Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Reactive oxygen species (ROS) generation is a usual phenomenon in a plant both under a normal and stressed condition. However, under unfavorable or adverse conditions, ROS production exceeds the capacity of the antioxidant defense system. Both non-enzymatic and enzymatic components of the antioxidant defense system either detoxify or scavenge ROS and mitigate their deleterious effects. The Ascorbate-Glutathione (AsA-GSH) pathway, also known as Asada–Halliwell pathway comprises of AsA, GSH, and four enzymes viz. ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase, and glutathione reductase, play a vital role in detoxifying ROS. Apart from ROS detoxification, they also interact with other defense systems in plants and protect the plants from various abiotic stress-induced damages. Several plant studies revealed that the upregulation or overexpression of AsA-GSH pathway enzymes and the enhancement of the AsA and GSH levels conferred plants better tolerance to abiotic stresses by reducing the ROS. In this review, we summarize the recent progress of the research on AsA-GSH pathway in terms of oxidative stress tolerance in plants. We also focus on the defense mechanisms as well as molecular interactions.

https://www.mdpi.com/2076-3921/8/9/384/pdf

Regulation of Ascorbate-Glutathione Pathway in Mitigating Oxidative Damage in Plants under Abiotic Stress

Senescence is an age-dependent process, ultimately leading to plant death, that in annual crop plants overlaps with the reproductive stage of development. Research on the molecular and biochemical mechanisms of leaf senescence has revealed a multi-layered regulatory network operating to control age-dependent processes. Abiotic stress-induced senescence challenges source-sink relationships and results in significant reduction in crop yields. Although processes associated with plant senescence are well studied, the mechanisms regulating stress-induced senescence are not well known. Here, we discuss the effects of abiotic stress on crop productivity, mechanisms associated with stress-induced senescence, and the possible use of these mechanisms for the generation of plant stress tolerance. We emphasize the involvement of source strength and stability of the photosynthetic apparatus in this process, and suggest a possible role of a perennial plant life strategy for the amelioration of stress-induced senescence.

Stress-induced senescence and plant tolerance to abiotic stress.

Although abscisic acid (ABA) is an important hormone that regulates seed dormancy, stomatal closure, plant development, as well as responses to environmental stimuli, the physiological mechanisms of ABA response to multiple stress in rice remain poorly understood. In the ABA biosynthetic pathway, 9-cis-epoxycarotenoid dioxygenase (NCED) is the key rate-limiting enzyme. Here, we report important functions of OsNCED3 in multi-abiotic stress tolerance in rice. The OsNCED3 is constitutively expressed in various tissues under normal condition, Its expression is highly induced by NaCl, PEG, and H2O2 stress, suggesting the roles for OsNCED3 in response to the multi-abiotic stress tolerance in rice. Compared with wild-type plants, nced3 mutants had earlier seed germination, longer post-germination seedling growth, increased sensitivity to water stress and H2O2 stress and increased stomata aperture under water stress and delayed leaf senescence. Further analysis found that nced3 mutants contained lower ABA content compared with wild-type plants, overexpression of OsNCED3 in transgenic plants could enhance water stress tolerance, promote leaf senescence and increase ABA content. We conclude that OsNCED3 mediates seed dormancy, plant growth, abiotic stress tolerance, and leaf senescence by regulating ABA biosynthesis in rice; and may provide a new strategy for improving the quality of crop.

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9-cis-Epoxycarotenoid Dioxygenase 3 Regulates Plant Growth and Enhances Multi-Abiotic Stress Tolerance in Rice.

Leaf senescence is an essential physiological process in plants that supports the recycling of nitrogen and other nutrients to support the growth of developing organs, including young leaves, seeds, and fruits. Thus, the regulation of senescence is crucial for evolutionary success in wild populations and for increasing yield in crops. Here, we describe the influence of a NAC transcription factor, SlNAP2 (Solanum lycopersicum NAC-like, activated by Apetala3/Pistillata), that controls both leaf senescence and fruit yield in tomato (S. lycopersicum). SlNAP2 expression increases during age-dependent and dark-induced leaf senescence. We demonstrate that SlNAP2 activates SlSAG113 (S. lycopersicum SENESCENCE-ASSOCIATED GENE113), a homolog of Arabidopsis (Arabidopsis thaliana) SAG113, chlorophyll degradation genes such as SlSGR1 (S. lycopersicum senescence-inducible chloroplast stay-green protein 1) and SlPAO (S. lycopersicum pheide a oxygenase), and other downstream targets by directly binding to their promoters, thereby promoting leaf senescence. Furthermore, SlNAP2 directly controls the expression of genes important for abscisic acid (ABA) biosynthesis, S. lycopersicum 9-cis-epoxycarotenoid dioxygenase 1 (SlNCED1); transport, S. lycopersicum ABC transporter G family member 40 (SlABCG40); and degradation, S. lycopersicum ABA 8′-hydroxylase (SlCYP707A2), indicating that SlNAP2 has a complex role in establishing ABA homeostasis during leaf senescence. Inhibiting SlNAP2 expression in transgenic tomato plants impedes leaf senescence but enhances fruit yield and sugar content likely due to prolonged leaf photosynthesis in aging tomato plants. Our data indicate that SlNAP2 has a central role in controlling leaf senescence and fruit yield in tomato.

The NAC Transcription Factor SlNAP2 Regulates Leaf Senescence and Fruit Yield in Tomato

It is well known that abscisic acid (ABA)-induced leaf senescence and premature leaf senescence negatively affect the yield of rice (Oryza sativa). However, the molecular mechanism underlying this relationship, especially the upstream transcriptional network that modulates ABA level during leaf senescence, remains largely unknown. Here, we demonstrate a rice NAC transcription factor, OsNAC2, that participates in ABA-induced leaf senescence. Overexpression of OsNAC2 dramatically accelerated leaf senescence, whereas its knockdown lines showed a delay in leaf senescence. Chromatin immunoprecipitation-quantitative PCR, dual-luciferase, and yeast one-hybrid assays demonstrated that OsNAC2 directly activates expression of chlorophyll degradation genes, OsSGR and OsNYC3. Moreover, ectopic expression of OsNAC2 leads to an increase in ABA levels via directly up-regulating expression of ABA biosynthetic genes (OsNCED3 and OsZEP1) as well as down-regulating the ABA catabolic gene (OsABA8ox1). Interestingly, OsNAC2 is upregulated by a lower level of ABA but downregulated by a higher level of ABA, indicating a feedback repression of OsNAC2 by ABA. Additionally, reduced OsNAC2 expression leads to about 10% increase in the grain yield of RNAi lines. The novel ABA-NAC-SAGs regulatory module might provide a new insight into the molecular action of ABA to enhance leaf senescence and elucidates the transcriptional network of ABA production during leaf senescence in rice.

A Rice NAC Transcription Factor Promotes Leaf Senescence via ABA Biosynthesis

Plant development and adaptation to environmental stresses are intimately associated with programmed cell death (PCD). Although some of the mechanisms regulating PCD [e.g., accumulation of reactive oxygen species (ROS)] are common among responses to different abiotic stresses, the pathways mediating salt-induced PCD remain largely uncharacterized. Here we report that overexpression of OsNAC2, which encodes a plant-specific transcription factor, promotes salt-induced cell death accompanied by the loss of plasma membrane integrity, nuclear DNA fragmentation, and changes to caspase-like activity. In OsNAC2-knockdown lines, cell death was markedly decreased in response to severe salt stress. Additionally, OsNAC2 expression was enhanced in rice seedlings exposed to a high NaCl concentration. Moreover, the results of quantitative real-time PCR, chromatin immunoprecipitation, dual-luciferase, and yeast one-hybrid assays indicated that OsNAC2 targeted genes that encoded an ROS scavenger (OsCOX11) and a caspase-like protease (OsAP37). Furthermore, K+ -efflux channels (OsGORK and OsSKOR) were clearly activated by OsNAC2. Overall, our results suggested that OsNAC2 accelerates NaCl-induced PCD and provide new insights into the mechanisms that affect ROS accumulation, plant caspase-like activity, and K+ efflux.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.13867

OsNAC2 positively affects salt-induced cell death and binds to the OsAP37 and OsCOX11 promoters.

The invention belongs to the technical field of gene engineering, and particularly relates to a coding sequence expressed in rice and belonging to a cytokinin oxidation/dehydrogenase gene (denoted asOsCKX4) as well as application of the gene. The coding sequence particularly comprises cloning of the gene OsCKX4, an expression mode of an OsCKX4 organ and the change of the expression quantity of the OsCKX4 treated by different hormones and different stress. The invention also discloses sequencing authentication of a Tilling mutant of the gene OsCKX4, which can influence the growth of the root of the rice and the yield of the rice. The gene OsCKX4 can be applied to plant variety improvement.

Coding sequence of rice cytokinin oxidation/dehydrogenase gene OsCKX4 as well as application of gene

The invention belongs to the technical field of gene engineering, and specifically relates to a coding sequence of an indole-3-acetic acid-amido synthetase gene OsGH3.6 expressed in paddy rice and applications thereof. The applications are as follows: the nucleotide coding sequence of the indole-3-acetic acid-amido synthetase gene OsGH3.6 is cloned; the spatial expression pattern of different endogenous organs and tissues of the gene of paddy rice is analyzed and identified; after treatments such as drought treatment, high salt stress, plant hormone treatment, and the like, the change of expression pattern is analyzed and identified; the tilling mutant of OsGH3.6 is detected, and the root length and output are analyzed.

Bin Zhang

Papers

A Rice NAC Transcription Factor Promotes Leaf Senescence via ABA Biosynthesis

OsNAC2 positively affects salt-induced cell death and binds to the OsAP37 and OsCOX11 promoters.

Coding sequence of rice cytokinin oxidation/dehydrogenase gene OsCKX4 as well as application of gene

Coding sequence of paddy rice indole-3-acetic acid-amido synthetase gene OsGH3.6 and applications thereof