Identification of tomato root growth regulatory genes and transcription factors through comparative transcriptomic profiling of different tissues

2021 ◽  
Author(s):  
Vinod Kumar ◽  
Deepika Singh ◽  
Adity Majee ◽  
Shikha Singh ◽  
Roohi ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Root Growth ◽  
Regulatory Genes ◽  
Tomato Root ◽  
Transcriptomic Profiling ◽  
Different Tissues

scholarly journals AtHB7/12 Regulate Root Growth in Response to Aluminum Stress

2020 ◽  
Vol 21 (11) ◽  
pp. 4080
Author(s):  
Yang Liu ◽  
Jiameng Xu ◽  
Siyi Guo ◽  
Xianzheng Yuan ◽  
Shan Zhao ◽  
...  
Keyword(s):  
Cell Wall ◽  
Transcription Factors ◽  
Root Growth ◽  
Crop Production ◽  
Expression Patterns ◽  
Acid Soils ◽  
Limiting Factor ◽  
Aluminum Stress ◽  
Al Stress

Aluminum (Al) stress is a major limiting factor for plant growth and crop production in acid soils. At present, only a few transcription factors involved in the regulation of Al resistance have been characterized. Here, we used reversed genetic approach through phenotype analysis of overexpressors and mutants to demonstrate that AtHB7 and AtHB12, two HD-Zip I transcription factors, participate in Al resistance. In response to Al stress, AtHB7 and AtHB12 displayed different dynamic expression patterns. Although both AtHB7 and AtHB12 positively regulate root growth in the absence of Al stress, our results showed that AtHB7 antagonizes with AtHB12 to control root growth in response to Al stress. The athb7/12 double mutant displayed a wild-type phenotype under Al stress. Consistently, our physiological analysis showed that AtHB7 and AtHB12 oppositely regulate the capacity of cell wall to bind Al. Yeast two hybrid assays showed that AtHB7 and AtHB12 could form homo-dimers and hetero-dimers in vitro, suggesting the interaction between AtHB7 and AtHB12 in the regulation of root growth. The conclusion was that AtHB7 and AtHB12 oppositely regulate Al resistance by affecting Al accumulation in root cell wall.

Napropamide Uptake, Transport, and Metabolism in Corn (Zea mays) and Tomato (Lycopersicon esculentum)

Weed Science ◽  
1981 ◽  
Vol 29 (6) ◽  
pp. 697-703 ◽  
Author(s):  
Michael Barrett ◽  
Floyd M. Ashton
Keyword(s):  
Zea Mays ◽  
Lycopersicon Esculentum ◽  
Root Growth ◽  
Shoot Growth ◽  
Root Tissue ◽  
Tomato Root ◽  
Corn Roots ◽  
Tomato Roots ◽  
Absorption Studies ◽  
Root And Shoot Growth

Napropamide [2-(α-napthoxy)-N,N-diethylpropionamide] inhibited root and shoot growth in corn (Zea maysL. ‘NC+ 59’) and tomato (Lycopersicon esculentumMill. ‘Niagara VF315’) seedlings. Shoot growth was reduced less than root growth in both species. Corn roots were approximately 10 times more sensitive to napropamide than were tomato roots. Translocation of napropamide from the roots to the shoot of tomato occurred within 0.5 h and followed an apoplastic pattern. Little movement of napropamide from the roots to the shoots occurred in corn. Metabolism of napropamide was not evident in either species during an 8-h exposure. Absorption studies showed that total napropamide levels were 60% higher in corn root tissue than in tomato root tissue. The greater napropamide content in the corn roots was associated with a tightly bound fraction of the total napropamide influx.

scholarly journals Prediction of condition-specific regulatory genes using machine learning

2020 ◽  
Vol 48 (11) ◽  
pp. e62-e62 ◽  
Author(s):  
Qi Song ◽  
Jiyoung Lee ◽  
Shamima Akter ◽  
Matthew Rogers ◽  
Ruth Grene ◽  
...  
Keyword(s):  
Machine Learning ◽  
Transcription Factors ◽  
Single Cell ◽  
Control Cell ◽  
Genomic Data ◽  
Regulatory Genes ◽  
Genomic Research ◽  
Open Chromatin ◽  
Data Set ◽  
Better Than

Abstract Recent advances in genomic technologies have generated data on large-scale protein–DNA interactions and open chromatin regions for many eukaryotic species. How to identify condition-specific functions of transcription factors using these data has become a major challenge in genomic research. To solve this problem, we have developed a method called ConSReg, which provides a novel approach to integrate regulatory genomic data into predictive machine learning models of key regulatory genes. Using Arabidopsis as a model system, we tested our approach to identify regulatory genes in data sets from single cell gene expression and from abiotic stress treatments. Our results showed that ConSReg accurately predicted transcription factors that regulate differentially expressed genes with an average auROC of 0.84, which is 23.5–25% better than enrichment-based approaches. To further validate the performance of ConSReg, we analyzed an independent data set related to plant nitrogen responses. ConSReg provided better rankings of the correct transcription factors in 61.7% of cases, which is three times better than other plant tools. We applied ConSReg to Arabidopsis single cell RNA-seq data, successfully identifying candidate regulatory genes that control cell wall formation. Our methods provide a new approach to define candidate regulatory genes using integrated genomic data in plants.

scholarly journals Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of Dryopteris fragrans (L.) Schott

2020 ◽  
Vol 21 (19) ◽  
pp. 7296
Author(s):  
Lingling Chen ◽  
Dongrui Zhang ◽  
Chunhua Song ◽  
Hemeng Wang ◽  
Xun Tang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Glandular Trichomes ◽  
Transcriptomic Analysis ◽  
Specific Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Transcription Factor Genes ◽  
Dryopteris Fragrans ◽  
Different Tissues

Background: Dryopteris fragrans, which is densely covered with glandular trichomes, is considered to be one of the ferns with the most medicinal potential. The transcriptomes from selected tissues of D. fragrans were collected and analyzed for functional and comparative genomic studies. The aim of this study was to determine the transcriptomic characteristics of wild D. fragrans sporangium in tissues from the SR (root), SL (sporophyll), and TRL (sporophyll with glandular trichomes removed). Results: Cluster analysis identified genes that were highly expressed in an organ-specific manner according to read mapping, feature counting, and normalization. The functional map identified gene clusters that can uniquely describe the function of each tissue. We identified a group of three tissue-specific transcription factors targeting the SL, SR, and TRL. In addition, highly expressed transcription factors (TFs) were found in each tissue-specific gene cluster, where ERF and bHLH transcription factors were the two types showing the most distinct expression patterns between the three different tissues. The specific expression of transcription factor genes varied between the different types of tissues. The numbers of transcription factors specifically expressed in the roots and sporophylls were 60 and 30, respectively, while only seven were found for the sporophylls with glandular trichomes removed. The expression of genes known to be associated with the development of glandular trichomes in flowering plants, including MIXTA, ATML1, and MYB106, were also validated and are discussed. In particular, a unigene encoding MIXTA was identified and exhibited the highest expression level in SL in D. fragrans. Conclusions: This study is the first report of global transcriptomic analysis in different tissues of D. fragrans, and the first to discuss these findings in the context of the development of homologous glandular trichomes. These results set the stage for further research on the development, stress resistance, and secondary metabolism of D. fragrans glandular trichomes.

Effective concentration and range of activity of abamectin as seed treatment against root-knot nematodes in tomato under glasshouse conditions

Nematology ◽  
2009 ◽  
Vol 11 (6) ◽  
pp. 909-915 ◽  
Author(s):  
J. Alfonso Cabrera ◽  
Sebastian Kiewnick ◽  
Christoph Grimm ◽  
Abd el-Fattah A. Dababat ◽  
Richard A. Sikora
Keyword(s):  
Root Growth ◽  
Active Ingredient ◽  
Meloidogyne Incognita ◽  
Growth And Development ◽  
Seed Treatment ◽  
Effective Concentration ◽  
Tomato Root ◽  
Root Knot Nematodes ◽  
Root Growth And Development ◽  
Meloidogyne Species

Abstract The objectives of this study were to determine the efficacy, range of activity and effective concentrations (EC50 and EC80) of abamectin as a seed treatment of tomato against Meloidogyne incognita, M. arenaria and M. javanica. The study revealed that abamectin seed treatment at concentrations ranging between 0.3 and 1 mg a.s. seed−1 is highly effective against the three species of root-knot nematodes, retaining its efficacy in the soil for 8 weeks. The highest EC50 found was reached at 0.2 mg a.s. seed−1. The highest EC80 for the number of egg masses per g root in the three Meloidogyne species was attained at 0.51 mg a.s. seed−1. Abamectin as a seed treatment is promising for the control of root-knot nematodes in the field since only low amounts of active ingredient are required to give adequate protection in the most sensitive stages of tomato root growth and development.

scholarly journals Exploratory Investigation on Functional Significance ofETS2andSIM2Genes in Down Syndrome

2011 ◽  
Vol 31 (5) ◽  
pp. 247-257 ◽  
Author(s):  
Arpita Chatterjee ◽  
Samikshan Dutta ◽  
Swagata Sinha ◽  
Kanchan Mukhopadhyay
Keyword(s):  
Down Syndrome ◽  
Transcription Factors ◽  
Functional Significance ◽  
Genomic Dna ◽  
Nonsynonymous Substitution ◽  
Regulatory Genes ◽  
Statistical Analyses ◽  
Exploratory Investigation

Trisomy of the 21st chromosome leads to an over dosage of several regulatory genes in Down syndrome (DS). Though allelic and genotypic combinations formed between genes are interesting, till date, this particular area has never been explored in DS. In the present investigation four SNPs in two transcription factors, Single minded 2 (SIM2) and V-ets erythroblastosis virus E26 oncogene homolog2 (ETS2), located in the 21st chromosome were genotyped to understand their role in DS. Genomic DNA of eastern Indian probands with DS (N= 132), their parents (N= 209) and ethnically matched controls (N= 149) was subjected to PCR-based analyses of functionally important SNPs followed by statistical analyses.ETS2rs461155 showed high heterozygosity in DS. Significantly lower frequency ofSIM2C-G haplotype (rs2073601-rs2073416) was noticed in individuals with DS (Pvalue = 0.01669) and their fathers (Pvalue = 0.01185). Significantly lower frequency of the A-C-C-G with higher frequency of A-C-A-G haplotypes was also noticed in subjects with DS (Pvalue = 0.02089 and 0.00588 respectively). Data obtained indicate that the rs2073601 ‘A’ allele, responsible for nonsynonymous substitution of leucine to methionine, may have some role in DS in this population.

scholarly journals TheYABBYGenes of Leaf and Leaf-Like Organ Polarity in Leafless PlantMonotropa hypopitys

2018 ◽  
Vol 2018 ◽  
pp. 1-16 ◽  
Author(s):  
Anna V. Shchennikova ◽  
Marya A. Slugina ◽  
Alexey V. Beletsky ◽  
Mikhail A. Filyushin ◽  
Andrey A. Mardanov ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Structural Analysis ◽  
Mycorrhizal Symbiosis ◽  
Vegetative Organs ◽  
Qrt Pcr ◽  
Physiological Processes ◽  
Lateral Organs ◽  
Monotropa Hypopitys ◽  
Different Tissues

Monotropa hypopitysis a mycoheterotrophic, nonphotosynthetic plant acquiring nutrients from the roots of autotrophic trees through mycorrhizal symbiosis, and, similar to other extant plants, forming asymmetrical lateral organs during development. The members of the YABBY family of transcription factors are important players in the establishment of leaf and leaf-like organ polarity in plants. This is the first report on the identification ofYABBYgenes in a mycoheterotrophic plant devoid of aboveground vegetative organs. SevenM. hypopitys YABBYmembers were identified and classified into four clades. By structural analysis of putative encoded proteins, we confirmed the presence of YABBY-defining conserved domains and identified novel clade-specific motifs. Transcriptomic and qRT-PCR analyses of different tissues revealedMhyYABBYtranscriptional patterns, which were similar to those of orthologousYABBYgenes from other angiosperms. These data should contribute to the understanding of the role of theYABBYgenes in the regulation of developmental and physiological processes in achlorophyllous leafless plants.

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