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Thomas SK, Hoek KV, Ogoti T, Duong H, Angelovici R, Pires JC, Mendoza-Cozatl D, Washburn J, Schenck CA. Halophytes and heavy metals: A multi-omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima. AMERICAN JOURNAL OF BOTANY 2024:e16310. [PMID: 38600732 DOI: 10.1002/ajb2.16310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 04/12/2024]
Abstract
PREMISE The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we used Cakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole-genome triplication with closely related salt-sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy. METHODS Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response in C. maritima and identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium. RESULTS Cakile maritima is tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool in C. maritima and likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved in C. maritima abiotic stress tolerance. CONCLUSIONS These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.
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Affiliation(s)
- Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, 65211, MO, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, 65211, MO, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
| | - Kathryn Vanden Hoek
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| | - Tasha Ogoti
- Department of Computer Science, University of Missouri, Columbia, 65211, MO, USA
| | - Ha Duong
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, 65211, MO, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, Fort Collins, 80523-1170, CO, USA
| | - David Mendoza-Cozatl
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Division of Plant Sciences and Technology, University of Missouri, Columbia, 65211, MO, USA
| | - Jacob Washburn
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Plant Genetics Research Unit, USDA-ARS, Columbia, 65211, MO, USA
| | - Craig A Schenck
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
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2
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Hurst JP, Sato S, Ferris T, Yobi A, Zhou Y, Angelovici R, Clemente TE, Holding DR. Editing the 19 kDa alpha-zein gene family generates non-opaque2-based quality protein maize. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:946-959. [PMID: 37988568 PMCID: PMC10955486 DOI: 10.1111/pbi.14237] [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: 06/16/2023] [Revised: 10/26/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023]
Abstract
Maize grain is deficient in lysine. While the opaque2 mutation increases grain lysine, o2 is a transcription factor that regulates a wide network of genes beyond zeins, which leads to pleiotropic and often negative effects. Additionally, the drastic reduction in 19 kDa and 22 kDa alpha-zeins causes a floury kernel, unsuitable for agricultural use. Quality protein maize (QPM) overcame the undesirable kernel texture through the introgression of modifying alleles. However, QPM still lacks a functional o2 transcription factor, which has a penalty on non-lysine amino acids due to the o2 mutation. CRISPR/cas9 gives researchers the ability to directly target genes of interest. In this paper, gene editing was used to specifically target the 19 kDa alpha zein gene family. This allows for proteome rebalancing to occur without an o2 mutation and without a total alpha-zein knockout. The results showed that editing some, but not all, of the 19 kDa zeins resulted in up to 30% more lysine. An edited line displayed an increase of 30% over the wild type. While not quite the 55% lysine increase displayed by QPM, the line had little collateral impact on other amino acid levels compared to QPM. Additionally, the edited line containing a partially reduced 19 kDa showed an advantage in kernel texture that had a complete 19 kDa knockout. These results serve as proof of concept that editing the 19 kDa alpha-zein family alone can enhance lysine while retaining vitreous endosperm and a functional O2 transcription factor.
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Affiliation(s)
- J. Preston Hurst
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
- Center for Plant Science InnovationLincolnNebraskaUSA
| | - Shirley Sato
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Tyler Ferris
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
- Center for Plant Science InnovationLincolnNebraskaUSA
| | - Abou Yobi
- University of Missouri‐ColumbiaColumbiaMissouriUSA
| | - You Zhou
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | | | - Tom E. Clemente
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - David R. Holding
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
- Center for Plant Science InnovationLincolnNebraskaUSA
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3
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Yoshida T, Fernie AR. Hormonal regulation of plant primary metabolism under drought. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1714-1725. [PMID: 37712613 DOI: 10.1093/jxb/erad358] [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: 06/28/2023] [Accepted: 09/13/2023] [Indexed: 09/16/2023]
Abstract
Phytohormones are essential signalling molecules globally regulating many processes of plants, including their growth, development, and stress responses. The promotion of growth and the enhancement of stress resistance have to be balanced, especially under adverse conditions such as drought stress, because of limited resources. Plants cope with drought stress via various strategies, including the transcriptional regulation of stress-responsive genes and the adjustment of metabolism, and phytohormones play roles in these processes. Although abscisic acid (ABA) is an important signal under drought, less attention has been paid to other phytohormones. In this review, we summarize progress in the understanding of phytohormone-regulated primary metabolism under water-limited conditions, especially in Arabidopsis thaliana, and highlight recent findings concerning the amino acids associated with ABA metabolism and signalling. We also discuss how phytohormones function antagonistically and synergistically in order to balance growth and stress responses.
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Affiliation(s)
- Takuya Yoshida
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
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4
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Sun Y, Zhou Y, Long Q, Xing J, Guo P, Liu Y, Zhang C, Zhang Y, Fernie AR, Shi Y, Luo Y, Luo J, Jin C. OsBCAT2, a gene responsible for the degradation of branched-chain amino acids, positively regulates salt tolerance by promoting the synthesis of vitamin B5. THE NEW PHYTOLOGIST 2024; 241:2558-2574. [PMID: 38258425 DOI: 10.1111/nph.19551] [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: 07/08/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Salt stress negatively affects rice growth, development and yield. Metabolic adjustments contribute to the adaptation of rice under salt stress. Branched-chain amino acids (BCAA) are three essential amino acids that cannot be synthesized by humans or animals. However, little is known about the role of BCAA in response to salt stress in plants. Here, we showed that BCAAs may function as scavengers of reactive oxygen species (ROS) to provide protection against damage caused by salinity. We determined that branched-chain aminotransferase 2 (OsBCAT2), a protein responsible for the degradation of BCAA, positively regulates salt tolerance. Salt significantly induces the expression of OsBCAT2 rather than BCAA synthesis genes, which indicated that salt mainly promotes BCAA degradation and not de novo synthesis. Metabolomics analysis revealed that vitamin B5 (VB5) biosynthesis pathway intermediates were higher in the OsBCAT2-overexpressing plants but lower in osbcat2 mutants under salt stress. The salt stress-sensitive phenotypes of the osbcat2 mutants are rescued by exogenous VB5, indicating that OsBCAT2 affects rice salt tolerance by regulating VB5 synthesis. Our work provides new insights into the enzymes involved in BCAAs degradation and VB5 biosynthesis and sheds light on the molecular mechanism of BCAAs in response to salt stress.
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Affiliation(s)
- Yangyang Sun
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
- Sanya Research Institute of Hainan Academy of Agricultural Sciences, Sanya, 572025, China
| | - Yutong Zhou
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Qiyuan Long
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Junwei Xing
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Peizhen Guo
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Yanchen Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Changjian Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Yuanyuan Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Yuheng Shi
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Yuehua Luo
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Jie Luo
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Cheng Jin
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
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5
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Zhu A, Liu M, Tian Z, Liu W, Hu X, Ao M, Jia J, Shi T, Liu H, Li D, Mao H, Su H, Yan W, Li Q, Lan C, Fernie AR, Chen W. Chemical-tag-based semi-annotated metabolomics facilitates gene identification and specialized metabolic pathway elucidation in wheat. THE PLANT CELL 2024; 36:540-558. [PMID: 37956052 PMCID: PMC10896294 DOI: 10.1093/plcell/koad286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023]
Abstract
The importance of metabolite modification and species-specific metabolic pathways has long been recognized. However, linking the chemical structure of metabolites to gene function in order to explore the genetic and biochemical basis of metabolism has not yet been reported in wheat (Triticum aestivum). Here, we profiled metabolic fragment enrichment in wheat leaves and consequently applied chemical-tag-based semi-annotated metabolomics in a genome-wide association study in accessions of wheat. The studies revealed that all 1,483 quantified metabolites have at least one known functional group whose modification is tailored in an enzyme-catalyzed manner and eventually allows efficient candidate gene mining. A Triticeae crop-specific flavonoid pathway and its underlying metabolic gene cluster were elucidated in further functional studies. Additionally, upon overexpressing the major effect gene of the cluster TraesCS2B01G460000 (TaOMT24), the pathway was reconstructed in rice (Oryza sativa), which lacks this pathway. The reported workflow represents an efficient and unbiased approach for gene mining using forward genetics in hexaploid wheat. The resultant candidate gene list contains vast molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets and will ultimately aid in achieving wheat crop improvement.
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Affiliation(s)
- Anting Zhu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Mengmeng Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Min Ao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingqi Jia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Taotao Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Department of Root Biology and Symbiosis, Potsdam-Golm 14476, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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6
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Chen C, Naveed H, Chen K. Research progress on branched-chain amino acid aminotransferases. Front Genet 2023; 14:1233669. [PMID: 38028625 PMCID: PMC10658711 DOI: 10.3389/fgene.2023.1233669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Branched-chain amino acid aminotransferases, widely present in natural organisms, catalyze bidirectional amino transfer between branched-chain amino acids and branched-chain α-ketoacids in cells. Branched-chain amino acid aminotransferases play an important role in the metabolism of branched-chain amino acids. In this paper, the interspecific evolution and biological characteristics of branched-chain amino acid aminotransferases are introduced, the related research of branched-chain amino acid aminotransferases in animals, plants, microorganisms and humans is summarized and the molecular mechanism of branched-chain amino acid aminotransferase is analyzed. It has been found that branched-chain amino acid metabolism disorders are closely related to various diseases in humans and animals and plants, such as diabetes, cardiovascular diseases, brain diseases, neurological diseases and cancer. In particular, branched-chain amino acid aminotransferases play an important role in the development of various tumors. Branched-chain amino acid aminotransferases have been used as potential targets for various cancers. This article reviews the research on branched-chain amino acid aminotransferases, aiming to provide a reference for clinical research on targeted therapy for various diseases and different cancers.
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Affiliation(s)
- Can Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hassan Naveed
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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7
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Wrobel TJ, Brilhaus D, Stefanski A, Stühler K, Weber APM, Linka N. Mapping the castor bean endosperm proteome revealed a metabolic interaction between plastid, mitochondria, and peroxisomes to optimize seedling growth. FRONTIERS IN PLANT SCIENCE 2023; 14:1182105. [PMID: 37868318 PMCID: PMC10588648 DOI: 10.3389/fpls.2023.1182105] [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: 03/08/2023] [Accepted: 08/07/2023] [Indexed: 10/24/2023]
Abstract
In this work, we studied castor-oil plant Ricinus communis as a classical system for endosperm reserve breakdown. The seeds of castor beans consist of a centrally located embryo with the two thin cotyledons surrounded by the endosperm. The endosperm functions as major storage tissue and is packed with nutritional reserves, such as oil, proteins, and starch. Upon germination, mobilization of the storage reserves requires inter-organellar interplay of plastids, mitochondria, and peroxisomes to optimize growth for the developing seedling. To understand their metabolic interactions, we performed a large-scale organellar proteomic study on castor bean endosperm. Organelles from endosperm of etiolated seedlings were isolated and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). Computer-assisted deconvolution algorithms were applied to reliably assign the identified proteins to their correct subcellular localization and to determine the abundance of the different organelles in the heterogeneous protein samples. The data obtained were used to build a comprehensive metabolic model for plastids, mitochondria, and peroxisomes during storage reserve mobilization in castor bean endosperm.
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Affiliation(s)
- Thomas J. Wrobel
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Dominik Brilhaus
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum (BMFZ), Universitätsklinikum, Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum (BMFZ), Universitätsklinikum, Düsseldorf, Germany
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Nicole Linka
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
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8
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Ingrisano R, Tosato E, Trost P, Gurrieri L, Sparla F. Proline, Cysteine and Branched-Chain Amino Acids in Abiotic Stress Response of Land Plants and Microalgae. PLANTS (BASEL, SWITZERLAND) 2023; 12:3410. [PMID: 37836150 PMCID: PMC10574504 DOI: 10.3390/plants12193410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
Proteinogenic amino acids are the building blocks of protein, and plants synthesize all of them. In addition to their importance in plant growth and development, growing evidence underlines the central role played by amino acids and their derivatives in regulating several pathways involved in biotic and abiotic stress responses. In the present review, we illustrate (i) the role of amino acids as an energy source capable of replacing sugars as electron donors to the mitochondrial electron transport chain and (ii) the role of amino acids as precursors of osmolytes as well as (iii) precursors of secondary metabolites. Among the amino acids involved in drought stress response, proline and cysteine play a special role. Besides the large proline accumulation occurring in response to drought stress, proline can export reducing equivalents to sink tissues and organs, and the production of H2S deriving from the metabolism of cysteine can mediate post-translational modifications that target protein cysteines themselves. Although our general understanding of microalgae stress physiology is still fragmentary, a general overview of how unicellular photosynthetic organisms deal with salt stress is also provided because of the growing interest in microalgae in applied sciences.
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Affiliation(s)
| | | | | | - Libero Gurrieri
- Department of Pharmacy and Biotechnology FaBiT, University of Bologna, 40126 Bologna, Italy; (R.I.); (E.T.); (P.T.); (F.S.)
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9
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Sui Y, Che Y, Zhong Y, He L. Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains. PLANTS (BASEL, SWITZERLAND) 2023; 12:2970. [PMID: 37631180 PMCID: PMC10459631 DOI: 10.3390/plants12162970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Rice (Oryza sativa L.) is a globally important food source providing carbohydrates, amino acids, and dietary fiber for humans and livestock. The branched-chain amino acid (BCAA) level is a complex trait related to the nutrient quality of rice. However, the genetic mechanism underlying the BCAA (valine, leucine, and isoleucine) accumulation in rice grains remains largely unclear. In this study, the grain BCAA contents and 239,055 SNPs of a diverse panel containing 422 rice accessions were adopted to perform a genome-wide association study (GWAS) using a recently proposed 3VmrMLM model. A total of 357 BCAA-content-associated main-effect quantitative trait nucleotides (QTNs) were identified from 15 datasets (12 BCAA content datasets and 3 BLUP datasets of BCAA). Furthermore, the allelic variation of two novel candidate genes, LOC_Os01g52530 and LOC_Os06g15420, responsible for the isoleucine (Ile) content alteration were identified. To reveal the genetic basis of the potential interactions between the gene and environmental factor, 53 QTN-by-environment interactions (QEIs) were detected using the 3VmrMLM model. The LOC_Os03g24460, LOC_Os01g55590, and LOC_Os12g31820 were considered as the candidate genes potentially contributing to the valine (Val), leucine (Leu), and isoleucine (Ile) accumulations, respectively. Additionally, 10 QTN-by-QTN interactions (QQIs) were detected using the 3VmrMLM model, which were putative gene-by-gene interactions related to the Leu and Ile contents. Taken together, these findings suggest that the implementation of the 3VmrMLM model in a GWAS may provide new insights into the deeper understanding of BCAA accumulation in rice grains. The identified QTNs/QEIs/QQIs serve as potential targets for the genetic improvement of rice with high BCAA levels.
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Affiliation(s)
| | | | | | - Liqiang He
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou 570228, China
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10
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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [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: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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Uchida K, Kim JS, Sato M, Tabeta H, Mochida K, Hirai MY. A metabolome genome-wide association study implicates histidine N-pi-methyltransferase as a key enzyme in N-methylhistidine biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1201129. [PMID: 37360714 PMCID: PMC10285387 DOI: 10.3389/fpls.2023.1201129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023]
Abstract
A genome-wide association study (GWAS), which uses information on single nucleotide polymorphisms (SNPs) from many accessions, has become a powerful approach to gene identification. A metabolome GWAS (mGWAS), which relies on phenotypic information based on metabolite accumulation, can identify genes that contribute to primary and secondary metabolite contents. In this study, we carried out a mGWAS using seed metabolomic data from Arabidopsis thaliana accessions obtained by liquid chromatography-mass spectrometry to identify SNPs highly associated with the contents of metabolites such as glucosinolates. These SNPs were present in genes known to be involved in glucosinolate biosynthesis, thus confirming the effectiveness of our analysis. We subsequently focused on SNPs detected in an unknown methyltransferase gene associated with N-methylhistidine content. Knockout and overexpression of A. thaliana lines of this gene had significantly decreased and increased N-methylhistidine contents, respectively. We confirmed that the overexpressing line exclusively accumulated histidine methylated at the pi position, not at the tau position. Our findings suggest that the identified methyltransferase gene encodes a key enzyme for N-methylhistidine biosynthesis in A. thaliana.
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Affiliation(s)
- Kai Uchida
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - June-Sik Kim
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Hiromitsu Tabeta
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan
- RIKEN Baton Zone Program, Yokohama, Kanagawa, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Department of Applied Biosciences, Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Japan
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12
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Yuxiao Z, Guo Y, Xinhua S. Comprehensive insight into an amino acid metabolic network in postharvest horticultural products: a review. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023. [PMID: 37066732 DOI: 10.1002/jsfa.12638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 06/19/2023]
Abstract
Amino acid (AA) metabolism plays a vital role in the central metabolism of plants. In addition to protein biosynthesis, AAs are involved in secondary metabolite biosynthesis, signal transduction, stress response, defense against pathogens, flavor formation, and so on. Besides these functions, AAs can be degraded into precursors or intermediates of the tricarboxylic acid cycle to substitute respiratory substrates and restore energy homeostasis, as well as directly acting as signal molecules or be involved in the regulation of plant signals to delay senescence of postharvest horticultural products (PHPs). AA metabolism and its role in plants growth have been clarified; however, only a few studies about their roles exist concerning the postharvest preservation of fruit and vegetables. This study reviews the potential functions of various AAs by comparing the difference in AA metabolism at the postharvest stage and then discusses the crosstalk of AA metabolism and energy metabolism, the target of rapamycin/sucrose nonfermenting-related kinase 1 signaling and secondary metabolism. Finally, the roles and effect mechanism of several exogenous AAs in the preservation of PHPs are highlighted. This review provides a comprehensive insight into the AA metabolism network in PHPs. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Zhang Yuxiao
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zi'bo, China
| | - Yanyin Guo
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zi'bo, China
| | - Song Xinhua
- College of Life Science, Shandong University of Technology, Zi'bo, China
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13
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Hurst JP, Yobi A, Li A, Sato S, Clemente TE, Angelovici R, Holding DR. Large and stable genome edits at the sorghum alpha kafirin locus result in changes in chromatin accessibility and globally increased expression of genes encoding lysine enrichment. FRONTIERS IN PLANT SCIENCE 2023; 14:1116886. [PMID: 36998682 PMCID: PMC10043997 DOI: 10.3389/fpls.2023.1116886] [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: 12/05/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Sorghum is a resilient and widely cultivated grain crop used for feed and food. However, it's grain is deficient in lysine, an essential amino acid. This is due to the primary seed storage proteins, the alpha-kafirins, lacking lysine. It has been observed that reductions in alpha-kafirin protein results in rebalancing of the seed proteome and a corresponding increase in non-kafirin proteins which leads to an increased lysine content. However, the mechanisms underlying proteome rebalancing are unclear. This study characterizes a previously developed gene edited sorghum line, with deletions at the alpha kafirin locus. METHODS A single consensus guide RNA leads to tandem deletion of multiple members of the gene family in addition to the small target site mutations in remaining genes. RNA-seq and ATAC-seq were utilized to identify changes in gene expression and chromatin accessibility in developing kernels in the absence of most alpha-kafirin expression. RESULTS Several differentially accessible chromatin regions and differentially expressed genes were identified. Additionally, several genes upregulated in the edited sorghum line were common with their syntenic orthologues differentially expressed in maize prolamin mutants. ATAC-seq showed enrichment of the binding motif for ZmOPAQUE 11, perhaps indicating the transcription factor's involvement in the kernel response to reduced prolamins. DISCUSSION Overall, this study provides a resource of genes and chromosomal regions which may be involved in sorghum's response to reduced seed storage proteins and the process of proteome rebalancing.
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Affiliation(s)
- J. Preston Hurst
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Abou Yobi
- School of Life Sciences, Ministry of Education, Shandong University, Jinan, China
| | - Aixia Li
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Shirley Sato
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Thomas E. Clemente
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Ruthie Angelovici
- School of Life Sciences, Ministry of Education, Shandong University, Jinan, China
| | - David R. Holding
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
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14
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Shim JS, Jeong HI, Bang SW, Jung SE, Kim G, Kim YS, Redillas MCFR, Oh SJ, Seo JS, Kim JK. DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE enhances drought tolerance in rice. PLANT PHYSIOLOGY 2023; 191:1435-1447. [PMID: 36493384 PMCID: PMC9922417 DOI: 10.1093/plphys/kiac560] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/13/2022] [Indexed: 06/17/2023]
Abstract
Plants accumulate several metabolites in response to drought stress, including branched-chain amino acids (BCAAs). However, the roles of BCAAs in plant drought responses and the underlying molecular mechanisms for BCAA accumulation remain elusive. Here, we demonstrate that rice (Oryza sativa) DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE (OsDIAT) mediates the accumulation of BCAAs in rice in response to drought stress. An in vitro enzyme activity assay indicated that OsDIAT is a branched-chain amino acid aminotransferase, and subcellular localization analysis revealed that OsDIAT localizes to the cytoplasm. The expression of OsDIAT was induced in plants upon exposure to abiotic stress. OsDIAT-overexpressing (OsDIATOX) plants were more tolerant to drought stress, whereas osdiat plants were more susceptible to drought stress compared with nontransgenic (NT) plants. Amino acid analysis revealed that BCAA levels were higher in OsDIATOX but lower in osdiat compared with in NT plants. Finally, the exogenous application of BCAAs improved plant tolerance to osmotic stress compared with that in control plants. Collectively, these findings suggest that OsDIAT mediates drought tolerance by promoting the accumulation of BCAAs.
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Affiliation(s)
| | | | - Seung Woon Bang
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Se Eun Jung
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Goeun Kim
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Mark Christian Felipe R Redillas
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
- Department of Biology, De La Salle University, Manila 1004, Philippines
| | - Se-Jun Oh
- LaSemilla Co. Ltd., Pyeongchang 25354, Korea
| | - Jun Sung Seo
- Author for correspondence: (J. S. S.); (J.-K. K.)
| | - Ju-Kon Kim
- Author for correspondence: (J. S. S.); (J.-K. K.)
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15
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Yuan W, Huang J, Li H, Ma Y, Gui C, Huang F, Feng X, Yu D, Wang H, Kan G. Genetic dissection reveals the complex architecture of amino acid composition in soybean seeds. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:17. [PMID: 36670242 DOI: 10.1007/s00122-023-04280-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Five loci related to soybean protein and amino acid contents were colocated by performing linkage mapping and GWAS. The haplotype analysis showed that Glyma.08G109100 may be useful to improve the soybean seed composition. Soybean (Glycine max (L.) Merr.) seeds are good protein sources. Although genetic variation is abundant, natural variation in seed amino acids and their derived traits is lacking across soybean accessions. Here, we determined the contents of protein and 17 amino acids, obtained 36 derived traits based on the protein and total amino acid contents, and derived 34 traits based on seven amino acid family groups. Furthermore, we performed a linkage analysis of the contents of 17 amino acids and 73 amino acid-derived traits based on the recombinant inbred line (RIL)-derived Kefeng No. 1 × Nannong 1138-2. Six hundred thirty-nine quantitative trait loci (QTLs) were identified, explaining 6.07-39.00% of the phenotypic variation. Among these loci, five were detected in diverse soybean accessions using a genome-wide association study. A network analysis revealed that some loci that were significantly associated with multiple amino acids were tightly linked on chromosome 8 based on linkage disequilibrium values, which also further confirmed the results of the correlation analysis among amino acid traits. Through a combination of a genome-wide association study, linkage analysis, qRT-PCR, and genomic polymorphism comparison, Glyma.08G109100 on chromosome 8, which may affect amino acid contents, was selected. The haplotype analysis showed that Hap-T of Glyma.08G109100 may be useful to improve the contents of protein and 16 amino acids in soybean. This study provides new insights into the genetic basis of the amino acid composition in soybean seeds and may facilitate marker-based breeding of soybean with improved nutritional value.
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Affiliation(s)
- Wenjie Yuan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jie Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Haiyang Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yujie Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chunju Gui
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Fang Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Hui Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
| | - Guizhen Kan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
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16
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He L, Wang H, Sui Y, Miao Y, Jin C, Luo J. Genome-wide association studies of five free amino acid levels in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1048860. [PMID: 36420042 PMCID: PMC9676653 DOI: 10.3389/fpls.2022.1048860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Rice (Oryza sativa L.) is one of the important staple foods for human consumption and livestock use. As a complex quality trait, free amino acid (FAA) content in rice is of nutritional importance. To dissect the genetic mechanism of FAA level, five amino acids' (Val, Leu, Ile, Arg, and Trp) content and 4,325,832 high-quality SNPs of 448 rice accessions were used to conduct genome-wide association studies (GWAS) with nine different methods. Of these methods, one single-locus method (GEMMA), seven multi-locus methods (mrMLM, pLARmEB, FASTmrEMMA, pKWmEB, FASTmrMLM, ISIS EM-BLASSO, and FarmCPU), and the recent released 3VmrMLM were adopted for methodological comparison of quantitative trait nucleotide (QTN) detection and identification of stable quantitative trait nucleotide loci (QTLs). As a result, 987 QTNs were identified by eight multi-locus GWAS methods; FASTmrEMMA detected the most QTNs (245), followed by 3VmrMLM (160), and GEMMA detected the least QTNs (0). Among 88 stable QTLs identified by the above methods, 3VmrMLM has some advantages, such as the most common QTNs, the highest LOD score, and the highest proportion of all detected stable QTLs. Around these stable QTLs, candidate genes were found in the GO classification to be involved in the primary metabolic process, biosynthetic process, and catalytic activity, and shown in KEGG analysis to have participated in metabolic pathways, biosynthesis of amino acids, and tryptophan metabolism. Natural variations of candidate genes resulting in the content alteration of five FAAs were identified in this association panel. In addition, 95 QTN-by-environment interactions (QEIs) of five FAA levels were detected by 3VmrMLM only. GO classification showed that the candidate genes got involved in the primary metabolic process, transport, and catalytic activity. Candidate genes of QEIs played important roles in valine, leucine, and isoleucine degradation (QEI_09_03978551 and candidate gene LOC_Os09g07830 in the Leu dataset), tryptophan metabolism (QEI_01_00617184 and candidate gene LOC_Os01g02020 in the Trp dataset), and glutathione metabolism (QEI_12_09153839 and candidate gene LOC_Os12g16200 in the Arg dataset) pathways through KEGG analysis. As an alternative of the multi-locus GWAS method, these findings suggested that the application of 3VmrMLM may provide new insights into better understanding FAA accumulation and facilitate the molecular breeding of rice with high FAA level.
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Affiliation(s)
- Liqiang He
- College of Tropical Crops, Hainan University, Haikou, China
| | - Huixian Wang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yao Sui
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yuanyuan Miao
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Cheng Jin
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
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17
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Wu L, Zheng Y, Jiao F, Wang M, Zhang J, Zhang Z, Huang Y, Jia X, Zhu L, Zhao Y, Guo J, Chen J. Identification of quantitative trait loci for related traits of stalk lodging resistance using genome-wide association studies in maize (Zea mays L.). BMC Genom Data 2022; 23:76. [PMID: 36319954 PMCID: PMC9623923 DOI: 10.1186/s12863-022-01091-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 10/10/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Stalk lodging is one of the main factors affecting maize (Zea mays L.) yield and limiting mechanized harvesting. Developing maize varieties with high stalk lodging resistance requires exploring the genetic basis of lodging resistance-associated agronomic traits. Stalk strength is an important indicator to evaluate maize lodging and can be evaluated by measuring stalk rind penetrometer resistance (RPR) and stalk buckling strength (SBS). Along with morphological traits of the stalk for the third internodes length (TIL), fourth internode length (FIL), third internode diameter (TID), and the fourth internode diameter (FID) traits are associated with stalk lodging resistance. RESULTS In this study, a natural population containing 248 diverse maize inbred lines genotyped with 83,057 single nucleotide polymorphism (SNP) markers was used for genome-wide association study (GWAS) for six stalk lodging resistance-related traits. The heritability of all traits ranged from 0.59 to 0.72 in the association mapping panel. A total of 85 significant SNPs were identified for the association mapping panel using best linear unbiased prediction (BLUP) values of all traits. Additionally, five candidate genes were associated with stalk strength traits, which were either directly or indirectly associated with cell wall components. CONCLUSIONS These findings contribute to our understanding of the genetic basis of maize stalk lodging and provide valuable theoretical guidance for lodging resistance in maize breeding in the future.
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Affiliation(s)
- Lifen Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Yunxiao Zheng
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Fuchao Jiao
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Shandong, Qingdao 266109 China
| | - Ming Wang
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Shandong, Qingdao 266109 China
| | - Jing Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Zhongqin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Yaqun Huang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Xiaoyan Jia
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Liying Zhu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Yongfeng Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Jinjie Guo
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Jingtang Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China ,grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Shandong, Qingdao 266109 China
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18
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Cai Y, Chen H, Tang X, Zhao J, Zhang H, Chen YQ, Chen W. The relationship between amino acid and lipid metabolism in oleaginous eukaryotic microorganism. Appl Microbiol Biotechnol 2022; 106:3405-3417. [PMID: 35503470 DOI: 10.1007/s00253-022-11931-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022]
Abstract
Amino acids are the building blocks of protein, promoting the balance between growth and lipid synthesis. However, the accumulation of microbial lipids involves multiple pathways, which requires the analysis of the global cellular metabolic network in which amino acid metabolism is involved. This review illustrates the dependence patterns of intracellular amino acids and lipids of oleaginous eukaryotic microorganisms in different environments and points out the contribution of amino acid metabolic precursors to the de novo synthesis of fatty acids. We emphasized the key role of amino acid metabolism in lipid remodeling and autophagy behavior and highlighted the regulatory effects of amino acids and their secondary metabolites as signal factors for microbial lipid synthesis. The application prospects of omics technology and genetic engineering technology in the field of microbial lipids are described. KEY POINTS: • Overview of microbial lipid synthesis mediated by amino acid metabolism • Insight into metabolic mechanisms founding multiple regulatory networks is provided • Description of microbial lipid homeostasis mediated by amino acid excitation signal.
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Affiliation(s)
- Yibo Cai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China. .,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China. .,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China.
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, 214122, People's Republic of China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 5: , 27127, USA
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China
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19
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Zhu F, Alseekh S, Koper K, Tong H, Nikoloski Z, Naake T, Liu H, Yan J, Brotman Y, Wen W, Maeda H, Cheng Y, Fernie AR. Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis. THE PLANT CELL 2022; 34:557-578. [PMID: 34623442 PMCID: PMC8774053 DOI: 10.1093/plcell/koab251] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 10/05/2021] [Indexed: 05/31/2023]
Abstract
Dark-induced senescence provokes profound metabolic shifts to recycle nutrients and to guarantee plant survival. To date, research on these processes has largely focused on characterizing mutants deficient in individual pathways. Here, we adopted a time-resolved genome-wide association-based approach to characterize dark-induced senescence by evaluating the photochemical efficiency and content of primary and lipid metabolites at the beginning, or after 3 or 6 days in darkness. We discovered six patterns of metabolic shifts and identified 215 associations with 81 candidate genes being involved in this process. Among these associations, we validated the roles of four genes associated with glycine, galactinol, threonine, and ornithine levels. We also demonstrated the function of threonine and galactinol catabolism during dark-induced senescence. Intriguingly, we determined that the association between tyrosine contents and TYROSINE AMINOTRANSFERASE 1 influences enzyme activity of the encoded protein and transcriptional activity of the gene under normal and dark conditions, respectively. Moreover, the single-nucleotide polymorphisms affecting the expression of THREONINE ALDOLASE 1 and the amino acid transporter gene AVT1B, respectively, only underlie the variation in threonine and glycine levels in the dark. Taken together, these results allow us to present a very detailed model of the metabolic aspects of dark-induced senescence, as well as the process itself.
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Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Kaan Koper
- Department of Botany, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Hao Tong
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
| | - Thomas Naake
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna 1030, Austria
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Weiwei Wen
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hiroshi Maeda
- Department of Botany, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
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Shrestha V, Yobi A, Slaten ML, Chan YO, Holden S, Gyawali A, Flint-Garcia S, Lipka AE, Angelovici R. Multiomics approach reveals a role of translational machinery in shaping maize kernel amino acid composition. PLANT PHYSIOLOGY 2022; 188:111-133. [PMID: 34618082 PMCID: PMC8774818 DOI: 10.1093/plphys/kiab390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Maize (Zea mays) seeds are a good source of protein, despite being deficient in several essential amino acids. However, eliminating the highly abundant but poorly balanced seed storage proteins has revealed that the regulation of seed amino acids is complex and does not rely on only a handful of proteins. In this study, we used two complementary omics-based approaches to shed light on the genes and biological processes that underlie the regulation of seed amino acid composition. We first conducted a genome-wide association study to identify candidate genes involved in the natural variation of seed protein-bound amino acids. We then used weighted gene correlation network analysis to associate protein expression with seed amino acid composition dynamics during kernel development and maturation. We found that almost half of the proteome was significantly reduced during kernel development and maturation, including several translational machinery components such as ribosomal proteins, which strongly suggests translational reprogramming. The reduction was significantly associated with a decrease in several amino acids, including lysine and methionine, pointing to their role in shaping the seed amino acid composition. When we compared the candidate gene lists generated from both approaches, we found a nonrandom overlap of 80 genes. A functional analysis of these genes showed a tight interconnected cluster dominated by translational machinery genes, especially ribosomal proteins, further supporting the role of translation dynamics in shaping seed amino acid composition. These findings strongly suggest that seed biofortification strategies that target the translation machinery dynamics should be considered and explored further.
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Affiliation(s)
- Vivek Shrestha
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Abou Yobi
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Marianne L Slaten
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Yen On Chan
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Samuel Holden
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Abiskar Gyawali
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Sherry Flint-Garcia
- U.S. Department of Agriculture-Agricultural Research Service, Columbia, Missouri 65211, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, USA
| | - Ruthie Angelovici
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
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21
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da Fonseca-Pereira P, Pham PA, Cavalcanti JHF, Omena-Garcia RP, Barros JAS, Rosado-Souza L, Vallarino JG, Mutwil M, Avin-Wittenberg T, Nunes-Nesi A, Fernie AR, Araújo WL. The Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase is required during normal seed development and germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:196-214. [PMID: 34741366 DOI: 10.1111/tpj.15566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
The importance of the alternative donation of electrons to the ubiquinol pool via the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) complex has been demonstrated. However, the functional significance of this pathway during seed development and germination remains to be elucidated. To assess the function of this pathway, we performed a detailed metabolic and transcriptomic analysis of Arabidopsis mutants to test the molecular consequences of a dysfunctional ETF/ETFQO pathway. We demonstrate that the disruption of this pathway compromises seed germination in the absence of an external carbon source and also impacts seed size and yield. Total protein and storage protein content is reduced in dry seeds, whilst sucrose levels remain invariant. Seeds of ETFQO and related mutants were also characterized by an altered fatty acid composition. During seed development, lower levels of fatty acids and proteins accumulated in the etfqo-1 mutant as well as in mutants in the alternative electron donors isovaleryl-CoA dehydrogenase (ivdh-1) and d-2-hydroxyglutarate dehydrogenase (d2hgdh1-2). Furthermore, the content of several amino acids was increased in etfqo-1 mutants during seed development, indicating that these mutants are not using such amino acids as alternative energy source for respiration. Transcriptome analysis revealed alterations in the expression levels of several genes involved in energy and hormonal metabolism. Our findings demonstrated that the alternative pathway of respiration mediated by the ETF/ETFQO complex affects seed germination and development by directly adjusting carbon storage during seed filling. These results indicate a role for the pathway in the normal plant life cycle to complement its previously defined roles in the response to abiotic stress.
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Affiliation(s)
- Paula da Fonseca-Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Phuong Anh Pham
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - João Henrique F Cavalcanti
- Instituto de Educação, Agricultura e Ambiente, Universidade Federal do Amazonas, Humaitá, Amazonas, Brazil
| | - Rebeca P Omena-Garcia
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Jessica A S Barros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Laise Rosado-Souza
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - José G Vallarino
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Tamar Avin-Wittenberg
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, 9190401, Israel
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
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22
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Joshi V, Nimmakayala P, Song Q, Abburi V, Natarajan P, Levi A, Crosby K, Reddy UK. Genome-wide association study and population structure analysis of seed-bound amino acids and total protein in watermelon. PeerJ 2021; 9:e12343. [PMID: 34722000 PMCID: PMC8533027 DOI: 10.7717/peerj.12343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/28/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Watermelon seeds are a powerhouse of value-added traits such as proteins, free amino acids, vitamins, and essential minerals, offering a paleo-friendly dietary option. Despite the availability of substantial genetic variation, there is no sufficient information on the natural variation in seed-bound amino acids or proteins across the watermelon germplasm. This study aimed to analyze the natural variation in watermelon seed amino acids and total protein and explore underpinning genetic loci by genome-wide association study (GWAS). METHODS The study evaluated the distribution of seed-bound free amino acids and total protein in 211 watermelon accessions of Citrullus spp, including 154 of Citrullus lanatus, 54 of Citrullus mucosospermus (egusi) and three of Citrullus amarus. We used the GWAS approach to associate seed phenotypes with 11,456 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS). RESULTS Our results demonstrate a significant natural variation in different free amino acids and total protein content across accessions and geographic regions. The accessions with high protein content and proportion of essential amino acids warrant its use for value-added benefits in the food and feed industries via biofortification. The GWAS analysis identified 188 SNPs coinciding with 167 candidate genes associated with watermelon seed-bound amino acids and total protein. Clustering of SNPs associated with individual amino acids found by principal component analysis was independent of the speciation or cultivar groups and was not selected during the domestication of sweet watermelon. The identified candidate genes were involved in metabolic pathways associated with amino acid metabolism, such as Argininosuccinate synthase, explaining 7% of the variation in arginine content, which validate their functional relevance and potential for marker-assisted analysis selection. This study provides a platform for exploring potential gene loci involved in seed-bound amino acids metabolism, useful in genetic analysis and development of watermelon varieties with superior seed nutritional values.
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Affiliation(s)
- Vijay Joshi
- Department of Horticultural Sciences, Texas A&M University, Uvalde, Texas, United States
- Texas A&M AgriLife Research and Extension Center, Uvalde, Texas, United States
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
| | - Qiushuo Song
- Department of Horticultural Sciences, Texas A&M University, Uvalde, Texas, United States
| | - Venkata Abburi
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
| | - Amnon Levi
- Vegetable Laboratory, USDA-ARS, Charleston, South Carolina, United States
| | - Kevin Crosby
- Department of Horticultural Sciences, Texas A&M University, Uvalde, Texas, United States
| | - Umesh K. Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
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23
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Breeding Canola ( Brassica napus L.) for Protein in Feed and Food. PLANTS 2021; 10:plants10102220. [PMID: 34686029 PMCID: PMC8539702 DOI: 10.3390/plants10102220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 01/12/2023]
Abstract
Interest in canola (Brassica napus L.). In response to this interest, scientists have been tasked with altering and optimizing the protein production chain to ensure canola proteins are safe for consumption and economical to produce. Specifically, the role of plant breeders in developing suitable varieties with the necessary protein profiles is crucial to this interdisciplinary endeavour. In this article, we aim to provide an overarching review of the canola protein chain from the perspective of a plant breeder, spanning from the genetic regulation of seed storage proteins in the crop to advancements of novel breeding technologies and their application in improving protein quality in canola. A review on the current uses of canola meal in animal husbandry is presented to underscore potential limitations for the consumption of canola meal in mammals. General discussions on the allergenic potential of canola proteins and the regulation of novel food products are provided to highlight some of the challenges that will be encountered on the road to commercialization and general acceptance of canola protein as a dietary protein source.
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24
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Heinemann B, Hildebrandt TM. The role of amino acid metabolism in signaling and metabolic adaptation to stress-induced energy deficiency in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4634-4645. [PMID: 33993299 DOI: 10.1093/jxb/erab182] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/26/2021] [Indexed: 05/26/2023]
Abstract
The adaptation of plant metabolism to stress-induced energy deficiency involves profound changes in amino acid metabolism. Anabolic reactions are suppressed, whereas respiratory pathways that use amino acids as alternative substrates are activated. This review highlights recent progress in unraveling the stress-induced amino acid oxidation pathways, their regulation, and the role of amino acids as signaling molecules. We present an updated map of the degradation pathways for lysine and the branched-chain amino acids. The regulation of amino acid metabolism during energy deprivation, including the coordinated induction of several catabolic pathways, is mediated by the balance between TOR and SnRK signaling. Recent findings indicate that some amino acids might act as nutrient signals in TOR activation and thus promote a shift from catabolic to anabolic pathways. The metabolism of the sulfur-containing amino acid cysteine is highly interconnected with TOR and SnRK signaling. Mechanistic details have recently been elucidated for cysteine signaling during the abscisic acid-dependent drought response. Local cysteine synthesis triggers abscisic acid production and, in addition, cysteine degradation produces the gaseous messenger hydrogen sulfide, which promotes stomatal closure via protein persulfidation. Amino acid signaling in plants is still an emerging topic with potential for fundamental discoveries.
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Affiliation(s)
- Björn Heinemann
- Institute for Plant Genetics, Department of Plant Proteomics, Leibniz University Hannover, Herrenhäuser Straße, Hannover, Germany
| | - Tatjana M Hildebrandt
- Institute for Plant Genetics, Department of Plant Proteomics, Leibniz University Hannover, Herrenhäuser Straße, Hannover, Germany
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25
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Parsons L, Ren Y, Yobi A, Angelovici R, Rodriguez O, Holding DR. Final Selection of Quality Protein Popcorn Hybrids. FRONTIERS IN PLANT SCIENCE 2021; 12:658456. [PMID: 33841483 PMCID: PMC8025670 DOI: 10.3389/fpls.2021.658456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
Quality Protein Popcorn (QPP) BC2F5 inbred lines were produced through an interpopulation breeding system between Quality Protein Maize dent (QPM) and elite popcorn germplasm. In 2019, five QPP F1 hybrids were selected for further evaluation due to superior agronomics, endosperm protein quality, and popping quality traits. Though these BC2F5 QPP hybrids were phenotypically similar to their popcorn parents, the QPP cultivars conveyed slightly inferior popping characteristics when compared to the original popcorn germplasm. The objective of this study was twofold. First, BC2F5 inbred lines were crossed to their popcorn parents and BC3F4 inbred lines were produced for hybridization to test the agronomic, protein, and popping trait effects from an additional QPP by popcorn backcross. Second, BC2- and BC3-hybrids were simultaneously evaluated alongside ConAgra Brands® elite cultivars and ranked for potential commercialization in the spring of 2020. These 10 QPP hybrids were grown alongside five ConAgra Brands® elite popcorn cultivars in three locations and agronomic, protein quality, and popping quality traits were evaluated. Significant improvements in popcorn quality traits were observed in the QPP BC3 cultivars compared to their BC2 counterparts, and yield averages were significantly lower in BC3-derived QPP hybrids compared to the BC2 population. Protein quality traits were not significantly different between QPP backcrossing populations and significantly superior to ConAgra elite popcorn varieties. Utilizing a previously published ranking system, six QPP hybrids, three from the BC2F5 population and three from the BC3F4 population, were evaluated as candidates for final selection. The successful evaluation and ranking system methodology employed is transferable to other hybrid production and testing programs. Incorporating this analysis with concurrent sensory studies, two QPP hybrids were chosen as premier cultivars for potential commercialization.
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Affiliation(s)
- Leandra Parsons
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Ying Ren
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Abou Yobi
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Ruthie Angelovici
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | | | - David R. Holding
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska–Lincoln, Lincoln, NE, United States
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26
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Yoshida T, Yamaguchi-Shinozaki K. Metabolic engineering: Towards water deficiency adapted crop plants. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153375. [PMID: 33609854 DOI: 10.1016/j.jplph.2021.153375] [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: 12/01/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Water deficiency caused by drought is one of the severe environmental conditions limiting plant growth, development, and yield. In this review article, we will summarize the changes in transcription, metabolism, and phytohormones under drought stress conditions and show the key transcription factors in these processes. We will also highlight the recent attempts to enhance stress tolerance without growth retardation and discuss the perspective on the development of stress adapted crops by engineering transcription factors.
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Affiliation(s)
- Takuya Yoshida
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany; Centre of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 113-8657, Tokyo, Japan; Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, 156-8502, Tokyo, Japan
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27
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Goto T, Shimamoto S, Takaya M, Sato S, Takahashi K, Nishimura K, Morii Y, Kunishige K, Ohtsuka A, Ijiri D. Impact on genetic differences among various chicken breeds on free amino acid contents of egg yolk and albumen. Sci Rep 2021; 11:2270. [PMID: 33500483 PMCID: PMC7838262 DOI: 10.1038/s41598-021-81660-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Eggs play important roles as food resources and nutraceuticals, to alleviate malnutrition and to improve health status in the world. Since free amino acids contribute to the nutritional values and food tastes, we investigated a total of 81 eggs from five chicken breeds, which are Australorp, Nagoya (NGY), Rhode Island Red (RIR), Shamo (SHA), Ukokkei, and two F1 hybrids (NGYxRIR and SHAxRIR) to test impact on genetic differences in 10 egg traits, 20 yolk amino acid traits, and 18 albumen amino acid traits. One-way ANOVA revealed significant breed effects on 10 egg traits, 20 yolk amino acid traits, and 15 albumen amino acid traits. Moreover, a significant heterosis effect on yolk aspartic acid was identified. In addition, positive correlations were found broadly among traits within each trait category (egg traits, yolk amino acid traits, and albumen amino acid traits), whereas there were basically no or weak correlations among the trait categories. These results suggest that almost all traits can be dramatically modified by genetic factor, and there will be partially independent production systems of amino acids into yolk and albumen. Since there will be typical quantitative genetic architecture of egg contents, further genetic analyses will be needed.
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Affiliation(s)
- Tatsuhiko Goto
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan. .,Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan.
| | - Saki Shimamoto
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, 890-0065, Japan.,Graduate School of Science and Technology, Niigata University, Niigata, 950-2181, Japan
| | - Masahiro Takaya
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan.,Hokkaido Tokachi Area Regional Food Processing Technology Center, Tokachi Foundation, Obihiro, Hokkaido, 080-2462, Japan
| | - Shun Sato
- Agricultural Research Department, Animal Research Center, Hokkaido Research Organization, Shintoku, Hokkaido, 081-0038, Japan
| | - Kanna Takahashi
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Kenji Nishimura
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Yasuko Morii
- Agricultural Research Department, Animal Research Center, Hokkaido Research Organization, Shintoku, Hokkaido, 081-0038, Japan
| | - Kyoko Kunishige
- Agricultural Research Department, Animal Research Center, Hokkaido Research Organization, Shintoku, Hokkaido, 081-0038, Japan
| | - Akira Ohtsuka
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, 890-0065, Japan
| | - Daichi Ijiri
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, 890-0065, Japan
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28
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Dong S, Sang L, Xie H, Chai M, Wang ZY. Comparative Transcriptome Analysis of Salt Stress-Induced Leaf Senescence in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2021; 12:666660. [PMID: 34305965 PMCID: PMC8299074 DOI: 10.3389/fpls.2021.666660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/14/2021] [Indexed: 05/20/2023]
Abstract
Leaves are the most critical portion of forage crops such as alfalfa (Medicago sativa). Leaf senescence caused by environmental stresses significantly impacts the biomass and quality of forages. To understand the molecular mechanisms and identify the key regulator of the salt stress-induced leaf senescence process, we conducted a simple and effective salt stress-induced leaf senescence assay in Medicago truncatula, which was followed by RNA-Seq analysis coupled with physiological and biochemical characterization. By comparing the observed expression data with that derived from dark-induced leaf senescence at different time points, we identified 3,001, 3,787, and 4,419 senescence-associated genes (SAGs) for salt stress-induced leaf senescence on day 2, 4, and 6, respectively. There were 1546 SAGs shared by dark and salt stress treatment across the three time points. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that the 1546 SAGs were mainly related to protein and amino acids metabolism, photosynthesis, chlorophyll metabolism, and hormone signaling during leaf senescence. Strikingly, many different transcription factors (TFs) families out of the 1546 SAGs, including NAC, bHLH, MYB, and ERF, were associated with salt stress-induced leaf senescence processes. Using the transient expression system in Nicotiana benthamiana, we verified that three functional NAC TF genes from the 1546 SAGs were related to leaf senescence. These results clarify SAGs under salt stress in M. truncatula and provide new insights and additional genetic resources for further forage crop breeding.
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Affiliation(s)
| | | | | | - Maofeng Chai
- *Correspondence: Maofeng Chai orcid.org/0000-0001-9915-0321
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29
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Li Y, Yang C, Ahmad H, Maher M, Fang C, Luo J. Benefiting others and self: Production of vitamins in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:210-227. [PMID: 33289302 DOI: 10.1111/jipb.13047] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Vitamins maintain growth and development in humans, animals, and plants. Because plants serve as essential producers of vitamins, increasing the vitamin contents in plants has become a goal of crop breeding worldwide. Here, we begin with a summary of the functions of vitamins. We then review the achievements to date in elucidating the molecular mechanisms underlying how vitamins are synthesized, transported, and regulated in plants. We also stress the exploration of variation in vitamins by the use of forward genetic approaches, such as quantitative trait locus mapping and genome-wide association studies. Overall, we conclude that exploring the diversity of vitamins could provide new insights into plant metabolism and crop breeding.
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Affiliation(s)
- Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hasan Ahmad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Mohamed Maher
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuanying Fang
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, 570228, China
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30
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Sun Y, Shi Y, Liu G, Yao F, Zhang Y, Yang C, Guo H, Liu X, Jin C, Luo J. Natural variation in the OsbZIP18 promoter contributes to branched-chain amino acid levels in rice. THE NEW PHYTOLOGIST 2020; 228:1548-1558. [PMID: 32654152 DOI: 10.1111/nph.16800] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/29/2020] [Indexed: 05/21/2023]
Abstract
Branched-chain amino acids (BCAAs) are essential amino acids that must be obtained from the diet for humans and animals, and they play important roles in various aspects of plant growth and development. Although BCAA biosynthetic pathways in higher plants have been uncovered, knowledge of their genetic control is still limited, and no positive regulators have been identified to date. Here, we showed that variation in BCAA levels in rice is attributable to differential transcription of OsbZIP18, a basic leucine zipper (bZIP) transcription factor, due to polymorphisms in its promoter. Functional analysis revealed that OsbZIP18 positively regulates BCAA synthesis by binding directly to the ACE and C-box cis-elements in the promoters of the biosynthetic genes branched-chain aminotransferase1 (OsBCAT1) and OsBCAT2. We further demonstrated that OsbZIP18 is strongly induced by nitrogen (N) deficiency and that N starvation results in enhanced BCAA levels in an OsbZIP18-dependent manner. Overall, we identified OsbZIP18, a positive regulator of BCAA biosynthesis, which contributed to natural variation in BCAA levels and mediated BCAA accumulation through de novo synthesis by directly modulating the key biosynthetic genes OsBCAT1 and OsBCAT2.
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Affiliation(s)
- Yangyang Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuheng Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Guige Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Yao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanyuan Zhang
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Guo
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Xianqing Liu
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Cheng Jin
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
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Genomic Prediction Informed by Biological Processes Expands Our Understanding of the Genetic Architecture Underlying Free Amino Acid Traits in Dry Arabidopsis Seeds. G3-GENES GENOMES GENETICS 2020; 10:4227-4239. [PMID: 32978264 PMCID: PMC7642941 DOI: 10.1534/g3.120.401240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Plant growth, development, and nutritional quality depends upon amino acid homeostasis, especially in seeds. However, our understanding of the underlying genetics influencing amino acid content and composition remains limited, with only a few candidate genes and quantitative trait loci identified to date. Improved knowledge of the genetics and biological processes that determine amino acid levels will enable researchers to use this information for plant breeding and biological discovery. Toward this goal, we used genomic prediction to identify biological processes that are associated with, and therefore potentially influence, free amino acid (FAA) composition in seeds of the model plant Arabidopsis thaliana. Markers were split into categories based on metabolic pathway annotations and fit using a genomic partitioning model to evaluate the influence of each pathway on heritability explained, model fit, and predictive ability. Selected pathways included processes known to influence FAA composition, albeit to an unknown degree, and spanned four categories: amino acid, core, specialized, and protein metabolism. Using this approach, we identified associations for pathways containing known variants for FAA traits, in addition to finding new trait-pathway associations. Markers related to amino acid metabolism, which are directly involved in FAA regulation, improved predictive ability for branched chain amino acids and histidine. The use of genomic partitioning also revealed patterns across biochemical families, in which serine-derived FAAs were associated with protein related annotations and aromatic FAAs were associated with specialized metabolic pathways. Taken together, these findings provide evidence that genomic partitioning is a viable strategy to uncover the relative contributions of biological processes to FAA traits in seeds, offering a promising framework to guide hypothesis testing and narrow the search space for candidate genes.
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32
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Dissecting the Seed Maturation and Germination Processes in the Non-Orthodox Quercus ilex Species Based on Protein Signatures as Revealed by 2-DE Coupled to MALDI-TOF/TOF Proteomics Strategy. Int J Mol Sci 2020; 21:ijms21144870. [PMID: 32660160 PMCID: PMC7402289 DOI: 10.3390/ijms21144870] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
Unlike orthodox species, seed recalcitrance is poorly understood, especially at the molecular level. In this regard, seed maturation and germination were studied in the non-orthodox Quercus ilex by using a proteomics strategy based on two-dimensional gel electrophoresis coupled to matrix-assisted laser desorption ionization/time of flight (2-DE-MALDI-TOF).Cotyledons and embryo/radicle were sampled at different developmental stages, including early (M1–M3), middle (M4–M7), and late (M8–M9) seed maturation, and early (G1–G3) and late (G4–G5) germination. Samples corresponding to non-germinating, inviable, seeds were also included. Protein extracts were subjected to 2-dimensional gel electrophoresis (2-DE) and changes in the protein profiles were analyzed. Identified variable proteins were grouped according to their function, being the energy, carbohydrate, lipid, and amino acid metabolisms, together with protein fate, redox homeostasis, and response to stress are the most represented groups. Beyond the visual aspect, morphometry, weight, and water content, each stage had a specific protein signature. Clear tendencies for the different protein groups throughout the maturation and germination stages were observed for, respectively, cotyledon and the embryo axis. Proteins related to metabolism, translation, legumins, proteases, proteasome, and those stress related were less abundant in non-germinating seeds, it related to the loss of viability. Cotyledons were enriched with reserve proteins and protein-degrading enzymes, while the embryo axis was enriched with proteins of cell defense and rescue, including heat-shock proteins (HSPs) and antioxidants. The peaks of enzyme proteins occurred at the middle stages (M6–M7) in cotyledons and at late ones (M8–M9) in the embryo axis. Unlike orthodox seeds, proteins associated with glycolysis, tricarboxylic acid cycle, carbohydrate, amino acid and lipid metabolism are present at high levels in the mature seed and were maintained throughout the germination stages. The lack of desiccation tolerance in Q. ilex seeds may be associated with the repression of some genes, late embryogenesis abundant proteins being one of the candidates.
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Tohge T, Scossa F, Wendenburg R, Frasse P, Balbo I, Watanabe M, Alseekh S, Jadhav SS, Delfin JC, Lohse M, Giavalisco P, Usadel B, Zhang Y, Luo J, Bouzayen M, Fernie AR. Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex. MOLECULAR PLANT 2020; 13:1027-1046. [PMID: 32305499 DOI: 10.1016/j.molp.2020.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 02/01/2020] [Accepted: 04/11/2020] [Indexed: 05/10/2023]
Abstract
While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species, those defining specialized metabolism are less well characterized and more highly variable across species. In this study, we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the metabolic network of polyphenols across eight different species of tomato. For this purpose, GC-MS- and LC-MS-based metabolomics of different tissues of Solanum lycopersicum and wild tomato species were carried out, in concert with the evaluation of cross-hybridized microarray data for MapMan-based transcriptomic analysis, and publicly available RNA-sequencing data for annotation of biosynthetic genes. The combined data were used to compile species-specific metabolic networks of polyphenolic metabolism, allowing the establishment of an entire pan-species biosynthetic framework as well as annotation of the functions of decoration enzymes involved in the formation of metabolic diversity of the flavonoid pathway. The combined results are discussed in the context of the current understanding of tomato flavonol biosynthesis as well as a global view of metabolic shifts during fruit ripening. Our results provide an example as to how large-scale biology approaches can be used for the definition and refinement of large specialized metabolism pathways.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via Ardeatina 546 00178 Rome, Italy
| | - Regina Wendenburg
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Pierre Frasse
- Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan 31326, France
| | - Ilse Balbo
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria
| | - Sagar Sudam Jadhav
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jay C Delfin
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Marc Lohse
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany
| | - Bjoern Usadel
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52056 Aachen, Germany
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Mondher Bouzayen
- Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan 31326, France
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria.
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Buffagni V, Vurro F, Janni M, Gullì M, Keller AA, Marmiroli N. Shaping Durum Wheat for the Future: Gene Expression Analyses and Metabolites Profiling Support the Contribution of BCAT Genes to Drought Stress Response. FRONTIERS IN PLANT SCIENCE 2020; 11:891. [PMID: 32719694 PMCID: PMC7350509 DOI: 10.3389/fpls.2020.00891] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Global climate change, its implications for agriculture, and the complex scenario presented by the scientific community are of worldwide concern. Drought is a major abiotic stress that can restrict plants growth and yields, thus the identification of genotypes with higher adaptability to drought stress represents one of the primary goals in breeding programs. During abiotic stress, metabolic adaptation is crucial for stress tolerance, and accumulation of specific amino acids and/or as secondary metabolites deriving from amino acid metabolism may correlate with the increased tolerance to adverse environmental conditions. This work, focused on the metabolism of branched chain-amino acids (BCAAs) in durum wheat and the role of branched-chain amino acid aminotransferases (BCATs) in stress response. The role of BCATs in plant response to drought was previously proposed for Arabidopsis, where the levels of BCAAs were altered at the transcriptional level under drought conditions, triggering the onset of defense response metabolism. However, in wheat the role of BCAAs as a trigger of the onset of the drought defense response has not been elucidated. A comparative genomic approach elucidated the composition of the BCAT gene family in durum wheat. Here we demonstrate a tissue and developmental stage specificity of BCATs regulation in the drought response. Moreover, a metabolites profiling was performed on two contrasting durum wheat cultivars Colosseo and Cappelli resulting in the detection of a specific pattern of metabolites accumulated among genotypes and, in particular, in an enhanced BCAAs accumulation in the tolerant cv Cappelli further supporting a role of BCAAs in the drought defense response. The results support the use of gene expression and target metabolomic in modern breeding to shape new cultivars more resilient to a changing climate.
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Affiliation(s)
- Valentina Buffagni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Filippo Vurro
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parma, Italy
| | - Michela Janni
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parma, Italy
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Bari, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Arturo A. Keller
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- CINSA Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
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35
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Shi T, Zhu A, Jia J, Hu X, Chen J, Liu W, Ren X, Sun D, Fernie AR, Cui F, Chen W. Metabolomics analysis and metabolite-agronomic trait associations using kernels of wheat (Triticum aestivum) recombinant inbred lines. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:279-292. [PMID: 32073701 PMCID: PMC7383920 DOI: 10.1111/tpj.14727] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/17/2020] [Accepted: 02/07/2020] [Indexed: 05/21/2023]
Abstract
Plants produce numerous metabolites that are important for their development and growth. However, the genetic architecture of the wheat metabolome has not been well studied. Here, utilizing a high-density genetic map, we conducted a comprehensive metabolome study via widely targeted LC-MS/MS to analyze the wheat kernel metabolism. We further combined agronomic traits and dissected the genetic relationship between metabolites and agronomic traits. In total, 1260 metabolic features were detected. Using linkage analysis, 1005 metabolic quantitative trait loci (mQTLs) were found distributed unevenly across the genome. Twenty-four candidate genes were found to modulate the levels of different metabolites, of which two were functionally annotated by in vitro analysis to be involved in the synthesis and modification of flavonoids. Combining the correlation analysis of metabolite-agronomic traits with the co-localization of methylation quantitative trait locus (mQTL) and phenotypic QTL (pQTL), genetic relationships between the metabolites and agronomic traits were uncovered. For example, a candidate was identified using correlation and co-localization analysis that may manage auxin accumulation, thereby affecting number of grains per spike (NGPS). Furthermore, metabolomics data were used to predict the performance of wheat agronomic traits, with metabolites being found that provide strong predictive power for NGPS and plant height. This study used metabolomics and association analysis to better understand the genetic basis of the wheat metabolism which will ultimately assist in wheat breeding.
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Affiliation(s)
- Taotao Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan430070China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Anting Zhu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan430070China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Jingqi Jia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan430070China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan430070China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan430070China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan430070China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Xifeng Ren
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Dongfa Sun
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdam‐Golm14476Germany
| | - Fa Cui
- Wheat Molecular Breeding Innovation Research GroupKey Laboratory of Molecular Module‐Based Breeding of High Yield and Abiotic Resistant Plants in Universities of ShandongSchool of AgricultureLudong UniversityYantaiChina
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan430070China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
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36
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Parsons L, Ren Y, Yobi A, Hurst P, Angelovici R, Rodriguez O, Holding DR. Production and Selection of Quality Protein Popcorn Hybrids Using a Novel Ranking System and Combining Ability Estimates. FRONTIERS IN PLANT SCIENCE 2020; 11:698. [PMID: 32655587 PMCID: PMC7325744 DOI: 10.3389/fpls.2020.00698] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/04/2020] [Indexed: 05/27/2023]
Abstract
Popcorn varieties are agronomically sub-optimal and genetically limited compared to other maize subspecies. To increase genetic diversity and improve popcorn agronomics, dent germplasm has been introduced to popcorn with limited success and generally, major loss of popping. Between 2013 and 2018, 12 Quality Protein Popcorn (QPP) inbreds containing Quality Protein Maize (QPM) and popcorn germplasm were produced that maintained popping while carrying the opaque-2 allele conferring elevated kernel lysine. This is an opportune trait in the growing market for healthier snacks and a model for mining QPM traits into popcorn. We crossed QPP inbreds to explore the effects of heterosis on popcorn protein, popping quality, and plant agronomics and selected hybrids for further production. To rank and intermediately prescreen hybrids, we utilized a novel hybrid-ranking model adapted from a rank summation index while examining the inbred general combining ability and hybrid specific combining ability estimates for all traits. We observed a biological manifestation of heterosis by categorizing hybrids by pedigree that resulted in a stepwise progression of trait improvement. These results corroborated our hybrid selection and offered insight in basic heterosis research. Estimates for popcorn quality and agronomic trait covariances also suggest the synergistic introgression of highly vitreous dent maize (QPM) into popcorn, providing a likely explanation for the successfully maintained vitreous endosperm, protein quality and popping traits in line with a remodeled proteome. QPP hybrids maintained improved amino acid profiles although different popping methods variably affected popcorn's protein bound and free amino acid levels. This preliminary screening of QPP hybrids is enabling further quantitative selection for large-scale, complex trait comparison to currently marketed elite popcorn varieties.
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Affiliation(s)
- Leandra Parsons
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
| | - Ying Ren
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
| | - Abou Yobi
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Preston Hurst
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
| | - Ruthie Angelovici
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | | | - David R. Holding
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
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37
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Slaten ML, Yobi A, Bagaza C, Chan YO, Shrestha V, Holden S, Katz E, Kanstrup C, Lipka AE, Kliebenstein DJ, Nour-Eldin HH, Angelovici R. mGWAS Uncovers Gln-Glucosinolate Seed-Specific Interaction and its Role in Metabolic Homeostasis. PLANT PHYSIOLOGY 2020; 183:483-500. [PMID: 32317360 PMCID: PMC7271782 DOI: 10.1104/pp.20.00039] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/26/2020] [Indexed: 05/04/2023]
Abstract
Gln is a key player in plant metabolism. It is one of the major free amino acids that is transported into the developing seed and is central for nitrogen metabolism. However, Gln natural variation and its regulation and interaction with other metabolic processes in seeds remain poorly understood. To investigate the latter, we performed a metabolic genome-wide association study (mGWAS) of Gln-related traits measured from the dry seeds of the Arabidopsis (Arabidopsis thaliana) diversity panel using all potential ratios between Gln and the other members of the Glu family as traits. This semicombinatorial approach yielded multiple candidate genes that, upon further analysis, revealed an unexpected association between the aliphatic glucosinolates (GLS) and the Gln-related traits. This finding was confirmed by an independent quantitative trait loci mapping and statistical analysis of the relationships between the Gln-related traits and the presence of specific GLS in seeds. Moreover, an analysis of Arabidopsis mutants lacking GLS showed an extensive seed-specific impact on Gln levels and composition that manifested early in seed development. The elimination of GLS in seeds was associated with a large effect on seed nitrogen and sulfur homeostasis, which conceivably led to the Gln response. This finding indicates that both Gln and GLS play key roles in shaping the seed metabolic homeostasis. It also implies that select secondary metabolites might have key functions in primary seed metabolism. Finally, our study shows that an mGWAS performed on dry seeds can uncover key metabolic interactions that occur early in seed development.
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Affiliation(s)
- Marianne L Slaten
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Abou Yobi
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Clement Bagaza
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Yen On Chan
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Vivek Shrestha
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Samuel Holden
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Ella Katz
- Department of Plant Sciences, University of California Davis, Davis, California 95616
| | - Christa Kanstrup
- DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, California 95616
| | - Hussam Hassan Nour-Eldin
- DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Ruthie Angelovici
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
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Sinha A, Haider T, Narula K, Ghosh S, Chakraborty N, Chakraborty S. Integrated Seed Proteome and Phosphoproteome Analyses Reveal Interplay of Nutrient Dynamics, Carbon–Nitrogen Partitioning, and Oxidative Signaling in Chickpea. Proteomics 2020; 20:e1900267. [DOI: 10.1002/pmic.201900267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/03/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Arunima Sinha
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Toshiba Haider
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Kanika Narula
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Sudip Ghosh
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
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39
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Kimani W, Zhang LM, Wu XY, Hao HQ, Jing HC. Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor). BMC Genomics 2020; 21:112. [PMID: 32005168 PMCID: PMC6995107 DOI: 10.1186/s12864-020-6538-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality. The nutritional quality and end use value of sorghum grains are primarily influenced by the proportions of tannins, starch and proteins, but the genetic basis of these grain quality traits remains largely unknown. This study aimed to dissect the natural variation of sorghum grain quality traits and identify the underpinning genetic loci by genome-wide association study. RESULTS Levels of starch, tannins and 17 amino acids were quantified in 196 diverse sorghum inbred lines, and 44 traits based on known metabolic pathways and biochemical interactions amongst the 17 amino acids calculated. A Genome-wide association study (GWAS) with 3,512,517 SNPs from re-sequencing data identified 14, 15 and 711 significant SNPs which represented 14, 14, 492 genetic loci associated with levels of tannins, starch and amino acids in sorghum grains, respectively. Amongst these significant SNPs, two SNPs were associated with tannin content on chromosome 4 and colocalized with three previously identified loci for Tannin1, and orthologs of Zm1 and TT16 genes. One SNP associated with starch content colocalized with sucrose phosphate synthase gene. Furthermore, homologues of opaque1 and opaque2 genes associated with amino acid content were identified. Using the KEGG pathway database, six and three candidate genes of tannins and starch were mapped into 12 and 3 metabolism pathways, respectively. Thirty-four candidate genes were mapped into 16 biosynthetic and catabolic pathways of amino acids. We finally reconstructed the biosynthetic pathways for aspartate and branched-chain amino acids based on 15 candidate genes identified in this study. CONCLUSION Promising candidate genes associated with grain quality traits have been identified in the present study. Some of them colocalized with previously identified genetic regions, but novel candidate genes involved in various metabolic pathways which influence grain quality traits have been dissected. Our study acts as an entry point for further validation studies to elucidate the complex mechanisms controlling grain quality traits such as tannins, starch and amino acids in sorghum.
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Affiliation(s)
- Wilson Kimani
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Min Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Xiao-Yuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Huai-Qing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Engineering Laboratory for Grass-based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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Pan Y, Hu F, Yu C, Li C, Huang T, Hu H. Amino Acid Catabolism During Nitrogen Limitation in Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2020; 11:589026. [PMID: 33408729 PMCID: PMC7780933 DOI: 10.3389/fpls.2020.589026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/23/2020] [Indexed: 05/08/2023]
Abstract
Diatoms can accumulate high levels of triacylglycerols (TAGs) under nitrogen depletion and have attracted increasing attention as a potential system for biofuel production. In Phaeodactylum tricornutum, a model diatom, about 40% of lipid is synthesized from the breakdown of cellular components under nitrogen starvation. Our previous studies indicated that carbon skeletons from enhanced branched-chain amino acid (BCAA) degradation under nitrogen deficiency contribute to TAG biosynthesis in P. tricornutum. In this review, we outlined the catabolic pathways of all 20 amino acids based on the genome, transcriptome, proteome, and metabolome data. The contribution of these amino acid catabolic pathways to TAG accumulation was also analyzed.
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Affiliation(s)
- Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fan Hu
- School of Foreign Languages, China University of Geosciences, Wuhan, China
| | - Chen Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenjie Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Teng Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Hanhua Hu,
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Cao P, Kim SJ, Xing A, Schenck CA, Liu L, Jiang N, Wang J, Last RL, Brandizzi F. Homeostasis of branched-chain amino acids is critical for the activity of TOR signaling in Arabidopsis. eLife 2019; 8:e50747. [PMID: 31808741 PMCID: PMC6937141 DOI: 10.7554/elife.50747] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/05/2019] [Indexed: 01/11/2023] Open
Abstract
The target of rapamycin (TOR) kinase is an evolutionarily conserved hub of nutrient sensing and metabolic signaling. In plants, a functional connection of TOR activation with glucose availability was demonstrated, while it is yet unclear whether branched-chain amino acids (BCAAs) are a primary input of TOR signaling as they are in yeast and mammalian cells. Here, we report on the characterization of an Arabidopsis mutant over-accumulating BCAAs. Through chemical interventions targeting TOR and by examining mutants of BCAA biosynthesis and TOR signaling, we found that BCAA over-accumulation leads to up-regulation of TOR activity, which causes reorganization of the actin cytoskeleton and actin-associated endomembranes. Finally, we show that activation of TOR is concomitant with alteration of cell expansion, proliferation and specialized metabolism, leading to pleiotropic effects on plant growth and development. These results demonstrate that BCAAs contribute to plant TOR activation and reveal previously uncharted downstream subcellular processes of TOR signaling.
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Affiliation(s)
- Pengfei Cao
- MSU-DOE Plant Research LabMichigan State UniversityEast LansingUnited States
- Department of Plant BiologyMichigan State UniversityEast LansingUnited States
| | - Sang-Jin Kim
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
| | - Anqi Xing
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
| | - Craig A Schenck
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
| | - Lu Liu
- MSU-DOE Plant Research LabMichigan State UniversityEast LansingUnited States
| | - Nan Jiang
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
| | - Jie Wang
- Department of Plant BiologyMichigan State UniversityEast LansingUnited States
| | - Robert L Last
- Department of Plant BiologyMichigan State UniversityEast LansingUnited States
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
| | - Federica Brandizzi
- MSU-DOE Plant Research LabMichigan State UniversityEast LansingUnited States
- Department of Plant BiologyMichigan State UniversityEast LansingUnited States
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
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Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon. Int J Mol Sci 2019; 20:ijms20215392. [PMID: 31671884 PMCID: PMC6862219 DOI: 10.3390/ijms20215392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/21/2019] [Accepted: 10/26/2019] [Indexed: 12/30/2022] Open
Abstract
Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection. The purpose of this study was to identify single nucleotide polymorphism (SNP) markers associated with citrulline metabolism using a genome-wide association study (GWAS) and understand the role of citrulline in watermelon domestication. A watermelon collection consisting of 187 wild, landraces, and cultivated accessions was used to estimate citrulline content. An association analysis involved a total of 12,125 SNPs with a minor allele frequency (MAF) >0.05 in understanding the population structure and phylogeny in light of citrulline accumulation. Wild egusi types and landraces contained low to medium citrulline content, whereas cultivars had higher content, which suggests that obtaining higher content of citrulline is a domesticated trait. GWAS analysis identified candidate genes (ferrochelatase and acetolactate synthase) showing a significant association of SNPs with citrulline content. Haplotype networking indicated positive selection from wild to domesticated watermelon. To our knowledge, this is the first study showing genetic regulation of citrulline variation in plants by using a GWAS strategy. These results provide new insights into the citrulline metabolism in plants and the possibility of incorporating high citrulline as a trait in watermelon breeding programs.
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Garg A, Kirchler T, Fillinger S, Wanke F, Stadelhofer B, Stahl M, Chaban C. Targeted manipulation of bZIP53 DNA-binding properties influences Arabidopsis metabolism and growth. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5659-5671. [PMID: 31257431 PMCID: PMC6812703 DOI: 10.1093/jxb/erz309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/24/2019] [Indexed: 05/21/2023]
Abstract
bZIP transcription factors regulate diverse processes in eukaryotic cells. Arabidopsis bZIP members of the C and S1 groups form heterodimers and synergistically control metabolic reprogramming during stress responses. However, their functional characterization is complicated due to an overlapping heterodimerization network and high redundancy. In this study, we develop a simple but powerful approach for generating dominant negative mutants of bZIP factors with high specificity. By applying in vitro DNA-binding, reporter gene and protoplast two-hybrid assays, and plant mutant analysis, we show that phosphorylation-mimicking substitution of conserved serines in the DNA-binding domain of bZIP monomeric subunits suffices for the disruption of the interaction of both bZIP homo- and heterodimers with cognate DNA. This results in the transcriptional inactivation of target genes. The dominant-negative effect is achieved by the unaltered function of the intrinsic nuclear localization signal and dimerization properties of the mutated bZIP protein. Our findings not only reveal an additional regulatory mechanism of bZIP10 intracellular localization, but also provide evidence of the involvement of bZIP53 in the diurnal adjustments of amino acid metabolism. Our data demonstrate the advantages and the suitability of this new approach for the artificial inactivation of bZIP transcription factors in plants, and it may also be of use for other organisms.
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Affiliation(s)
| | | | | | | | | | - Mark Stahl
- ZMBP, University of Tübingen, Tübingen, Germany
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Qanmber G, Lu L, Liu Z, Yu D, Zhou K, Huo P, Li F, Yang Z. Genome-wide identification of GhAAI genes reveals that GhAAI66 triggers a phase transition to induce early flowering. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4721-4736. [PMID: 31106831 PMCID: PMC6760319 DOI: 10.1093/jxb/erz239] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/11/2019] [Indexed: 05/20/2023]
Abstract
Plants undergo a phase transition from vegetative to reproductive development that triggers floral induction. Genes containing an AAI (α-amylase inhibitor) domain form a large gene family, but there have been no comprehensive analyses of this gene family in any plant species. Here, we identified 336 AAI genes from nine plant species including122 AAI genes in cotton (Gossypium hirsutum). The AAI gene family has evolutionarily conserved amino acid residues throughout the plant kingdom. Phylogenetic analysis classified AAI genes into five major clades with significant polyploidization and showing effects of genome duplication. Our study identified 42 paralogous and 216 orthologous gene pairs resulting from segmental and whole-genome duplication, respectively, demonstrating significant contributions of gene duplication to expansion of the cotton AAI gene family. Further, GhAAI66 was preferentially expressed in flower tissue and as responses to phytohormone treatments. Ectopic expression of GhAAI66 in Arabidopsis and silencing in cotton revealed that GhAAI66 triggers a phase transition to induce early flowering. Further, GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of RNA sequencing data and qRT-PCR (quantitative reverse transcription-PCR) analysis indicated that GhAAI66 integrates multiple flower signaling pathways including gibberellin, jasmonic acid, and floral integrators to trigger an early flowering cascade in Arabidopsis. Therefore, characterization of the AAI family provides invaluable insights for improving cotton breeding.
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Affiliation(s)
- Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhao Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Daoqian Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Kehai Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Peng Huo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan, China
- Correspondence: or
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan, China
- Correspondence: or
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Xu G, Cao J, Wang X, Chen Q, Jin W, Li Z, Tian F. Evolutionary Metabolomics Identifies Substantial Metabolic Divergence between Maize and Its Wild Ancestor, Teosinte. THE PLANT CELL 2019; 31:1990-2009. [PMID: 31227559 PMCID: PMC6751114 DOI: 10.1105/tpc.19.00111] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/03/2019] [Accepted: 06/17/2019] [Indexed: 05/04/2023]
Abstract
Maize (Zea mays subsp mays) was domesticated from its wild ancestor, teosinte (Zea mays subsp parviglumis). Maize's distinct morphology and adaptation to diverse environments required coordinated changes in various metabolic pathways. However, how the metabolome was reshaped since domestication remains poorly understood. Here, we report a comprehensive assessment of divergence in the seedling metabolome between maize and teosinte. In total, 461 metabolites exhibited significant divergence due to selection. Interestingly, teosinte and tropical and temperate maize, representing major stages of maize evolution, targeted distinct sets of metabolites. Alkaloids, terpenoids, and lipids were specifically targeted in the divergence between teosinte and tropical maize, while benzoxazinoids were specifically targeted in the divergence between tropical and temperate maize. To identify genetic factors controlling metabolic divergence, we assayed the seedling metabolome of a large maize-by-teosinte cross population. We show that the recent metabolic divergence between tropical and temperate maize tended to have simpler genetic architecture than the divergence between teosinte and tropical maize. Through integrating transcriptome data, we identified candidate genes contributing to metabolic divergence, many of which were under selection at the nucleotide and transcript levels. Through overexpression or mutant analysis, we verified the roles of Flavanone 3-hydroxylase1, Purple aleurone1, and maize terpene synthase1 in the divergence of their related biosynthesis pathways. Our findings not only provide important insights into domestication-associated changes in the metabolism but also highlight the power of combining omics data for trait dissection.
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Affiliation(s)
- Guanghui Xu
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Jingjing Cao
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xufeng Wang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Qiuyue Chen
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
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Meena MK, Prajapati R, Krishna D, Divakaran K, Pandey Y, Reichelt M, Mathew M, Boland W, Mithöfer A, Vadassery J. The Ca 2+ Channel CNGC19 Regulates Arabidopsis Defense Against Spodoptera Herbivory. THE PLANT CELL 2019; 31:1539-1562. [PMID: 31076540 PMCID: PMC6635850 DOI: 10.1105/tpc.19.00057] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/18/2019] [Accepted: 05/07/2019] [Indexed: 05/18/2023]
Abstract
Cellular calcium elevation is an important signal used by plants for recognition and signaling of environmental stress. Perception of the generalist insect, Spodoptera litura, by Arabidopsis (Arabidopsis thaliana) activates cytosolic Ca2+ elevation, which triggers downstream defense. However, not all the Ca2+ channels generating the signal have been identified, nor are their modes of action known. We report on a rapidly activated, leaf vasculature- and plasma membrane-localized, CYCLIC NUCLEOTIDE GATED CHANNEL19 (CNGC19), which activates herbivory-induced Ca2+ flux and plant defense. Loss of CNGC19 function results in decreased herbivory defense. The cngc19 mutant shows aberrant and attenuated intravascular Ca2+ fluxes. CNGC19 is a Ca2+-permeable channel, as hyperpolarization of CNGC19-expressing Xenopus oocytes in the presence of both cyclic adenosine monophosphate and Ca2+ results in Ca2+ influx. Breakdown of Ca2+-based defense in cngc19 mutants leads to a decrease in herbivory-induced jasmonoyl-l-isoleucine biosynthesis and expression of JA responsive genes. The cngc19 mutants are deficient in aliphatic glucosinolate accumulation and hyperaccumulate its precursor, methionine. CNGC19 modulates aliphatic glucosinolate biosynthesis in tandem with BRANCHED-CHAIN AMINO ACID TRANSAMINASE4, which is involved in the chain elongation pathway of Met-derived glucosinolates. Furthermore, CNGC19 interacts with herbivory-induced CALMODULIN2 in planta. Together, our work reveals a key mechanistic role for the Ca2+ channel CNGC19 in the recognition of herbivory and the activation of defense signaling.
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Affiliation(s)
- Mukesh Kumar Meena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ramgopal Prajapati
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepthi Krishna
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Keerthi Divakaran
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - Yogesh Pandey
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - Michael Reichelt
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - M.K. Mathew
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - Wilhelm Boland
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Axel Mithöfer
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
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Wang S, Alseekh S, Fernie AR, Luo J. The Structure and Function of Major Plant Metabolite Modifications. MOLECULAR PLANT 2019; 12:899-919. [PMID: 31200079 DOI: 10.1016/j.molp.2019.06.001] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/27/2019] [Accepted: 06/04/2019] [Indexed: 05/23/2023]
Abstract
Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality.
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Affiliation(s)
- Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Onda Y, Inoue K, Sawada Y, Shimizu M, Takahagi K, Uehara-Yamaguchi Y, Hirai MY, Garvin DF, Mochida K. Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon. Int J Mol Sci 2019; 20:ijms20092348. [PMID: 31083584 PMCID: PMC6540107 DOI: 10.3390/ijms20092348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 12/27/2022] Open
Abstract
Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses.
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Affiliation(s)
- Yoshihiko Onda
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Minami Shimizu
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yukiko Uehara-Yamaguchi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Masami Y Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - David F Garvin
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Institute of Plant Science and Resource, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Yobi A, Batushansky A, Oliver MJ, Angelovici R. Adaptive responses of amino acid metabolism to the combination of desiccation and low nitrogen availability in Sporobolus stapfianus. PLANTA 2019; 249:1535-1549. [PMID: 30725176 DOI: 10.1007/s00425-019-03105-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Depending on nitrogen availability, S. stapfianus uses different amino acid metabolism strategies to cope with desiccation stress. The different metabolic strategies support essential processes for the desiccation tolerance phenotype. To provide a comprehensive assessment of the role played by amino acids in the adaptation of Sporobolus stapfianus to a combination of desiccation and nitrogen limitation, we used an absolute quantification of free and protein-bound amino acids (FAAs and PBAAs) as well as their gamma-glutamyl (gg-AA) derivatives in four different tissues grown under high- and low-nitrogen regimes. We demonstrate that although specific FAAs and gg-AAs increased in desiccating immature leaves under both nitrogen regimes, the absolute change in the total amount of either is small or negligible, negating their proposed role in nitrogen storage. FAAs and PBAAs decrease in underground tissues during desiccation, when nitrogen is abundant. In contrast, PBAAs are drastically reduced from the mature leaves, when nitrogen is limiting. Nevertheless, the substantial reduction in PBAA and FAA fractions in both treatments is not manifested in the immature leaves, which strongly suggests that these amino acids are further metabolized to fuel central metabolism or other metabolic adjustments that are essential for the acquisition of desiccation tolerance (DT).
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Affiliation(s)
- Abou Yobi
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65311, USA
| | - Albert Batushansky
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65311, USA
- Aging and Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Melvin J Oliver
- U.S. Department of Agriculture-Agricultural Research Service, Plant Genetic Research Unit, University of Missouri, Columbia, MO, 65211, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65311, USA.
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Do TD, Vuong TD, Dunn D, Clubb M, Valliyodan B, Patil G, Chen P, Xu D, Nguyen HT, Shannon JG. Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping. BMC Genomics 2019; 20:318. [PMID: 31023240 PMCID: PMC6485111 DOI: 10.1186/s12864-019-5662-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/31/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplasm. In this study, a genome-wide association study (GWAS) was performed to map genomic regions for salt tolerance in a diverse panel of 305 soybean accessions using a single nucleotide polymorphism (SNP) dataset derived from the SoySNP50K iSelect BeadChip. A second GWAS was also conducted in a subset of 234 accessions using another 3.7 M SNP dataset derived from a whole-genome resequencing (WGRS) study. In addition, three gene-based markers (GBM) of the known gene, Glyma03g32900, on Chr. 3 were also integrated into the two datasets. Salt tolerance among soybean lines was evaluated by leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC). RESULTS For both association studies, a major locus for salt tolerance on Chr. 3 was confirmed by a number of significant SNPs, of which three gene-based SNP markers, Salt-20, Salt14056 and Salt11655, had the highest association with all four traits studied. Also, additional genomic regions on Chrs. 1, 8, and 18 were found to be associated with various traits measured in the second GWAS using the WGRS-derived SNP dataset. CONCLUSIONS A region identified on Chr. 8 was identified to be associated with all four traits and predicted as a new minor locus for salt tolerance in soybean. The candidate genes harbored in this minor locus may help reveal the molecular mechanism involved in salt tolerance and to improve tolerance in soybean cultivars. The significant SNPs will be useful for marker-assisted selection for salt tolerance in soybean breeding programs.
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Affiliation(s)
- Tuyen D. Do
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
- Present address: The Cuu Long Delta Rice Research Institute, Thoi Lai District, Can Tho City, Vietnam
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - David Dunn
- Division of Plant Sciences, University of Missouri, Portageville, MO 63873 USA
| | - Michael Clubb
- Division of Plant Sciences, University of Missouri, Portageville, MO 63873 USA
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Gunvant Patil
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
- Present Address: Department Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 USA
| | - Pengyin Chen
- Division of Plant Sciences, University of Missouri, Portageville, MO 63873 USA
| | - Dong Xu
- Department of Electric Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - J. Grover Shannon
- Division of Plant Sciences, University of Missouri, Portageville, MO 63873 USA
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