Improving vanadium stress tolerance of watermelon by grafting onto bottle gourd and pumpkin rootstock

Vanadium (V) is a transition metal found in the Earth crust. V adversely affects plant growth and development. Besides several other management practices, grafting of scion cultivars onto appropriate rootstock provides a suitable solution. Grafting is an important agro-technical procedure utilized to enhance the capacity of plants to tolerate biotic and abiotic stresses. In this study, watermelon was grafted onto bottle gourd and pumpkin rootstock, and self-grafted watermelon plants were utilized as a control. V was applied at the rate of 50 mg/L under hydroponic conditions. The result showed that V application substantially reduces the growth of watermelon plants, however, grafting of watermelon onto bottle gourd and pumpkin rootstock improves V stress tolerance of watermelon by reducing the V concentration in leaf tissues, improving the relative chlorophyll content (SPAD index) and photosynthetic assimilation, up-regulating the expression of SOD (Cla008698, Cla0012125, Cla009820 and Cla001158), glutathione S-transferase (Cla013224) and glutathione peroxidase (Cla021039) genes in the leaves, and enhancing the activities of antioxidant enzymes (SOD, CAT). The scanning electron microscopy (SEM) of the root tips showed that minimal damage of roots was observed for pumpkin roots compared with the roots of watermelon and bottle gourd under V stress conditions. So far as we know, these results are the first evidence that grafting mitigates V stress in plants.     

蒙古沙冬青保守microRNAs的鉴定及靶基因预测

蒙古沙冬青(Ammopiptanthus mongolicus)是生长在荒漠中的木本植物, 对于我国西北部干旱、半干旱区域的植被维护与恢复具有重要价值。蒙古沙冬青对干旱、低温等多种逆境具有较高的耐受性, 是研究林木耐受逆境生理与分子机制的合适材料。MicroRNA(miRNA)是一类长度约为21个核苷酸的内源性非编码小分子RNA, 在植物生长发育和逆境应答等生物学过程中发挥着重要的调控作用。目前, 许多植物物种的miRNAs已经获得鉴定, 但未见蒙古沙冬青miRNAs的相关报道。文章应用高通量测序和生物信息学分析方法对蒙古沙冬青幼苗保守miRNAs的类型、表达丰度以及靶基因进行了分析和预测。共鉴定了10个家族的19种保守miRNAs, 其表达丰度介于55~1920269个拷贝之间。通过在线软件psRNATarget预测了其中14个保守miRNAs的靶基因。对于这些靶基因的功能分析表明, 蒙古沙冬青的保守miRNA主要通过转录调控、激素信号途径、物质代谢和胁迫应答等生物学过程参与植物生长发育和环境响应。     

Dynamic Regulation of Novel and Conserved miRNAs Across Various Tissues of Diverse Cucurbit Species

MicroRNA genes (miRNAs) encoding small non-coding RNAs are abundant in plant genomes and play a key role in regulating several biological mechanisms. Five conserved miRNAs, miR156, miR168-1, miR168-2, miR164, and miR166 were selected for analysis from the 21 known plant miRNA families that were recovered from deep sequencing data of small RNA libraries of pumpkin and squash. A total of six novel miRNAs that were not reported before were found to have precursors with reliable fold-back structures and hence considered novel and were designated as cuc_nov_miRNAs. A set of five conserved, six novel miRNAs, and five uncharacterized small RNAs from the deep sequencing data were profiled for their dynamic regulation using qPCR. The miRNAs were evaluated for differential regulation across the tissues among four diverse cucurbit species, including pumpkin and squash (Cucurbita moschata Duch. Ex Poir. and Cucurbita pepo L.), bitter melon (Momordica charantia L.), and Luffa (Loofah) (Luffa acutangula Roxb.). Expression analysis revealed differential regulation of various miRNAs in leaf, stem, and fruit tissues. Importantly, differences in the expression levels were also found in the leaves and fruits of closely related C. moschata and C. pepo. Comparative miRNA profiling and expression analysis in four cucurbits led to identification of conserved miRNAs in cucurbits. Predicted targets for two of the conserved miRNAs suggested miRNAs are involved in regulating similar biological mechanisms in various species of cucurbits.     

MicroRNA profiles in Sorghum exposed to individual drought or heat or their combination

Sorghum is largely grown for food, fodder and for biofuel production in semi-arid regions where the drought or high temperature or their combination co-occur. Plant microRNAs (miRNAs) are integral to the gene regulatory networks that control almost all biological processes including adaptation to stress conditions. Thus far, plant miRNA profiles under separate drought or heat stresses have been reported but not under combined drought and heat. In this study, we report miRNA profiles in leaves of sorghum exposed to individual drought or heat or their combination. Approximately 29 conserved miRNA families represented by 80 individual miRNAs, 26 families represented by 47 members of less conserved or sorghum-specific miRNA families as well as 8 novel miRNA families have been identified. Of these, 25 miRNAs were found to be differentially regulated in response to stress treatments. The comparative profiling revealed that the miRNA regulation was stronger under heat or combination of heat and drought compared to the drought alone. Furthermore, using degradome sequencing, 48 genes were confirmed as targets for the miRNAs in sorghum. Overall, this study provides a framework for understanding of the miRNA-guided gene regulations under combined stresses.

     

利用深度测序技术检测玉米根系和叶片中已知的microRNAs

microRNA(miRNA)是一类具有20～24nt核苷酸长度的非蛋白质编码的内源小分子RNA,它在植物生长发育和逆境胁迫响应等过程中发挥着重要作用。文章利用基于Illumina/Solexa原理的小分子RNA深度测序技术,结合生物信息学的方法对玉米根系和叶片中已知miRNA的类型、丰度及靶基因进行了分析。研究发现,在根系中共检测到92个已知的miRNA,分别属于18个miRNA家族,其表达丰度在1～105943之间;在叶片中,共发现86个已知的miRNA,分别属于17个miRNA家族,其表达丰度在1～85973之间。靶基因预测结果表明,根系中的18个miRNA家族共靶向54个蛋白,进一步的功能预测发现,这些基因涉及了转录调控、物质能量代谢、电子传递、胁迫响应和信号转导等过程。以上研究结果表明,就已知的miRNA而言,无论是miRNA的类型还是表达丰度,在玉米根系和叶片中都存在较大差异。     

Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium

MicroRNAs (miRNAs) are a distinct class of small RNAs in plants that not only regulate biological processes but also regulate response to environmental stresses. The toxic heavy metal cadmium (Cd) induces expression of several miRNAs in rapeseed (Brassica napus), but it is not known on a genome-wide scale how the expression of miRNAs and their target genes, is regulated by Cd. In this study, four small RNA libraries and four degradome libraries were constructed from Cd-treated and non-Cd-treated roots and shoots of B. napus seedlings. Using high-throughput sequencing, the study identified 84 conserved and non-conserved miRNAs (belonging to 37 miRNA families) from Cd-treated and non-treated B. napus, including 19 miRNA members that were not identified before. Some of the miRNAs were validated by RNA gel blotting. Most of the identified miRNAs were found to be differentially expressed in roots/shoots or regulated by Cd exposure. The study simultaneously identified 802 targets for the 37 (24 conserved and 13 non-conserved) miRNA families, from which there are 200, 537, and 65 targets, belonging to categories I, II, and III, respectively. In category I alone, many novel targets for miRNAs were identified and shown to be involved in plant response to Cd.     

Identification of MicroRNAs and Transcript Targets in Camelina sativa by Deep Sequencing and Computational Methods

Camelina sativa is an annual oilseed crop that is under intensive development for renewable resources of biofuels and industrial oils. MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play key roles in diverse plant biological processes. Here, we conducted deep sequencing on small RNA libraries prepared from camelina leaves, flower buds and two stages of developing seeds corresponding to initial and peak storage products accumulation. Computational analyses identified 207 known miRNAs belonging to 63 families, as well as 5 novel miRNAs. These miRNAs, especially members of the miRNA families, varied greatly in different tissues and developmental stages. The predicted miRNA target genes are involved in a broad range of physiological functions including lipid metabolism. This report is the first step toward elucidating roles of miRNAs in C. sativa and will provide additional tools to improve this oilseed crop for biofuels and biomaterials.     

Common functions for diverse small RNAs of land plants

Endogenous small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), are critical components of plant gene regulation. Some abundant miRNAs involved in developmental control are conserved between anciently diverged plants, while many other less-abundant miRNAs appear to have recently emerged in the Arabidopsis thaliana lineage. Using large-scale sequencing of small RNAs, we extended the known diversity of miRNAs in basal plants to include 88 confidently annotated miRNA families in the moss Physcomitrella patens and 44 in the lycopod Selaginella moellendorffii. Cleavage of 29 targets directed by 14 distinct P. patens miRNA families and a trans-acting siRNA (ta-siRNA) was experimentally confirmed. Despite a core set of 12 miRNA families also expressed in angiosperms, weakly expressed and apparently lineage-specific miRNAs accounted for the majority of miRNA diversity in both species. Nevertheless, the molecular functions of several of these lineage-specific small RNAs matched those of angiosperms, despite dissimilarities in the small RNA sequences themselves, including small RNAs that mediated negative feedback regulation of the miRNA pathway and miR390-dependent ta-siRNAs that guided the cleavage of AUXIN RESPONSE FACTOR mRNAs. Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants.     

Discovery and profiling of novel and conserved microRNAs during flower development in Carya cathayensis via deep sequencing

Hickory (Carya cathayensis Sarg.) is an economically important woody plant in China, but its long juvenile phase delays yield. MicroRNAs (miRNAs) are critical regulators of genes and important for normal plant development and physiology, including flower development. We used Solexa technology to sequence two small RNA libraries from two floral differentiation stages in hickory to identify miRNAs related to flower development. We identified 39 conserved miRNA sequences from 114 loci belonging to 23 families as well as two novel and ten potential novel miRNAs belonging to nine families. Moreover, 35 conserved miRNA*s and two novel miRNA*s were detected. Twenty miRNA sequences from 49 loci belonging to 11 families were differentially expressed; all were up-regulated at the later stage of flower development in hickory. Quantitative real-time PCR of 12 conserved miRNA sequences, five novel miRNA families, and two novel miRNA*s validated that all were expressed during hickory flower development, and the expression patterns were similar to those detected with Solexa sequencing. Finally, a total of 146 targets of the novel and conserved miRNAs were predicted. This study identified a diverse set of miRNAs that were closely related to hickory flower development and that could help in plant floral induction.     

Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules

miRNAs are ～21 nt non-coding RNAs and play important roles in plant development and response to stress. Symbiotic nitrogen fixation (SNF) is agronomically important for reducing the need of nitrogen fertilizers. The soybean root nodule is the place where SNF takes place. To identify miRNAs that are possibly involved in nitrogen fixation in soybean functional nitrogen-fixing nodules, a small library of RNAs was constructed from the functional nodules harvested 28 days after inoculation with rhizobium. Thirty-two small RNA sequences were identified as belonging to 11 miRNA families. Eight miRNAs are conserved across plant species, twenty are specific to soybean, and the four remaining miRNAs are novel. Expression analysis revealed that miRNAs were differentially expressed in the different tissues. Combinatorial miRNA target prediction identified genes that are involved in multiple biological processes. The results suggest that miRNAs play critical and diverse roles in SNF, nutrient acquisition, and plant development.