scholarly journals Comparative Analysis of Proteomics and Transcriptomics during Fertility Transition in a Two-Line Hybrid Rice Line Wuxiang S

2019 ◽  
Vol 20 (18) ◽  
pp. 4542
Author(s):  
Hao Chen ◽  
Jing Jin ◽  
Hongyuan Zhang ◽  
Ying Wang ◽  
Qian Li ◽  
...  
Keyword(s):  
Hybrid Rice ◽  
Fertility Transition ◽  
Cell Formation ◽  
Rice Line ◽  
Transition Mechanism ◽  
Formation Stage ◽  
Stress Response Pathway ◽  
Related Proteins ◽  
Ptgms Rice ◽  
Differentially Abundant Proteins

The two-line hybrid rice is an important factor of a global crop, but its fertility transition mechanism is unclear. Here, a comparative proteomics and transcriptomics analysis was completed on the two-line hybrid rice line Wuxiang S (WXS) to explore its molecular mechanism and protein regulation during fertility transition. A total of 340 differentially abundant proteins (DAPs) were identified using iTRAQ between the pollen mother cell formation stage (P2) and the meiosis stage (P3). There were 3541 and 4247 differentially expressed genes (DEGs) in P2 and P3 between WXS (Sterile, S)-WXS(S) and WXS (Fertile, F)-WXS(F), respectively, of which 92 and 71 DEGs had corresponding DAPs. Among the DAPs and DEGs, 65 (SP2 vs. FP2) and 55 (SP3 vs. FP3) corresponding DEGs and DAPs (cor-DEGs-DAPs) showed the same expression trend, indicating the cor-DEGs-DAPs genes might play vital roles in WXS fertility transition. Further analysis indicated that cor-DEGs-DAPs proteins were related to energy metabolism-related proteins in anther development and were accompanied by the activation of the stress response pathway and modifications to the cell wall, which ultimately affected the fertility transition of the PTGMS rice line WXS.

scholarly journals Genome-Wide Identification of lncRNAs Involved in Fertility Transition in the Photo-Thermosensitive Genic Male Sterile Rice Line Wuxiang S

2021 ◽  
Vol 11 ◽  
Author(s):  
Ying Wang ◽  
Hongyuan Zhang ◽  
Qian Li ◽  
Jing Jin ◽  
Hao Chen ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Fertility Transition ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Male Sterile ◽  
Rice Line ◽  
Genome Wide ◽  
Reporter Assays ◽  
Mother Cells ◽  
Ptgms Rice

Long non-coding RNAs (lncRNAs) act as universal regulators of various biological processes, but no genome-wide screening of lncRNAs involved in the fertility transition of the photo-thermosensitive genic male sterile (PTGMS) rice line has been reported. Here, we performed strand-specific RNA sequencing at three developmental stages of a novel PTGMS line Wuxiang S (WXS). A total of 3,948 lncRNAs were identified; 622 of these were detected as differentially expressed lncRNAs (DE-lncRNAs) between male-sterile WXS (WXS-S) and male-fertile WXS (WXS-F). A large proportion of lncRNAs differentially expressed at the stage of pollen mother cells meiosis, suggested that it may be the most critical stage for fertility transition of WXS. Furthermore, functional annotation of the cis- and trans- targets of DE-lncRNAs showed that 150 targets corresponding to 141 DE-lncRNAs were identified as involved in anther and pollen development. Moreover, computational analysis predicted 97 lncRNAs as precursors for 72 miRNAs, and 94 DE-lncRNAs as potential endogenous target mimics (eTMs) for 150 miRNAs. Finally, using the dual luciferase reporter assays, we demonstrated that two lncRNAs act as eTMs to regulate the expression of the SPL and GRF genes by competing for the shared osa-miR156 and osa-miR396, respectively. These genomic characteristics, differential expression, and interaction of lncRNAs with miRNAs and mRNAs contribute to our understanding of the roles of lncRNAs during the fertility transition in PTGMS rice lines.

scholarly journals Performance of Hybrid Rice (Bio-453) In Variation of Spacing and Number of Seedling Per Hill

2020 ◽  
Vol 22 (1) ◽  
pp. 27-37
Author(s):  
D Chowdhury ◽  
M Biswas ◽  
MNH Miah ◽  
P Mandal ◽  
MS Hossain
Keyword(s):  
Hybrid Rice ◽  
Research Work ◽  
Maximum Yield ◽  
Growth And Yield ◽  
Plant Spacing ◽  
Rice Line ◽  
Biological Yield ◽  
Main Plot ◽  
1000 Grain Weight ◽  
Plot Design

Hybrid rice production can ensure to get more yields per unit land. The research work was carried out to evaluate the effect of number of seedling hill-1 and spacing on the growth and yield of hybrid rice line Bio-453. The experiment was laid out in a split-plot design with 3 replications at the field of Agronomy and Haor Agriculture Department of Sylhet Agricultural University, under the AEZ 20 in Kharif-II (Aman) season of 2013. Number of seedling hill-1 was assigned in the main plot and plant spacing in the sub-plot. Two levels of seedling hill-1 viz. NS1 (1 seedling hill-1) and NS2 (2 seedlings hill-1) and five levels of plant spacing viz. Sp1 (15 cm  X 15 cm), Sp2 (15 cm X 20 cm) and Sp3 (20 cm X 20 cm), Sp4 (20 cm X 25 cm) and Sp5 (20 cm X 30 cm) were the treatments. Number of seedling hill-1 and plant spacing showed significant effect in yield and yield contributing parameters except days to maturity, plant height, 1000-grain weight, total tillers hill-1, number of effective tillers hill-1, harvest index and grains panicle-1. Maximum grain yield (9.43 t ha-1), straw yield (16.27 t ha-1) and biological yield (25.70 t ha-1) were obtained from 1 seedling hill-1 (NS1) with the closest spacing 15 cm X 15 cm Therefore,  one seedling hill-1 with 15 cm distance for plant and row to row distance could  ensure maximum yield of hybrid rice line Bio-453. Bangladesh Agron. J. 2019, 22(1): 27-37

scholarly journals Photosynthetic analysis of mid-vein and leaf lamina in high-yield hybrid rice in fields during senescence

2020 ◽  
Author(s):  
Zhiping Gao ◽  
Minli Xu ◽  
Haizi Zhang ◽  
Guoxiang Chen
Keyword(s):  
Heat Dissipation ◽  
Hybrid Rice ◽  
Photosynthetic Apparatus ◽  
High Yield ◽  
Leaf Lamina ◽  
Two Dimensional Gel Electrophoresis ◽  
Leaf Physiology ◽  
Functional Aspects ◽  
Underlying Mechanisms ◽  
Related Proteins

Abstract Previous studies on rice (Oryza sativa L.) have shown that different components of the photosynthetic apparatus are not uniformly synthesized or degraded during senescence. However, most of these senescence-related studies focused on leaf lamina, while few have addressed functional aspects on chloroplasts or leaf physiology. Here, we investigated the photosynthetic properties of the mid-vein and leaf lamina in a super high-yield hybrid rice (LYP9) during senescence. We found that assimilation and transpiration decreased more slowly in the mid-vein than in the lamina during senescence, suggesting more sustained photosynthesis in the mid-vein, as well as stronger heat dissipation. Two-dimensional gel electrophoresis revealed that the mid-vein had a higher abundance of proteins involved with energy and lower levels of disease or defense-related proteins, suggesting that photosynthesis and energy metabolism were less affected by senescence in the mid-vein than in leaf lamina. In late senescence stage, the excess energy dissipation in the mid-vein through the xanthophyll cycle had a higher active photosynthetic capacity than in the leaf lamina, and we inferred that the mid-vein and leaf lamina of LYP9 rice aged heterogeneously. Taken together, these results provide new insights into the underlying mechanisms of senescence and associated physiology of the rice mid-vein.

scholarly journals Oryza sativa cv. Nipponbare and Oryza barthii as Unexpected Tolerance and Susceptibility Sources Against Schizotetranychus oryzae (Acari: Tetranychidae) Mite Infestation

2021 ◽  
Vol 12 ◽  
Author(s):  
Giseli Buffon ◽  
Édina Aparecida dos Reis Blasi ◽  
Thainá Inês Lamb ◽  
Janete Mariza Adamski ◽  
Joséli Schwambach ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Energy Production ◽  
Leaf Damage ◽  
Mite Infestation ◽  
Weedy Rice ◽  
Oryza Glaberrima ◽  
Primary Metabolism ◽  
Related Proteins ◽  
Oryza Barthii ◽  
Differentially Abundant Proteins

Cultivated rice (Oryza sativa L.) is frequently exposed to multiple stresses, including Schizotetranychus oryzae mite infestation. Rice domestication has narrowed the genetic diversity of the species, leading to a wide susceptibility. This work aimed to analyze the response of two African rice species (Oryza barthii and Oryza glaberrima), weedy rice (O. sativa f. spontanea), and O. sativa cv. Nipponbare to S. oryzae infestation. Surprisingly, leaf damage, histochemistry, and chlorophyll concentration/fluorescence indicated that the African species present a higher level of leaf damage, increased accumulation of H2O2, and lower photosynthetic capacity when compared to O. sativa plants under infested conditions. Infestation decreased tiller number, except in Nipponbare, and caused the death of O. barthii and O. glaberrima plants during the reproductive stage. While infestation did not affect the weight of 1,000 grains in both O. sativa, the number of panicles per plant was affected only in O. sativa f. spontanea, and the percentage of full seeds per panicle and seed length were increased only in Nipponbare. Using proteomic analysis, we identified 195 differentially abundant proteins when comparing susceptible (O. barthii) and tolerant (Nipponbare) plants under control and infested conditions. O. barthii presents a less abundant antioxidant arsenal and is unable to modulate proteins involved in general metabolism and energy production under infested condition. Nipponbare presents high abundance of detoxification-related proteins, general metabolic processes, and energy production, suggesting that the primary metabolism is maintained more active compared to O. barthii under infested condition. Also, under infested conditions, Nipponbare presents higher levels of proline and a greater abundance of defense-related proteins, such as osmotin, ricin B-like lectin, and protease inhibitors (PIs). These differentially abundant proteins can be used as biotechnological tools in breeding programs aiming at increased tolerance to mite infestation.

scholarly journals Characteristics of Fertility Transition Response to the Cumulative Effective Low Temperature in a Two-Line Male Sterile Rice Cultivar

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Linxuan Wu ◽  
Huazhen Rong ◽  
Chun Chen ◽  
Xin Lin ◽  
Jiafeng Wang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Seed Production ◽  
Pollen Fertility ◽  
Hybrid Rice ◽  
Fertility Transition ◽  
Day Length ◽  
Sensitive Period ◽  
Rice Seed ◽  
Night Temperature ◽  
Male Sterile

Abstract Background Photo-thermo-sensitive genic male sterile (PTGMS) rice (Oryza sativa L.) is usually considered two-line male sterile rice because of its dual-purpose in two-line hybrid rice system: under short days and low temperatures, it is fertile and used for self-propagation, but under long days and high temperatures, it is sterile and used for hybrid seed production. Therefore, photoperiod and temperature conditions are extremely important for the fertility transition of two-line male sterile rice. In recent years, there have been frequent occurrences of abnormally low-temperature (ALT) resulting in failure of two-line hybrid rice seed production. The daily average temperature (DAT) during ALT events is sometimes higher than the critical sterility-inducing temperature (CSIT) of two-line male sterile rice, of which the night temperature is lower than the CSIT. DAT has been traditionally used as the single indicator of pollen fertility transition, but it is unknown why the fertility of two-line male sterile rice in seed production restored fertility under ALT conditions. Results For Hang93S (H93S), a newly released PTGMS line, we hypothesized fertility transition is determined mainly by the cumulative effective low temperature (ELT) and only a certain duration of low temperature is required every day during the fertility-sensitive period. This study simulated ALTs where the DAT was higher than the CSIT while some segments of night temperature were lower than the CSIT. The results showed H93S exhibited a fertility transition to varying degrees. Moreover, fertility was restored under simulated ALT conditions and pollen fertility increased with increasing cumulative ELT, indicating that the fertility transition was affected primarily by the cumulative ELT. Results also indicated that pollen fertility increased as the number of treatment days increased. Conclusions The fertility transition is caused mainly by the cumulative ELT. In two-line male sterile rice breeding, the effects of day length, ALT at night, and continuous response days should be considered together. The present study provides new insight into fertility transition so breeders can more effectively utilize the two-line male sterile rice, H93S, in breeding programs.

scholarly journals TMT-based quantitative proteomic profiling of human monocyte-derived macrophages and foam cells

2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Yali Zhang ◽  
Yu Fu ◽  
Linying Jia ◽  
Chenyang Zhang ◽  
Wenbin Cao ◽  
...  
Keyword(s):  
Immune Response ◽  
Endoplasmic Reticulum ◽  
Protein Interaction ◽  
Cholesterol Metabolism ◽  
Foam Cell ◽  
Cell Formation ◽  
Foam Cells ◽  
Foam Cell Formation ◽  
Differentially Expressed Proteins ◽  
Related Proteins

Abstract Background Cardiovascular diseases remain the leading cause of morbidity and mortality worldwide, most of which are caused by atherosclerosis. Discerning processes that participate in macrophage-to-foam cell formation are critical for understanding the basic mechanisms underlying atherosclerosis. To explore the molecular mechanisms of foam cell formation, differentially expressed proteins were identified. Methods Human peripheral blood mononuclear cells were stimulated with macrophage colony-stimulating factor, and obtained macrophages were transformed into foam cells by oxidized low-density lipoprotein. Tandem mass tag (TMT) labeling combined with mass spectrometry was performed to find associations between foam cell transformation and proteome profiles. Results Totally, 5146 quantifiable proteins were identified, among which 1515 and 182 differentially expressed proteins (DEPs) were found in macrophage/monocyte and foam cell/macrophage, respectively. Subcellular localization analysis revealed that downregulated DEPs of macrophages/monocytes were mostly located in the nucleus, whereas upregulated DEPs of foam cells/macrophages were mostly extracellular or located in the plasma membrane. Functional analysis of DEPs demonstrated that cholesterol metabolism-related proteins were upregulated in foam cells, whereas immune response-related proteins were downregulated in foam cells. The protein interaction network showed that the DEPs with the highest interaction scores between macrophages and foam cells were mainly concentrated in lysosomes and the endoplasmic reticulum. Conclusions Proteomics analysis suggested that cholesterol metabolism was upregulated, while the immune response was suppressed in foam cells. KEGG enrichment analysis and protein-protein interaction analysis indicated that DEPs located in the endoplasmic reticulum and lysosomes might be key drivers of foam cell formation. These data provide a basis for identifying the potential proteins associated with the molecular mechanism underlying macrophage transformation to foam cells.

scholarly journals Proteogenomic analysis of pitaya reveals cold stress-related molecular signature

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8540
Author(s):  
Junliang Zhou ◽  
Zhuang Wang ◽  
Yongya Mao ◽  
Lijuan Wang ◽  
Tujian Xiao ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Crop Production ◽  
Molecular Signature ◽  
Reference Database ◽  
Label Free ◽  
Tropical Fruit ◽  
Temperature Damage ◽  
Related Proteins ◽  
Differentially Abundant Proteins

Pitayas (Hylocereus spp.) is an attractive, highly nutritious and commercially valuable tropical fruit. However, low-temperature damage limits crop production. Genome of pitaya has not been sequenced yet. In this study, we sequenced the transcriptome of pitaya as the reference and further investigated the proteome under low temperature. By RNAseq technique, approximately 25.3 million reads were obtained, and further trimmed and assembled into 81,252 unigene sequences. The unigenes were searched against UniProt, NR and COGs at NCBI, Pfam, InterPro and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and 57,905 unigenes were retrieved annotations. Among them, 44,337 coding sequences were predicted by Trandecoder (v2.0.1), which served as the reference database for label-free proteomic analysis study of pitaya. Here, we identified 116 Differentially Abundant Proteins (DAPs) associated with the cold stress in pitaya, of which 18 proteins were up-regulated and 98 proteins were down-regulated. KEGG analysis and other results showed that these DAPs mainly related to chloroplasts and mitochondria metabolism. In summary, chloroplasts and mitochondria metabolism-related proteins may play an important role in response to cold stress in pitayas.

Pathogenesis-related proteins in somatic hybrid rice induced by bacterial blight

2008 ◽  
Vol 69 (10) ◽  
pp. 1989-1996 ◽  
Author(s):  
Chu L. Yu ◽  
Shun P. Yan ◽  
Chang C. Wang ◽  
Hai T. Hu ◽  
Wei N. Sun ◽  
...  
Keyword(s):  
Somatic Hybrid ◽  
Bacterial Blight ◽  
Hybrid Rice ◽  
Pathogenesis Related Proteins ◽  
Pathogenesis Related ◽  
Related Proteins
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