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Lin W, Bai M, Peng C, Kuang H, Kong F, Guan Y. Genome editing toward biofortified soybean with minimal trade-off between low phytic acid and yield. ABIOTECH 2024; 5:196-201. [PMID: 38974864 PMCID: PMC11224060 DOI: 10.1007/s42994-024-00158-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/02/2024] [Indexed: 07/09/2024]
Abstract
Phytic acid (PA) in grain seeds reduces the bioavailability of nutrient elements in monogastric animals, and an important objective for crop seed biofortification is to decrease the seed PA content. Here, we employed CRISPR/Cas9 to generate a PA mutant population targeting PA biosynthesis and transport genes, including two multi-drug-resistant protein 5 (MRP5) and three inositol pentose-phosphate kinases (IPK1). We characterized a variety of lines containing mutations on multiple IPK and MRP5 genes. The seed PA was more significantly decreased in higher-order mutant lines with multiplex mutations. However, such mutants also exhibited poor agronomic performance. In the population, we identified two lines carrying single mutations in ipk1b and ipk1c, respectively. These mutants exhibited moderately reduced PA content, and regular agronomic performance compared to the wild type. Our study indicates that moderately decreasing PA by targeting single GmIPK1 genes, rather than multiplex mutagenesis toward ultra-low PA, is an optimal strategy for low-PA soybean with a minimal trade-off in yield performance. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-024-00158-4.
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Affiliation(s)
- Wenxin Lin
- Sanya Institute of China Agricultural University, Sanya, 572000 China
- College of Agronomy, China Agricultural University, Beijing, 100193 China
| | - Mengyan Bai
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Chunyan Peng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Huaqin Kuang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Yuefeng Guan
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
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Liu S, Yang S, Liu H, Hu Q, Liu X, Wang J, Wang J, Xin W, Chen Q. Physiological and transcriptomic analysis of the mangrove species Kandelia obovata in response to flooding stress. MARINE POLLUTION BULLETIN 2023; 196:115598. [PMID: 37839131 DOI: 10.1016/j.marpolbul.2023.115598] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
Flooding stress on mangroves is growing continually with rising sea level. In this study, the physiology and transcriptome of the mangrove species Kandelia obovata under flooding stress were analyzed. With increasing inundation time, malondialdehyde (MDA), superoxide dismutase (SOD), glutathione (GSH), soluble sugar (SS), soluble protein (SP), and proline (Pro) content declined, while peroxidase (POD) and ascorbate peroxidase (APX) activity rose significantly. According to the KEGG pathway enrichment analysis, upregulated differentially expressed genes (DEGs) were enriched in the plant hormone signaling pathway. Furthermore, MYB44 and MYB108 genes from the MYB transcription factor family and RAP2.12, DREB2B, and ERF4 genes from the AP2/ERF family were up-regulated under flooding conditions. A strong correlation was established between the expression levels of 12 DEGs under flooding stress and RNA sequencing data and was verified by qRT-PCR. These results provide new insights into the molecular mechanism of K. obovata in response to flooding stress.
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Affiliation(s)
- Shuangshuang Liu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China; College of Forestry and Biotechnology, Zhejiang Agricultural and Forestry University, Hangzhou 311300, China
| | - Sheng Yang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Huizi Liu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Qingdi Hu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Xing Liu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Jinwang Wang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Jiayu Wang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China; College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Wenzhen Xin
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China; College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Qiuxia Chen
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China.
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Wen Z, Juliana P, Dhugga HS, Pacheco M, Martínez UI, Aguilar A, Ibba MI, Govindan V, Singh RP, Dhugga KS. Genome-Wide Association Study of Phytic Acid in Wheat Grain Unravels Markers for Improving Biofortification. FRONTIERS IN PLANT SCIENCE 2022; 13:830147. [PMID: 35242157 PMCID: PMC8886111 DOI: 10.3389/fpls.2022.830147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/10/2022] [Indexed: 06/07/2023]
Abstract
Biofortification of cereal grains offers a lasting solution to combat micronutrient deficiency in developing countries where it poses developmental risks to children. Breeding efforts thus far have been directed toward increasing the grain concentrations of iron (Fe) and zinc (Zn) ions. Phytic acid (PA) chelates these metal ions, reducing their bioavailability in the digestive tract. We present a high-throughput assay for quantification of PA and its application in screening a breeding population. After extraction in 96-well megatiter plates, PA content was determined from the phosphate released after treatment with a commercially available phytase enzyme. In a set of 330 breeding lines of wheat grown in the field over 3 years as part of a HarvestPlus breeding program for high grain Fe and Zn, our assay unraveled variation for PA that ranged from 0.90 to 1.72% with a mean of 1.24%. PA content was not associated with grain yield. High yielding lines were further screened for low molar PA/Fe and PA/Zn ratios for increased metal ion bioavailability, demonstrating the utility of our assay. Genome-wide association study revealed 21 genetic associations, six of which were consistent across years. Five of these associations mapped to chromosomes 1A, 2A, 2D, 5A, and 7D. Additivity over four of these haplotypes accounted for an ∼10% reduction in PA. Our study demonstrates it is possible to scale up assays to directly select for low grain PA in forward breeding programs.
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Wang L, Gao Y, Wang S, Zhang Q, Yang S. Genome-wide identification of PME genes, evolution and expression analyses in soybean (Glycine max L.). BMC PLANT BIOLOGY 2021; 21:578. [PMID: 34872520 PMCID: PMC8647493 DOI: 10.1186/s12870-021-03355-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Pectin methylesterase (PME) is one of pectin-modifying enzyme that affects the pectin homeostasis in cell wall and regulates plant growth and diverse biological processes. The PME genes have been well explored and characterized in different plants. Nevertheless, systematic research on the soybean (Glycine max L.) PME genes remain lacking. RESULTS We identified 127 Glycine max PME genes (GmPME) from the soybean Wm82.a2.v1 genome, which unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis classified the GmPME genes into four clades (Group I, Group II, Group III and Group IV). GmPME gene members in the same clades displayed similar gene structures and motif patterns. The gene family expansion analysis demonstrated that segmental duplication was the major driving force to acquire novel GmPME genes compared to the tandem duplication events. Further synteny and evolution analyses showed that the GmPME gene family experienced strong purifying selective pressures during evolution. The cis-element analyses together with the expression patterns of the GmPME genes in various tissues suggested that the GmPME genes broadly participate in distinct biological processes and regulate soybean developments. Importantly, based on the transcriptome data and quantitative RT-PCR validations, we examined the potential roles of the GmPME genes in regulating soybean flower bud development and seed germination. CONCLUSION In conclusion, we provided a comprehensive characterization of the PME genes in soybean, and our work laid a foundation for the functional study of GmPME genes in the future.
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Affiliation(s)
- Liang Wang
- Soybean Research Institute, National Center for Soybean, Key Improvement Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yingqi Gao
- Soybean Research Institute, National Center for Soybean, Key Improvement Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Songming Wang
- Soybean Research Institute, National Center for Soybean, Key Improvement Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qiqi Zhang
- Soybean Research Institute, National Center for Soybean, Key Improvement Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean, Key Improvement Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
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DeMers LC, Raboy V, Li S, Saghai Maroof MA. Network Inference of Transcriptional Regulation in Germinating Low Phytic Acid Soybean Seeds. FRONTIERS IN PLANT SCIENCE 2021; 12:708286. [PMID: 34531883 PMCID: PMC8438133 DOI: 10.3389/fpls.2021.708286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/23/2021] [Indexed: 05/14/2023]
Abstract
The low phytic acid (lpa) trait in soybeans can be conferred by loss-of-function mutations in genes encoding myo-inositol phosphate synthase and two epistatically interacting genes encoding multidrug-resistance protein ATP-binding cassette (ABC) transporters. However, perturbations in phytic acid biosynthesis are associated with poor seed vigor. Since the benefits of the lpa trait, in terms of end-use quality and sustainability, far outweigh the negatives associated with poor seed performance, a fuller understanding of the molecular basis behind the negatives will assist crop breeders and engineers in producing variates with lpa and better germination rate. The gene regulatory network (GRN) for developing low and normal phytic acid soybean seeds was previously constructed, with genes modulating a variety of processes pertinent to phytic acid metabolism and seed viability being identified. In this study, a comparative time series analysis of low and normal phytic acid soybeans was carried out to investigate the transcriptional regulatory elements governing the transitional dynamics from dry seed to germinated seed. GRNs were reverse engineered from time series transcriptomic data of three distinct genotypic subsets composed of lpa soybean lines and their normal phytic acid sibling lines. Using a robust unsupervised network inference scheme, putative regulatory interactions were inferred for each subset of genotypes. These interactions were further validated by published regulatory interactions found in Arabidopsis thaliana and motif sequence analysis. Results indicate that lpa seeds have increased sensitivity to stress, which could be due to changes in phytic acid levels, disrupted inositol phosphate signaling, disrupted phosphate ion (Pi) homeostasis, and altered myo-inositol metabolism. Putative regulatory interactions were identified for the latter two processes. Changes in abscisic acid (ABA) signaling candidate transcription factors (TFs) putatively regulating genes in this process were identified as well. Analysis of the GRNs reveal altered regulation in processes that may be affecting the germination of lpa soybean seeds. Therefore, this work contributes to the ongoing effort to elucidate molecular mechanisms underlying altered seed viability, germination and field emergence of lpa crops, understanding of which is necessary in order to mitigate these problems.
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Affiliation(s)
- Lindsay C. DeMers
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Victor Raboy
- National Small Grains Germplasm Research Center, Agricultural Research Service (USDA), Aberdeen, ID, United States
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - M. A. Saghai Maroof
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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Jin H, Yu X, Yang Q, Fu X, Yuan F. Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants. Sci Rep 2021; 11:8740. [PMID: 33888781 PMCID: PMC8062490 DOI: 10.1038/s41598-021-88055-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Phytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3-InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.
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Affiliation(s)
- Hangxia Jin
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiaomin Yu
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Qinghua Yang
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xujun Fu
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Fengjie Yuan
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
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7
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Yu X, Jin H, Fu X, Yang Q, Yuan F. Quantitative proteomic analyses of two soybean low phytic acid mutants to identify the genes associated with seed field emergence. BMC PLANT BIOLOGY 2019; 19:569. [PMID: 31856712 PMCID: PMC6921446 DOI: 10.1186/s12870-019-2201-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 12/12/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Seed germination is essential to crop growth and development, and ultimately affects its harvest. It is difficult to breed soybeans low in phytic acid with a higher seed field emergence. Although additional management and selection could overcome the phytate reduction, the mechanisms of seed germination remain unknown. RESULTS A comparative proteomic analysis was conducted between two low phytic acid (LPA) soybean mutants (TW-1-M and TW-1), both of which had a deletion of 2 bp in the GmMIPS1 gene. However, the TW-1 seeds showed a significantly lower field emergence compared to the TW-1-M. There were 282 differentially accumulated proteins (DAPs) identified between two mutants at the three stages. Among these DAPs, 80 were down-accumulated and 202 were up-accumulated. Bioinformatic analysis showed that the identified proteins were related to functional categories of oxidation reduction, response to stimulus and stress, dormancy and germination processes and catalytic activity. KEGG analysis showed that these DAPs were mainly involved in energy metabolism and anti-stress pathways. Based upon the conjoint analysis of DAPs with the differentially expressed genes (DEGs) previously published among three germination stages in two LPA mutants, 30 shared DAPs/DEGs were identified with different patterns, including plant seed protein, beta-amylase, protein disulfide-isomerase, disease resistance protein, pyrophosphate-fructose 6-phosphate 1-phosphotransferase, cysteine proteinase inhibitor, non-specific lipid-transfer protein, phosphoenolpyruvate carboxylase and acyl-coenzyme A oxidase. CONCLUSIONS Seed germination is a very complex process in LPA soybean mutants. The TW-1-M and TW-1 showed many DAPs involved in seed germination. The differential accumulation of these proteins could result in the difference of seed field emergence between the two mutants. The high germination rate in the TW-1-M might be strongly attributed to reactive oxygen species-related and plant hormone-related genes. All these findings would help us further explore the germination mechanisms in LPA crops.
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Affiliation(s)
- Xiaomin Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hangxia Jin
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xujun Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qinghua Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fengjie Yuan
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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8
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Mohanapriya G, Bharadwaj R, Noceda C, Costa JH, Kumar SR, Sathishkumar R, Thiers KLL, Santos Macedo E, Silva S, Annicchiarico P, Groot SP, Kodde J, Kumari A, Gupta KJ, Arnholdt-Schmitt B. Alternative Oxidase (AOX) Senses Stress Levels to Coordinate Auxin-Induced Reprogramming From Seed Germination to Somatic Embryogenesis-A Role Relevant for Seed Vigor Prediction and Plant Robustness. FRONTIERS IN PLANT SCIENCE 2019; 10:1134. [PMID: 31611888 PMCID: PMC6776121 DOI: 10.3389/fpls.2019.01134] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 08/16/2019] [Indexed: 05/21/2023]
Abstract
Somatic embryogenesis (SE) is the most striking and prominent example of plant plasticity upon severe stress. Inducing immature carrot seeds perform SE as substitute to germination by auxin treatment can be seen as switch between stress levels associated to morphophysiological plasticity. This experimental system is highly powerful to explore stress response factors that mediate the metabolic switch between cell and tissue identities. Developmental plasticity per se is an emerging trait for in vitro systems and crop improvement. It is supposed to underlie multi-stress tolerance. High plasticity can protect plants throughout life cycles against variable abiotic and biotic conditions. We provide proof of concepts for the existing hypothesis that alternative oxidase (AOX) can be relevant for developmental plasticity and be associated to yield stability. Our perspective on AOX as relevant coordinator of cell reprogramming is supported by real-time polymerase chain reaction (PCR) analyses and gross metabolism data from calorespirometry complemented by SHAM-inhibitor studies on primed, elevated partial pressure of oxygen (EPPO)-stressed, and endophyte-treated seeds. In silico studies on public experimental data from diverse species strengthen generality of our insights. Finally, we highlight ready-to-use concepts for plant selection and optimizing in vivo and in vitro propagation that do not require further details on molecular physiology and metabolism. This is demonstrated by applying our research & technology concepts to pea genotypes with differential yield performance in multilocation fields and chickpea types known for differential robustness in the field. By using these concepts and tools appropriately, also other marker candidates than AOX and complex genomics data can be efficiently validated for prebreeding and seed vigor prediction.
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Affiliation(s)
- Gunasekaran Mohanapriya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Carlos Noceda
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Cell and Molecular Biology of Plants (BPOCEMP)/Industrial Biotechnology and Bioproducts, Department of Sciences of the Vidaydela Agriculture, University of the Armed Forces-ESPE, Milagro, Ecuador
- Faculty of Engineering, State University of Milagro (UNEMI), Milagro, Ecuador
| | - José Hélio Costa
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Sarma Rajeev Kumar
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Karine Leitão Lima Thiers
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Elisete Santos Macedo
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Sofia Silva
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Paolo Annicchiarico
- Council for Agricultural Research and Economics (CREA), Research Centre for Animal Production and Aquaculture, Lodi, Italy
| | - Steven P.C. Groot
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Jan Kodde
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Aprajita Kumari
- National Institute of Plant Genome Research, New Delhi, India
| | - Kapuganti Jagadis Gupta
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- National Institute of Plant Genome Research, New Delhi, India
| | - Birgit Arnholdt-Schmitt
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- CERNAS-Research Center for Natural Resources, Environment and Society, Department of Environment, Escola Superior Agrária de Coimbra, Coimbra, Portugal
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Comparative transcriptome and metabolite profiling of four tissues from Alisma orientale (Sam.) Juzep reveals its inflorescence developmental and medicinal characteristics. Sci Rep 2019; 9:12310. [PMID: 31444376 PMCID: PMC6707231 DOI: 10.1038/s41598-019-48806-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Alisma orientale (Sam.) Juzep (A. orientale) is an important medicinal plant in traditional Chinese medicine. In this study, de novo RNA-seq of A. orientale was performed based on the cDNA libraries from four different tissues, roots, leaves, scapes and inflorescences. A total of 41,685 unigenes were assembled, 25,024 unigene functional annotations were obtained by searching against the five public sequence databases, and 3,411 simple sequence repeats in A. orientale were reported for the first time. 15,402 differentially expressed genes were analysed. The morphological characteristics showed that compared to the other tissues, the leaves had more chlorophyll, the scapes had more vascular bundles, and the inflorescences contained more starch granules and protein. In addition, the metabolic profiles of eight kinds of alisols metabolite profiling, which were measured by ultra-Performance liquid chromatography-triple quadrupole-mass spectrometry showed that alisol B 23-acetate and alisol B were the major components of the four tissues at amounts of 0.068~0.350 mg/g and 0.046~0.587 mg/g, respectively. In addition, qRT-PCR validated that farnesyl pyrophosphate synthase and 3-hydroxy-3-methylglutaryl-CoA reductase should be considered the critical candidate genes involved in alisol biosynthesis. These transcriptome and metabolic profiles of A. orientale may help clarify the molecular mechanisms underlying the medicinal characteristics of A. orientale.
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Goßner S, Yuan F, Zhou C, Tan Y, Shu Q, Engel KH. Stability of the Metabolite Signature Resulting from the MIPS1 Mutation in Low Phytic Acid Soybean ( Glycine max L. Merr.) Mutants upon Cross-Breeding. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5043-5052. [PMID: 30977368 DOI: 10.1021/acs.jafc.9b00817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The low phytic acid ( lpa) soybean ( Glycine max L. Merr.) mutant Gm-lpa-TW-1-M, resulting from a 2 bp deletion in GmMIPS1, was crossed with a commercial cultivar. F3 and F5 progenies were subjected to nontargeted GC-based metabolite profiling, allowing analysis of a broad array of low molecular weight constituents. In the homozygous lpa mutant progenies the intended phytic acid reduction was accompanied by remarkable metabolic changes of nutritionally relevant constituents such as reduced contents of raffinose oligosaccharides and galactosyl cyclitols as well as increased concentrations in sucrose and various free amino acids. The mutation-induced metabolite signature was nearly unaffected by the cross-breeding and consistently expressed over generations and in different growing seasons. Therefore, not only the primary MIPS1 lpa mutant but also its progenies might be valuable genetic resources for commercial breeding programs to produce soybean seeds stably exhibiting improved phytate-related and nutritional properties.
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Affiliation(s)
- Sophia Goßner
- Chair of General Food Technology , Technical University of Munich , Maximus-von-Imhof-Forum 2 , Freising-Weihenstephan D-85354 , Germany
| | - Fengjie Yuan
- Institute of Crop Science and Nuclear Technology Utilization , Zhejiang Academy of Agricultural Sciences , Hangzhou 310021 , China
| | - Chenguang Zhou
- Chair of General Food Technology , Technical University of Munich , Maximus-von-Imhof-Forum 2 , Freising-Weihenstephan D-85354 , Germany
| | - Yuanyuan Tan
- State Key Laboratory of Rice Biology and Zhejiang Provincial Key Laboratory of Plant Germplasm, Institute of Crop Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Qingyao Shu
- State Key Laboratory of Rice Biology and Zhejiang Provincial Key Laboratory of Plant Germplasm, Institute of Crop Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Karl-Heinz Engel
- Chair of General Food Technology , Technical University of Munich , Maximus-von-Imhof-Forum 2 , Freising-Weihenstephan D-85354 , Germany
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11
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Goßner S, Yuan F, Zhou C, Tan Y, Shu Q, Engel KH. Impact of Cross-Breeding of Low Phytic Acid MIPS1 and IPK1 Soybean ( Glycine max L. Merr.) Mutants on Their Contents of Inositol Phosphate Isomers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:247-257. [PMID: 30541281 DOI: 10.1021/acs.jafc.8b06117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The knowledge on consequences of cross-breeding of induced low phytic acid ( lpa) soybean ( Glycine max L. Merr.) mutants on the contents of phytic acid (InsP6) and lower inositol phosphate isomers (InsP2-InsP5) in the resulting progenies is limited. Therefore, MIPS1 and IPK1 lpa soybean mutants were crossed with wild-type (WT) cultivars or among themselves to generate homozygous lpa and WT progenies and double lpa mutants. The lpa trait of the MIPS1 mutant was not altered by cross-breeding with a WT cultivar; lpa progenies had InsP6 reductions of about 44% compared to WT progenies. IPK1 progenies showed pronounced accumulations of specific InsP3-InsP5 isomers (up to 12.4 mg/g) compared to the progenitor lpa mutant (4.7 mg/g); the extent of InsP6 reduction (43-71%) was depending on the WT crossing parent. Double mutants exhibited the most pronounced InsP6 reductions (up to 87%), accompanied by moderate accumulations of InsP3-InsP5 (2.5 mg/g). Cross-breeding offers the potential to modulate the amounts of both InsP6 and InsP3-InsP5 contents in lpa soybean mutants and thus to improve their nutritional quality.
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Affiliation(s)
- Sophia Goßner
- Chair of General Food Technology , Technical University of Munich , Maximus-von-Imhof-Forum 2 , D-85354 Freising-Weihenstephan , Germany
| | - Fengjie Yuan
- Institute of Crop Science and Nuclear Technology Utilization , Zhejiang Academy of Agricultural Sciences , Hangzhou 310021 , China
| | - Chenguang Zhou
- Chair of General Food Technology , Technical University of Munich , Maximus-von-Imhof-Forum 2 , D-85354 Freising-Weihenstephan , Germany
| | - Yuanyuan Tan
- State Key Laboratory of Rice Biology and Zhejiang Provincial Key Laboratory of Plant Germplasm, Institute of Crop Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Qingyao Shu
- State Key Laboratory of Rice Biology and Zhejiang Provincial Key Laboratory of Plant Germplasm, Institute of Crop Sciences , Zhejiang University , Hangzhou 310058 , China
| | - Karl-Heinz Engel
- Chair of General Food Technology , Technical University of Munich , Maximus-von-Imhof-Forum 2 , D-85354 Freising-Weihenstephan , Germany
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12
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Wayne LL, Gachotte DJ, Walsh TA. Transgenic and Genome Editing Approaches for Modifying Plant Oils. Methods Mol Biol 2019; 1864:367-394. [PMID: 30415347 DOI: 10.1007/978-1-4939-8778-8_23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Vegetable oils are important for human and animal nutrition and as renewable resources for chemical feedstocks. We provide an overview of transgenic and genome editing approaches for modifying plant oils, describing useful model and crop systems and different strategies for transgenic modifications. We also describe new genome editing approaches that are beginning to be applied to oilseed plants and crops. These approaches are illustrated with examples for modifying the nutritional quality of vegetable oils by altering fatty acid desaturation, producing non-native fatty acids in oilseeds, and enhancing the overall accumulation of oil in seeds and leaves.
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Affiliation(s)
- Laura L Wayne
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA.
| | - Daniel J Gachotte
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
| | - Terence A Walsh
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
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