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Kovacik M, Nowicka A, Zwyrtková J, Strejčková B, Vardanega I, Esteban E, Pasha A, Kaduchová K, Krautsova M, Červenková M, Šafář J, Provart NJ, Simon R, Pecinka A. The transcriptome landscape of developing barley seeds. THE PLANT CELL 2024:koae095. [PMID: 38635902 DOI: 10.1093/plcell/koae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4-32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains.
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Affiliation(s)
- Martin Kovacik
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Anna Nowicka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30 239 Kraków, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Beáta Strejčková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Isaia Vardanega
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Kateřina Kaduchová
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Maryna Krautsova
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Marie Červenková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
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Xu Y, Shang W, Li L, Song Y, Wang G, Shi L, Shen Y, Sun Y, He S, Wang Z. Transcriptome Landscape Analyses of the Regulatory Network for Zygotic Embryo Development in Paeonia ostii. Int J Mol Sci 2023; 24:10715. [PMID: 37445891 DOI: 10.3390/ijms241310715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Paeonia ostii is a worldwide ornamental flower and an emerging oil crop. Zyotic embryogenesis is a critical process during seed development, and it can provide a basis for improving the efficiency of somatic embryogenesis (SE). In this study, transcriptome sequencing of embryo development was performed to investigate gene expression profiling in P. ostii and identified Differentially expressed genes (DEGs) related to transcription factors, plant hormones, and antioxidant enzymes. The results indicated that IAA (Indole-3-acetic acid), GA (Gibberellin), BR (Brassinosteroid) and ETH (Ethylene) were beneficial to early embryonic morphogenesis, while CTK (Cytokinin) and ABA (Abscisic Acid) promoted embryo morphogenesis and maturation. The antioxidant enzymes' activity was the highest in early embryos and an important participant in embryo formation. The high expression of the genes encoding fatty acid desaturase was beneficial to fast oil accumulation. Representative DEGs were selected and validated using qRT-PCR. Protein-protein interaction network (PPI) was predicted, and six central node proteins, including AUX1, PIN1, ARF6, LAX3, ABCB19, PIF3, and PIF4, were screened. Our results provided new insights into the formation of embryo development and even somatic embryo development in tree peonies.
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Affiliation(s)
- Yufeng Xu
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Wenqian Shang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Linda Li
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Yinglong Song
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Guiqing Wang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Liyun Shi
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuxiao Shen
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuke Sun
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Songlin He
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
- Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Zheng Wang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
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Geng L, He X, Ye L, Zhang G. Identification of the genes associated with β-glucan synthesis and accumulation during grain development in barley. FOOD CHEMISTRY. MOLECULAR SCIENCES 2022; 5:100136. [PMID: 36177107 PMCID: PMC9513732 DOI: 10.1016/j.fochms.2022.100136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/08/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
The presence of β-glucan in barley grains is one of its important quality traits. Lower β-glucan content is required for the barley used in beer and feed production, while higher β-glucan content is beneficial for food barley. Although intensive research has been carried out on the genotypic and environmental differences in β-glucan content in barley grains, little information is available on the molecular mechanisms underlying their genotypic differences and genetic regulation of β-glucan synthesis and accumulation. In this study, RNA sequencing analysis was conducted to compare the transcriptome profiles of two barley genotypes (BCS192 and BCS297) that greatly differ in grain β-glucan content, in order to identify the key genes responsible for β-glucan synthesis and accumulation during grain development. The results showed that carbohydrate metabolic processes and starch and sucrose metabolism play significant roles in β-glucan synthesis. The identified differently expressed genes (DEGs), which are closely associated with grain β-glucan content, are mainly involved in hydrolase activity and glucan metabolic processes. In addition, β-glucan accumulation in barley grains is predominantly regulated by photosynthesis and carbon metabolism. The DEGs identified in this study and their functions may provide new insights into the molecular mechanisms of β-glucan synthesis and genotypic differences in barley grains.
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Affiliation(s)
- La Geng
- Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Xinyi He
- Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Lingzhen Ye
- Department of Agronomy, Zhejiang University, Hangzhou 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi 276000, China
| | - Guoping Zhang
- Department of Agronomy, Zhejiang University, Hangzhou 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi 276000, China
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Xu C, Abbas HMK, Zhan C, Huang Y, Huang S, Yang H, Wang Y, Yuan H, Luo J, Zeng X. Integrative metabolomic and transcriptomic analyses reveal the mechanisms of Tibetan hulless barley grain coloration. FRONTIERS IN PLANT SCIENCE 2022; 13:1038625. [PMID: 36388537 PMCID: PMC9641248 DOI: 10.3389/fpls.2022.1038625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Cereal grains accumulate anthocyanin during developmental process. The anthocyanin content increases at grain filling stages to develop grain coloration in cereals. However, anthocyanin biosynthesis responsible for grain coloring and its regulatory mechanisms controlled by structural and functional genes remain unclear. Therefore, this study aimed to explore the global map of metabolic changes linked to grain coloration of Tibetan hulless barley (qingke) using an integrative metabolome and transcriptome approach. Grains from three colored qingke cultivars at different developmental stages were considered for molecular and metabolic investigations. A total of 120 differentially accumulated metabolites (DAMs) and 8,327 differentially expressed genes (DEGs) were filtered. DEGs were mainly enriched in the phenylpropanoid and flavonoid pathways. The transcript levels of anthocyanin biosynthesis genes (PAL, C4H, 4CL, CHS, FLS, F3H, F3'H, DFR, ANS, GT, OMT, and MAT) significantly upregulate in colored qingke compared to the non-colored variety. During grain development and maturation, the strong correlation of HvMYC2 expression with anthocyanin contents and anthocyanin biosynthesis genes suggested it as a critical gene in anthocyanin accumulation. Further results confirmed that HvMYC2 could be activated by HvMYB and be a positive regulator of UV-B and cold tolerance in qingke. In addition, verification based on enzymatic assays indicated that six key modifier enzymes could catalyze glycosylation, malonylation, and methylation of anthocyanins, thereby dissecting the major anthocyanin modification pathway in colored qingke. Overall, our study provides global insight into anthocyanin accumulation and the mechanism underlying grain coloration in qingke.
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Affiliation(s)
- Congping Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | | | - Chuansong Zhan
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yuxiao Huang
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Sishu Huang
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Haizhen Yang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Jie Luo
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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Jiang L, Liu C, Fan Y, Wu Q, Ye X, Li Q, Wan Y, Sun Y, Zou L, Xiang D, Lv Z. Dynamic transcriptome analysis suggests the key genes regulating seed development and filling in Tartary buckwheat (Fagopyrum tataricum Garetn.). Front Genet 2022; 13:990412. [PMID: 36072657 PMCID: PMC9441574 DOI: 10.3389/fgene.2022.990412] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Tartary buckwheat is highly attractive for the richness of nutrients and quality, yet post-embryonic seed abortion greatly halts the yield. Seed development is crucial for determining grain yield, whereas the molecular basis and regulatory network of Tartary buckwheat seed development and filling is not well understood at present. Here, we assessed the transcriptional dynamics of filling stage Tartary buckwheat seeds at three developmental stages by RNA sequencing. Among the 4249 differentially expressed genes (DEGs), genes related to seed development were identified. Specifically, 88 phytohormone biosynthesis signaling genes, 309 TFs, and 16 expansin genes participating in cell enlargement, 37 structural genes involved in starch biosynthesis represented significant variation and were candidate key seed development genes. Cis-element enrichment analysis indicated that the promoters of differentially expressed expansin genes and starch biosynthesis genes are rich of hormone-responsive (ABA-, AUX-, ET-, and JA-), and seed growth-related (MYB, MYC and WRKY) binding sites. The expansin DEGs showed strong correlations with DEGs in phytohormone pathways and transcription factors (TFs). In total, phytohormone ABA, AUX, ET, BR and CTK, and related TFs could substantially regulate seed development in Tartary buckwheat through targeting downstream expansin genes and structural starch biosynthetic genes. This transcriptome data could provide a theoretical basis for improving yield of Tartary buckwheat.
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Affiliation(s)
- Liangzhen Jiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yu Fan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xueling Ye
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yan Wan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yanxia Sun
- College of Tourism and Culture Industry, Chengdu University, Chengdu, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
- *Correspondence: Dabing Xiang, ; Zhibin Lv,
| | - Zhibin Lv
- Department of Medical Instruments and Information, College of Biomedical Engineering, Sichuan University, Chengdu, China
- *Correspondence: Dabing Xiang, ; Zhibin Lv,
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Wu XT, Xiong ZP, Chen KX, Zhao GR, Feng KR, Li XH, Li XR, Tian Z, Huo FL, Wang MX, Song W. Genome-Wide Identification and Transcriptional Expression Profiles of PP2C in the Barley (Hordeum vulgare L.) Pan-Genome. Genes (Basel) 2022; 13:genes13050834. [PMID: 35627219 PMCID: PMC9140614 DOI: 10.3390/genes13050834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
The gene family protein phosphatase 2C (PP2C) is related to developmental processes and stress responses in plants. Barley (Hordeum vulgare L.) is a popular cereal crop that is primarily utilized for human consumption and nutrition. However, there is little knowledge regarding the PP2C gene family in barley. In this study, a total of 1635 PP2C genes were identified in 20 barley pan-genome accessions. Then, chromosome localization, physical and chemical feature predictions and subcellular localization were systematically analyzed. One wild barley accession (B1K-04-12) and one cultivated barley (Morex) were chosen as representatives to further analyze and compare the differences in HvPP2Cs between wild and cultivated barley. Phylogenetic analysis showed that these HvPP2Cs were divided into 12 subgroups. Additionally, gene structure, conserved domain and motif, gene duplication event detection, interaction networks and gene expression profiles were analyzed in accessions Morex and B1K-04-12. In addition, qRT-PCR experiments in Morex indicated that seven HvMorexPP2C genes were involved in the response to aluminum and low pH stresses. Finally, a series of positively selected homologous genes were identified between wild accession B1K-04-12 and another 14 cultivated materials, indicating that these genes are important during barley domestication. This work provides a global overview of the putative physiological and biological functions of PP2C genes in barley. We provide a broad framework for understanding the domestication- and evolutionary-induced changes in PP2C genes between wild and cultivated barley.
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Affiliation(s)
- Xiao-Tong Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Zhu-Pei Xiong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Kun-Xiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Guo-Rong Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Ke-Ru Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Xiu-Hua Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Xi-Ran Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Zhao Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Fu-Lin Huo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Meng-Xing Wang
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
- Correspondence: (M.-X.W.); (W.S.)
| | - Weining Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
- Correspondence: (M.-X.W.); (W.S.)
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Genome-wide investigation and functional analysis of RNA editing sites in wheat. PLoS One 2022; 17:e0265270. [PMID: 35275970 PMCID: PMC8916659 DOI: 10.1371/journal.pone.0265270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
Wheat is an important cereal and half of the world population consumed it. Wheat faces environmental stresses and different techniques (CRISPR, gene silencing, GWAS, etc.) were used to enhance its production but RNA editing (RESs) is not fully explored in wheat. RNA editing has a special role in controlling environmental stresses. The genome-wide identification and functional characterization of RESs in different types of wheat genotypes was done. We employed six wheat genotypes by RNA-seq analyses to achieve RESs. The findings revealed that RNA editing events occurred on all chromosomes equally. RNA editing sites were distributed randomly and 10–12 types of RESs were detected in wheat genotypes. Higher number of RESs were detected in drought-tolerant genotypes. A-to-I RNA editing (2952, 2977, 1916, 2576, 3422, and 3459) sites were also identified in six wheat genotypes. Most of the genes were found to be engaged in molecular processes after a Gene Ontology analysis. PPR (pentatricopeptide repeat), OZ1 (organelle zinc-finger), and MORF/RIP gene expression levels in wheat were also examined. Normal growth conditions diverge gene expression of these three different gene families, implying that normal growth conditions for various genotypes can modify RNA editing events and have an impact on gene expression levels. While the expression of PPR genes was not change. We used Variant Effect Predictor (VEP) to annotate RNA editing sites, and Local White had the highest RESs in the CDS region of the protein. These findings will be useful for prediction of RESs in other crops and will be helpful in drought tolerance development in wheat.
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Luo G, Shen L, Zhao S, Li R, Song Y, Song S, Yu K, Yang W, Li X, Sun J, Wang Y, Gao C, Liu D, Zhang A. Genome-wide identification of seed storage protein gene regulators in wheat through coexpression analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1704-1720. [PMID: 34634158 DOI: 10.1111/tpj.15538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 09/27/2021] [Indexed: 12/31/2022]
Abstract
Only a few transcriptional regulators of seed storage protein (SSP) genes have been identified in common wheat (Triticum aestivum L.). Coexpression analysis could be an efficient approach to characterize novel transcriptional regulators at the genome-scale considering the correlated expression between transcriptional regulators and target genes. As the A genome donor of common wheat, Triticum urartu is more suitable for coexpression analysis than common wheat considering the diploid genome and single gene copy. In this work, the transcriptome dynamics in endosperm of T. urartu throughout grain filling were revealed by RNA-Seq analysis. In the coexpression analysis, a total of 71 transcription factors (TFs) from 23 families were found to be coexpressed with SSP genes. Among these TFs, TuNAC77 enhanced the transcription of SSP genes by binding to cis-elements distributed in promoters. The homolog of TuNAC77 in common wheat, TaNAC77, shared an identical function, and the total SSPs were reduced by about 24% in common wheat when TaNAC77 was knocked down. This is the first genome-wide identification of transcriptional regulators of SSP genes in wheat, and the newly characterized transcriptional regulators will undoubtedly expand our knowledge of the transcriptional regulation of SSP synthesis.
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Affiliation(s)
- Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Lisha Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Ruidong Li
- Graduate Program in Genetics, Genomics and Bioinformatics, University of California, Riverside, CA, USA
| | - Yanhong Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Shuyi Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Kang Yu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Wenlong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, China
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9
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Fan Y, Han Z, Lu X, Arbab AAI, Nazar M, Yang Y, Yang Z. Short Time-Series Expression Transcriptome Data Reveal the Gene Expression Patterns of Dairy Cow Mammary Gland as Milk Yield Decreased Process. Genes (Basel) 2021; 12:genes12060942. [PMID: 34203058 PMCID: PMC8235497 DOI: 10.3390/genes12060942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/29/2022] Open
Abstract
The existing research on dairy cow mammary gland genes is extensive, but there have been few reports about dynamic changes in dairy cow mammary gland genes as milk yield decrease. For the first time, transcriptome analysis based on short time-series expression miner (STEM) and histological observations were performed using the Holstein dairy cow mammary gland to explore gene expression patterns in this process of decrease (at peak, mid-, and late lactation). Histological observations suggested that the number of mammary acinous cells at peak/mid-lactation was significantly higher than that at mid-/late lactation, and the lipid droplets area secreted by dairy cows was almost unaltered across the three stages of lactation (p > 0.05). Totals of 882 and 1439 genes were differentially expressed at mid- and late lactation, respectively, compared to peak lactation. Function analysis showed that differentially expressed genes (DEGs) were mainly related to apoptosis and energy metabolism (fold change ≥ 2 or fold change ≤ 0.5, p-value ≤ 0.05). Transcriptome analysis based on STEM identified 16 profiles of differential gene expression patterns, including 5 significant profiles (false discovery rate, FDR ≤ 0.05). Function analysis revealed DEGs involved in milk fat synthesis were downregulated in Profile 0 and DEGs in Profile 12 associated with protein synthesis. These findings provide a foundation for future studies on the molecular mechanisms underlying mammary gland development in dairy cows.
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Affiliation(s)
- Yongliang Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Ziyin Han
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Abdelaziz Adam Idriss Arbab
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Mudasir Nazar
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Yi Yang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou 225009, China;
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-0514-87979269
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10
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Genome-Wide Identification of Barley Long Noncoding RNAs and Analysis of Their Regulatory Interactions during Shoot and Grain Development. Int J Mol Sci 2021; 22:ijms22105087. [PMID: 34064912 PMCID: PMC8150791 DOI: 10.3390/ijms22105087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 11/17/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of RNA molecules with gene regulatory functions in plant development and the stress response. Although the number of lncRNAs identified in plants is rapidly increasing, very little is known about their role in barley development. In this study, we performed global identification of barley lncRNAs based on 53 RNAseq libraries derived from nine different barley tissues and organs. In total, 17,250 lncRNAs derived from 10,883 loci were identified, including 8954 novel lncRNAs. Differential expression of lncRNAs was observed in the developing shoot apices and grains, the two organs that have a direct influence on the final yield. The regulatory interaction of differentially expressed lncRNAs with the potential target genes was evaluated. We identified 176 cis-acting lncRNAs in shoot apices and 424 in grains, while the number of trans-acting lncRNAs in these organs was 1736 and 540, respectively. The potential target protein-coding genes were identified, and their biological function was annotated using MapMan ontology. This is the first insight into the roles of lncRNAs in barley development on the genome-wide scale, and our results provide a solid background for future functional studies.
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11
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Milne L, Bayer M, Rapazote-Flores P, Mayer CD, Waugh R, Simpson CG. EORNA, a barley gene and transcript abundance database. Sci Data 2021; 8:90. [PMID: 33767193 DOI: 10.1038/s41597-021-00872-874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/22/2021] [Indexed: 05/27/2023] Open
Abstract
A high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EORNA*) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EORNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eòrna is the Scottish Gaelic word for Barley.
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Affiliation(s)
- Linda Milne
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Micha Bayer
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Paulo Rapazote-Flores
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Claus-Dieter Mayer
- Biomathematics and Statistics Scotland, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
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12
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Milne L, Bayer M, Rapazote-Flores P, Mayer CD, Waugh R, Simpson CG. EORNA, a barley gene and transcript abundance database. Sci Data 2021; 8:90. [PMID: 33767193 PMCID: PMC7994555 DOI: 10.1038/s41597-021-00872-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/22/2021] [Indexed: 01/31/2023] Open
Abstract
A high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EORNA*) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EORNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eòrna is the Scottish Gaelic word for Barley.
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Affiliation(s)
- Linda Milne
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Micha Bayer
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Paulo Rapazote-Flores
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Claus-Dieter Mayer
- Biomathematics and Statistics Scotland, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
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13
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Zhang G, Zhang G, Zeng X, Xu Q, Wang Y, Yuan H, Zhang Y, Nyima T. Quantitative Proteome Profiling Provides Insight into the Proteins Associated with β-Glucan Accumulation in Hull-less Barley Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:568-583. [PMID: 33371680 DOI: 10.1021/acs.jafc.0c05284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The hull-less barley (Qingke) is widely planted as a staple food crop in the Tibetan area, China, and the grains contains high content of β-glucan (BG). The mechanisms of BG synthesis and accumulation in qingke has not been studied at the protein level. This study characterized the proteins associated with BG synthesis and accumulation during qingke seed development. The proteome profiles of qingke seeds taken at 20, 30, and 40 days after flowering were compared using the TMT-based quantitative proteomics. A total of 4283 proteins were identified, with 759 being differentially expressed (DEPs) throughout seed development. Comparisons of protein expression pattern, functions, and pathway enrichment tests highlight cell wall modification, carbon and energy metabolism, polysaccharide metabolism, post-transcriptional modifications, and vesicular transport as critical biological processes related to qingke BG accumulation. Furthermore, induction of starch synthase, starch branching enzyme, pectin acetyl esterases, beta-glucosidases, beta-amylases, 1,4-beta-xylan, xyloglucan, α-amylase inhibitors, and glycosyltransferases underpinned BG synthesis. The results also indicated that the proteins involved in glycolytic, gluconeogenesis, and glyoxylate bypass pathways provided energy and reducing power for BG storage. Parallel reaction monitoring (PRM) and quantitative real-time PCR (qPCR) analyses confirmed the expression profile of the proteins obtained by TMT-based proteomics. The current results provided an insight into the mechanisms of BG synthesis and accumulation during qingke seed development.
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Affiliation(s)
- Guoqiang Zhang
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Guoping Zhang
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Xingquan Zeng
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Qijun Xu
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Yulin Wang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Hongjun Yuan
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Yuhong Zhang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Tashi Nyima
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
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14
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The Impact of Zinc Oxide Nanoparticles on Cytotoxicity, Genotoxicity, and miRNA Expression in Barley ( Hordeum vulgare L.) Seedlings. ScientificWorldJournal 2020; 2020:6649746. [PMID: 33343237 PMCID: PMC7725555 DOI: 10.1155/2020/6649746] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 01/14/2023] Open
Abstract
Zinc oxide nanoparticles are one of the most commonly engineered nanomaterials and necessarily enter the environment because of the large quantities produced and their widespread application. Understanding the impacts of nanoparticles on plant growth and development is crucial for the assessment of probable environmental risks to food safety and human health, because plants are a fundamental living component of the ecosystem and the most important source in the human food chain. The objective of this study was to examine the impact of different concentrations of zinc oxide nanoparticles on barley Hordeum vulgare L. seed germination, seedling morphology, root cell viability, stress level, genotoxicity, and expression of miRNAs. The results demonstrate that zinc oxide nanoparticles enhance barley seed germination, shoot/root elongation, and H2O2 stress level and decrease root cell viability and genomic template stability and up- and downregulated miRNAs in barley seedlings.
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15
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Wu TY, Müller M, Gruissem W, Bhullar NK. Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains. RICE (NEW YORK, N.Y.) 2020; 13:62. [PMID: 32894395 PMCID: PMC7477059 DOI: 10.1186/s12284-020-00421-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/20/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. MAIN TEXT Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. CONCLUSION Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.
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Affiliation(s)
- Ting-Ying Wu
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Present address: Temasek Life Science Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Marlen Müller
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Present address: Roche Glycart AG, Wagistrasse 10, 8952, Schlieren, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Advanced Plant Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Navreet K Bhullar
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland.
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16
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Seven M, Akdemir H. DOF, MYB and TCP transcription factors: Their possible roles on barley germination and seedling establishment. Gene Expr Patterns 2020; 37:119116. [PMID: 32603687 DOI: 10.1016/j.gep.2020.119116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/03/2020] [Indexed: 12/28/2022]
Abstract
Seed germination is a multi-staged complex process during seed plant life cycle, and it is tightly regulated through a coordinated expression of diverse genes in diverse tissues. As regulatory molecules of gene expression, determination of transcription factors is crucial to understanding molecular basis and regulatory network of germination process and seedling establishment. However, limited data on the contributions of these transcription factors to the germination of crop barley (Hordeum vulgare L.) are available. Here, we investigated the expression profiles of selected transcription factors from different families (DOF, MYB and TCP) with qRT-PCR analysis in various tissues including coleoptiles, leaves and roots following the germination. Analysis of MYB and DOF gene expression profiles indicated that there were differing expressions in different aged tissues, HvMYB5 and HvDOF2 being the most outstanding one in the oldest tissue, 15-day-old root. On the other hand, investigated TCP genes were lowly expressed compared to selected MYB and DOF genes, except HvTCP3, where the highest expression was observed in 15-day-old root tissue. The obtained expression profiles illustrate the importance of potential regulatory roles of transcription factors in early developmental stages of barley germination and seedling establishment.
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Affiliation(s)
- Merve Seven
- Yeditepe University, Department of Genetics and Bioengineering, 34755, Istanbul, Turkey
| | - Hulya Akdemir
- Gebze Technical University, Faculty of Science, Department of Molecular Biology and Genetics, 41400, Kocaeli, Turkey.
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17
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Hu H, Gutierrez‐Gonzalez JJ, Liu X, Yeats TH, Garvin DF, Hoekenga OA, Sorrells ME, Gore MA, Jannink J. Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1211-1222. [PMID: 31677224 PMCID: PMC7152608 DOI: 10.1111/pbi.13286] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/24/2019] [Accepted: 10/26/2019] [Indexed: 05/04/2023]
Abstract
Oat ranks sixth in world cereal production and has a higher content of health-promoting compounds compared with other cereals. However, there is neither a robust oat reference genome nor transcriptome. Using deeply sequenced full-length mRNA libraries of oat cultivar Ogle-C, a de novo high-quality and comprehensive oat seed transcriptome was assembled. With this reference transcriptome and QuantSeq 3' mRNA sequencing, gene expression was quantified during seed development from 22 diverse lines across six time points. Transcript expression showed higher correlations between adjacent time points. Based on differentially expressed genes, we identified 22 major temporal co-expression (TCoE) patterns of gene expression and revealed enriched gene ontology biological processes. Within each TCoE set, highly correlated transcripts, putatively commonly affected by genetic background, were clustered and termed genetic co-expression (GCoE) sets. Seventeen of the 22 TCoE sets had GCoE sets with median heritabilities higher than 0.50, and these heritability estimates were much higher than that estimated from permutation analysis, with no divergence observed in cluster sizes between permutation and non-permutation analyses. Linear regression between 634 metabolites from mature seeds and the PC1 score of each of the GCoE sets showed significantly lower p-values than permutation analysis. Temporal expression patterns of oat avenanthramides and lipid biosynthetic genes were concordant with previous studies of avenanthramide biosynthetic enzyme activity and lipid accumulation. This study expands our understanding of physiological processes that occur during oat seed maturation and provides plant breeders the means to change oat seed composition through targeted manipulation of key pathways.
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Affiliation(s)
- Haixiao Hu
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | | | - Xinfang Liu
- Corn Research InstituteLiaoning Academy of Agricultural SciencesShenyangChina
| | - Trevor H. Yeats
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | | | | | - Mark E. Sorrells
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Michael A. Gore
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Jean‐Luc Jannink
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- USDA‐ARSRobert W. Holley Center for Agriculture and HealthIthacaNYUSA
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18
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Watt C, Zhou G, Li C. Harnessing Transcription Factors as Potential Tools to Enhance Grain Size Under Stressful Abiotic Conditions in Cereal Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:1273. [PMID: 33013947 PMCID: PMC7461896 DOI: 10.3389/fpls.2020.01273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/05/2020] [Indexed: 05/07/2023]
Abstract
Predicted climate change is widely cited to significantly reduce yields of the major cereal crop species in a period where demand is rapidly rising due to a growing global population. This requires exhaustive research to develop genetic resources in order to address the expected production deficiencies which will largely be driven by abiotic stress. Modification of multiple genes is an approach that can address the predicted challenges; however, it is time-consuming and costly to modify multiple genes simultaneously. Transcription factors represent a group of proteins regulating multiple genes simultaneously and are therefore promising targets to concurrently improve multiple traits concurrently, such as abiotic stress tolerance and grain size (a contributor to yield). Many studies have identified the complex role that transcription factors of multiple families have contributed toward abiotic stress tolerance or grain size, although research addressing both simultaneously is in its infancy despite its potential significance for cereal crop improvement. Here we discuss the potential role that transcription factors may contribute toward improving cereal crop productivity under adverse environmental conditions and offer research objectives that need to be addressed before the modification of transcription factors becomes routinely used to positively manipulate multiple target traits.
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Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat ( Fagopyrum esculentum). Int J Mol Sci 2019; 20:ijms20174303. [PMID: 31484314 PMCID: PMC6747174 DOI: 10.3390/ijms20174303] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/16/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022] Open
Abstract
Seed development is an essential and complex process, which is involved in seed size change and various nutrients accumulation, and determines crop yield and quality. Common buckwheat (Fagopyrum esculentum Moench) is a widely cultivated minor crop with excellent economic and nutritional value in temperate zones. However, little is known about the molecular mechanisms of seed development in common buckwheat (Fagopyrum esculentum). In this study, we performed RNA-Seq to investigate the transcriptional dynamics and identify the key genes involved in common buckwheat seed development at three different developmental stages. A total of 4619 differentially expressed genes (DEGs) were identified. Based on the results of Gene Ontology (GO) and KEGG analysis of DEGs, many key genes involved in the seed development, including the Ca2+ signal transduction pathway, the hormone signal transduction pathways, transcription factors (TFs), and starch biosynthesis-related genes, were identified. More importantly, 18 DEGs were identified as the key candidate genes for seed size through homologous query using the known seed size-related genes from different seed plants. Furthermore, 15 DEGs from these identified as the key genes of seed development were selected to confirm the validity of the data by using quantitative real-time PCR (qRT-PCR), and the results show high consistency with the RNA-Seq results. Taken together, our results revealed the underlying molecular mechanisms of common buckwheat seed development and could provide valuable information for further studies, especially for common buckwheat seed improvement.
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20
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Editorial for Special Issue "Molecular Advances in Wheat and Barley". Int J Mol Sci 2019; 20:ijms20143501. [PMID: 31315309 PMCID: PMC6678518 DOI: 10.3390/ijms20143501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/15/2019] [Accepted: 07/15/2019] [Indexed: 12/02/2022] Open
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