Transcriptome Analysis of Two Near-Isogenic Lines with Different NUE under Normal Nitrogen Conditions in Wheat

Nitrogen (N) is an essential nutrient element for crop productivity. Unfortunately, the nitrogen use efficiency (NUE) of crop plants gradually decreases with the increase of the N application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling of flag leaves at the stage of anthesis in wheat NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions (300 kg N ha−1, corresponding to 1.6 g N pot−1). We identified 7023 DEGs (4738 upregulated and 2285 downregulated) in the comparison between lines 1Y and 1W. The responses of 1Y and 1W to normal N differed in the transcriptional regulatory mechanisms. Several genes belonging to the GS and GOGAT gene families were upregulated in 1Y compared with 1W, and the enhanced carbon metabolism might lead 1Y to produce more C skeletons, metabolic energy, and reductants for nitrogen metabolism. A subset of transcription factors (TFs) family members, such as ERF, WRKY, NAC, and MYB, were also identified. Collectively, these identified candidate genes provided new information for a further understanding of the genotypic difference in NUE.

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Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides

BMC Genomics ◽

10.1186/s12864-019-6397-3 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 5

Author(s):

Adam Pym ◽

Kumar Saurabh Singh ◽

Åsa Nordgren ◽

T. G. Emyr Davies ◽

Christoph T. Zimmer ◽

...

Keyword(s):

Gene Expression ◽

Host Plants ◽

Large Scale ◽

Molecular Mechanisms ◽

Wide Spectrum ◽

Transcriptome Profiling ◽

Gene Families ◽

Trialeurodes Vaporariorum ◽

Specific Gene ◽

Natural And Synthetic

Abstract Background The glasshouse whitefly, Trialeurodes vaporariorum, is a damaging crop pest and an invasive generalist capable of feeding on a broad range of host plants. As such this species has evolved mechanisms to circumvent the wide spectrum of anti-herbivore allelochemicals produced by its host range. T. vaporariorum has also demonstrated a remarkable ability to evolve resistance to many of the synthetic insecticides used for control. Results To gain insight into the molecular mechanisms that underpin the polyphagy of T. vaporariorum and its resistance to natural and synthetic xenobiotics, we sequenced and assembled a reference genome for this species. Curation of genes putatively involved in the detoxification of natural and synthetic xenobiotics revealed a marked reduction in specific gene families between this species and another generalist whitefly, Bemisia tabaci. Transcriptome profiling of T. vaporariorum upon transfer to a range of different host plants revealed profound differences in the transcriptional response to more or less challenging hosts. Large scale changes in gene expression (> 20% of genes) were observed during adaptation to challenging hosts with a range of genes involved in gene regulation, signalling, and detoxification differentially expressed. Remarkably, these changes in gene expression were associated with significant shifts in the tolerance of host-adapted T. vaporariorum lines to natural and synthetic insecticides. Conclusions Our findings provide further insights into the ability of polyphagous insects to extensively reprogram gene expression during host adaptation and illustrate the potential implications of this on their sensitivity to synthetic insecticides.

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Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development

BMC Plant Biology ◽

10.1186/s12870-020-02702-y ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Xiaobo Zhao ◽

Chunjuan Li ◽

Hao Zhang ◽

Caixia Yan ◽

Quanxi Sun ◽

...

Keyword(s):

Cell Wall ◽

Alternative Splicing ◽

Signaling Pathways ◽

Molecular Mechanisms ◽

Mechanical Response ◽

Root Apex ◽

Transcriptome Profiling ◽

Calcium Dependent ◽

Pod Development ◽

Transcriptional Regulatory Mechanisms

Abstract Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, and the generation of pegs and formation of subterranean pods are essential processes in peanut reproductive development. However, little information has been reported about alternative splicing (AS) in peanut peg formation and development. Results Herein, we presented a comprehensive full-length (FL) transcriptome profiling of AS isoforms during peanut peg and early pod development. We identified 1448, 1102, 832, and 902 specific spliced transcripts in aerial pegs, subterranean pegs, subterranean unswollen pegs, and early swelling pods, respectively. A total of 184 spliced transcripts related to gravity stimulation, light and mechanical response, hormone mediated signaling pathways, and calcium-dependent proteins were identified as possibly involved in peanut peg development. For aerial pegs, spliced transcripts we got were mainly involved in gravity stimulation and cell wall morphogenetic processes. The genes undergoing AS in subterranean peg were possibly involved in gravity stimulation, cell wall morphogenetic processes, and abiotic response. For subterranean unswollen pegs, spliced transcripts were predominantly related to the embryo development and root formation. The genes undergoing splice in early swelling pods were mainly related to ovule development, root hair cells enlargement, root apex division, and seed germination. Conclusion This study provides evidence that multiple genes are related to gravity stimulation, light and mechanical response, hormone mediated signaling pathways, and calcium-dependent proteins undergoing AS express development-specific spliced isoforms or exhibit an obvious isoform switch during the peanut peg development. AS isoforms in subterranean pegs and pods provides valuable sources to further understand post-transcriptional regulatory mechanisms of AS in the generation of pegs and formation of subterranean pods.

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Transcriptome profiling reveals potential genes involved in browning of fresh-cut eggplant (Solanum melongena L.)

Scientific Reports ◽

10.1038/s41598-021-94831-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xiaohui Liu ◽

Aidong Zhang ◽

Jie Zhao ◽

Jing Shang ◽

Zongwen Zhu ◽

...

Keyword(s):

Regulatory Networks ◽

Fruits And Vegetables ◽

Molecular Mechanisms ◽

Solanum Melongena ◽

Transcriptome Profiling ◽

Gene Families ◽

Enzymatic Browning ◽

Specific Expression ◽

Fruit Samples ◽

Fresh Cut

AbstractFresh-cut processing promotes enzymatic browning of fresh fruits and vegetables, which negatively affects the product appearance and impacts their nutrition. We used RNA-sequencing to analyze the transcriptomic changes occurring during the browning of fresh-cut eggplant fruit samples from both browning-sensitive and browning-resistant cultivars to investigate the molecular mechanisms involved in browning. A total of 8347 differentially expressed genes were identified, of which 62 genes were from six gene families (i.e., PPO, PAL, POD, CAT, APX, and GST) potentially associated with enzymatic browning. Furthermore, using qRT-PCR, we verified 231 differentially regulated transcription factors in fresh-cut eggplant fruits. The enzyme activities of PPO, POD, PAL, and CAT in ‘36’ were significantly higher than those of ‘F’ fresh-cut for 15 min. Both PPO and POD play a major role in the browning of eggplant pulp and might therefore act synergistically in the browning process. Meanwhile, qPCR results of 18 browning related genes randomly screened in 15 eggplant materials with different browning tolerance showed variant-specific expression of genes. Lastly, gene regulatory networks were constructed to identify the browning-related genes. This work provides a basis for future molecular studies of eggplants, and lays a theoretical foundation for the development of browning-resistant fresh-cut fruits and vegetables.

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Transcriptomic Analysis of Short-Term Salt-Stress Response in Mega Hybrid Rice Seedlings

Agronomy ◽

10.3390/agronomy11071328 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1328

Author(s):

Noushin Jahan ◽

Yang Lv ◽

Mengqiu Song ◽

Yu Zhang ◽

Liangguang Shang ◽

...

Keyword(s):

Salt Stress ◽

Molecular Mechanisms ◽

Oryza Sativa L ◽

Transcriptome Profiling ◽

Bhlh Transcription Factor ◽

F1 Hybrid ◽

Salt Stress Response ◽

Productivity Losses ◽

Expression Of Genes ◽

Trait Locus

Salinity is a major abiotic stressor that leads to productivity losses in rice (Oryza sativa L.). In this study, transcriptome profiling and heterosis-related genes were analyzed by ribonucleic acid sequencing (RNA-Seq) in seedlings of a mega rice hybrid, Liang-You-Pei-Jiu (LYP9), and its two parents 93–11 and Pei-ai64s (PA64s), under control and two different salinity levels, where we found 8292, 8037, and 631 salt-induced differentially expressed genes (DEGs), respectively. Heterosis-related DEGs were obtained higher after 14 days of salt treatment than after 7 days. There were 631 and 4237 salt-induced DEGs related to heterosis under 7-day and 14-day salt stresses, respectively. Gene functional classification showed the expression of genes involved in photosynthesis activity after 7-day stress treatment, and in metabolic and catabolic activity after 14 days. In addition, we correlated the concurrence of an expression of DEGs for the bHLH transcription factor and a shoot length/salinity-related quantitative trait locus qSL7 that we fine-mapped previously, providing a confirmed case of heterosis-related genes. This experiment reveals the transcriptomic divergence of the rice F1 hybrid and its parental lines under control and salt stress state, and enlightens about the significant molecular mechanisms developed over time in response to salt stress.

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Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa042 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Qian-Hao Zhu ◽

Warwick Stiller ◽

Philippe Moncuquet ◽

Stuart Gordon ◽

Yuman Yuan ◽

...

Keyword(s):

Molecular Mechanisms ◽

Agronomic Traits ◽

Gene Families ◽

Mutant Phenotype ◽

Wild Type ◽

Calcium Dependent ◽

Dependent Protein ◽

Flanking Region ◽

Comparative Transcriptomic Analysis

Abstract Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

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Exploring Suitable Biochar Application Rates with Compost to Improve Upland Field Environment

Agronomy ◽

10.3390/agronomy11061136 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1136

Author(s):

Se-Won Kang ◽

Jin-Ju Yun ◽

Jae-Hyuk Park ◽

Ju-Sik Cho

Keyword(s):

Soil Quality ◽

Chinese Cabbage ◽

Early Period ◽

Crop Productivity ◽

Application Rate ◽

Control Treatment ◽

N2o Emissions ◽

Treatment Area ◽

Application Rates ◽

Upland Field

A field experiment was carried out to investigate crop productivity, emissions of carbon dioxide (CO2) and nitrous oxide (N2O), and soil quality of an upland field treated with compost and varying rates of biochar (BC) derived from soybean stalks during crop growing periods in a corn and Chinese cabbage rotation system. Compost was supplemented with BC derived from soybean stalks at varying rates of 5, 10, 15, and 20 t ha−1 (BC5, BC10, BC15, and BC20, respectively); the control (BC0) area was untreated. Our results reveal that crop productivity and emissions of CO2 and N2O varied significantly with the biochar application rate. Moreover, irrespective of the biochar application rate, crop productivity was improved after BC application as compared to the control treatment area, by 11.2–29.3% (average 17.0 ± 8.3%) for corn cultivation and 10.3–39.7% (average 27.8 ± 12.7%) for Chinese cabbage cultivation. Peak emissions of CO2 and N2O were mainly observed in the early period of crop cultivation, whereas low CO2 and N2O emissions were determined during the fallow period. Compared to the control area, significant differences were obtained for CO2 emissions produced by the different biochar application rates for both crops. During the two cropping periods, the overall N2O emission was significantly decreased with BC5, BC10, BC15, and BC20 applications as compared to the control, ranging from 11.1 to 13.6%, 8.7 to 15.4%, 23.1 to 26.0%, and 15.0 to 19.6%, respectively (average 16.9% decrease in the corn crop period and 16.3% in the Chinese cabbage crop period). Soil quality results after the final crop harvest show that bulk density, soil organic carbon (SOC), pH, and cation exchange capacity (CEC) were significantly improved by biochar application, as compared to the control. Taken together, our results indicate that compost application supplemented with biochar is potentially an appropriate strategy for achieving high crop productivity and improving soil quality in upland field conditions. In conclusion, appropriate application of biochar with compost has the concomitant advantages of enriching soil quality for long-term sustainable agriculture and reducing the use of inorganic fertilizers.

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Amynthas corticis genome reveals molecular mechanisms behind global distribution

Communications Biology ◽

10.1038/s42003-021-01659-4 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Xing Wang ◽

Yi Zhang ◽

Yufeng Zhang ◽

Mingming Kang ◽

Yuanbo Li ◽

...

Keyword(s):

Genome Assembly ◽

Molecular Mechanisms ◽

Gene Families ◽

The Body ◽

Gene Family Evolution ◽

Complex Environments ◽

Protein Coding ◽

Itraq Analysis ◽

Rdna Sequencing ◽

Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

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Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia

International Journal of Molecular Sciences ◽

10.3390/ijms22052683 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2683

Author(s):

Princess D. Rodriguez ◽

Hana Paculova ◽

Sophie Kogut ◽

Jessica Heath ◽

Hilde Schjerven ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

B Cell ◽

Molecular Mechanisms ◽

Lymphoblastic Leukemia ◽

Transcriptome Profiling ◽

Rna Seq ◽

Protein Coding ◽

Non Coding Rna ◽

Technological Developments ◽

Cell Acute Lymphoblastic Leukemia

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

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Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

BioMed Research International ◽

10.1155/2016/3702789 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 5

Author(s):

Liangbin Zeng ◽

Airong Shen ◽

Jia Chen ◽

Zhun Yan ◽

Touming Liu ◽

...

Keyword(s):

Protein Function ◽

Molecular Mechanisms ◽

Defense Mechanism ◽

Natural Fiber ◽

De Novo ◽

Average Length ◽

Expression Patterns ◽

Transcriptome Profiling ◽

Cdna Libraries ◽

Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

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Overexpression of SgGH3.1 from Fine-Stem Stylo (Stylosanthes guianensis var. intermedia) Enhances Chilling and Cold Tolerance in Arabidopsis thaliana

Genes ◽

10.3390/genes12091367 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1367

Author(s):

Ming Jiang ◽

Long-Long Ma ◽

Huai-An Huang ◽

Shan-Wen Ke ◽

Chun-Sheng Gui ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Cold Stress ◽

Stress Responses ◽

Molecular Mechanisms ◽

Transcriptome Profiling ◽

Pasture Legumes ◽

Cold Tolerant ◽

Whole Transcriptome ◽

Altered Sensitivity ◽

Exogenous Iaa

Stylosanthes (stylo) species are commercially significant tropical and subtropical forage and pasture legumes that are vulnerable to chilling and frost. However, little is known about the molecular mechanisms behind stylos’ responses to low temperature stress. Gretchen-Hagen 3 (GH3) proteins have been extensively investigated in many plant species for their roles in auxin homeostasis and abiotic stress responses, but none have been reported in stylos. SgGH3.1, a cold-responsive gene identified in a whole transcriptome profiling study of fine-stem stylo (S. guianensis var. intermedia) was further investigated for its involvement in cold stress tolerance. SgGH3.1 shared a high percentage of identity with 14 leguminous GH3 proteins, ranging from 79% to 93%. Phylogenetic analysis classified SgGH3.1 into Group Ⅱ of GH3 family, which have been proven to involve with auxins conjugation. Expression profiling revealed that SgGH3.1 responded rapidly to cold stress in stylo leaves. Overexpression of SgGH3.1 in Arabidopsis thaliana altered sensitivity to exogenous IAA, up-regulated transcription of AtCBF1-3 genes, activated physiological responses against cold stress, and enhanced chilling and cold tolerances. This is the first report of a GH3 gene in stylos, which not only validated its function in IAA homeostasis and cold responses, but also gave insight into breeding of cold-tolerant stylos.

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