Sample Collection Protocol Effects on Quantification of Gene Expression in Potato Leaf Tissue

New platforms allow quantification of gene expression from large, replicated experiments but current sampling protocols for plant tissue using immediate flash freezing in liquid nitrogen are a barrier to these high-throughput studies. In this study, we compared four sampling methods for RNA extraction for gene expression analysis: (1) the standard sampling method of flash freezing whole leaves in liquid nitrogen immediately upon removal from the plant; (2) incubation of excised leaf disks for 2 min at field temperature followed by flash freezing; (3) incubation of excised leaf disks for 1 h on ice followed by flash freezing; and (4) incubation of excised leaf disks for 1 h at field temperature followed by flash freezing. Gene expression analysis was done for 23 genes using nCounter, and normalization of the data was done using the geometric mean of five housekeeping genes. Quality of RNA was highest for protocol A and lowest for protocol D. Despite some differences in RNA quality, gene expression was not significantly different among protocols A, B, and C for any of the 23 genes. Expression of some genes was significantly different between protocol D and the other protocols. This study demonstrates that when sampling leaf disks for gene expression analysis, the time between tissue removal from the plant and flash freezing in liquid nitrogen can be extended. This increase in time allowable during sampling provides greater flexibility in sampling large replicated field experiments for statistical analysis of gene expression data.     

RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize

The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize.     

Neonatal Maternal Deprivation Response and Developmental Changes in Gene Expression Revealed by Hypothalamic Gene Expression Profiling in Mice

Neonatal feeding problems are observed in several genetic diseases including Prader-Willi syndrome (PWS). Later in life, individuals with PWS develop hyperphagia and obesity due to lack of appetite control. We hypothesized that failure to thrive in infancy and later-onset hyperphagia are related and could be due to a defect in the hypothalamus. In this study, we performed gene expression microarray analysis of the hypothalamic response to maternal deprivation in neonatal wild-type and Snord116del mice, a mouse model for PWS in which a cluster of imprinted C/D box snoRNAs is deleted. The neonatal starvation response in both strains was dramatically different from that reported in adult rodents. Genes that are affected by adult starvation showed no expression change in the hypothalamus of 5 day-old pups after 6 hours of maternal deprivation. Unlike in adult rodents, expression levels of Nanos2 and Pdk4 were increased, and those of Pgpep1, Ndp, Brms1l, Mett10d, and Snx1 were decreased after neonatal deprivation. In addition, we compared hypothalamic gene expression profiles at postnatal days 5 and 13 and observed significant developmental changes. Notably, the gene expression profiles of Snord116del deletion mice and wild-type littermates were very similar at all time points and conditions, arguing against a role of Snord116 in feeding regulation in the neonatal period.     

Effects of Different Tissue Microenvironments on Gene Expression in Breast Cancer Cells

In metastasis, circulating tumor cells penetrate the walls of blood vessels and enter the metastatic target tissue, thereby becoming exposed to novel and relatively unsupportive microenvironments. In the new microenvironments, the tumor cells often remain in a dormant state indefinitely and must adapt before they are able to successfully colonize the tissue. Very little is known about this adaptive process. We studied temporal changes in gene expression when breast cancer cells adapt to survive and grow on brain, bone marrow, and lung tissue maintained in an in vivo culture system, as models of the metastatic colonization of these tissues. We observed the transient activation of genes typically associated with homeostasis and stress during the initial stages of adaptation, followed by the activation of genes that mediate more advanced functions, such as elaboration of cell morphology and cell division, as the cells adapted to thrive in the host tissue microenvironment. We also observed the temporary induction of genes characteristic of the host tissue, which was particularly evident when tumor cells were grown on brain tissue. These early transient gene expression events suggest potential points of therapeutic intervention that are not evident in data from well-established tumors.     

Effects of Drought Stress on the Photosynthesis in Maize

To clarify how the components of the entire photosynthetic electron transport chain in response to drought stress in maize. The activities of photosystem II (PSII), photosystem I (PSI), and the electron transport chain between PSII and PSI of maize were investigated by prompt fluorescence (PF), delayed fluorescence (DF) and 820 nm modulated reflection (MR). Maize (Zea mays L.) plants were subjected to different levels of soil water availability including control, moderate and severe drought stress. A significant decrease in ?E₀, Ψ₀ and PI_ABS was found in maize treated with moderate drought stress. A significant increase in ABS/RC was observed, but there were no significant change in the fast MR phase and the amplitude of DF under moderate drought stress compared to the control. Under severe drought stress, the exchange capacity between Q_A to Q_B, reoxidation capacity of plastoquinol, and the oxidation and re-reduction rates of PC and P₇₀₀ all decreased. These results demonstrated that moderate drought stress reduced the photochemical activity of PSII from Q_A to PQH₂, while the photochemical activity of PSI was unscathed. However, severe drought stress inhibited the entire electron transport chain from the donor side of PSII to PSI-end electron acceptors. In addition, the photochemical activity of PSII is more sensitive to drought stress than PSI.     

Profiles of Leaf Senescence During Reproductive Growth of Sunflower and Maize

We investigated the effect of reproductive growth on the profilesof leaf senescence in maize (Zea mays L.) and sunflower (Helianthusannuus L.). Leaf senescence after flowering was assessed usingboth structural (leaf chlorophyll, nitrogen and dry matter)and functional (photosynthesis) variables in undisturbed plants(+G) and in plants in which grain set was prevented (-G). Twoweeks after flowering, lack of grain accelerated senescencein maize and delayed senescence in sunflower as indicated byleaf chlorophyll; leaf nitrogen and dry matter were less sensitiveresponse variables. Lack of interaction between reproductivetreatment and leaf position indicates that the senescence signal,whatever its nature, was equally effective throughout the plantin both species. In both species, feedback inhibition of photosynthesiswas first detected 30–35 d after flowering; excess carbohydratein the leaves was therefore an unlikely trigger of acceleratedsenescence in maize. As reproductive development progressed,differences between +G and -G plants were more marked in sunflower,and tended to disappear or reverse in maize. In sunflower, interactionsbetween leaf position and reproductive treatment—attributableto the local effect of grain—were detected around 20–27d after flowering. Copyright 2000 Annals of Botany Company Helianthus annuus, Zea mays, chlorophyll, light, nitrogen, photosynthesis, reproductive growth, senescence, source-sink, SPAD.     

Genetic Control of the Leaf Angle and Leaf Orientation Value as Revealed by Ultra-High Density Maps in Three Connected Maize Populations

Plant architecture is a key factor for high productivity maize because ideal plant architecture with an erect leaf angle and optimum leaf orientation value allow for more efficient light capture during photosynthesis and better wind circulation under dense planting conditions. To extend our understanding of the genetic mechanisms involved in leaf-related traits, three connected recombination inbred line (RIL) populations including 538 RILs were genotyped by genotyping-by-sequencing (GBS) method and phenotyped for the leaf angle and related traits in six environments. We conducted single population quantitative trait locus (QTL) mapping and joint linkage analysis based on high-density recombination bin maps constructed from GBS genotype data. A total of 45 QTLs with phenotypic effects ranging from 1.2% to 29.2% were detected for four leaf architecture traits by using joint linkage mapping across the three populations. All the QTLs identified for each trait could explain approximately 60% of the phenotypic variance. Four QTLs were located on small genomic regions where candidate genes were found. Genomic predictions from a genomic best linear unbiased prediction (GBLUP) model explained 45±9% to 68±8% of the variation in the remaining RILs for the four traits. These results extend our understanding of the genetics of leaf traits and can be used in genomic prediction to accelerate plant architecture improvement.     

植物叶片衰老过程中的基因表达与调控

衰老是一种器官或组织逐步走向功能衰退和死亡的变化过程〔１〕。它除了代表器官或组织生命周期的终结之外,在发育生物学上也有着重要的意义。叶片的衰老是植物的一个重要发育阶段。在这段时期内,植物在成熟叶片内积累的物质,包括大量的氮、碳有机化合物和矿物质,将被分解并运送至植物其它生长旺盛的部分,其中大部分被转移到种子内,为下一代的生长做好准备〔１１〕。对于产生种子的作物,包括绝大多数农作物,这种转移使营养重新分配,对植株保持正常的生长发育与繁殖是十分必要的〔３〕。衰老过程中,叶片细胞在组成成分上有很大的变…     

Effects of S-Abscisic Acid (S-ABA) on Seed Germination,Seedling Growth,and Asr1 Gene Expression Under Drought Stress in Maize

The objective of this study was to evaluate the ability of the phytohormone S-abscisic acid (S-ABA) to protect maize seedlings grown under drought stress and to measure their increased drought tolerance. The maize hybrids ‘Zhengdan 958’ (ZD958; drought tolerant) and ‘Xundan 20’ (XD20; drought sensitive) were treated with nutrient solutions of different concentrations (1, 2, 4, 8, and 10 mg/kg) of S-ABA under polyethylene glycol (PEG, 15% w/v, MW 6000) simulated drought stress. Optimal concentrations of S-ABA were designed to be sprayed onto the leaves of seedlings, and their effect on endogenous ABA, malondialdehyde (MDA), osmotic substances, antioxidant enzyme activities, and Asr1 gene expression in seedlings were studied. Results indicated that, under drought stress, S-ABA treatment significantly improved maize seed germination rate (GR), germination energy (GE), and seedling biomass (p < 0.05). After spraying 4 mg/kg S-ABA onto leaves, the endogenous hormone ABA, osmotic substances, antioxidant enzyme activities, and expressive quantity of the Asr1 gene were extended and MDA content dropped significantly (p < 0.05). Moreover, ZD 958 endogenous ABA content, osmotic substances content, antioxidant enzyme activity and Asr1 gene expressive quantity were higher than that of XD 20 (p < 0.05). In conclusion, S-ABA treatment increased the content of endogenous ABA, induced an increase in antioxidant enzyme activity and Asr1 gene expression level, reduced the oxidative damage caused by drought to maize leaves, and improved the adaptability of maize seedlings to withstand drought stress. The promoting effect of S-ABA on the drought-tolerant variety ZD 958 was more obvious (p < 0.05). These results serve as a reference for the use of S-ABA in mitigating drought stress in maize.

     

Root Morphology and Gene Expression Analysis in Response to Drought Stress in Maize (Zea mays)

Water-deficit stress tolerance is a complex trait, and water deficit results in various physiological and chemical changes in maize (Zea mays L.) and exacerbates pre-harvest aflatoxin contamination. The objective of this study was to characterize the variations in morphology, physiology, and gene expression in two contrasting inbred lines, Lo964 and Lo1016, in order to understand the differences in response to water-deficit stress. The results revealed that Lo964 was less sensitive to water-deficit stress, and had a strong lateral root system and a higher root/shoot ratio in comparison to Lo1016. In response to water-deficit stress by comparing stressed versus well-watered conditions, abscisic acid syntheses were increased in leaves, roots, and kernels of both Lo964 and Lo1016, but by different magnitudes. Indole-3-acetic acid (IAA) was undetectable in the leaves and roots of either genotype regardless of treatments, but increases of 58% and 8% in IAA concentration were observed in 20 DAP kernels, in response to water-deficit stress, respectively. The expression of the MIPS was up-regulated 7-fold in leaf tissues of Lo964 compared to Lo1016 at watered conditions, but decreased significantly to similar levels in both genotypes at water-deficit conditions. ZmPR10 and ZmFer1 expressions tended to up-regulate although ZmPR10 was expressed higher in root tissue while ZmFer1 was expressed higher in leaf tissue. Further study is needed to confirm if Lo964 has reduced aflatoxin contamination associated with the drought tolerance in the field in order to utilize the resistant trait in breeding.