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Costes C, Navarro Sanz S, Calatayud C, Soriano A, Mameri H, Terrier N, Francin-Allami M. Transcriptomic analysis of developing sorghum grains to detect genes related to cell wall biosynthesis and remodelling. BMC Genom Data 2024; 25:14. [PMID: 38321382 PMCID: PMC10848504 DOI: 10.1186/s12863-024-01198-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
OBJECTIVE Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important grain produced in the world. Interest for cultivating sorghum is increasing all over the world in the context of climate change, due to its low input and water requirements. Like other cultivated cereals, sorghum has significant nutritional value thanks to its protein, carbohydrate and dietary fiber content, these latter mainly consisting of cell wall polysaccharides. This work describes for the first time a transcriptomic analysis dedicated to identify the genes involved in the biosynthesis and remodelling of cell walls both in the endosperm and outer layers of sorghum grain during its development. Further analysis of these transcriptomic data will improve our understanding of cell wall assembly, which is a key component of grain quality. DATA DESCRIPTION This research delineates the steps of our analysis, starting with the cultivation conditions and the grain harvest at different stages of development, followed by the laser microdissection applied to separate the endosperm from the outer layers. It also describes the procedures implemented to generate RNA libraries and to obtain a normalized and filtered table of transcript counts, and finally determine the number of putative cell wall-related genes already listed in literature.
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Affiliation(s)
| | - Sergi Navarro Sanz
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- CIRAD, INRAE, UMR AGAP Institut, Univ Montpellier, Institut Agro, Montpellier, France
- Montpellier Ressources Imagerie, BioCampus, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Caroline Calatayud
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- CIRAD, INRAE, UMR AGAP Institut, Univ Montpellier, Institut Agro, Montpellier, France
| | - Alexandre Soriano
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- CIRAD, INRAE, UMR AGAP Institut, Univ Montpellier, Institut Agro, Montpellier, France
| | - Hamza Mameri
- UMR IATE, Univ Montpellier, INRAE, Institut-Agro Montpellier, 34060, Montpellier, France
| | - Nancy Terrier
- CIRAD, INRAE, UMR AGAP Institut, Univ Montpellier, Institut Agro, Montpellier, France.
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Chen J, Watson-Lazowski A, Kamble NU, Vickers M, Seung D. Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis. BMC Plant Biol 2023; 23:363. [PMID: 37460981 DOI: 10.1186/s12870-023-04369-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/11/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Durum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. Like in bread wheat, the starch and protein accumulated in the endosperm during grain development are the primary contributors to the calorific value of durum grains. RESULTS To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. We demonstrate the potential of our dataset to provide new insights into key processes that occur during endosperm development, using starch metabolism as an example. CONCLUSION We provide a valuable resource for studying endosperm development in this increasingly important crop species.
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Affiliation(s)
- Jiawen Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alexander Watson-Lazowski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | | | - Martin Vickers
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - David Seung
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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Pei H, Li Y, Liu Y, Liu P, Zhang J, Ren X, Lu Z. Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development. aBIOTECH 2023; 4:8-19. [PMID: 37220536 PMCID: PMC10199822 DOI: 10.1007/s42994-023-00095-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/22/2023] [Indexed: 05/25/2023]
Abstract
Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential transcriptomic expressions, and the proportion of distal ACRs was increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed light on the improvement of wheat yields and qualities. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00095-8.
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Affiliation(s)
- Hongcui Pei
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yushan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yanhong Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Pan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jialin Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xueni Ren
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zefu Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Chen P, Liu Q, Sun B, Lv S, Jiang L, Zhang J, Mao X, Yu H, Chen Y, Chen W, Fan Z, Pan D, Li C. Creation and gene expression analysis of a giant embryo rice mutant with high GABA content. Mol Breed 2023; 43:3. [PMID: 37312870 PMCID: PMC10248637 DOI: 10.1007/s11032-022-01353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/27/2022] [Indexed: 06/15/2023]
Abstract
Gamma-amino butyric acid (GABA) is a natural non-protein amino acid involved in stress, signal transmission, carbon and nitrogen balance, and other physiological processes in plants. In the human body, GABA has the effects of lowering blood pressure, anti-aging, and activating the liver and kidneys. However, there are few studies on the molecular regulation mechanism of genes in the metabolic pathways of GABA during grain development of giant embryo rice with high GABA content. In this study, three glant embryo (ge) mutants of different embryo sizes were obtained by CRISPR/Cas9 knockout, and it was found that GABA, protein, crude fat, and various mineral contents of the ge mutants were significantly increased. RNA-seq and qRT-PCR analysis showed that in the GABA shunt and polyamine degradation pathways, the expression levels of most of the genes encoding enzymes promoting GABA accumulation were significantly upregulated in the ge-1 mutant, whereas, the expression levels of most of the genes encoding enzymes involved GABA degradation were significantly downregulated in the ge-1 mutant. This is most likely responsible for the significant increase in GABA content of the ge mutant. These results help reveal the molecular regulatory network of GABA metabolism in giant embryo rice and provide a theoretical basis for the study of its development mechanisms, which is conducive to the rapid cultivation of GABA-rich rice varieties, promoting human nutrition, and ensuring health. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01353-1.
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Affiliation(s)
- Pingli Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Shuwei Lv
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Yangyang Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Dajian Pan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
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Li W, Yu Y, Chen X, Fang Q, Yang A, Chen X, Wu L, Wang C, Wu D, Ye S, Wu D, Sun G. N6-Methyladenosine dynamic changes and differential methylation in wheat grain development. Planta 2022; 255:125. [PMID: 35567638 DOI: 10.1007/s00425-022-03893-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/02/2022] [Indexed: 06/15/2023]
Abstract
More methylation changes occur in late interval than in early interval of wheat seed development with protein and the starch synthesis-related pathway enriched in the later stages. Wheat seed development is a critical process to determining wheat yield and quality, which is controlled by genetics, epigenetics and environments. The N6-methyladenosine (m6A) modification is a reversible and dynamic process and plays regulatory role in plant development and stress responses. To better understand the role of m6A in wheat grain development, we characterized the m6A modification at 10 day post-anthesis (DPA), 20 DPA and 30 DPA in wheat grain development. m6A-seq identified 30,615, 30,326, 27,676 high confidence m6A peaks from the 10DPA, 20DPA, and 30DPA, respectively, and enriched at 3'UTR. There were 29,964, 29,542 and 26,834 unique peaks identified in AN0942_10d, AN0942_20d and AN0942_30d. One hundred and forty-two genes were methylated by m6A throughout seed development, 940 genes methylated in early grain development (AN0942_20d vs AN0942_10d), 1542 genes in late grain development (AN0942_30d vs AN0942_20d), and 1190 genes between early and late development stage (AN0942_30d vs AN0942_10d). KEGG enrichment analysis found that protein-related pathways and the starch synthesis-related pathway were significantly enriched in the later stages of seed development. Our results provide novel knowledge on m6A dynamic changes and its roles in wheat grain development.
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Affiliation(s)
- Wenxiang Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yi Yu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xuanrong Chen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Qian Fang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Anqi Yang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xinyu Chen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Lei Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Chengyu Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, China
| | - Dechuan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Sihong Ye
- Cotton Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001, Anhui, China.
| | - Dexiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, NS, B3H 3C3, Canada.
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Deng Y, Liu R, Wang Z, Zhang L, Yu S, Zhou Z, Diao J. The stereoselectivity of metconazole on wheat grain filling and harvested seeds germination: Implication for the application of triazole chiral pesticides. J Hazard Mater 2021; 416:125911. [PMID: 34492845 DOI: 10.1016/j.jhazmat.2021.125911] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/26/2021] [Accepted: 04/14/2021] [Indexed: 06/13/2023]
Abstract
Plant growth can be influenced by the application of triazole pesticides as these regulate physiological processes such as plant hormonal levels and enzyme activity. Homology modeling and molecular docking studies suggested that inhibition of ADP-glucose pyrophosphorylase activity in two trans-stereoisomers treatments hinders starch accumulation during the grain filling stage. A field experiment investigated the effects of metconazole racemate, cis-1R,5S-stereostereoisomer, and cis-1S,5R-stereoisomer application at the flowering stage on wheat grain ripening and yield. The concentrations of racemate and both cis-stereoisomers were detected in wheat plant and grain samples. Compared with the racemate, both cis-stereoisomers were more persistent in the matrices. Treatment with cis-1R,5S-stereoisomer decreased grain weight and yield of wheat by delaying chlorophyll degradation, increasing the ethylene content, and decreasing the level of abscisic acid. The germination of harvested seeds was adversely affected by racemate treatment as a result of gibberellin and abscisic acid metabolism regulation and the transcription of signaling-related genes. Therefore, cis-1S,5R-stereoisomer was recommended to be used as metconazole pesticide at the flowering stage.
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Affiliation(s)
- Yue Deng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, PR China
| | - Rui Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, PR China
| | - Zikang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, PR China
| | - Luyao Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, PR China
| | - Simin Yu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, PR China
| | - Zhiqiang Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, PR China
| | - Jinling Diao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, PR China.
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Fan Y, Yan J, Lai D, Yang H, Xue G, He A, Guo T, Chen L, Cheng XB, Xiang DB, Ruan J, Cheng J. Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]. BMC Genomics 2021; 22:509. [PMID: 34229611 PMCID: PMC8259154 DOI: 10.1186/s12864-021-07848-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background GRAS, an important family of transcription factors, have played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. Since the sequencing of the sorghum genome, a plethora of genetic studies were mainly focused on the genomic information. The indepth identification or genome-wide analysis of GRAS family genes, especially in Sorghum bicolor, have rarely been studied. Results A total of 81 SbGRAS genes were identified based on the S. bicolor genome. They were named SbGRAS01 to SbGRAS81 and grouped into 13 subfamilies (LISCL, DLT, OS19, SCL4/7, PAT1, SHR, SCL3, HAM-1, SCR, DELLA, HAM-2, LAS and OS4). SbGRAS genes are not evenly distributed on the chromosomes. According to the results of the gene and motif composition, SbGRAS members located in the same group contained analogous intron/exon and motif organizations. We found that the contribution of tandem repeats to the increase in sorghum GRAS members was slightly greater than that of fragment repeats. By quantitative (q) RT-PCR, the expression of 13 SbGRAS members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. We further investigated the relationship between DELLA genes, GAs and grain development in S. bicolor. The paclobutrazol treatment significantly increased grain weight, and affected the expression levels of all DELLA subfamily genes. SbGRAS03 is the most sensitive to paclobutrazol treatment, but also has a high response to abiotic stresses. Conclusions Collectively, SbGRAs play an important role in plant development and response to abiotic stress. This systematic analysis lays the foundation for further study of the functional characteristics of GRAS genes of S. bicolor. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07848-z.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, 610106, Chengdu, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Tianrong Guo
- Chengdu Institute of Food Inspection, 610030, Chengdu, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, 618200, Mianzhu, People's Republic of China
| | - Xiao-Bin Cheng
- Department of Environmental and Life Sciences, Sichuan MinZu College, 626001, Kangding, People's Republic of China
| | - Da-Bing Xiang
- School of Food and Biological engineering, Chengdu University, 610106, Chengdu, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China.
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Call L, Haider E, D'Amico S, Reiter E, Grausgruber H. Synthesis and accumulation of amylase-trypsin inhibitors and changes in carbohydrate profile during grain development of bread wheat (Triticum aestivum L.). BMC Plant Biol 2021; 21:113. [PMID: 33627080 PMCID: PMC7905651 DOI: 10.1186/s12870-021-02886-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Recent studies indicate that amylase-trypsin inhibitors (ATIs) and certain carbohydrates referred to as FODMAPs (fermentable oligo-, di-, monosaccharides and polyols) play an important role in promoting wheat sensitivity. Hitherto, no study has investigated the accumulation of ATIs during the development of the wheat caryopsis. We collected caryopses of common wheat cv. 'Arnold' at eight different grain developmental stages to study compositional changes in ATI and FODMAP content. RESULTS The harvested caryopses were analysed for their size, protein and carbohydrate concentrations. ATIs were further characterized by MALDI-TOF MS, and their trypsin inhibition was evaluated by an enzymatic assay. The results showed that ATI accumulation started about 1 week after anthesis and subsequently increased steadily until physiological maturity. However, the biological activity of ATIs in terms of enzyme inhibition was not detectable before about 4 weeks after anthesis. Carbohydrate analysis revealed the abundance of short-chain fructans in early stages of grain development, whereas non-water-soluble carbohydrates increased during later developmental stages. CONCLUSIONS The results provide new insights into the complex metabolisms during grain filling and maturation, with particular emphasis on the ATI content as well as the inhibitory potential towards trypsin. The time lag between ATI accumulation and development of their biological activity is possibly attributed to the assembling of ATIs to dimers and tetramers, which seems to be crucial for their inhibitory potential.
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Affiliation(s)
- Lisa Call
- Institute of Animal Nutrition and Feeding, AGES - Austrian Agency for Health and Food Safety, Spargelfeldstr. 191, 1220, Vienna, Austria
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Elisabeth Haider
- Institute of Animal Nutrition and Feeding, AGES - Austrian Agency for Health and Food Safety, Spargelfeldstr. 191, 1220, Vienna, Austria
| | - Stefano D'Amico
- Institute of Animal Nutrition and Feeding, AGES - Austrian Agency for Health and Food Safety, Spargelfeldstr. 191, 1220, Vienna, Austria
| | - Elisabeth Reiter
- Institute of Animal Nutrition and Feeding, AGES - Austrian Agency for Health and Food Safety, Spargelfeldstr. 191, 1220, Vienna, Austria
| | - Heinrich Grausgruber
- Department of Crop Sciences, BOKU - University of Natural Resources and Life Sciences, Vienna, Konrad Lorenz-Str. 24, 3430, Tulln an der Donau, Austria.
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Zhu Y, Li T, Xu J, Wang J, Wang L, Zou W, Zeng D, Zhu L, Chen G, Hu J, Gao Z, Dong G, Ren D, Shen L, Zhang Q, Guo L, Hu S, Qian Q, Zhang G. Leaf width gene LW5/D1 affects plant architecture and yield in rice by regulating nitrogen utilization efficiency. Plant Physiol Biochem 2020; 157:359-369. [PMID: 33189056 DOI: 10.1016/j.plaphy.2020.10.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/28/2020] [Indexed: 06/11/2023]
Abstract
Leaves are the primary structures responsible for photosynthesis, making leaf morphology one of the most important traits of rice plant architecture. Both plant architecture and nutrient utilization jointly affect rice yield, however, their molecular association is still poorly understood. We identified a rice mutant, leaf width 5 (lw5), that displayed small grains and wide leaves and possesses characteristics typical of a small "sink" and a large "source". Map-based cloning and CRISPR-Cas9 gene editing indicated that LW5 affects both the plant architecture and yield. It is an allele of D1, encoding the rice G protein α subunit. The loss of LW5 functioning leads to an increase in the rate of photosynthesis, vascular bundles, and chlorophyll content. However, the grain-straw ratio and the rate of grain filling decreased significantly. The detection results of 15N-ammonium nitrate and an expression analysis of genes associated with nitrogen demonstrated that LW5 serves an important role in nitrate uptake and transport. LW5 affects plant architecture and grain size by regulating nitrogen transfer. These results provide a theoretical foundation for further research surrounding the molecular mechanism of "source-sink" balance in rice and suggest novel methods of molecular design for the cultivation of breeding super rice in ideal plant types.
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Affiliation(s)
- Yuchen Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ting Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jing Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiajia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Li Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Weiwei Zou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guang Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Songping Hu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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Zhu L, Cheng H, Peng G, Wang S, Zhang Z, Ni E, Fu X, Zhuang C, Liu Z, Zhou H. Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles. Genomics Proteomics Bioinformatics 2020; 18:305-320. [PMID: 33147495 PMCID: PMC7801245 DOI: 10.1016/j.gpb.2019.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 12/06/2018] [Accepted: 01/11/2019] [Indexed: 02/04/2023]
Abstract
Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.
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Affiliation(s)
- Liya Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Han Cheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guoqing Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shuansuo Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing 100101, China
| | - Zhiguo Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Erdong Ni
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiangdong Fu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing 100101, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zexian Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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11
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Tahir A, Kang J, Choulet F, Ravel C, Romeuf I, Rasouli F, Nosheen A, Branlard G. Deciphering carbohydrate metabolism during wheat grain development via integrated transcriptome and proteome dynamics. Mol Biol Rep 2020; 47:5439-49. [PMID: 32627139 DOI: 10.1007/s11033-020-05634-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/27/2020] [Indexed: 10/23/2022]
Abstract
Grain development of Triticum aestivum is being studied extensively using individual OMICS tools. However, integrated transcriptome and proteome studies are limited mainly due to complexity of genome. Current study focused to unravel the transcriptome-proteome coordination of key mechanisms underlying carbohydrate metabolism during whole wheat grain development. Wheat grains were manually dissected to obtain grain tissues for proteomics and transcriptomics analyses. Differentially expressed proteins and transcripts at the 11 stages of grain development were compared. Computational workflow for integration of two datasets related to carbohydrate metabolism was designed. For CM proteins, output peptide sequences of proteomic analyses (via LC-MS/MS) were used as source to search corresponding transcripts. The transcript that turned out with higher number of peptides was selected as bona fide ribonucleotide sequence for respective protein synthesis. More than 90% of hits resulted in successful identification of respective transcripts. Comparative analysis of protein and transcript expression profiles resulted in overall 32% concordance between these two series of data. However, during grain development correlation of two datasets gradually increased up to ~ tenfold from 152 to 655 °Cd and then dropped down. Proteins involved in carbohydrate metabolism were divided in five categories in accordance with their functions. Enzymes involved in starch and sucrose biosynthesis showed the highest correlations between proteome-transcriptome profiles. High percentage of identification and validation of protein-transcript hits highlighted the power of omics data integration approach over existing gene functional annotation tools. We found that correlation of two datasets is highly influenced by stage of grain development. Further, gene regulatory networks would be helpful in unraveling the mechanisms underlying the complex and significant traits such as grain weight and yield.
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12
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Kino RI, Pellny TK, Mitchell RAC, Gonzalez-Uriarte A, Tosi P. High post-anthesis temperature effects on bread wheat (Triticum aestivum L.) grain transcriptome during early grain-filling. BMC Plant Biol 2020; 20:170. [PMID: 32299364 PMCID: PMC7164299 DOI: 10.1186/s12870-020-02375-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/31/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND High post-anthesis (p.a) temperatures reduce mature grain weights in wheat and other cereals. However, the causes of this reduction are not entirely known. Control of grain expansion by the maternally derived pericarp of the grain has previously been suggested, although this interaction has not been investigated under high p.a. temperatures. Down-regulation of pericarp localised genes that regulate cell wall expansion under high p.a. temperatures may limit expansion of the encapsulated endosperm due to a loss of plasticity in the pericarp, reducing mature grain weight. Here the effect of high p.a. temperatures on the transcriptome of the pericarp and endosperm of the wheat grain during early grain-filling was investigated via RNA-Seq and is discussed alongside grain moisture dynamics during early grain development and mature grain weight. RESULTS High p.a. temperatures applied from 6-days after anthesis (daa) and until 18daa reduced the grain's ability to accumulate water, with total grain moisture and percentage grain moisture content being significantly reduced from 14daa onwards. Mature grain weight was also significantly reduced by the same high p.a. temperatures applied from 6daa for 4-days or more, in a separate experiment. Comparison of our RNA-Seq data from whole grains, with existing data sets from isolated pericarp and endosperm tissues enabled the identification of subsets of genes whose expression was significantly affected by high p.a. temperature and predominantly expressed in either tissue. Hierarchical clustering and gene ontology analysis resulted in the identification of a number of genes implicated in the regulation of cell wall expansion, predominantly expressed in the pericarp and significantly down-regulated under high p.a. temperatures, including endoglucanase, xyloglucan endotransglycosylases and a β-expansin. An over-representation of genes involved in the 'cuticle development' functional pathway that were expressed in the pericarp and affected by high p.a. temperatures was also observed. CONCLUSIONS High p.a. temperature induced down-regulation of genes involved in regulating pericarp cell wall expansion. This concomitant down-regulation with a reduction in total grain moisture content and grain weight following the same treatment period, adds support to the theory that high p.a. temperatures may cause a reduction in mature grain weight as result of decreased pericarp cell wall expansion.
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Affiliation(s)
- Richard I. Kino
- School of Agriculture Policy and Development, University of Reading, Whiteknights, PO Box 237, Reading, RG6 6AR UK
| | - Till K. Pellny
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ UK
| | | | - Asier Gonzalez-Uriarte
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ UK
- Current affiliation: European Bioinformatics Institute, Wellcome Genome Campus, Cambridgeshire, CB10 1SD UK
| | - Paola Tosi
- School of Agriculture Policy and Development, University of Reading, Whiteknights, PO Box 237, Reading, RG6 6AR UK
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13
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Hou G, Du C, Gao H, Liu S, Sun W, Lu H, Kang J, Xie Y, Ma D, Wang C. Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels. BMC Plant Biol 2020; 20:87. [PMID: 32103721 PMCID: PMC7045451 DOI: 10.1186/s12870-020-2296-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/20/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) play crucial roles in the regulation of plant development and growth, but little information is available concerning their roles during grain development under different nitrogen (N) application levels. Our objective was to identify miRNAs related to the regulation of grain characteristics and the response to different N fertilizer conditions. RESULTS A total of 79 miRNAs (46 known and 33 novel miRNAs) were identified that showed significant differential expression during grain development under both high nitrogen (HN) and low nitrogen (LN) treatments. The miRNAs that were significantly upregulated early in grain development target genes involved mainly in cell differentiation, auxin-activated signaling, and transcription, which may be associated with grain size; miRNAs abundant in the middle and later stages target genes mainly involved in carbohydrate and nitrogen metabolism, transport, and kinase activity and may be associated with grain filling. Additionally, we identified 50 miRNAs (22 known and 28 novel miRNAs), of which 11, 9, and 39 were differentially expressed between the HN and LN libraries at 7, 17, and 27 days after anthesis (DAA). The miRNAs that were differentially expressed in response to nitrogen conditions target genes involved mainly in carbohydrate and nitrogen metabolism, the defense response, and transport as well as genes that encode ubiquitin ligase. Only one novel miRNA (PC-5p-2614_215) was significantly upregulated in response to LN treatment at all three stages, and 21 miRNAs showed significant differential expression between HN and LN conditions only at 27 DAA. We therefore propose a model for target gene regulation by miRNAs during grain development with N-responsive patterns. CONCLUSIONS The potential targets of the identified miRNAs are related to various biological processes, such as carbohydrate/nitrogen metabolism, transcription, cellular differentiation, transport, and defense. Our results indicate that miRNA-mediated networks, via posttranscriptional regulation, play crucial roles in grain development and the N response, which determine wheat grain weight and quality. Our study provides useful information for future research of regulatory mechanisms that focus on improving grain yield and quality.
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Affiliation(s)
- Gege Hou
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chenyang Du
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Honghuan Gao
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Sujun Liu
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wan Sun
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongfang Lu
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Juan Kang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingxin Xie
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dongyun Ma
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Chenyang Wang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
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14
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Hong MJ, Kim DY, Choi HI, Seo YW, Kim JB. Isolation and characterization of kelch repeat-containing F-box proteins from colored wheat. Mol Biol Rep 2020; 47:1129-41. [PMID: 31907740 DOI: 10.1007/s11033-019-05210-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/26/2019] [Indexed: 12/30/2022]
Abstract
F-box proteins play important roles in the regulation of various developmental processes in plants. Approximately 1796 F-box genes have been identified in the wheat genome, but details of their functions remain unknown. Moreover, not much was known about the roles of kelch repeat domain-containing F-box genes (TaKFBs) in wheat. In the present study, we isolated five TaKFBs to investigate the roles of KFBs at different stages of colored wheat grain development. The cDNAs encoding TaKFB1, TaKFB2, TaKFB3, TaKFB4, and TaKFB5 contained 363, 449, 353, 382, and 456 bp open reading frames, respectively. All deduced TaKFBs contained an F-box domain (IPR001810) and a kelch repeat type 1 domain (IPR006652), except TaKFB2. Expression of TaKFBs was elevated during the pigmentation stages of grain development. To clarify how TaKFB and SKP interact in wheat, we investigated whether five TaKFB proteins showed specificity for six SKP proteins using a yeast two-hybrid (Y2H) assay. An Y2H screen was performed to search for proteins capable of binding the TaKFBs and interaction was identified between TaKFB1 and aquaporin PIP1. To examine the subcellular localization of TaKFBs, we transiently expressed TaKFB-green fluorescent protein (GFP) fusions in tobacco leaves; the TaKFB-GFP fusions were detected in the nucleus and the cytoplasm. Y2H and bimolecular fluorescence complementation (BiFC) assays revealed that TaKFB1 specifically interacts with aquaporin PIP1. These results will provide useful information for further functional studies on wheat F-box proteins and their possible roles.
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15
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Le TDQ, Alvarado C, Girousse C, Legland D, Chateigner-Boutin AL. Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development. Plant Methods 2019; 15:84. [PMID: 31384289 PMCID: PMC6668075 DOI: 10.1186/s13007-019-0468-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/23/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Wheat is one of the most important staple source in the world for human consumption, animal feed and industrial raw materials. To deal with the global and increasing population demand, enhancing crop yield by increasing the final weight of individual grain is considered as a feasible solution. Morphometric analysis of wheat grain plays an important role in tracking and understanding developmental processes by assessing potential impacts on grains properties, size and shape that are major determinants of final grain weight. X-ray micro computed tomography (μCT) is a very powerful non-invasive imaging tool that is able to acquire 3D images of an individual grain, enabling to assess the morphology of wheat grain and of its different compartments. Our objective is to quantify changes of morphology during growth stages of wheat grain from 3D μCT images. METHODS 3D μCT images of wheat grains were acquired at various development stages ranging from 60 to 310 degree days after anthesis. We developed robust methods for the identification of outer and inner tissues within the grains, and the extraction of morphometric features using 3D μCT images. We also developed a specific workflow for the quantification of the shape of the grain crease. RESULTS The different compartments of the grain could be semi-automatically segmented. Variations of volumes of the compartments adequately describe the different stages of grain developments. The evolution of voids within wheat grain reflects lysis of outer tissues and growth of inner tissues. The crease shape could be quantified for each grain and averaged for each stage of development, helping us understand the genesis of the grain shape. CONCLUSION This work shows that μCT acquisitions and image processing methodologies are powerful tools to extract morphometric parameters of developing wheat grain. The results of quantitative analysis revealed remarkable features of wheat grain growth. Further work will focus on building a computational model of wheat grain growth based on real 3D imaging data.
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Affiliation(s)
| | | | - Christine Girousse
- UMR GDEC, INRA, Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
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16
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Wei J, Cao H, Liu JD, Zuo JH, Fang Y, Lin CT, Sun RZ, Li WL, Liu YX. Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq. Funct Integr Genomics 2019; 19:919-932. [PMID: 31168755 DOI: 10.1007/s10142-019-00693-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 03/21/2019] [Accepted: 05/17/2019] [Indexed: 11/28/2022]
Abstract
Bread wheat (Triticum aestivum L.) is an allohexaploid, and the transcriptional characteristics of the wheat embryo and endosperm during grain development remain unclear. To analyze the transcriptome, we performed isoform sequencing (Iso-Seq) for wheat grain and RNA sequencing (RNA-Seq) for the embryo and de-embryonated kernels. The differential regulation between the embryo and de-embryonated kernels was found to be greater than the difference between the two time points for each tissue. Exactly 2264 and 4790 tissue-specific genes were found at 14 days post-anthesis (DPA), while 5166 and 3784 genes were found at 25 DPA in the embryo and de-embryonated kernels, respectively. Genes expressed in the embryo were more likely to be related to nucleic acid and enzyme regulation. In de-embryonated kernels, genes were rich in substance metabolism and enzyme activity functions. Moreover, 4351, 4641, 4516, and 4453 genes with the A, B, and D homoeoloci were detected for each of the four tissues. Expression characteristics suggested that the D genome may be the largest contributor to the transcriptome in developing grain. Among these, 48, 66, and 38 silenced genes emerged in the A, B, and D genomes, respectively. Gene ontology analysis showed that silenced genes could be inclined to different functions in different genomes. Our study provided specific gene pools of the embryo and de-embryonated kernels and a homoeolog expression bias model on a large scale. This is helpful for providing new insights into the molecular physiology of wheat.
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Affiliation(s)
- Jun Wei
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing-Dong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing-Hong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Fang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chih-Ta Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Run-Ze Sun
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wen-Long Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,Science and Technology Daily, Beijing, 100093, China
| | - Yong-Xiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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17
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Chi Q, Guo L, Ma M, Zhang L, Mao H, Wu B, Liu X, Ramirez-Gonzalez RH, Uauy C, Appels R, Zhao H. Global transcriptome analysis uncovers the gene co-expression regulation network and key genes involved in grain development of wheat (Triticum aestivum L.). Funct Integr Genomics 2019; 19:853-66. [PMID: 31115762 DOI: 10.1007/s10142-019-00678-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 03/24/2019] [Accepted: 04/12/2019] [Indexed: 02/07/2023]
Abstract
Wheat grain development is a robust biological process that largely determines grain quality and yield. In this study, we investigated the grain transcriptome of winter wheat cv. Xiaoyan-6 at four developmental stages (5, 10, 15, and 20 days post-anthesis), using high-throughput RNA sequencing (RNA-Seq). We identified 427 grain-specific transcription factors (TFs) and 1653 differentially expressed TFs during grain development as well as a grain co-expression regulation network (GrainNet) of the TFs and their predicted co-expressed genes. Our study identified ten putative key TFs and the predicted regulatory genes of these TFs in wheat grain development of Xiaoyan-6. The analysis was given a firm basis through the study of additional wheat tissues, including root, stem, leaf, flag leaf, grain, spikes (from wheat plants at booting or heading stages) to provide a dataset of 92,478 high-confidence protein-coding genes that were mostly evenly distributed among subgenomes, but unevenly distributed across each of the chromosomes or each of the seven homeologous groups. Within this larger framework of the transcriptomes, we identified 4659 grain-specific genes (SEGs) and 26,500 differentially expressed genes (DEGs) throughout grain development stages tested. The SEGs identified mainly associate with regulation and signaling-related biological processes, while the DEGs mainly involve in cellular component organization or biogenesis and nutrient reservoir activity during grain development of Xiaoyan-6. This study establishes new targets for modifying genes related to grain development and yield, to fine-tune expression in different varieties and environments.
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18
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Francin-Allami M, Alvarado C, Daniel S, Geairon A, Saulnier L, Guillon F. Spatial and temporal distribution of cell wall polysaccharides during grain development of Brachypodium distachyon. Plant Sci 2019; 280:367-382. [PMID: 30824016 DOI: 10.1016/j.plantsci.2018.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/14/2018] [Accepted: 12/15/2018] [Indexed: 06/09/2023]
Abstract
Brachypodium distachyon (Brachypodium) is now well considered as being a suitable plant model for studying temperate cereal crops. Its cell walls are phylogenetically intermediate between rice and poaceae, with a greater proximity to these latter. By microscopic and biochemical approaches, this work gives an overview of the temporal and spatial distribution of cell wall polysaccharides in the grain of Brachypodium from the end of the cellularization step to the maturation of grain. Variation in arabinoxylan chemical structure and distribution were demonstrated according to development and different grain tissues. In particular, the kinetic of arabinoxylan feruloylation was shown occuring later in the aleurone layers compared to storage endosperm. Mixed linked β-glucan was detected in whole the tissues of Brachypodium grain even at late stage of development. Cellulose was found in both the storage endosperm and the outer layers. Homogalacturonan and rhamnogalacturonan I epitopes were differentially distributed within the grain tissues. LM5 galactan epitope was restricted to the aleurone layers contrary to LM6 arabinan epitope which was detected in the whole endosperm. A massive deposition of highly methylated homogalacturonans in vesicular bodies was observed underneath the cell wall of the testa t2 layer at early stage of development. At maturity, low-methylated homogalacturonans totally fulfilled the lumen of the t2 cell layer, suggesting pectin remodeling during grain development. Xyloglucans were only detected in the cuticle above the testa early in the development of the grain while feruloylated arabinoxylans were preferentially deposited into the cell wall of t1 layer. Indeed, the circumscribed distribution of some of the cell wall polysaccharides raises questions about their role in grain development and physiology.
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Affiliation(s)
| | - Camille Alvarado
- INRA, UR 1268 Biopolymères Interactions Assemblages, 44000, Nantes, France
| | - Sylviane Daniel
- INRA, UR 1268 Biopolymères Interactions Assemblages, 44000, Nantes, France
| | - Audrey Geairon
- INRA, UR 1268 Biopolymères Interactions Assemblages, 44000, Nantes, France
| | - Luc Saulnier
- INRA, UR 1268 Biopolymères Interactions Assemblages, 44000, Nantes, France
| | - Fabienne Guillon
- INRA, UR 1268 Biopolymères Interactions Assemblages, 44000, Nantes, France
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19
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Bian J, Deng P, Zhan H, Wu X, Nishantha MDLC, Yan Z, Du X, Nie X, Song W. Transcriptional Dynamics of Grain Development in Barley ( Hordeum vulgare L.). Int J Mol Sci 2019; 20:E962. [PMID: 30813307 PMCID: PMC6412674 DOI: 10.3390/ijms20040962] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/06/2019] [Accepted: 02/19/2019] [Indexed: 11/29/2022] Open
Abstract
Grain development, as a vital process in the crop's life cycle, is crucial for determining crop quality and yield. However, the molecular basis and regulatory network of barley grain development is not well understood at present. Here, we investigated the transcriptional dynamics of barley grain development through RNA sequencing at four developmental phases, including early prestorage phase (3 days post anthesis (DPA)), late prestorage or transition phase (8 DPA), early storage phase (13 DPA), and levels off stages (18 DPA). Transcriptome profiling found that pronounced shifts occurred in the abundance of transcripts involved in both primary and secondary metabolism during grain development. The transcripts' activity was decreased during maturation while the largest divergence was observed between the transitions from prestorage phase to storage phase, which coincided with the physiological changes. Furthermore, the transcription factors, hormone signal transduction-related as well as sugar-metabolism-related genes, were found to play a crucial role in barley grain development. Finally, 4771 RNA editing events were identified in these four development stages, and most of the RNA editing genes were preferentially expressed at the prestore stage rather than in the store stage, which was significantly enriched in "essential" genes and plant hormone signal transduction pathway. These results suggested that RNA editing might act as a 'regulator' to control grain development. This study systematically dissected the gene expression atlas of barley grain development through transcriptome analysis, which not only provided the potential targets for further functional studies, but also provided insights into the dynamics of gene regulation underlying grain development in barley and beyond.
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Affiliation(s)
- Jianxin Bian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Haoshuang Zhan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaotong Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Mutthanthirige D L C Nishantha
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Zhaogui Yan
- Huazhong Agricultural University, Wuhan 430070, China.
| | - Xianghong Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
- Joint Research Center for Agriculture Research in Arid Areas, Yangling, Shaanxi 712100, China.
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Mandal PK, Rai S, Kaushik M, Sinha SK, Gupta RK, Mahendru A. Transcriptome data of cultivated tetraploid and hexaploid wheat variety during grain development. Data Brief 2018; 22:551-556. [PMID: 30627606 PMCID: PMC6321973 DOI: 10.1016/j.dib.2018.12.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/07/2018] [Accepted: 12/17/2018] [Indexed: 11/17/2022] Open
Abstract
Wheat is a major food crop and an important component of human diet throughout the world. There are two major types of cultivated wheat; one is tetraploid durum (pasta) wheat and another one is hexaploid bread wheat. Wheat grain is the reservoir of two major dietary components – carbohydrate and protein, which get accumulated during seed maturation and directly affects yield and quality. Hexaploid, having 6 copies of each chromosome differs to a great extent from tetraploid having 4 copies of each chromosome. Studying the gene expression pattern in developing grain would help in understanding the difference in metabolic process as well as involvement of the genes in these two types of wheat. A transcriptional comparison of developing grains was carried out between the two wheat genotypes; tetraploid (AABB:PDW233) and hexaploid (AABBDD:PBW343) using RNA-seq. Approximately 194 million raw reads were obtained from both libraries. After removal of contaminations, a huge proportion (>99%), of high quality reads were obtained, were aligned to reference genome. A total of 2324 up-regulated and 522 down-regulated genes were identified as differentially expressed between PDW233 vs PBW343. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes between durum and bread wheat. This information will help in understanding process grain reserve in tetraploid and hexaploid wheat in relation to their nutritional quality.
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Affiliation(s)
- Pranab Kumar Mandal
- Indian Council of Agricultural Research – National Research Centre on Plant Biotechnology (ICAR-NRCPB), LBS Building, Pusa Campus, New Delhi 110012, India
- Corresponding author.
| | - Shubham Rai
- Indian Council of Agricultural Research – National Research Centre on Plant Biotechnology (ICAR-NRCPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Megha Kaushik
- Indian Council of Agricultural Research – National Research Centre on Plant Biotechnology (ICAR-NRCPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Subodh Kumar Sinha
- Indian Council of Agricultural Research – National Research Centre on Plant Biotechnology (ICAR-NRCPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Rajesh Kumar Gupta
- Indian Council of Agricultural Research – National Research Centre on Plant Biotechnology (ICAR-NRCPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Anju Mahendru
- Indian Agriculture Research Institute – Division of Genetics, Pusa Campus, New Delhi 110012, India
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Gao J, Shi J, Dong S, Liu P, Zhao B, Zhang J. Grain development and endogenous hormones in summer maize (Zea mays L.) submitted to different light conditions. Int J Biometeorol 2018; 62:2131-2138. [PMID: 30244320 DOI: 10.1007/s00484-018-1613-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 08/17/2018] [Accepted: 09/09/2018] [Indexed: 05/27/2023]
Abstract
Low light is a type of abiotic stress that seriously affects plant growth and production efficiency. We investigated the response mechanisms of summer maize to low light by measuring the changes in endogenous hormones in the grains and during grain filling in summer maize at different light intensities to provide a theoretical basis for the production and management of summer maize under light stress. We applied different light treatments in a field experiment as follows: S, shading from tassel stage (VT) to maturity stage (R6); CK, natural lighting in the field; and L, increasing light from VT to R6. The shading level was 60%, and the maximum illumination intensity of the increasing light treatment on cloudy days was 1600-1800 μmol m-2 s-1. Compared with the control, shading significantly increased the grain abscisic acid (ABA) content at 5-20 days after pollination and decreased the indole acetic acid (IAA), zeatin riboside (ZR), and gibberellin (GA) contents (P < 0.05). The grain-filling rate decreased under shading conditions. Meanwhile, the grain volume, grain weight, and yield all decreased; the yields in 2013 and 2014 decreased by 61 and 60%, respectively. The grain IAA, ZR, and GA contents were increased by increasing light. The grain ABA content at 5-20 days after pollination did not significantly differ from that of CK (P < 0.05). After 20 days after pollination, the ABA content decreased, the grain-filling rate and the filling duration increased, and the yield increased. However, shading after anthesis increased the grain ABA content and reduced the IAA, ZR, and GA contents. Grain growth and development were inhibited, and the yield decreased. The grain ABA content decreased; the IAA, ZR, and GA contents increased; and the yield increased after increasing light. The results indicate that different light intensities regulated the levels of grains endogenous hormones, which influenced the grain-filling rate and duration, and consequently, regulated grain weight and yield.
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Affiliation(s)
- Jia Gao
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Jianguo Shi
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Shuting Dong
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Peng Liu
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Bin Zhao
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Jiwang Zhang
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
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22
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Ma D, Huang X, Hou J, Ma Y, Han Q, Hou G, Wang C, Guo T. Quantitative analysis of the grain amyloplast proteome reveals differences in metabolism between two wheat cultivars at two stages of grain development. BMC Genomics 2018; 19:768. [PMID: 30355308 PMCID: PMC6201562 DOI: 10.1186/s12864-018-5174-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/16/2018] [Indexed: 01/15/2023] Open
Abstract
Background Wheat (Triticum aestivum L.) is one of the world’s most important grain crops. The amyloplast, a specialized organelle, is the major site for starch synthesis and storage in wheat grain. Understanding the metabolism in amyloplast during grain development in wheat cultivars with different quality traits will provide useful information for potential yield and quality improvement. Results Two wheat cultivars, ZM366 and YM49–198 that differ in kernel hardness and starch characteristics, were used to examine the metabolic changes in amyloplasts at 10 and 15 days after anthesis (DAA) using label-free-based proteome analysis. We identified 523 differentially expressed proteins (DEPs) between 10 DAA and 15 DAA, and 229 DEPs between ZM366 and YM49–198. These DEPs mainly participate in eight biochemical processes: carbohydrate metabolism, nitrogen metabolism, stress/defense, transport, energetics-related, signal transduction, protein synthesis/assembly/degradation, and nucleic acid-related processes. Among these proteins, the DEPs showing higher expression levels at 10 DAA are mainly involved in carbohydrate metabolism, stress/defense, and nucleic acid related processes, whereas DEPs with higher expression levels at 15 DAA are mainly carbohydrate metabolism, energetics-related, and transport-related proteins. Among the DEPs between the two cultivars, ZM366 had more up-regulated proteins than YM49–198, and these are mainly involved in carbohydrate metabolism, nucleic acid-related processes, and transport. Conclusions The results of our study indicate that wheat grain amyloplast has the broad metabolic capability. The DEPs involved in carbohydrate metabolism, nucleic acids, stress/defense, and transport processes, with grain development and cultivar differences, are possibly responsible for different grain characteristics, especially with respect to yield and quality-related traits. Electronic supplementary material The online version of this article (10.1186/s12864-018-5174-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dongyun Ma
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China. .,The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Xin Huang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Junfeng Hou
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ying Ma
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiaoxia Han
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Gege Hou
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chenyang Wang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.,The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Tiancai Guo
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
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Zhen S, Deng X, Li M, Zhu D, Yan Y. 2D-DIGE comparative proteomic analysis of developing wheat grains under high-nitrogen fertilization revealed key differentially accumulated proteins that promote storage protein and starch biosyntheses. Anal Bioanal Chem 2018; 410:6219-35. [PMID: 30058028 DOI: 10.1007/s00216-018-1230-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/26/2018] [Accepted: 06/26/2018] [Indexed: 12/30/2022]
Abstract
Nitrogen (N) serves as a macronutrient that is essential to plant growth and development, and significantly influences storage protein and starch biosyntheses and, ultimately, grain yield and quality. In this study, we performed the first comparative proteomic analysis of developing wheat grains under high-N conditions using 2D-DIGE and tandem mass spectrometry. High-N fertilizer application caused significant increases in ear number, ear grain number, and grain yield. 2D-DIGE identified 142 differentially accumulated proteins (DAPs) during grain development in the elite Chinese bread wheat cultivar Zhongmai 175, of which 132 (93%) were identified by MALDI-TOF/TOF-MS, representing 92 unique proteins. These proteins are involved mainly in energy, N and protein metabolism, carbon metabolism, and starch biosynthesis. Subcellular localization prediction and fluorescence confocal microscopic analysis showed that the DAPs identified were localized mainly in the cytosol and chloroplast. Principal component analysis (PCA) revealed a greater proteomic difference among grain developmental periods than between the high-N and control groups. Protein-protein interaction analysis highlighted a complex network centered around enzymes involved in energy, N and protein metabolism, and starch biosynthesis. Six key DAP genes showed expression patterns consistent with their protein accumulation trends during grain development. A putative metabolic pathway was proposed, with synergistic regulatory networks of grain storage protein and starch biosyntheses in response to high-N application.
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24
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Geng J, Li L, Lv Q, Zhao Y, Liu Y, Zhang L, Li X. TaGW2-6A allelic variation contributes to grain size possibly by regulating the expression of cytokinins and starch-related genes in wheat. Planta 2017; 246:1153-1163. [PMID: 28825220 DOI: 10.1007/s00425-017-2759-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/11/2017] [Indexed: 05/21/2023]
Abstract
Functional allelic variants of TaGW2 - 6A produce large grains, possibly via changes in endosperm cells and dry matter by regulating the expression of cytokinins and starch-related genes via the ubiquitin-proteasome system. In wheat, TaGW2-6A coding region allelic variants are closely related to the grain width and weight, but how this region affects grain development has not been fully elucidated; thus, we explored its influence on grain development based mainly on histological and grain filling analyses. We found that the insertion type (NIL31) TaGW2-6A allelic variants exhibited increases in cell numbers and cell size, thereby resulting in a larger (wider) grain size with an accelerated grain milk filling rate, and increases in grain width and weight. We also found that cytokinin (CK) synthesis genes and key starch biosynthesis enzyme AGPase genes were significantly upregulated in the TaGW2-6A allelic variants, while CK degradation genes and starch biosynthesis-negative regulators were downregulated in the TaGW2-6A allelic variants, which was consistent with the changes in cells and grain filling. Thus, we speculate that TaGW2-6A allelic variants are linked with CK signaling, but they also influence the accumulation of starch by regulating the expression of related genes via the ubiquitin-proteasome system to control the grain size and grain weight.
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Affiliation(s)
- Juan Geng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Liqun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qian Lv
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yi Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Li Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China.
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Brennan M, Shepherd T, Mitchell S, Topp CFE, Hoad SP. Husk to caryopsis adhesion in barley is influenced by pre- and post-anthesis temperatures through changes in a cuticular cementing layer on the caryopsis. BMC Plant Biol 2017; 17:169. [PMID: 29058624 PMCID: PMC5651604 DOI: 10.1186/s12870-017-1113-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND At ripeness, the outer husk of "covered" barley grains firmly adheres to the underlying caryopsis. A cuticular cementing layer on the caryopsis is required for husk adhesion, however the quality of adhesion varies significantly among cultivars which produce the cementing layer, resulting in the economically important malting defect, grain skinning. The composition of the cementing layer, and grain organ development have been hypothesised to influence the quality of husk adhesion. Plants of Hordeum vulgare 'Concerto' were grown at different temperatures pre- and post-anthesis to effect changes in the development of the husk, caryopsis and cuticular cementing layer, to determine how these variables influence the quality of husk-to-caryopsis adhesion. RESULTS Warm conditions pre-anthesis decreased the quality of husk adhesion, and consequently increased the incidence of grain skinning. Cool post-anthesis conditions further decreased the quality of husk adhesion. The composition of the cementing layer, rather than its structure, differed with respect to husk adhesion quality. This cementing layer was produced at the late milk stage, occurring between nine and 29 days post-anthesis, conditional on the temperature-dependent growth rate. The compounds octadecanol, tritriacontane, campesterol and β-sitosterol were most abundant in caryopses with high-quality husk adhesion. The differences in adhesion quality were not due to incompatible husk and caryopsis dimensions affecting organ contact. CONCLUSIONS This study shows that husk-to-caryopsis adhesion is dependent on cementing layer composition, and implies that this composition is regulated by temperature before, and during grain development. Understanding this regulation will be key to improving husk-to-caryopsis adhesion.
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Affiliation(s)
- M. Brennan
- Scotland’s Rural College, King’s Buildings, West Mains Road, EH9 3JG Edinburgh, Scotland
| | - T. Shepherd
- James Hutton Institute, Invergowrie, DD2 5DA Dundee, Scotland
| | - S. Mitchell
- University of Edinburgh, King’s Buildings, Mayfield Road, EH9 3JH Edinburgh, Scotland
| | - C. F. E. Topp
- Scotland’s Rural College, King’s Buildings, West Mains Road, EH9 3JG Edinburgh, Scotland
| | - S. P. Hoad
- Scotland’s Rural College, King’s Buildings, West Mains Road, EH9 3JG Edinburgh, Scotland
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Abid M, Shao Y, Liu S, Wang F, Gao J, Jiang D, Tian Z, Dai T. Pre-drought priming sustains grain development under post-anthesis drought stress by regulating the growth hormones in winter wheat (Triticum aestivum L.). Planta 2017; 246:509-524. [PMID: 28526982 DOI: 10.1007/s00425-017-2698-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/13/2017] [Indexed: 05/03/2023]
Abstract
Drought stress during grain filling is the most yield-damaging to wheat. Pre-drought priming facilitated the wheat plants to sustain grain development against the post-anthesis drought stress by modulating the levels of growth hormones. Post-anthesis drought stress substantially reduces grain yield in wheat (Triticum aestivum L.) due to impaired grain development associated with imbalanced levels of growth hormones. To investigate whether pre-drought priming could sustain grain development in wheat by regulating favorable levels of growth hormones under post-anthesis drought conditions, the plants of a drought-sensitive (Yangmai-16) and drought-tolerant (Luhan-7) wheat cultivar were exposed to a moderate drought stress during tillering (Feekes 2 stage) for priming, and then, a subsequent severe drought stress was applied from 7 to 14 days after anthesis. The results showed that drought-stressed plants of both cultivars showed a decline in flag leaf water potential, chlorophyll contents, photosynthetic rate, grain size initiation, and grain filling as compared to well-watered plants; however, decline in these traits was less in pre-drought primed (PD) plants than in nonprimed (ND) plants. Under drought stress, the PD plants regulated higher concentrations of zeatin and zeatin riboside, indole-3-acetic acid, gibberellins, and lower abscisic acid content in grains, resulting in higher endosperm cell division and expansion, grain size initiation, grain-filling rate and duration, and finally higher grain dry weights as compared to ND plants. The PD plants of both cultivars showed higher potential to tolerate the post-anthesis drought stress, but more effect was displayed by drought-tolerant cultivar. From the achieved results, it was concluded that pre-drought priming facilitated the wheat plants to sustain higher grain development and yield against the most yield-damaging post-anthesis drought stress by modulating the levels of growth hormones.
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Affiliation(s)
- Muhammad Abid
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- Department of Soil and Water Conservation, Soon Valley, Khushab, Punjab, 41000, Pakistan
| | - Yuhang Shao
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Sixi Liu
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Feng Wang
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jingwen Gao
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Dong Jiang
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhongwei Tian
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Tingbo Dai
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
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Yu T, Li G, Dong S, Liu P, Zhang J, Zhao B. Proteomic analysis of maize grain development using iTRAQ reveals temporal programs of diverse metabolic processes. BMC Plant Biol 2016; 16:241. [PMID: 27809771 PMCID: PMC5095984 DOI: 10.1186/s12870-016-0878-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 08/18/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Grain development in maize is an essential process in the plant's life cycle and is vital for use of the plant as a crop for animals and humans. However, little is known regarding the protein regulatory networks that control grain development. Here, isobaric tag for relative and absolute quantification (iTRAQ) technology was used to analyze temporal changes in protein expression during maize grain development. RESULTS Maize grain proteins and changes in protein expression at eight developmental stages from 3 to 50 d after pollination (DAP) were performed using iTRAQ-based proteomics. Overall, 4751 proteins were identified; 2639 of these were quantified and 1235 showed at least 1.5-fold changes in expression levels at different developmental stages and were identified as differentially expressed proteins (DEPs). The DEPs were involved in different cellular and metabolic processes with a preferential distribution to protein synthesis/destination and metabolism categories. A K-means clustering analysis revealed coordinated protein expression associated with different functional categories/subcategories at different development stages. CONCLUSIONS Our results revealed developing maize grain display different proteomic characteristics at distinct stages, such as numerous DEPs for cell growth/division were highly expressed during early stages, whereas those for starch biosynthesis and defense/stress accumulated in middle and late stages, respectively. We also observed coordinated expression of multiple proteins of the antioxidant system, which are essential for the maintenance of reactive oxygen species (ROS) homeostasis during grain development. Particularly, some DEPs, such as zinc metallothionein class II, pyruvate orthophosphate dikinase (PPDK) and 14-3-3 proteins, undergo major changes in expression at specific developmental stages, suggesting their roles in maize grain development. These results provide a valuable resource for analyzing protein function on a global scale and also provide new insights into the potential protein regulatory networks that control grain yield and quality.
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Affiliation(s)
- Tao Yu
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, 271018 Shandong People’s Republic of China
| | - Geng Li
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, 271018 Shandong People’s Republic of China
| | - Shuting Dong
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, 271018 Shandong People’s Republic of China
| | - Peng Liu
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, 271018 Shandong People’s Republic of China
| | - Jiwang Zhang
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, 271018 Shandong People’s Republic of China
| | - Bin Zhao
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Taian, 271018 Shandong People’s Republic of China
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28
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Kim NH, Kwak J, Baik JY, Yoon MR, Lee JS, Yoon SW, Kim IH. Changes in lipid substances in rice during grain development. Phytochemistry 2015; 116:170-179. [PMID: 26021733 DOI: 10.1016/j.phytochem.2015.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 04/27/2015] [Accepted: 05/13/2015] [Indexed: 05/13/2023]
Abstract
Lipid substances, such as fatty acids, γ-oryzanol, policosanols, and tocol (tocopherol+tocotrienol), were investigated in two rice cultivars, Ilpum and Dasan, during rice development. In both cultivars, the lipid extract level decreased steadily after it reached its maximum level. Additionally, there were differences in the fatty acid composition, depending on the rice developmental stage, between the two cultivars. The γ-oryzanol level increased during rice development, and there were differences in the composition of γ-oryzanol between the two cultivars. The levels of policosanols drastically decreased during the early stage of rice development in the two cultivars. The total tocol level showed a downward trend during rice development. The predominant tocol isomer in Ilpum was α-tocopherol during rice development. In Dasan, the predominant tocol isomer was α-tocopherol at the early stage, but γ-tocotrienol at the later stage. This study provided information on the levels and composition of lipid substances, such as fatty acids, γ-oryzanol, policosanols, and tocol during rice development.
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Affiliation(s)
- Nam Ho Kim
- Department of Food and Nutrition, Korea University, Seoul, Republic of Korea; BK21PLUS Program in Embodiment: Health-Society Interaction, Department of Public Health Sciences, Graduate School, Korea University, Seoul 136 703, Republic of Korea
| | - Jieun Kwak
- National Institute of Crop Science, Rural Development Administration, Suwon, Gyunggi-do, Republic of Korea
| | - Ji Yeon Baik
- Department of Food and Nutrition, Korea University, Seoul, Republic of Korea; BK21PLUS Program in Embodiment: Health-Society Interaction, Department of Public Health Sciences, Graduate School, Korea University, Seoul 136 703, Republic of Korea
| | - Mi-Ra Yoon
- National Institute of Crop Science, Rural Development Administration, Suwon, Gyunggi-do, Republic of Korea
| | - Jeom-Sig Lee
- National Institute of Crop Science, Rural Development Administration, Suwon, Gyunggi-do, Republic of Korea
| | - Sung Won Yoon
- Department of Food and Nutrition, Korea University, Seoul, Republic of Korea
| | - In-Hwan Kim
- Department of Food and Nutrition, Korea University, Seoul, Republic of Korea; BK21PLUS Program in Embodiment: Health-Society Interaction, Department of Public Health Sciences, Graduate School, Korea University, Seoul 136 703, Republic of Korea.
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