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Wang B, Bu Y, Zhang G, Liu N, Feng Z, Gong Y. Comparative transcriptome analysis of vegetable soybean grain discloses genes essential for grain quality. BMC PLANT BIOLOGY 2024; 24:491. [PMID: 38825702 PMCID: PMC11145879 DOI: 10.1186/s12870-024-05214-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
BACKGROUND Vegetable soybean is an important vegetable crop in world. Seed size and soluble sugar content are considered crucial indicators of quality in vegetable soybean, and there is a lack of clarity on the molecular basis of grain quality in vegetable soybean. RESULTS In this context, we performed a comprehensive comparative transcriptome analysis of seeds between a high-sucrose content and large-grain variety (Zhenong 6, ZN6) and a low-sucrose content and small-grain variety (Williams 82, W82) at three developmental stages, i.e. stage R5 (Beginning Seed), stage R6 (Full Seed), and stage R7 (Beginning Maturity). The transcriptome analysis showed that 17,107 and 13,571 differentially expressed genes (DEGs) were identified in ZN6 at R6 (vs. R5) and R7 (vs. R6), respectively, whereas 16,203 and 16,032 were detected in W82. Gene expression pattern and DEGs functional enrichment proposed genotype-specific biological processes during seed development. The genes participating in soluble sugar biosynthesis such as FKGP were overexpressed in ZN6, whereas those responsible for lipid and protein metabolism such as ALDH3 were more enhanced in W82, exhibiting different dry material accumulation between two genotypes. Furthermore, hormone-associated transcriptional factors involved in seed size regulation such as BEH4 were overrepresented in ZN6, exhibiting different seed size regulation processes between two genotypes. CONCLUSIONS Herein, we not only discovered the differential expression of genes encoding metabolic enzymes involved in seed composition, but also identified a type of hormone-associated transcriptional factors overexpressed in ZN6, which may regulate seed size and soluble content. This study provides new insights into the underlying causes of differences in the soybean metabolites and appearance, and suggests that genetic data can be used to improve its appearance and textural quality.
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Affiliation(s)
- Bin Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
| | - Yuanpeng Bu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Guwen Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Zhijuan Feng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Yaming Gong
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
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2
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Jiang H, Xie L, Gu Z, Mei H, Wang H, Zhang J, Wang M, Xu Y, Zhou C, Han L. MtPIN4 plays critical roles in amino acid biosynthesis and metabolism of seed in Medicago truncatula. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38701004 DOI: 10.1111/tpj.16787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024]
Abstract
The regulation of seed development is critical for determining crop yield. Auxins are vital phytohormones that play roles in various aspects of plant growth and development. However, its role in amino acid biosynthesis and metabolism in seeds is not fully understood. In this study, we identified a mutant with small seeds through forward genetic screening in Medicago truncatula. The mutated gene encodes MtPIN4, an ortholog of PIN1. Using molecular approaches and integrative omics analyses, we discovered that auxin and amino acid content significantly decreased in mtpin4 seeds, highlighting the role of MtPIN4-mediated auxin distribution in amino acid biosynthesis and metabolism. Furthermore, genetic analysis revealed that the three orthologs of PIN1 have specific and overlapping functions in various developmental processes in M. truncatula. Our findings emphasize the significance of MtPIN4 in seed development and offer insights into the molecular mechanisms governing the regulation of seed size in crops. This knowledge could be applied to enhance crop quality by targeted manipulation of seed protein regulatory pathways.
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Affiliation(s)
- Hongjiao Jiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Lijun Xie
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Zhiqun Gu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Hongyao Mei
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Haohao Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Jing Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Minmin Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Yiteng Xu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
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Basu U, Parida SK. The developmental dynamics in cool season legumes with focus on chickpea. PLANT MOLECULAR BIOLOGY 2023; 111:473-491. [PMID: 37016106 DOI: 10.1007/s11103-023-01340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Chickpea is one of the most widely consumed grain legume world-wide. Advances in next-generation sequencing and genomics tools have led to genetic dissection and identification of potential candidate genes regulating agronomic traits in chickpea. However, the developmental particularities and its potential in reforming the yield and nutritional value remain largely unexplored. Studies in crops such as rice, maize, tomato and pea have highlighted the contribution of key regulator of developmental events in yield related traits. A comprehensive knowledge on the development aspects of a crop can pave way for new vistas to explore. Pea and Medicago are the close relatives of genus Cicer and the basic developmental events in these legumes are similar. However, there are some distinct developmental features in chickpea which hold potential for future crop improvement endeavours. The global chickpea germplasm encompasses wide range of diversities in terms of morphology at both vegetative and reproductive stages. There is an immediate need for understanding the genetic and molecular basis of this diversity and utilizing them for the yield contributing trait improvement. The review discusses some of the key developmental events which have potential in yield enhancement and the lessons which can be learnt from model legumes in this regard.
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Affiliation(s)
- Udita Basu
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box: 10531, New Delhi, 110067, India
| | - Swarup K Parida
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box: 10531, New Delhi, 110067, India.
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Zou X, Sun H. DOF transcription factors: Specific regulators of plant biological processes. FRONTIERS IN PLANT SCIENCE 2023; 14:1044918. [PMID: 36743498 PMCID: PMC9897228 DOI: 10.3389/fpls.2023.1044918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/03/2023] [Indexed: 06/12/2023]
Abstract
Plant biological processes, such as growth and metabolism, hormone signal transduction, and stress responses, are affected by gene transcriptional regulation. As gene expression regulators, transcription factors activate or inhibit target gene transcription by directly binding to downstream promoter elements. DOF (DNA binding with One Finger) is a classic transcription factor family exclusive to plants that is characterized by its single zinc finger structure. With breakthroughs in taxonomic studies of different species in recent years, many DOF members have been reported to play vital roles throughout the plant life cycle. They are not only involved in regulating hormone signals and various biotic or abiotic stress responses but are also reported to regulate many plant biological processes, such as dormancy, tissue differentiation, carbon and nitrogen assimilation, and carbohydrate metabolism. Nevertheless, some outstanding issues remain. This article mainly reviews the origin and evolution, protein structure, and functions of DOF members reported in studies published in many fields to clarify the direction for future research on DOF transcription factors.
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Affiliation(s)
- Xiaoman Zou
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hongmei Sun
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang, China
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5
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Experimental Evidence for Seed Metabolic Allometry in Barrel Medic (Medicago truncatula Gaertn.). Int J Mol Sci 2022; 23:ijms23158484. [PMID: 35955618 PMCID: PMC9369157 DOI: 10.3390/ijms23158484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 12/10/2022] Open
Abstract
Seed size is often considered to be an important trait for seed quality, i.e., vigour and germination performance. It is believed that seed size reflects the quantity of reserve material and thus the C and N sources available for post-germinative processes. However, mechanisms linking seed size and quality are poorly documented. In particular, specific metabolic changes when seed size varies are not well-known. To gain insight into this aspect, we examined seed size and composition across different accessions of barrel medic (Medicago truncatula Gaertn.) from the genetic core collection. We conducted multi-elemental analyses and isotope measurements, as well as exact mass GC–MS metabolomics. There was a systematic increase in N content (+0.17% N mg−1) and a decrease in H content (–0.14% H mg−1) with seed size, reflecting lower lipid and higher S-poor protein quantity. There was also a decrease in 2H natural abundance (δ2H), due to the lower prevalence of 2H-enriched lipid hydrogen atoms that underwent isotopic exchange with water during seed development. Metabolomics showed that seed size correlates with free amino acid and hexoses content, and anticorrelates with amino acid degradation products, disaccharides, malic acid and free fatty acids. All accessions followed the same trend, with insignificant differences in metabolic properties between them. Our results show that there is no general, proportional increase in metabolite pools with seed size. Seed size appears to be determined by metabolic balance (between sugar and amino acid degradation vs. utilisation for storage), which is in turn likely determined by phloem source metabolite delivery during seed development.
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6
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Wang Y, Wang P, Wang W, Kong L, Tian S, Qin G. Genome-wide binding analysis of the tomato transcription factor SlDof1 reveals its regulatory impacts on fruit ripening. MOLECULAR HORTICULTURE 2021; 1:9. [PMID: 37789424 PMCID: PMC10514982 DOI: 10.1186/s43897-021-00011-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/15/2021] [Indexed: 10/05/2023]
Abstract
The DNA binding with one finger (Dof) proteins are plant-specific transcription factors involved in a variety of biological processes. However, little is known about their functions in fruit ripening, a flowering-plant-specific process that is required for seed maturation and dispersal. Here, we found that the tomato Dof transcription factor SlDof1, is necessary for normal fruit ripening. Knockdown of SlDof1 expression by RNA interference delayed ripening-related processes, including lycopene synthesis and ethylene production. Transcriptome profiling indicated that SlDof1 influences the expression of hundreds of genes, and a chromatin immunoprecipitation sequencing revealed a large number of SlDof1 binding sites. A total of 312 genes were identified as direct targets of SlDof1, among which 162 were negatively regulated by SlDof1 and 150 were positively regulated. The SlDof1 target genes were involved in a variety of metabolic pathways, and follow-up analyses verified that SlDof1 directly regulates some well-known ripening-related genes including ACS2 and PG2A as well as transcriptional repressor genes such as SlIAA27. Our findings provide insights into the transcriptional regulatory networks underlying fruit ripening and highlight a gene potentially useful for genetic engineering to control ripening.
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Affiliation(s)
- Yuying Wang
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Peiwen Wang
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weihao Wang
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lingxi Kong
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Malovichko YV, Shikov AE, Nizhnikov AA, Antonets KS. Temporal Control of Seed Development in Dicots: Molecular Bases, Ecological Impact and Possible Evolutionary Ramifications. Int J Mol Sci 2021; 22:ijms22179252. [PMID: 34502157 PMCID: PMC8430901 DOI: 10.3390/ijms22179252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 12/21/2022] Open
Abstract
In flowering plants, seeds serve as organs of both propagation and dispersal. The developing seed passes through several consecutive stages, following a conserved general outline. The overall time needed for a seed to develop, however, may vary both within and between plant species, and these temporal developmental properties remain poorly understood. In the present paper, we summarize the existing data for seed development alterations in dicot plants. For genetic mutations, the reported cases were grouped in respect of the key processes distorted in the mutant specimens. Similar phenotypes arising from the environmental influence, either biotic or abiotic, were also considered. Based on these data, we suggest several general trends of timing alterations and how respective mechanisms might add to the ecological plasticity of the families considered. We also propose that the developmental timing alterations may be perceived as an evolutionary substrate for heterochronic events. Given the current lack of plausible models describing timing control in plant seeds, the presented suggestions might provide certain insights for future studies in this field.
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Affiliation(s)
- Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence:
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8
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Genome-wide association study identified candidate genes for seed size and seed composition improvement in M. truncatula. Sci Rep 2021; 11:4224. [PMID: 33608604 PMCID: PMC7895968 DOI: 10.1038/s41598-021-83581-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/19/2021] [Indexed: 12/20/2022] Open
Abstract
Grain legumes are highly valuable plant species, as they produce seeds with high protein content. Increasing seed protein production and improving seed nutritional quality represent an agronomical challenge in order to promote plant protein consumption of a growing population. In this study, we used the genetic diversity, naturally present in Medicago truncatula, a model plant for legumes, to identify genes/loci regulating seed traits. Indeed, using sequencing data of 162 accessions from the Medicago HAPMAP collection, we performed genome-wide association study for 32 seed traits related to seed size and seed composition such as seed protein content/concentration, sulfur content/concentration. Using different GWAS and postGWAS methods, we identified 79 quantitative trait nucleotides (QTNs) as regulating seed size, 41 QTNs for seed composition related to nitrogen (i.e. storage protein) and sulfur (i.e. sulfur-containing amino acid) concentrations/contents. Furthermore, a strong positive correlation between seed size and protein content was revealed within the selected Medicago HAPMAP collection. In addition, several QTNs showed highly significant associations in different seed phenotypes for further functional validation studies, including one near an RNA-Binding Domain protein, which represents a valuable candidate as central regulator determining both seed size and composition. Finally, our findings in M. truncatula represent valuable resources to be exploitable in many legume crop species such as pea, common bean, and soybean due to its high synteny, which enable rapid transfer of these results into breeding programs and eventually help the improvement of legume grain production.
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9
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Rodas AL, Roque E, Hamza R, Gómez-Mena C, Minguet EG, Wen J, Mysore KS, Beltrán JP, Cañas LA. MtSUPERMAN plays a key role in compound inflorescence and flower development in Medicago truncatula. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:816-830. [PMID: 33176041 DOI: 10.1111/tpj.15075] [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: 08/06/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Legumes have unique features, such as compound inflorescences and a complex floral ontogeny. Thus, the study of regulatory genes in these species during inflorescence and floral development is essential to understand their role in the evolutionary origin of developmental novelties. The SUPERMAN (SUP) gene encodes a C2H2 zinc-finger transcriptional repressor that regulates the floral organ number in the third and fourth floral whorls of Arabidopsis thaliana. In this work, we present the functional characterization of the Medicago truncatula SUPERMAN (MtSUP) gene based on gene expression analysis, complementation and overexpression assays, and reverse genetic approaches. Our findings provide evidence that MtSUP is the orthologous gene of SUP in M. truncatula. We have unveiled novel functions for a SUP-like gene in eudicots. MtSUP controls not only the number of floral organs in the inner two whorls, but also in the second whorl of the flower. Furthermore, MtSUP regulates the activity of the secondary inflorescence meristem, thus controlling the number of flowers produced. Our work provides insight into the regulatory network behind the compound inflorescence and flower development in this angiosperm family.
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Affiliation(s)
- Ana L Rodas
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Edelín Roque
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Rim Hamza
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Concepción Gómez-Mena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Eugenio G Minguet
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Jiangqi Wen
- Plant Biology Division, Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Kirankumar S Mysore
- Plant Biology Division, Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - José P Beltrán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Luis A Cañas
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
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10
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Into the Seed: Auxin Controls Seed Development and Grain Yield. Int J Mol Sci 2020; 21:ijms21051662. [PMID: 32121296 PMCID: PMC7084539 DOI: 10.3390/ijms21051662] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 11/17/2022] Open
Abstract
Seed development, which involves mainly the embryo, endosperm and integuments, is regulated by different signaling pathways, leading to various changes in seed size or seed weight. Therefore, uncovering the genetic and molecular mechanisms of seed development has great potential for improving crop yields. The phytohormone auxin is a key regulator required for modulating different cellular processes involved in seed development. Here, we provide a comprehensive review of the role of auxin biosynthesis, transport, signaling, conjugation, and catabolism during seed development. More importantly, we not only summarize the research progress on the genetic and molecular regulation of seed development mediated by auxin but also discuss the potential of manipulating auxin metabolism and its signaling pathway for improving crop seed weight.
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11
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Henriet C, Aimé D, Térézol M, Kilandamoko A, Rossin N, Combes-Soia L, Labas V, Serre RF, Prudent M, Kreplak J, Vernoud V, Gallardo K. Water stress combined with sulfur deficiency in pea affects yield components but mitigates the effect of deficiency on seed globulin composition. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4287-4304. [PMID: 30855667 PMCID: PMC6698706 DOI: 10.1093/jxb/erz114] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/20/2019] [Accepted: 02/28/2019] [Indexed: 05/08/2023]
Abstract
Water stress and sulfur (S) deficiency are two constraints increasingly faced by crops due to climate change and low-input agricultural practices. To investigate their interaction in the grain legume pea (Pisum sativum), sulfate was depleted at the mid-vegetative stage and a moderate 9-d water stress period was imposed during the early reproductive phase. The combination of the stresses impeded reproductive processes in a synergistic manner, reducing seed weight and seed number, and inducing seed abortion, which highlighted the paramount importance of sulfur for maintaining seed yield components under water stress. On the other hand, the moderate water stress mitigated the negative effect of sulfur deficiency on the accumulation of S-rich globulins (11S) in seeds, probably due to a lower seed sink strength for nitrogen, enabling a readjustment of the ratio of S-poor (7S) to 11S globulins. Transcriptome analysis of developing seeds at the end of the combined stress period indicated that similar biological processes were regulated in response to sulfur deficiency and to the combined stress, but that the extent of the transcriptional regulation was greater under sulfur deficiency. Seeds from plants subjected to the combined stresses showed a specific up-regulation of a set of transcription factor and SUMO ligase genes, indicating the establishment of unique regulatory processes when sulfur deficiency is combined with water stress.
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Affiliation(s)
- Charlotte Henriet
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Delphine Aimé
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Morgane Térézol
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Anderson Kilandamoko
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Nadia Rossin
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Lucie Combes-Soia
- Physiologie de la Reproduction et des Comportements (PRC) UMR85, INRA, CNRS, Université de Tours, IFCE, Nouzilly, France
| | - Valerie Labas
- Physiologie de la Reproduction et des Comportements (PRC) UMR85, INRA, CNRS, Université de Tours, IFCE, Nouzilly, France
| | - Rémy-Félix Serre
- GeT-PlaGe, US INRA 1426, INRA Auzeville, Castanet-Tolosan, Cedex, France
| | - Marion Prudent
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Vanessa Vernoud
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
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12
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Abstract
The size of seeds affects not only evolutionary fitness but also grain yield of crops. Understanding the mechanisms controlling seed size has become an important research field in plant science. Seed size is determined by the integrated signals of maternal and zygotic tissues, which control the coordinated growth of the embryo, endosperm, and seed coat. Recent advances have identified several signaling pathways that control seed size through maternal tissues, including or involving the ubiquitin-proteasome pathway, G-protein signaling, mitogen-activated protein kinase (MAPK) signaling, phytohormone perception and homeostasis, and some transcriptional regulators. Meanwhile, growth of the zygotic tissues is regulated in part by the HAIKU (IKU) pathway and phytohormones. This review provides a general overview of current findings in seed size control and discusses the emerging molecular mechanisms and regulatory networks found to be involved.
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Affiliation(s)
- Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering and Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
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13
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Savadi S. Molecular regulation of seed development and strategies for engineering seed size in crop plants. PLANT GROWTH REGULATION 2018; 84:401-422. [PMID: 0 DOI: 10.1007/s10725-017-0355-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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14
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Le Signor C, Vernoud V, Noguero M, Gallardo K, Thompson RD. Functional Genomics and Seed Development in Medicago truncatula: An Overview. Methods Mol Biol 2018; 1822:175-195. [PMID: 30043305 DOI: 10.1007/978-1-4939-8633-0_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The study of seed development in the model species Medicago truncatula has made a significant contribution to our understanding of this process in crop legumes. Thanks to the availability of comprehensive proteomics and transcriptomics databases, coupled with exhaustive mutant collections, the roles of several regulatory genes in development and maturation are beginning to be deciphered and functionally validated. Advances in next-generation sequencing and the availability of a genomic sequence have made feasible high-density SNP genotyping, allowing the identification of markers tightly linked to traits of agronomic interest. A further major advance is to be expected from the integration of omics resources in functional network construction, which has been used recently to identify "hub" genes central to important traits.
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Affiliation(s)
- Christine Le Signor
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Vanessa Vernoud
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Mélanie Noguero
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Richard D Thompson
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France.
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15
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McAdam EL, Meitzel T, Quittenden LJ, Davidson SE, Dalmais M, Bendahmane AI, Thompson R, Smith JJ, Nichols DS, Urquhart S, Gélinas-Marion A, Aubert G, Ross JJ. Evidence that auxin is required for normal seed size and starch synthesis in pea. THE NEW PHYTOLOGIST 2017; 216:193-204. [PMID: 28748561 DOI: 10.1111/nph.14690] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/31/2017] [Indexed: 05/02/2023]
Abstract
In recent years the biosynthesis of auxin has been clarified with the aid of mutations in auxin biosynthesis genes. However, we know little about the effects of these mutations on the seed-filling stage of seed development. Here we investigate a key auxin biosynthesis mutation of the garden pea, which results in auxin deficiency in developing seeds. We exploit the large seed size of this model species, which facilitates the measurement of compounds in individual seeds. The mutation results in small seeds with reduced starch content and a wrinkled phenotype at the dry stage. The phenotypic effects of the mutation were fully reversed by introduction of the wild-type gene as a transgene, and partially reversed by auxin application. The results indicate that auxin is required for normal seed size and starch accumulation in pea, an important grain legume crop.
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Affiliation(s)
- Erin L McAdam
- School of Biological Sciences, University of Tasmania, Sandy Bay, 7001, Australia
| | - Tobias Meitzel
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, D-06466, Germany
| | - Laura J Quittenden
- School of Biological Sciences, University of Tasmania, Sandy Bay, 7001, Australia
| | - Sandra E Davidson
- School of Biological Sciences, University of Tasmania, Sandy Bay, 7001, Australia
| | - Marion Dalmais
- Institute of Plant Sciences - Paris-Saclay, Bâtiment 630, Plateau du Moulon Rue Noetzlin CS 80004, 91192, Gif-sur-Yvette Cedex, France
| | - Abdelhafid I Bendahmane
- Institute of Plant Sciences - Paris-Saclay, Bâtiment 630, Plateau du Moulon Rue Noetzlin CS 80004, 91192, Gif-sur-Yvette Cedex, France
| | - Richard Thompson
- INRA (National Institute for Agronomic Research), UMR 1347 Agroécologie, BP 86510, Dijon, France
| | - Jennifer J Smith
- School of Biological Sciences, University of Tasmania, Sandy Bay, 7001, Australia
| | - David S Nichols
- Central Science Laboratory, University of Tasmania, Sandy Bay, 7001, Australia
| | - Shelley Urquhart
- School of Biological Sciences, University of Tasmania, Sandy Bay, 7001, Australia
| | | | - Gregoire Aubert
- INRA (National Institute for Agronomic Research), UMR 1347 Agroécologie, BP 86510, Dijon, France
| | - John J Ross
- School of Biological Sciences, University of Tasmania, Sandy Bay, 7001, Australia
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16
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17
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Ingram GC. Dying to live: cell elimination as a developmental strategy in angiosperm seeds. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:785-796. [PMID: 27702990 DOI: 10.1093/jxb/erw364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The complete elimination of unwanted cells during development is a repeated theme in both multicellular animals and in plants. In plants, such events have been extensively studied and reviewed in terms of their molecular regulation, of marker genes and proteins expressed, and in terms of cellular changes associated with their progression. This review will take a slightly different view of developmental cell elimination and will concentrate specifically on the numerous elimination events that occur during ovule and seed development (here grouped together as seed development). It asks why this cell elimination occurs in specific seed tissues, in order to understand something about the commonalities underlying how seemingly disparate events are triggered and regulated. Finally, by placing the seed in its broader evolutionary context, the question of why cell elimination may have emerged as such a key component of the seed developmental toolbox will be considered.
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Affiliation(s)
- Gwyneth C Ingram
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, CNRS (UMR 5667), INRA (UMR 0879), UCB Lyon 1, Ecole Normale Supérieure de Lyon, F-69342 Lyon, France
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18
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Analysis of Large Seeds from Three Different Medicago truncatula Ecotypes Reveals a Potential Role of Hormonal Balance in Final Size Determination of Legume Grains. Int J Mol Sci 2016; 17:ijms17091472. [PMID: 27618017 PMCID: PMC5037750 DOI: 10.3390/ijms17091472] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/21/2016] [Accepted: 08/23/2016] [Indexed: 11/16/2022] Open
Abstract
Legume seeds are important as protein and oil source for human diet. Understanding how their final seed size is determined is crucial to improve crop yield. In this study, we analyzed seed development of three accessions of the model legume, Medicago truncatula, displaying contrasted seed size. By comparing two large seed accessions to the reference accession A17, we described mechanisms associated with large seed size determination and potential factors modulating the final seed size. We observed that early events during embryogenesis had a major impact on final seed size and a delayed heart stage embryo development resulted to large seeds. We also observed that the difference in seed growth rate was mainly due to a difference in embryo cell number, implicating a role of cell division rate. Large seed accessions could be explained by an extended period of cell division due to a longer embryogenesis phase. According to our observations and recent reports, we observed that auxin (IAA) and abscisic acid (ABA) ratio could be a key determinant of cell division regulation at the end of embryogenesis. Overall, our study highlights that timing of events occurring during early seed development play decisive role for final seed size determination.
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19
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Fatihi A, Boulard C, Bouyer D, Baud S, Dubreucq B, Lepiniec L. Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 250:198-204. [PMID: 27457996 DOI: 10.1016/j.plantsci.2016.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 05/11/2023]
Abstract
Increasing yield and quality of seed storage compounds in a sustainable way is a key challenge for our societies. Genome-wide analyses conducted in both monocot and dicot angiosperms emphasized drastic transcriptional switches that occur during seed development. In Arabidopsis thaliana, a reference species, genetic and molecular analyses have demonstrated the key role of LAFL (LEC1, ABI3, FUS3, and LEC2) transcription factors (TFs), in controlling gene expression programs essential to accomplish seed maturation and the accumulation of storage compounds. Here, we summarize recent progress obtained in the characterization of these LAFL proteins, their regulation, partners and target genes. Moreover, we illustrate how these evolutionary conserved TFs can be used to engineer new crops with altered seed compositions and point out the current limitations. Last, we discuss about the interest of investigating further the environmental and epigenetic regulation of this network for the coming years.
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Affiliation(s)
- Abdelhak Fatihi
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
| | - Céline Boulard
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Daniel Bouyer
- Institut de Biologie de l'ENS, CNRS UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris cedex 05, France
| | - Sébastien Baud
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Bertrand Dubreucq
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Loïc Lepiniec
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
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20
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Kang Y, Li M, Sinharoy S, Verdier J. A Snapshot of Functional Genetic Studies in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2016; 7:1175. [PMID: 27555857 PMCID: PMC4977297 DOI: 10.3389/fpls.2016.01175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 07/21/2016] [Indexed: 05/21/2023]
Abstract
In the current context of food security, increase of plant protein production in a sustainable manner represents one of the major challenges of agronomic research, which could be partially resolved by increased cultivation of legume crops. Medicago truncatula is now a well-established model for legume genomic and genetic studies. With the establishment of genomics tools and mutant populations in M. truncatula, it has become an important resource to answer some of the basic biological questions related to plant development and stress tolerance. This review has an objective to overview a decade of genetic studies in this model plant from generation of mutant populations to nowadays. To date, the three biological fields, which have been extensively studied in M. truncatula, are the symbiotic nitrogen fixation, the seed development, and the abiotic stress tolerance, due to their significant agronomic impacts. In this review, we summarize functional genetic studies related to these three major biological fields. We integrated analyses of a nearly exhaustive list of genes into their biological contexts in order to provide an overview of the forefront research advances in this important legume model plant.
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Affiliation(s)
- Yun Kang
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Minguye Li
- University of Chinese Academy of SciencesBeijing, China
- Shanghai Plant Stress Center, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Senjuti Sinharoy
- Department of Biotechnology, University of CalcuttaCalcutta, India
| | - Jerome Verdier
- Shanghai Plant Stress Center, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, China
- *Correspondence: Jerome Verdier
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Ingram G, Gutierrez-Marcos J. Peptide signalling during angiosperm seed development. JOURNAL OF EXPERIMENTAL BOTANY 2015. [PMID: 26195729 DOI: 10.1093/jxb/erv336] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Cell-cell communication is pivotal for the coordination of various features of plant development. Recent studies in plants have revealed that, as in animals, secreted signal peptides play critical roles during reproduction. However, the precise signalling mechanisms in plants are not well understood. In this review, we discuss the known and putative roles of secreted peptides present in the seeds of angiosperms as key signalling factors involved in coordinating different aspects of seed development.
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Affiliation(s)
- Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, UMR 5667 CNRS/UMR 0879 INRA, ENS de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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22
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Versatility of germin-like proteins in their sequences, expressions, and functions. Funct Integr Genomics 2015; 15:533-48. [DOI: 10.1007/s10142-015-0454-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/28/2015] [Accepted: 07/02/2015] [Indexed: 12/19/2022]
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23
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Curto M, Krajinski F, Schlereth A, Rubiales D. Transcriptional profiling of Medicago truncatula during Erysiphe pisi infection. FRONTIERS IN PLANT SCIENCE 2015; 6:517. [PMID: 26217367 PMCID: PMC4496563 DOI: 10.3389/fpls.2015.00517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/26/2015] [Indexed: 05/21/2023]
Abstract
Resistance to powdery mildew has been studied in a number of plant species, yet the molecular mechanisms remain largely unknown. Transcription factors (TFs) play a critical role in the plant defense response by regulating the transcriptional machinery which coordinates the expression of a large group of genes involved in plant defense. Using high-throughput quantitative real-time PCR (qPCR) technology more than 1000 Medicago truncatula TFs were screened in a pair of susceptible and resistant genotypes of M. truncatula after 4 h of Erysiphe pisi infection. Seventy nine TF genes, belonging to 33 families showed a significant transcriptional change in response to E. pisi infection. Forty eight TF genes were differentially expressed in the resistant genotypes compared to the susceptible one in response to E. pisi infection, including pathogenesis-related transcriptional factors, AP2/EREBP (APETALA2/ETHYLENE-RESPONSIVE ELEMENT BINDING FACTORS), WRKY (highly conserved WRKYGQK amino-acid sequence), MYB (Myeloblastoma), homeodomain (HD) and zinc finger C2C2 (CYS2-CYS2), C2H2, (CYS2-HIS2), LIM (Lin-11, Isl-1, Mec-3) gene families, which are involved in known defense responses. Our results suggest that these TF genes are among the E. pisi responsive genes in resistant M. truncatula that may constitute a regulatory network which controls the transcriptional changes in defense genes involved in resistance to E. pisi.
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Affiliation(s)
- Miguel Curto
- Department of Plant Breeding, Institute for Sustainable Agriculture, Spanish National Research CouncilCórdoba, Spain
| | - Franziska Krajinski
- Department of Plant-Microbe Interactions, Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Armin Schlereth
- Department of Plant-Microbe Interactions, Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Diego Rubiales
- Department of Plant Breeding, Institute for Sustainable Agriculture, Spanish National Research CouncilCórdoba, Spain
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