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Jain R, Dhaka N, Krishnan K, Yadav G, Priyam P, Sharma MK, Sharma RA. Temporal Gene Expression Profiles From Pollination to Seed Maturity in Sorghum Provide Core Candidates for Engineering Seed Traits. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39248611 DOI: 10.1111/pce.15134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/12/2024] [Accepted: 08/19/2024] [Indexed: 09/10/2024]
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development and the associated agronomic traits remain unexplored. In this study, we performed a comprehensive transcriptomic analysis of pistils collected 1-2 days before pollination, and developing seeds collected -2, 10, 20 and 30 days after pollination of S. bicolor variety M35-1. Out of 31 337 genes expressed in these stages, 12 804 were differentially expressed in the consecutive stages of seed development. These exhibited 10 dominant expression patterns correlated with the distinct pathways and gene functions. Functional analysis, based on the pathway mapping, transcription factor enrichment and orthology, delineated the key patterns associated with pollination, fertilization, early seed development, grain filling and seed maturation. Furthermore, colocalization with previously reported quantitative trait loci (QTLs) for grain weight/size revealed 48 differentially expressed genes mapping to these QTL regions. Comprehensive literature mining integrated with QTL mapping and expression data shortlisted 25, 17 and 8 core candidates for engineering grain size, starch and protein content, respectively.
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Affiliation(s)
- Rubi Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Kushagra Krishnan
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Garima Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Prachi Priyam
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | | | - Rita A Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani, Rajasthan, India
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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2
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Zhang Y, Wang Y, Liu R, Fei Z, Fan X, Jiang J, Sun L, Meng X, Liu C. Antibody array-based proteome approach reveals proteins involved in grape seed development. PLANT PHYSIOLOGY 2024; 195:462-478. [PMID: 38395446 PMCID: PMC11060674 DOI: 10.1093/plphys/kiad682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 10/16/2023] [Indexed: 02/25/2024]
Abstract
Grape (Vitis vinifera) is one of the most widely cultivated fruits globally, primarily used for processing and fresh consumption. Seedless grapes are favored by consumers for their convenience, making the study of seedlessness a subject of great interest to scientists. To identify regulators involved in this process in grape, a monoclonal antibody (mAb)-array-based proteomics approach, which contains 21,120 mAbs, was employed for screening proteins/antigens differentially accumulated in grape during development. Differences in antigen signals were detected between seeded and seedless grapes revealing the differential accumulation of 2,587 proteins. After immunoblotting validation, 71 antigens were further immunoprecipitated and identified by mass spectrometry (MS). An in planta protein-protein interaction (PPI) network of those differentially accumulated proteins was established using mAb antibody by immunoprecipitation (IP)-MS, which reveals the alteration of pathways related to carbon metabolism and glycolysis. To validate our result, a seedless-related protein, DUF642 domain-containing protein (VvDUF642), which is functionally uncharacterized in grapes, was ectopically overexpressed in tomato (Solanum lycopersicum "MicroTom") and led to a reduction in seed production. PPI network indicated that VvDUF642 interacts with pectin acetylesterase (VvPAE) in grapes, which was validated by BiFC and Co-IP. As anticipated, overexpression of VvPAE substantially reduced seed production in tomato. Moreover, S. lycopersicum colourless non-ripening expression was altered in VvDUF642- and VvPAE-overexpressing plants. Taken together, we provided a high-throughput method for the identification of proteins involved in the seed formation process. Among those, VvDUF642 and VvPAE are potential targets for breeding seedless grapes and other important fruits in the future.
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Affiliation(s)
- Ying Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
- Chuxiong Yunguo Agriculture Technology Research Institute (Yunnan), Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Henan 450008, China
| | - Yiming Wang
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruitao Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853-1801, USA
| | - Xiucai Fan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
| | - Jianfu Jiang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
| | - Lei Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
| | - Xun Meng
- School of Life Science, Northwest University, Xi’an, Shanxi 710069, China
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Chonghuai Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
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Park M, Shin SY, Moon H, Choi W, Shin C. Analysis of the global transcriptome and miRNAome associated with seed dormancy during seed maturation in rice (Oryza sativa L. cv. Nipponbare). BMC PLANT BIOLOGY 2024; 24:215. [PMID: 38532331 DOI: 10.1186/s12870-024-04928-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Seed dormancy is a biological mechanism that prevents germination until favorable conditions for the subsequent generation of plants are encountered. Therefore, this mechanism must be effectively established during seed maturation. Studies investigating the transcriptome and miRNAome of rice embryos and endosperms at various maturation stages to evaluate seed dormancy are limited. This study aimed to compare the transcriptome and miRNAome of rice seeds during seed maturation. RESULTS Oryza sativa L. cv. Nipponbare seeds were sampled for embryos and endosperms at three maturation stages: 30, 45, and 60 days after heading (DAH). The pre-harvest sprouting (PHS) assay was conducted to assess the level of dormancy in the seeds at each maturation stage. At 60 DAH, the PHS rate was significantly increased compared to those at 30 and 45 DAH, indicating that the dormancy is broken during the later maturation stage (45 DAH to 60 DAH). However, the largest number of differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) were identified between 30 and 60 DAH in the embryo and endosperm, implying that the gradual changes in genes and miRNAs from 30 to 60 DAH may play a significant role in breaking seed dormancy. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses confirmed that DEGs related to plant hormones were most abundant in the embryo during 45 DAH to 60 DAH and 30 DAH to 60 DAH transitions. Alternatively, most of the DEGs in the endosperm were related to energy and abiotic stress. MapMan analysis and quantitative real-time polymerase chain reaction identified four newly profiled auxin-related genes (OsSAUR6/12/23/25) and one ethylene-related gene (OsERF087), which may be involved in seed dormancy during maturation. Additionally, miRNA target prediction (psRNATarget) and degradome dataset (TarDB) indicated a potential association between osa-miR531b and ethylene biosynthesis gene (OsACO4), along with osa-miR390-5p and the abscisic acid (ABA) exporter-related gene (OsMATE19) as factors involved in seed dormancy. CONCLUSIONS Analysis of the transcriptome and miRNAome of rice embryos and endosperms during seed maturation provided new insights into seed dormancy, particularly its relationship with plant hormones such as ABA, auxin, and ethylene.
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Affiliation(s)
- Minsu Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang-Yoon Shin
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongman Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Woochang Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea.
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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] [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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Yoon J, Min CW, Kim J, Baek G, Kim D, Jang JW, Gupta R, Kim ST, Cho LH. Quantitative Proteomic Analysis Deciphers the Molecular Mechanism for Endosperm Nuclear Division in Early Rice Seed Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3715. [PMID: 37960070 PMCID: PMC10650807 DOI: 10.3390/plants12213715] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Understanding the molecular mechanisms underlying early seed development is important in improving the grain yield and quality of crop plants. We performed a comparative label-free quantitative proteomic analysis of developing rice seeds for the WT and osctps1-2 mutant, encoding a cytidine triphosphate synthase previously reported as the endospermless 2 (enl2) mutant in rice, harvested at 0 and 1 d after pollination (DAP) to understand the molecular mechanism of early seed development. In total, 5231 proteins were identified, of which 902 changed in abundance between 0 and 1 DAP seeds. Proteins that preferentially accumulated at 1 DAP were involved in DNA replication and pyrimidine biosynthetic pathways. Notably, an increased abundance of OsCTPS1 was observed at 1 DAP; however, no such changes were observed at the transcriptional level. We further observed that the inhibition of phosphorylation increased the stability of this protein. Furthermore, in osctps1-2, minichromosome maintenance (MCM) proteins were significantly reduced compared with those in the WT at 1 DAP, and mutations in OsMCM5 caused defects in seed development. These results highlight the molecular mechanisms underlying early seed development in rice at the post-transcriptional level.
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Affiliation(s)
- Jinmi Yoon
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea;
- Department of Biological Sciences and Bioengineering, Industry-Academia Interactive R&E Center for Bioprocess Innovation, Inha University, Incheon 22212, Republic of Korea
| | - Cheol Woo Min
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
| | - Jiyoung Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Gibeom Baek
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Dohyeon Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Jeong Woo Jang
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea;
| | - Sun Tae Kim
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Lae-Hyeon Cho
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
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Hake AA, Ballichatla S, Barbadikar KM, Magar N, Dutta S, Gokulan CG, Awalellu K, Patel HK, Sonti RV, Phule AS, Varma EP, Ayeella PG, Vamshi P, Sundaram RM, Maganti SM. Combined strategy employing MutMap and RNA-seq reveals genomic regions and genes associated with complete panicle exsertion in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:69. [PMID: 37622088 PMCID: PMC10444938 DOI: 10.1007/s11032-023-01412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023]
Abstract
Complete panicle exsertion (CPE) in rice is an important determinant of yield and a desirable trait in breeding. However, the genetic basis of CPE in rice still remains to be completely characterized. An ethyl methane sulfonate (EMS) mutant line of an elite cultivar Samba Mahsuri (BPT 5204), displaying stable and consistent CPE, was identified and named as CPE-110. MutMap and RNA-seq were deployed for unraveling the genomic regions, genes, and markers associated with CPE. Two major genomic intervals, on chromosome 8 (25668481-25750456) and on chromosome 11 (20147154-20190400), were identified to be linked to CPE through MutMap. A non-synonymous SNP (G/A; Chr8:25683828) in the gene LOC_Os08g40570 encoding pyridoxamine 5'-phosphate oxidase with the SNP index 1 was converted to Kompetitive allele-specific PCR (KASP) marker. This SNP (KASP 8-1) exhibited significant association with CPE and further validated through assay in the F2 mapping population, released varieties and CPE exhibiting BPT 5204 mutant lines. RNA-seq of the flag leaves at the booting stage, 1100 genes were upregulated and 1305 downregulated differentially in CPE-110 and BPT 5204. Metabolic pathway analysis indicated an enrichment of genes involved in photosynthesis, glyoxylate, dicarboxylate, porphyrin, pyruvate, chlorophyll, carotenoid, and carbon metabolism. Further molecular and functional studies of the candidate genes could reveal the mechanistic aspects of CPE. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01412-1.
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Affiliation(s)
- Anil A. Hake
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - Suneel Ballichatla
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | | | - Nakul Magar
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - Shubhankar Dutta
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007 India
- Research and Education in Cancer, Advanced Centre for Treatment, Navi Mumbai, Maharashtra 410210 India
| | - CG Gokulan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007 India
| | - Komal Awalellu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007 India
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Ramesh V. Sonti
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007 India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
| | - Amol S. Phule
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | | | | | - Poloju Vamshi
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - R. M. Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - Sheshu Madhav Maganti
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
- ICAR-Central Tobacco Research Institute, Rajahmundry, Andhra Pradesh 533105 India
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7
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Zhou H, Deng XW, He H. Gene expression variations and allele-specific expression of two rice and their hybrid in caryopses at single-nucleus resolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1171474. [PMID: 37287712 PMCID: PMC10242081 DOI: 10.3389/fpls.2023.1171474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/26/2023] [Indexed: 06/09/2023]
Abstract
Seeds are an indispensable part of the flowering plant life cycle and a critical determinant of agricultural production. Distinct differences in the anatomy and morphology of seeds separate monocots and dicots. Although some progress has been made with respect to understanding seed development in Arabidopsis, the transcriptomic features of monocotyledon seeds at the cellular level are much less understood. Since most important cereal crops, such as rice, maize, and wheat, are monocots, it is essential to study transcriptional differentiation and heterogeneity during seed development at a finer scale. Here, we present single-nucleus RNA sequencing (snRNA-seq) results of over three thousand nuclei from caryopses of the rice cultivars Nipponbare and 9311 and their intersubspecies F1 hybrid. A transcriptomics atlas that covers most of the cell types present during the early developmental stage of rice caryopses was successfully constructed. Additionally, novel specific marker genes were identified for each nuclear cluster in the rice caryopsis. Moreover, with a focus on rice endosperm, the differentiation trajectory of endosperm subclusters was reconstructed to reveal the developmental process. Allele-specific expression (ASE) profiling in endosperm revealed 345 genes with ASE (ASEGs). Further pairwise comparisons of the differentially expressed genes (DEGs) in each endosperm cluster among the three rice samples demonstrated transcriptional divergence. Our research reveals differentiation in rice caryopsis from the single-nucleus perspective and provides valuable resources to facilitate clarification of the molecular mechanism underlying caryopsis development in rice and other monocots.
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Affiliation(s)
- Han Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
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8
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Hertig C, Rutten T, Melzer M, Schippers JHM, Thiel J. Dissection of Developmental Programs and Regulatory Modules Directing Endosperm Transfer Cell and Aleurone Identity in the Syncytial Endosperm of Barley. PLANTS (BASEL, SWITZERLAND) 2023; 12:1594. [PMID: 37111818 PMCID: PMC10142620 DOI: 10.3390/plants12081594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/10/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Endosperm development in barley starts with the formation of a multinucleate syncytium, followed by cellularization in the ventral part of the syncytium generating endosperm transfer cells (ETCs) as first differentiating subdomain, whereas aleurone (AL) cells will originate from the periphery of the enclosing syncytium. Positional signaling in the syncytial stage determines cell identity in the cereal endosperm. Here, we performed a morphological analysis and employed laser capture microdissection (LCM)-based RNA-seq of the ETC region and the peripheral syncytium at the onset of cellularization to dissect developmental and regulatory programs directing cell specification in the early endosperm. Transcriptome data revealed domain-specific characteristics and identified two-component signaling (TCS) and hormone activities (auxin, ABA, ethylene) with associated transcription factors (TFs) as the main regulatory links for ETC specification. On the contrary, differential hormone signaling (canonical auxin, gibberellins, cytokinin) and interacting TFs control the duration of the syncytial phase and timing of cellularization of AL initials. Domain-specific expression of candidate genes was validated by in situ hybridization and putative protein-protein interactions were confirmed by split-YFP assays. This is the first transcriptome analysis dissecting syncytial subdomains of cereal seeds and provides an essential framework for initial endosperm differentiation in barley, which is likely also valuable for comparative studies with other cereal crops.
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Affiliation(s)
- Christian Hertig
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Twan Rutten
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Michael Melzer
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Jos H. M. Schippers
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Johannes Thiel
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
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9
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Ren ZW, Kopittke PM, Zhao FJ, Wang P. Nutrient accumulation and transcriptome patterns during grain development in rice. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:909-930. [PMID: 36272142 PMCID: PMC9899419 DOI: 10.1093/jxb/erac426] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/21/2022] [Indexed: 06/13/2023]
Abstract
Rice is an important source of calories and mineral nutrients for more than half of the world's population. The accumulation of essential and toxic mineral elements in rice grain affects its nutritional quality and safety. However, the patterns and processes by which different elements progressively accumulate during grain filling remain largely unknown. In the present study, we investigated temporal changes in dry matter, elemental concentrations, and the transcriptome in the grain of field-grown rice. We also investigated the effects of seed setting rate and the position of the grain within the rice panicle on element accumulation. Three different patterns of accumulation were observed: (i) elements including K, Mn, B, and Ca showed an early accumulation pattern; (ii) dry matter and elements including N, P, S, Mg, Cu, Zn, Mo, As, and Cd showed a mid accumulation pattern; and (iii) elements such as Fe showed a gradual increase pattern. These different accumulation patterns can be explained by the differences in the biogeochemical behavior of the various elements in the soil, as well as differences in plant nutrient redistribution, gene expression, and the sink-source relationship. These results improve our knowledge of the dynamics of elemental accumulation in rice grain and are helpful for identification of functional genes mediating the translocation of elements to grain.
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Affiliation(s)
- Zi-Wen Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Peter M Kopittke
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland, 4072, Australia
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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10
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Viana VE, Maltzahn LE, Costa de Oliveira A, Pegoraro C. Genetic Approaches for Iron and Zinc Biofortification and Arsenic Decrease in Oryza sativa L. Grains. Biol Trace Elem Res 2022; 200:4505-4523. [PMID: 34773578 DOI: 10.1007/s12011-021-03018-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/04/2021] [Indexed: 12/29/2022]
Abstract
Rice is the staple diet to half of the world's population, being a major source of carbohydrates, vitamins, and some essential elements. However, rice naturally contains low amounts of essential minerals such as iron (Fe) and zinc (Zn), which are drastically decreased after milling. Thus, populations that consume mostly rice may have micronutrient deficiency, which is associated with different diseases. On the other hand, rice irrigated by flooding has a high ability to accumulate arsenic (As) in the grain. Therefore, when rice is grown in areas with contaminated soil or irrigation water, it represents a risk factor for consumers, since As is associated with cancer and other diseases. Different strategies have been used to mitigate micronutrient deficiencies such as Fe and Zn and to prevent As from entering the food chain. Each strategy has its positive and its negative sides. The development of genetically biofortified rice plants with Fe and Zn and with low As accumulation is one of the most promising strategies, since it does not represent an additional cost for farmers, and gives benefits to consumers as well. Considering the importance of genetic improvement (traditional or molecular) to decrease the impact of micronutrient deficiencies such as Fe and Zn and contamination with As, this review aimed to summarize the major efforts, advances, and challenges for genetic biofortification of Fe and Zn and decrease in As content in rice grains.
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Affiliation(s)
- Vívian Ebeling Viana
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Latóia Eduarda Maltzahn
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Antonio Costa de Oliveira
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Camila Pegoraro
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil.
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The molecular basis of cereal grain proteostasis. Essays Biochem 2022; 66:243-253. [PMID: 35818971 PMCID: PMC9400069 DOI: 10.1042/ebc20210041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/07/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022]
Abstract
Storage proteins deposited in the endosperm of cereal grains are both a nitrogen reserve for seed germination and seedling growth and a primary protein source for human nutrition. Detailed surveys of the patterns of storage protein accumulation in cereal grains during grain development have been undertaken, but an in-depth understanding of the molecular mechanisms that regulate these patterns is still lacking. Accumulation of storage proteins in cereal grains involves a series of subcellular compartments, a set of energy-dependent events that compete with other cellular processes, and a balance of protein synthesis and protein degradation rates at different times during the developmental process. In this review, we focus on the importance of rates in cereal grain storage protein accumulation during grain development and outline the potential implications and applications of this information to accelerate modern agriculture breeding programmes and optimize energy use efficiency in proteostasis.
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12
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Ishimaru T, Parween S, Saito Y, Masumura T, Kondo M, Sreenivasulu N. Laser microdissection transcriptome data derived gene regulatory networks of developing rice endosperm revealed tissue- and stage-specific regulators modulating starch metabolism. PLANT MOLECULAR BIOLOGY 2022; 108:443-467. [PMID: 35098404 PMCID: PMC8894313 DOI: 10.1007/s11103-021-01225-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Laser microdissection applied on the developing rice endosperm revealed tissue- and stage-specific regulators modulating programmed cell death and desiccation tolerance mechanisms in the central starchy endosperm following starch metabolism. Rice (Oryza sativa L.) filial seed tissues are heterozygous in its function, which accumulate distinct storage compounds spatially in starchy endosperm and aleurone. In this study, we identified the 18 tissue- and stage-specific gene co-regulons in the developing endosperm by isolating four fine tissues dorsal aleurone layer (AL), central starchy endosperm (CSE), dorsal starchy endosperm (DSE), and lateral starchy endosperm (LSE) at two developmental stages (7 days after flowering, DAF and 12DAF) using laser microdissection (LM) coupled with gene expression analysis of a 44 K microarray. The derived co-expression regulatory networks depict that distinct set of starch biosynthesis genes expressed preferentially at first in CSE at 7 DAF and extend its spatial expression to LSE and DSE by 12 DAF. Interestingly, along with the peak of starch metabolism we noticed accumulation of transcripts related to phospholipid and glycolipid metabolism in CSE during 12 DAF. The spatial distribution of starch accumulation in distinct zones of starchy endosperm contains specific transcriptional factors and hormonal-regulated genes. Genes related to programmed cell death (PCD) were specifically expressed in CSE at 12DAF, when starch accumulation was already completed in that tissue. The aleurone layer present in the outermost endosperm accumulates transcripts of lipid, tricarboxylic acid metabolism, several transporters, while starch metabolism and PCD is not pronounced. These regulatory cascades are likely to play a critical role in determining the positional fate of cells and offer novel insights into the molecular physiological mechanisms of endosperm development from early to middle storage phase.
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Affiliation(s)
- Tsutomu Ishimaru
- NARO Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518 Japan
- Hokuriku Research Station, Central Region Agricultural Research Center, National Agriculture and Food Research Organization (CARC/NARO), 1-2-1 Inada, Joetsu, Niigata 941-0193 Japan
| | - Sabiha Parween
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, The Philippines
| | - Yuhi Saito
- Graduate School of Life and Environmental Science, Kyoto Prefectural University, Shimogamo, Sakyo-ku, Kyoto, 606-8522 Japan
| | - Takehiro Masumura
- Graduate School of Life and Environmental Science, Kyoto Prefectural University, Shimogamo, Sakyo-ku, Kyoto, 606-8522 Japan
| | - Motohiko Kondo
- NARO Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518 Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo, Chikusa, Nagoya, 464-8601 Japan
| | - Nese Sreenivasulu
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, The Philippines
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13
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Kawakami Y, Bhullar NK. Delineating the future of iron biofortification studies in rice: challenges and future perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2099-2113. [PMID: 32974681 DOI: 10.1093/jxb/eraa446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
Iron (Fe) deficiency in humans is a widespread problem worldwide. Fe biofortification of rice (Oryza sativa) is a promising approach to address human Fe deficiency. Since its conceptualization, various biofortification strategies have been developed, some of which have resulted in significant increases in grain Fe concentration. However, there are still many aspects that have not yet been addressed in the studies to date. In this review, we first overview the important rice Fe biofortification strategies reported to date and the complications associated with them. Next, we highlight the key outstanding questions and hypotheses related to rice Fe biofortification. Finally, we make suggestions for the direction of future rice biofortification studies.
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Affiliation(s)
- Yuta Kawakami
- Plant Biotechnology, Department of Biology, ETH Zurich, Universitätstrasse 2, Zurich, Switzerland
| | - Navreet K Bhullar
- Plant Biotechnology, Department of Biology, ETH Zurich, Universitätstrasse 2, Zurich, Switzerland
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Ram H, Singh A, Katoch M, Kaur R, Sardar S, Palia S, Satyam R, Sonah H, Deshmukh R, Pandey AK, Gupta I, Sharma TR. Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2212-2230. [PMID: 33197257 DOI: 10.1093/jxb/eraa536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/12/2020] [Indexed: 06/11/2023]
Abstract
Rice, a staple food worldwide, contains varying amounts of nutrients in different grain tissues. The underlying molecular mechanism of such distinct nutrient partitioning remains poorly investigated. Here, an optimized rapid laser capture microdissection (LCM) approach was used to individually collect pericarp, aleurone, embryo and endosperm from grains 10 days after fertilization. Subsequent RNA-Seq analysis in these tissues identified 7760 differentially expressed genes. Analysis of promoter sequences of tissue-specific genes identified many known and novel cis-elements important for grain filling and seed development. Using the identified differentially expressed genes, comprehensive spatial gene expression pathways were built for accumulation of starch, proteins, lipids, and iron. The extensive transcriptomic analysis provided novel insights about nutrient partitioning mechanisms; for example, it revealed a gradient in seed storage protein accumulation across the four tissue types analysed. The analysis also revealed that the partitioning of various minerals, such as iron, is most likely regulated through transcriptional control of their transporters. We present the extensive analysis from this study as an interactive online tool that provides a much-needed resource for future functional genomics studies aimed to improve grain quality and seed development.
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Affiliation(s)
- Hasthi Ram
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Anmol Singh
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Megha Katoch
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Ravneet Kaur
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Shaswati Sardar
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Shubham Palia
- Department of Biochemical Engineering and Biotechnology, Block I, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Rohit Satyam
- Department of Biochemical Engineering and Biotechnology, Block I, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Ajay Kumar Pandey
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Block I, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
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