System analysis of microRNAs in the development and aluminium stress responses of the maize root system

MicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that down‐regulate target genes through mRNA cleavage or translational inhibition. miRNA is known to play an important role in the root development and environmental responses in both the Arabidopsis and rice. However, little information is available to form a complete view of miRNAs in the development of the maize root system and Al stress responses in maize. Four sRNA libraries were generated and sequenced from the early developmental stage of primary roots (PRY), the later developmental stage of maize primary roots (PRO), seminal roots (SR) and crown roots (CR). Through integrative analysis, we identified 278 miRNAs (246 conserved and 32 novel ones) and found that the expression patterns of miRNAs differed dramatically in different maize roots. The potential targets of the identified conserved and novel miRNAs were also predicted. In addition, our data showed that CR is more resistant to Al stress compared with PR and SR, and the differentially expressed miRNAs are likely to play significant roles in different roots in response to environmental stress such as Al stress. Here, we demonstrate that the expression patterns of miRNAs are highly diversified in different maize roots. The differentially expressed miRNAs are correlated with both the development and environmental responses in the maize root. This study not only improves our knowledge about the roles of miRNAs in maize root development but also reveals the potential role of miRNAs in the environmental responses of different maize roots.     

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.     

Primary and Lateral Root Development of Dark- and Light-Grown Cotton Seedlings under Salinity Stress*

Primary root growth dynamics and lateral root development of dark- and light grown cotton seedlings (Gossypium hirsutum L., cv. Acala SJ-2) were studied under control and salinity stress conditions. The seedlings were grown by two methods: A) in paper-lined, vermiculite-filled beakers with the plants growing between the paper and the glass wall (Gladish and Rost, 1993), and B) in hydroponics after germination and initial growth in germination paper rolls saturated with the treatment solutions (Kent and Läuchli, 1985). After germination, daily primary root elongation rate gradually incrased to a maximum, then gradually declined to close to zero for dark-grown seedlings, or to sustained rates of about 10 mm per day for light-grown control plants. Salinity stress delayed primary root growth and reduced peak elongation rates, without changing the general primary root growth pattern. These results suggest that salinity changed the time-scale, but did not modify the normal developmental sequence. Lateral root growth was more inhibited by salinity than primary root growth. In addition, elongation of lateral roots was more inhibited by salinity than their initiation and emergence. Light exposure of the shoot favored both sustained primary root growth from 7 days after planting, and lateral root emergence and growth. Salinity effects were more severe on seedlings germinated and grown in hydroponics (method B) than on vermiculite-grown plants (method A). These results emphasize the importance of growing conditions for the NaCl-induced effects on cotton root development. In addition, the differential effects of salinity on primary and lateral roots became evident, pointing to diverse control mechanisms for the development of these root types.     

玉米苗期SR蛋白基因家族的干旱胁迫应答

基因表达的选择性剪接(Alternative splicing, AS)调控与植物对逆境胁迫应答密切相关, SR蛋白(Serine/ arginine-rich proteins)是其中关键的调节因子。文章对玉米B73参考基因组进行分析显示: 多数SR蛋白家族基因成员启动子区域含有3~8种与发育或胁迫相关的顺式调控元件; 27个基因成员编码碱性蛋白, 其中23个成员的编码蛋白依照其N′端的首个RRM(RNA recognition motif)结构域特征大体上可划分为5个亚组。利用双向分级聚类方法, 对三叶期干旱胁迫下玉米杂交种郑单958及其亲本郑58和昌7-2的SR蛋白基因家族的分析显示, 该基因家族的表达模式具有明显的组织表达特异性和基因型依赖性特征; 其中在干旱胁迫下地下组织以下调表达模式为主, 而地上组织中以上调表达模式为主。在重度干旱胁迫后的3个不同时段复水过程中, 地上和地下组织中SR蛋白基因家族的表达皆以下调表达模式为主。另外, 尽管不同基因成员的表达模式在干旱胁迫及其后的复水过程中存在明显差异, 但普遍存在自身选择性剪接现象。SR蛋白基因家族在玉米干旱胁迫的应答规律, 为从AS-network视角解析玉米的抗逆分子机制提供了新思路。     

Genetic Analysis of Maize Root Characteristics in Response to Low Nitrogen Stress

Under low-input cropping systems, nitrogen (N) can be a limiting factor in plant growth and yield. Identifying genotypes that are more efficient at capturing limited N resources and the traits and mechanisms responsible for this ability is important. Root trait has a substantial influence on N acquisition from soils. Nevertheless, inconsistencies still exist as to the effect of low N on root length and its architecture in terms of lateral and axial roots. For maize, a crop utilizing heterosis, little is known about the relationship between parents and their crosses in the response of root architecture to N availability. Here 7 inbred maize lines and 21 of their crosses created by diallel mating were used to study the effect of N stress on root morphology as well as the relationship between the inbreds and their crosses. With large genotypic differences, low N generally suppresses shoot growth and increases the root to shoot ratio with or without increasing root biomass in maize. Maize plants responded to N deficiency by increasing total root length and altering root architecture by increasing the elongation of individual axial roots and enhancing lateral root growth, but with a reduction in the number of axial roots. Here, the inbreds showed weaker responses in root biomass and other root parameters than their crosses. Heterosis of root traits was significant at both N levels and was attributed to both the general combining ability (GCA) and special combining ability (SCA). Low N had substantial affects on the pattern of heterosis, GCA and SCA affects on root traits for each of the crosses suggesting that selection under N stress is necessary in generating low N-tolerant maize genotypes.     

Genetic variability of oxalate oxidase?activity and elongation in water-stressed primary roots of diverse maize and rice lines

A previous study of maize primary roots under water stress showed pronounced increases in oxalate oxidase activity and apoplastic hydrogen peroxide in the apical region of the growth zone where cell elongation is maintained. We examined whether increased oxalate oxidase activity in water-stressed roots is conserved across diverse lines of maize and rice. The maize lines exhibited varied patterns of activity, with some lines lacking activity in the apical region. Moreover, none of the rice lines showed activity in the apical region. Also, although the genotypic response of root elongation to water stress was variable in both maize and rice, this was not correlated with the pattern of oxalate oxidase activity. Implications of these findings for root growth regulation under water stress are discussed.     

Maize protein phosphatase gene family: identification and molecular characterization

Background

Protein phosphatases (PPs) play critical roles in various cellular processes through the reversible protein phosphorylation that dictates many signal transduction pathways among organisms. Recently, PPs in Arabidopsis and rice have been identified, while the whole complement of PPs in maize is yet to be reported.

Results

In this study, we have identified 159 PP-encoding genes in the maize genome. Phylogenetic analyses categorized the ZmPP gene family into 3 classes (PP2C, PTP, and PP2A) with considerable conservation among classes. Similar intron/exon structural patterns were observed in the same classes. Moreover, detailed gene structures and duplicative events were then researched. The expression profiles of ZmPPs under different developmental stages and abiotic stresses (including salt, drought, and cold) were analyzed using microarray and RNA-seq data. A total of 152 members were detected in 18 different tissues representing distinct stages of maize plant developments. Under salt stress, one gene was significantly up-expressed in seed root (SR) and one gene was down-expressed in primary root (PR) and crown root (CR), respectively. As for drought stress condition, 13 genes were found to be differentially expressed in leaf, out of which 10 were up-regulated and 3 exhibited down-regulation. Additionally, 13 up-regulated and 3 down-regulated genes were found in cold-tolerant line ETH-DH7. Furthermore, real-time PCR was used to confirm the expression patterns of ZmPPs.

Conclusions

Our results provide new insights into the phylogenetic relationships and characteristic functions of maize PPs and will be useful in studies aimed at revealing the global regulatory network in maize abiotic stress responses, thereby contributing to the maize molecular breeding with enhanced quality traits.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-773) contains supplementary material, which is available to authorized users.