Guidelines to use tomato in experiments with a controlled environment

Schwarz, Dietmar; Thompson, Andrew J.; Kläring, Hans‐Peter

doi:10.3389/fpls.2014.00625

Cited by 112 publications

(81 citation statements)

References 51 publications

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“…For seed production, phenotyping and detached leaf experiments, Murashige and Skoog (MS) medium-grown wild-type and SlTAF1 transgenic tomato seedlings were transferred to soil, as previously reported (Schwarz et al, 2014;Thirumalaikumar et al, 2018) and grown in a glasshouse under a 16 h : 8 h, day : night regime, 450 µmol photons m À2 s À1 light, 24°C, and 65% relative humidity. After preparation of the nutrient medium, the pH was adjusted to 5.8 using H 2 SO 4 .…”

Section: Plant Materials and Growth Conditionsmentioning

confidence: 99%

Multifaceted regulatory function of tomato SlTAF1 in the response to salinity stress

et al. 2019

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Salinity stress limits plant growth and has a major impact on agricultural productivity. Here, we identify NAC transcription factor SlTAF1 as a regulator of salt tolerance in cultivated tomato (Solanum lycopersicum).While overexpression of SlTAF1 improves salinity tolerance compared with wild-type, lowering SlTAF1 expression causes stronger salinity-induced damage. Under salt stress, shoots of SlTAF1 knockdown plants accumulate more toxic Na + ions, while SlTAF1 overexpressors accumulate less ions, in accordance with an altered expression of the Na + transporter genes SlHKT1;1 and SlHKT1;2. Furthermore, stomatal conductance and pore area are increased in SlTAF1 knockdown plants during salinity stress, but decreased in SlTAF1 overexpressors.We identified stress-related transcription factor, abscisic acid metabolism and defence-related genes as potential direct targets of SlTAF1, correlating it with reactive oxygen species scavenging capacity and changes in hormonal response. Salinity-induced changes in tricarboxylic acid cycle intermediates and amino acids are more pronounced in SlTAF1 knockdown than wild-type plants, but less so in SlTAF1 overexpressors. The osmoprotectant proline accumulates more in SlTAF1 overexpressors than knockdown plants.In summary, SlTAF1 controls the tomato's response to salinity stress by combating both osmotic stress and ion toxicity, highlighting this gene as a promising candidate for the future breeding of stress-tolerant crops.

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Section: Plant Materials and Growth Conditionsmentioning

confidence: 99%

Multifaceted regulatory function of tomato SlTAF1 in the response to salinity stress

et al. 2019

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“…Tomato is the most widely cultivated vegetables worldwide (30). It belongs to the Solanaceae, whose members produce important foods, spices, and medicines.…”

Section: Introductionmentioning

confidence: 99%

Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling

Song

Walley

et al. 2019

Preprint

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25mRNA translation is a critical step in gene expression, but our understanding of the 26 landscape and control of translation in diverse crops remains lacking. Here, we combined de 27 novo transcriptome assembly and ribosome profiling to study global mRNA translation in tomato 28 roots. Taking advantage of the 3-nucleotide periodicity displayed by translating ribosomes, we 29 identified 354 novel small ORFs (sORFs) translated from previously unannotated transcripts, as 30 well as 1329 upstream ORFs (uORFs) translated within the 5' UTRs of annotated protein-coding 31 genes. Proteomic analysis confirmed that some of these novel uORFs and sORFs generate 32 stable proteins in planta. Compared with the annotated ORFs, the uORFs use more flexible 33 Kozak sequences around translation start sites. Interestingly, uORF-containing genes are 34 enriched for protein phosphorylation/dephosphorylation and signaling transduction pathways, 35 suggesting a regulatory role for uORFs in these processes. We also demonstrated that 36 ribosome profiling is useful to facilitate the annotation of translated ORFs and noncanonical 37 translation initiation sites. In addition to defining the translatome, our results revealed the global 38 control of mRNA translation by uORFs and microRNAs in tomato. In summary, our approach 39 provides a high-throughput method to discover unannotated ORFs, elucidates evolutionarily 40 conserved translational features, and identifies new regulatory mechanisms hidden in a crop 41 genome. 42 43 48 transcriptome assembly and ribosome profiling, we mapped and quantified translating 49 ribosomes across the entire transcriptome in tomato roots. This is the first experiment-based 50 survey to systematically identify actively translated ORFs in a crop. Our results reveal numerous 51 unannotated translation events and uncover new regulatory mechanisms of gene expression in 52 tomato. Our approach not only facilitates our understanding of the tomato translational 53 landscape but also provides a practical strategy to study the translatomes of other species. 54 55 56 Introduction 57Besides being an essential step in gene expression, mRNA translation directly shapes 58 the proteome, which contributes to cellular structure, function, and activity in all organisms. The 59 characterization of translational regulation has enabled crop improvement, including increasing 60 tomato sweetness, rice immunity and lettuce resistance to oxidative stress (1-3). However, due 61 to limited genomic resources and methods, most crop translatomes remain understudied. 62Ribosome profiling, or Ribo-seq, has emerged as a high-throughput technique to study 63 global translation (4-6). In a Ribo-seq experiment, ribosomes in the sample of interest are 64 immobilized, and the lysate is treated with nucleases to obtain ribosome-protected mRNA 65 fragments (i.e. ribosome footprints). Finally, sequencing of the ribosome footprints reveals the 66 quantity and positions of ribosomes on a given transcript. Features corresponding to active 67 translat...

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“…While both T and RH interact to drive insect biology, abundance and dynamics, temperature largely plays a more significant part in influencing pest population trends. Nevertheless, relative humidity (RH) also plays a critical role in host plant (Schwarz, Thompson, & Kläring, 2014) and insect pest development (Guimapi et al, 2016). The spatio-environmental heterogeneity in a changing climate (IPCC, 2014) makes universal model use unreliable, underpinning the need for location-specific models.…”

Section: Introductionmentioning

confidence: 99%

Disentangling factors limiting diamondback moth, Plutella xylostella (L.), spatio‐temporal population abundance: A tool for pest forecasting

Machekano

Mutamiswa

Mvumi

et al. 2019

J Applied Entomology

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Data-mining techniques play an important role in hyperparameter optimization of heterogeneous environmental factors and their relative contribution as determinants of incidences in insect pest ecological studies. A multidimensional field-based surveillance was conducted in two seasons (24 months), July-June of each season (2015/2016 -season 1 and 2016/2017 -season 2) using sex-pheromone-baited traps and Thermocron i-Buttons to identify key determinants of population abundance of diamondback moth, Plutella xylostella L., across spatial horticultural hotspots of Botswana. The moth is a notorious global brassica pest. Pearson's product moment correlation matrix showed month of the year (M), mean temperature (T mean ) and maximum temperature (T max ) as positively correlated (p < 0.001) to number of moths (N), while minimum temperature (T min ), minimum relative humidity (RH min ), mean relative humidity (RH mean ), maximum relative humidity (RH max ) and host plant (h) were negatively correlated (p < 0.001) to N. Using Waikato Environment for Knowledge Analysis (WEKA) data-mining techniques, two models were developed: (a) M5P decision-tree algorithm associated with nine linear models (LMs) and (b) principal component analysis (PCA) based on four principal components. Both approaches identified M as the major predictor of moth abundance, followed by h and farming region (R). However, R was a function of T max (positive auto-correlation) and RH max (negative auto-correlation). These results provide simplified relative contribution of heterogeneous factors in influencing P. xylostella spatio-temporal abundance, essential for early warning systems in pest management. This is an important component of sustainable pest management aimed at managing insect pests and minimizing pesticides abuse in brassica production systems. K E Y W O R D S hyperparameter optimization, insect population dynamics, integrated pest management, predictive models, small-scale farmers, Waikato Environment for Knowledge Analysis (WEKA) | 671 MACHEKANO Et Al.

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Guidelines to use tomato in experiments with a controlled environment

Cited by 112 publications

References 51 publications

Multifaceted regulatory function of tomato SlTAF1 in the response to salinity stress

Multifaceted regulatory function of tomato SlTAF1 in the response to salinity stress

Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling

Disentangling factors limiting diamondback moth, Plutella xylostella (L.), spatio‐temporal population abundance: A tool for pest forecasting

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