmental control and stress responses. The whole complement of ZFP genes has been identified in Arabidopsis and rice, while the genome-scale identification and functional analysis of maize ZFPs is not yet reported. Hence, we performed a comprehensive analysis, including gene structure, chromosome location, duplicated event, selective pressure, phylogeny, gene ontology annotation, and expression profiling under developmental stages and abiotic stresses. Phylogenetic analyses suggested that the ZmZFP gene family can be grouped into three classes (A, B, and C). The analysis of differential gene expression in different developmental stages and stress treatments (drought, salt, and cold) was conducted based on microarray and RNA-seq data. A total of 99.05 % (209 genes) of the total ZmZFP genes (211 genes) were detected in 60 different tissues in microarray data. Under drought stress, 13 differentially expressed genes were found in leaf, of which 7 and 6 genes were up-regulated and down-regulated, respectively. For salt stress, crown root (CR), primary root (PR) and seed root (SR) each had one significantly elevated gene, while 2, 1, and 7 genes were obviously down-regulated in CR, PR and SR, respectively. Additionally, 8 and 3 genes were significantly up-regulated and down-regulated, respectively, in the cold-tolerant line ETH-DH7. This study will lay the foundation for understanding the roles of ZFPs in maize growth and stress resistance, contributing to the molecular breeding of maize for food.