scholarly journals Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

2017 ◽  
Author(s):  
Jemima Brinton ◽  
James Simmonds ◽  
Cristobal Uauy
Keyword(s):  
Cell Size ◽  
Crop Yields ◽  
Grain Weight ◽  
Differentially Expressed ◽  
Reference Sequence ◽  
Complex Nature ◽  
Grain Development ◽  
Diverse Range ◽  
Isogenic Lines ◽  
Gene Models

AbstractBackgroundThere is an urgent need to increase global crop production. Identifying and combining genes controlling indidviual yield components, such as grain weight, holds the potential to enhance crop yields. Transcriptomics is a powerful tool to gain insights into the complex gene regulatory networks that underlie such traits, but relies on the availability of a high-quality reference sequence and accurate gene models. Previously, we identified a grain weight QTL on wheat chromosome 5A (5A QTL) which acts during early grain development to increase grain length through cell expansion in the pericarp. In this study, we performed RNA-sequencing on near isogenic lines (NILs) segregating for the 5A QTL and used the latest gene models to identify differentially expressed (DE) genes and pathways that potentially influence pericarp cell size and grain weight in wheat.ResultsWe sampled grains at four and eight days post anthesis and found genes associated with metabolism, biosynthesis, proteoloysis and defence response to be upregulated during this stage of grain development in both NILs. We identified a specific set of 112 transcripts DE between 5A NILs at either time point, including seven potential candidates for the causal gene underlying the 5A QTL. The 112 DE transcripts had functional annotations including non-coding RNA, transpon-associated, cell-cycle control, and ubiquitin-related processes. Many of the wheat genes identified belong to families that have been previously associated with seed/grain development in other species. However, few of these wheat genes are the direct orthologs and none have been previously characterised in wheat. Notably, we identified DE transcripts at almost all steps of the pathway associated with ubiquitin-mediated protein degradation. In the promoters of a subset of DE transcripts we identified enrichment of binding sites associated with C2H2, MYB/SANT, YABBY, AT HOOK and Trihelix transcription factor families.ConclusionsIn this study, we identified DE transcripts with a diverse range of predicted biological functions, reflecting the complex nature of the pathways that control early grain development. Further functional characterisation of these candidates and how they interact could provide new insights into the control of grain size in cereals, ultimately improving crop yield.

scholarly journals Polyphenol Supplementation Reverses Age-Related Changes in Microglial Signaling Cascades

2021 ◽  
Vol 22 (12) ◽  
pp. 6373
Author(s):  
Ahmad Jalloh ◽  
Antwoine Flowers ◽  
Charles Hudson ◽  
Dale Chaput ◽  
Jennifer Guergues ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Control Diet ◽  
Bioinformatic Analysis ◽  
Diet Group ◽  
Differentially Expressed ◽  
Signaling Cascades ◽  
Complex Nature ◽  
Differentially Expressed Proteins ◽  
Ms Analysis ◽  
Age Related

Microglial activity in the aging neuroimmune system is a central player in aging-related dysfunction. Aging alters microglial function via shifts in protein signaling cascades. These shifts can propagate neurodegenerative pathology. Therapeutics require a multifaceted approach to understand and address the stochastic nature of this process. Polyphenols offer one such means of rectifying age-related decline. Our group used mass spectrometry (MS) analysis to explicate the complex nature of these aging microglial pathways. In our first experiment, we compared primary microglia isolated from young and aged rats and identified 197 significantly differentially expressed proteins between these groups. Then, we performed bioinformatic analysis to explore differences in canonical signaling cascades related to microglial homeostasis and function with age. In a second experiment, we investigated changes to these pathways in aged animals after 30-day dietary supplementation with NT-020, which is a blend of polyphenols. We identified 144 differentially expressed proteins between the NT-020 group and the control diet group via MS analysis. Bioinformatic analysis predicted an NT-020 driven reversal in the upregulation of age-related canonical pathways that control inflammation, cellular metabolism, and proteostasis. Our results highlight salient aspects of microglial aging at the level of protein interactions and demonstrate a potential role of polyphenols as therapeutics for age-associated dysfunction.

scholarly journals Abiotic Stress Response of Near-Isogenic Spring Durum Wheat Lines under Different Sowing Densities

2021 ◽  
Vol 22 (4) ◽  
pp. 2053
Author(s):  
Judit Bányai ◽  
Marco Maccaferri ◽  
László Láng ◽  
Marianna Mayer ◽  
Viola Tóth ◽  
...  
Keyword(s):  
Drought Stress ◽  
Durum Wheat ◽  
Chlorophyll Content ◽  
Vegetation Index ◽  
Flag Leaf ◽  
Kernel Weight ◽  
Grain Weight ◽  
Abiotic Stress Response ◽  
Grain Number ◽  
Isogenic Lines

A detailed study was made of changes in the plant development, morphology, physiology and yield biology of near-isogenic lines of spring durum wheat sown in the field with different plant densities in two consecutive years (2013–2014). An analysis was made of the drought tolerance of isogenic lines selected for yield QTLs (QYld.idw-2B and QYld.idw-3B), and the presence of QTL effects was examined in spring sowings. Comparisons were made of the traits of the isogenic pairs QYld.idw-3B++ and QYld.idw-3B−− both within and between the pairs. Changes in the polyamine content, antioxidant enzyme activity, chlorophyll content of the flag leaf and the normalized difference vegetation index (NDVI) of the plot were monitored in response to drought stress, and the relationship between these components and the yield was analyzed. In the case of moderate stress, differences between the NIL++ and NIL−− pairs appeared in the early dough stage, indicating that the QYld.idw-3B++ QTL region was able to maintain photosynthetic activity for a longer period, resulting in greater grain number and grain weight at the end of the growing period. The chlorophyll content of the flag leaf in phenophases Z77 and Z83 was significantly correlated with the grain number and grain weight of the main spike. The grain yield was greatly influenced by the treatment, while the genotype had a significant effect on the thousand-kernel weight and on the grain number and grain weight of the main spike. When the lines were compared in the non-irrigated treatment, significantly more grains and significantly higher grain weight were observed in the main spike in NIL++ lines, confirming the theory that the higher yields of the QYld.idw-3B++ lines when sown in spring and exposed to drought stress could be attributed to the positive effect of the “Kofa” QTL on chromosome 3B.

scholarly journals The study of the nature of the inheritance of quantitative traits in F1 hybrids of winter soft wheat

2020 ◽  
Vol 17 ◽  
pp. 00084
Author(s):  
Olga Antoshina ◽  
Julia Odnodushnova ◽  
Gennadiy Fadkin ◽  
Irina Kondakova ◽  
Olga Fedosova
Keyword(s):  
Quantitative Traits ◽  
First Generation ◽  
Grain Weight ◽  
Soft Wheat ◽  
F1 Hybrids ◽  
Complex Nature ◽  
Intraspecific Hybridization ◽  
Quantitative Characteristics ◽  
Economically Valuable Traits ◽  
Ear Number

In the conditions of the south of the Nonchernozem Zone, intraspecific hybridization of winter soft wheat was carried out. When selecting parental forms used in crossing, special attention was paid to such economically valuable traits as productive tilling capacity, the number of grains and the mass of grain per spike. The true (Htru) and hypothetical heterosis (Hhyp) on the basis of “plant height”, “length of the lower internode”, “length of the upper internode”, “general tilling capacity”, “productive tilling capacity”, “spike length”, “number of spikelets”, “number of grains” and “grain weight per spike” were determined. It was established that the inheritance of quantitative traits in hybrids of the first generation was distinguished by the complex nature of distribution by types. Studies have made possible to identify 5 hybrid combinations F1, in which the effect of heterosis manifests itself simultaneously on five quantitative characteristics (ear length, number of spikelets per ear, number of grains per ear, grain weight per ear, mass grain from a plant).

scholarly journals Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shenghui Zhou ◽  
Jinpeng Zhang ◽  
Haiming Han ◽  
Jing Zhang ◽  
Huihui Ma ◽  
...  
Keyword(s):  
Single Molecule ◽  
Sequence Data ◽  
Full Length ◽  
Grain Weight ◽  
Agropyron Cristatum ◽  
Reference Sequence ◽  
Translocation Line ◽  
Thousand Grain Weight ◽  
Sequencing Platform ◽  
Transcriptome Sequences

Abstract Background Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies. Results Single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies. By analyzing RNA-Seq data, we identified tissue-enriched transcripts and assessed their GO term enrichment; the results indicated that tissue-enriched transcripts were enriched for particular molecular functions that varied by tissue. We identified 3398 novel and 1352 A. cristatum-specific transcripts compared with the wheat gene model set. To better apply this A. cristatum transcriptome, the A. cristatum transcripts were integrated with the wheat genome as a reference sequence to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line, Pubing 3035. Conclusions Full-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.

scholarly journals Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

2019 ◽  
Vol 20 (10) ◽  
pp. 2391 ◽  
Author(s):  
Jiayang Xu ◽  
Qiansi Chen ◽  
Pingping Liu ◽  
Wei Jia ◽  
Zheng Chen ◽  
...  
Keyword(s):  
Salinity Stress ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Crop Yields ◽  
Antioxidant Activities ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Alkali Stress ◽  
Rna Seq ◽  
Alkali Tolerance

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as “photosynthesis” and “starch and sucrose metabolism,” were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

scholarly journals Analysis of QTL Interaction for Grain Weight using Near Isogenic Lines in Rice

2015 ◽  
Vol 3 (1) ◽  
pp. 30-38 ◽  
Author(s):  
Hae-hwang Kim ◽  
Dong-min Kim ◽  
Ju-won Kang ◽  
Hyun-Sook Lee ◽  
Yun-ju Kang ◽  
...  
Keyword(s):  
Grain Weight ◽  
Near Isogenic Lines ◽  
Isogenic Lines
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