Epigenetic chromatin modifiers in barley: I. Cloning, mapping and expression analysis of the plant specific HD2 family of histone deacetylases from barley, during seed development and after hormonal treatment

Epigenetic phenomena have been associated with modifications of chromatin structure. These are achieved, in part, by histone post-translational modifications including acetylations and deacetylations, the later being catalyzed by histone deacetylaces (HDACs). Eukaryotic HDACs are grouped into three major families, RPD3/HDA1, SIR2 and the plant-specific HD2. HDAC genes have been analyzed from model plants such as Arabidopsis , rice and maize and have been shown to be involved in various cellular processes including seed development, vegetative and reproductive growth and responses to abiotic and biotic stress, but reports on HDACs from other crops are limited. In this work two full-length cDNAs ( HvHDAC2-1 and HvHDAC2-2 ) encoding two members of the plant-specific HD2 family, respectively, were isolated and characterized from barley ( Hordeum vulgare ), an agronomically important cereal crop. HvHDAC2-1 and HvHDAC2-2 were mapped on barley chromosomes 1H and 3H, respectively, which could prove useful in developing markers for marker-assisted selection in breeding programs. Expression analysis of the barley HD2 genes demonstrated that they are expressed in all tissues and seed developmental stages examined. Significant differences were observed among tissues and seed stages, and between cultivars with varying seed size, suggesting an association of these genes with seed development. Furthermore, the HD2 genes from barley were found to respond to treatments with plant stress-related hormones such as jasmonic acid (JA), abscisic acid (ABA) and salicylic acid (SA) implying an association of these genes with plant resistance to biotic and abiotic stress. The expression pattern of HD2 genes suggests a possible role for these genes in the epigenetic regulation of seed development and stress response.     

Deep Sequencing of Maize Small RNAs Reveals a Diverse Set of MicroRNA in Dry and Imbibed Seeds

Seed germination plays a pivotal role during the life cycle of plants. As dry seeds imbibe water, the resumption of energy metabolism and cellular repair occur and miRNA-mediated gene expression regulation is involved in the reactivation events. This research was aimed at understanding the role of miRNA in the molecular control during seed imbibition process. Small RNA libraries constructed from dry and imbibed maize seed embryos were sequenced using the Illumina platform. Twenty-four conserved miRNA families were identified in both libraries. Sixteen of them showed significant expression differences between dry and imbibed seeds. Twelve miRNA families, miR156, miR159, miR164, miR166, miR167, miR168, miR169, miR172, miR319, miR393, miR394 and miR397, were significantly down-regulated; while four families, miR398, miR408, miR528 and miR529, were significantly up-regulated in imbibed seeds compared to that in dry seeds. Furthermore, putative novel maize miRNAs and their target genes were predicted. Target gene GO analysis was performed for novel miRNAs that were sequenced more than 50 times in the normalized libraries. The result showed that carbohydrate catabolic related genes were specifically enriched in the dry seed, while in imbibed seed target gene enrichment covered a broad range of functional categories including genes in amino acid biosynthesis, isomerase activity, ligase activity and others. The sequencing results were partially validated by quantitative RT-PCR for both conserved and novel miRNAs and the predicted target genes. Our data suggested that diverse and complex miRNAs are involved in the seed imbibition process. That miRNA are involved in plant hormone regulation may play important roles during the dry-imbibed seed transition.     

The calcium sensor calcineurin B-like 9 modulates abscisic acid sensitivity and biosynthesis in Arabidopsis

Calcium plays a pivotal role in plant responses to several stimuli, including pathogens, abiotic stresses, and hormones. However, the molecular mechanisms underlying calcium functions are poorly understood. It is hypothesized that calcium serves as second messenger and, in many cases, requires intracellular protein sensors to transduce the signal further downstream in the pathways. The calcineurin B-like proteins (CBLs) represent a unique family of calcium sensors in plant cells. Here, we report our analysis of the CBL9 member of this gene family. Expression of CBL9 was inducible by multiple stress signals and abscisic acid (ABA) in young seedlings. When CBL9 gene function was disrupted in Arabidopsis thaliana plants, the responses to ABA were drastically altered. The mutant plants became hypersensitive to ABA in the early developmental stages, including seed germination and post-germination seedling growth. In addition, seed germination in the mutant also showed increased sensitivity to inhibition by osmotic stress conditions produced by high concentrations of salt and mannitol. Further analyses indicated that increased stress sensitivity in the mutant may be a result of both ABA hypersensitivity and increased accumulation of ABA under the stress conditions. The cbl9 mutant plants showed enhanced expression of genes involved in ABA signaling, such as ABA-INSENSITIVE 4 and 5. This study has identified a calcium sensor as a common element in the ABA signaling and stress-induced ABA biosynthesis pathways.     

Genome‐wide identification,expression analysis of auxin‐responsive GH3 family genes in maize (Zea mays L.) under abiotic stresses

Auxin is involved in different aspects of plant growth and development by regulating the expression of auxinresponsive family genes. As one of the three major auxinresponsive families, GH3(Gretchen Hagen3) genes participate in auxin homeostasis by catalyzing auxin conjugation and bounding free indole-3-acetic acid(IAA) to amino acids.However, how GH3 genes function in responses to abiotic stresses and various hormones in maize is largely unknown.Here, the latest updated maize(Zea mays L.) reference genome sequence was used to characterize and analyze the Zm GH3 family genes from maize. The results showed that 13 Zm GH3 genes were mapped on fi ve maize chromosomes(total10 chromosomes). Highly diversi fi ed gene structures and tissue-speci fi c expression patterns suggested the possibility of function diversi fi cation for these genes in response to environmental stresses and hormone stimuli. The expression patterns of Zm GH3 genes are responsive to several abiotic stresses(salt, drought and cadmium) and major stress-relatedhormones(abscisic acid, salicylic acid and jasmonic acid)Various environmental factors suppress auxin free IAA contents in maize roots suggesting that these abiotic stresses and hormones might alter GH3-mediated auxin levels. The respon siveness of Zm GH3 genes to a wide range of abiotic stresses and stress-related hormones suggested that Zm GH3 s are involved in maize tolerance to environmental stresses.     

东乡野生稻苗期响应低温胁迫的转录组分析

为了解东乡野生稻（Oryza rufipogon）对低温胁迫的响应机制,对苗期的RNA-seq转录表达谱进行了研究。结果表明,与对照相比,共检测到10 200个差异表达基因（DEGs）,其中5 201个上调表达,4 999个下调表达,其中有426个DEGs位于已报道的水稻耐冷QTL区间,且37个为耐冷调控相关的家族基因。GO功能分类和KEGG代谢路径分析表明,核酸结合转录因子活性、氨基酸生物合成以及光合作用代谢等均参与响应低温胁迫过程。实时荧光定量分析表明,ABA响应蛋白基因、MYB转录因子和40S核糖体蛋白SA基因等12个可能与低温胁迫响应相关的DEGs表达模式与RNA-seq的一致。可见,植物激素传导途径和转录因子相关调控基因在东乡野生稻苗期响应低温胁迫过程中起重要作用。     

Cloning and expression analysis of some genes involved in the phosphoinositide and phospholipid signaling pathways from maize (Zea mays L.)

Previous studies have indicated the phosphoinositide and phospholipid signaling pathways play a key role in plant growth, development and responses to environmental stresses. However, little is known about the phosphoinositide and phospholipid signaling pathways in maize (Zea mays L.). To better understand the function of genes involved in the phosphoinositide and phospholipid signaling pathways in maize, the cDNA sequences of ZmPIS2, ZmPLC2, ZmDGK1, ZmDGK2 and ZmDGK3 were obtained by RACE (rapid amplification of cDNA ends) or in silico cloning combined with PCR. RT-PCR analysis of cDNA from five tissues (roots, stems, leaves, tassels, and ears) indicated that the expression patterns of the five cDNAs we isolated as well as ZmPIS, ZmPLC, ZmPLD varied in different tissues. To determine the effects of different environmental conditions such as cold, drought and various phytohormones (abscisic acid, indole-3-acetic acid and gibberellic acid) on gene expression, we analyzed expression by Real-Time (RT-PCR), and found that the different isoforms of these gene families involved in the phosphoinositide and phospholipid signaling pathways have specific expression patterns. Our results suggested that these genes may be involved in the responses to environmental stresses, but have different functions. The isolation and analysis of expression patterns of genes involved in the phosphoinositide and phospholipid signaling pathways provides a good basis for further research of the phosphoinositide and phospholipid signaling pathways in maize and is a novel supplement to our comprehension of these pathways in plants.     

Early changes of gene activity in developing seedlings of Arabidopsis hybrids relative to parents may contribute to hybrid vigour

Hybrid vigour (heterosis) has been used for decades in crop industries, especially in the production of maize and rice. Hybrid varieties usually exceed their parents in plant biomass and seed yield. But the molecular basis of hybrid vigour is not fully understood. In this project, we studied heterosis at early stages of seedling development in Arabidopsis hybrids derived from crossing Ler and C24 accessions. We found that early heterosis is associated with non‐additive gene expression that resulted from earlier changes in gene expression in the hybrids relative to the parents. The non‐additively expressed genes are involved in metabolic pathways, including photosynthesis, critical for plant growth. The early increased expression levels of genes involved in energy production in hybrids is associated with heterosis in the young seedlings that could be essential for biomass heterosis at later developmental stages of the plant.