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Zhang RJ, Liu B, Song SS, Salah R, Song CJ, Xia SW, Hao Q, Liu YJ, Li Y, Lai YS. Lipid-Related Domestication Accounts for the Extreme Cold Sensitivity of Semiwild and Tropic Xishuangbanna Cucumber ( Cucumis sativus L. var. xishuangbannanesis). Int J Mol Sci 2023; 25:79. [PMID: 38203249 PMCID: PMC10779220 DOI: 10.3390/ijms25010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 12/10/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannanesis) is a semiwild variety originating from low latitude tropic areas, and therefore shows extreme cold sensitivity and heat tolerance. Here, we mapped the quantitative trait loci (QTLs) that control the cold sensitivity and heat tolerance of XIS cucumber seedlings. Using bulked segregant analysis (BSA), we identified three QTLs (HTT1.1, HTT3.1, and HTT3.2, with a total length of 11.98 Mb) for heat tolerance and two QTLs (LTT6.1 and LTT6.2, with a total length of 8.74 Mb) for cold sensitivity. The QTL LTT6.1 was then narrowed down to a length of 641 kb by using kompetitive allele-specific PCR (KASP) markers. Based on structural variants (SVs) and single-nucleotide polymorphisms (SNPs), we found the LTT6.1 is covered by a high divergent region including a 50 kb deletion in the XIS49 genome, which affects the gene structure of lipase abhydrolase domain containing 6 (ABHD6, Csa_6G032560). Accordingly, there is a very big difference in lipid composition, but not in other osmoprotectants like free amino acids and fatty acids, between XIS49 and cultivated cucumber CL. Moreover, we calculated the composite likelihood ratio (CLR) and identified selective sweeps from 115 resequencing data, and found that lipid- and fatty-acid-related processes are major aspects in the domestication of the XIS group cucumber. LTT6.1 is a particularly special region positioned nearby lipid-related selective sweeps. These studies above suggested that the lipid-related domestication of XIS cucumbers should account for their extreme cold sensitivity.
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Affiliation(s)
- Rui-Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Bin Liu
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Shan-Shan Song
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Radwa Salah
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Chang-Jiang Song
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Shi-Wei Xia
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Qian Hao
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Yan-Jun Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Yu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Yun-Song Lai
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
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Habib Z, Ijaz S, Haq IU. Comparative metabolomic profiling and nutritional chemistry of Chenopodium quinoa of diverse panicle architecture and agroecological zones. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1959-1979. [PMID: 38222284 PMCID: PMC10784447 DOI: 10.1007/s12298-023-01398-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/01/2023] [Accepted: 11/24/2023] [Indexed: 01/16/2024]
Abstract
Chenopodium quinoa possesses remarkable nutritional value and adaptability to various agroecological conditions. Panicle architecture influences the number of spikelets and grains in a panicle, ultimately leading to productivity and yield. Therefore, this study aimed to investigate the metabolites, nutrients, and minerals in Chenopodium quinoa accessions of varying panicle architecture. Metabolic profiling using liquid chromatography-mass spectrometry (LC-MS) analysis identified seventeen metabolites, including flavonoids, phenolics, fatty acids, terpenoids, phenylbutenoid dimers, amino acids, and saccharides. Eight metabolic compounds were reported in this study for the first time in quinoa. Some metabolites were detected as differentially expressed. The compound (Z)-1-(2,4,5-trimethoxyphenyl) butadiene and chrysin were found only in SPrecm. Sodium ((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxtetrahydrofuran-2-yl) methyl hydrogen phosphate and elenolic acid were detected only in CHEN-33, and quercetin, 3-hydroxyphloretin-3'-C-glucoside, kurarinone, and rosmarinic acid were identified only in D-12175. Variable importance in projection (VIP) scores annotated ten metabolites contributing to variability. Mineral analysis using atomic absorption spectrophotometry indicated that the quantity of magnesium and calcium is high in D-12175. In comparison, SPrecm showed a high quantity of magnesium compared to CHEN-33, while CHEN-33 showed a high quantity of calcium compared to SPrecm. However, the proximate composition showed no significant difference among quinoa accessions. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01398-2.
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Affiliation(s)
- Zakia Habib
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, University Road, Faisalabad, Pakistan
| | - Siddra Ijaz
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, University Road, Faisalabad, Pakistan
| | - Imran Ul Haq
- Department of Plant Pathology, University of Agriculture, University Road, Faisalabad, Pakistan
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3
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Zhang L, Zhang N, Wang S, Tian H, Liu L, Pei D, Yu X, Zhao L, Chen F. A TaSnRK1α Modulates TaPAP6L-Mediated Wheat Cold Tolerance through Regulating Endogenous Jasmonic Acid. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303478. [PMID: 37740426 PMCID: PMC10625090 DOI: 10.1002/advs.202303478] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/22/2023] [Indexed: 09/24/2023]
Abstract
Here, a sucrose non-fermenting-1-related protein kinase alpha subunit (TaSnRK1α-1A) is identified as associated with cold stress through integration of genome-wide association study, bulked segregant RNA sequencing, and virus-induced gene silencing. It is confirmed that TaSnRK1α positively regulates cold tolerance by transgenes and ethyl methanesulfonate (EMS) mutants. A plastid-lipid-associated protein 6, chloroplastic-like (TaPAP6L-2B) strongly interacting with TaSnRK1α-1A is screened. Molecular chaperone DJ-1 family protein (TaDJ-1-7B) possibly bridged the interaction of TaSnRK1α-1A and TaPAP6L-2B. It is further revealed that TaSnRK1α-1A phosphorylated TaPAP6L-2B. Subsequently, a superior haplotype TaPAP6L-2B30S /38S is identified and confirmed that both R30S and G38S are important phosphorylation sites that influence TaPAP6L-2B in cold tolerance. Overexpression (OE) and EMS-mutant lines verified TaPAP6L positively modulating cold tolerance. Furthermore, transcriptome sequencing revealed that TaPAP6L-2B-OE lines significantly increased jasmonic acid (JA) content, possibly by improving precursor α-linolenic acid contributing to JA synthesis and by repressing JAR1 degrading JA. Exogenous JA significantly improved the cold tolerance of wheat plants. In summary, TaSnRK1α profoundly regulated cold stress, possibly through phosphorylating TaPAP6L to increase endogenous JA content of wheat plants.
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Affiliation(s)
- Lingran Zhang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhou450046China
| | - Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhou450046China
| | - Sisheng Wang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhou450046China
| | - Hongyan Tian
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhou450046China
| | - Lu Liu
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhou450046China
| | - Dan Pei
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhou450046China
| | - Xiaodong Yu
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhou450046China
| | - Lei Zhao
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhou450046China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhou450046China
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Zheng P, Shen M, Liu R, Cai X, Lin J, Wang L, Chen Y, Chen G, Cao S, Qin Y. Revealing Further Insights into Astringent Seeds of Chinese Fir by Integrated Metabolomic and Lipidomic Analyses. Int J Mol Sci 2023; 24:15103. [PMID: 37894783 PMCID: PMC10607028 DOI: 10.3390/ijms242015103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) stands as one of the pivotal afforestation tree species and timber resources in southern China. Nevertheless, the occurrence of seed abortion and a notably high proportion of astringent seeds significantly curtail the yield and quality of elite seeds, resulting in substantial economic losses. The development of astringent seeds is accompanied by significant physiological and biochemical alterations. Here, the first combined lipidomic and metabolomic analysis was performed to gain a comprehensive understanding of astringent seed traits. A total of 744 metabolites and 616 lipids were detected, of which 489 differential metabolites and 101 differential lipids were identified. In astringent seeds, most flavonoids and tannins, as well as proline and γ-aminobutyric acid, were more accumulated, along with a notable decrease in lipid unsaturation, indicating oxidative stress in the cells of astringent seeds. Conversely, numerous elemental metabolites were less accumulated, including amino acids and their derivatives, saccharides and alcohols, organic acids and nucleotides and their derivatives. Meanwhile, most lipid subclasses, mainly associated with energy storage (triglyceride and diglyceride) and cell membrane composition (phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine), also exhibited significant reductions. These results reflected a disruption in the cellular system or the occurrence of cell death, causing a reduction in viable cells within astringent seeds. Furthermore, only one lipid subclass, sphingosine phosphate (SoP), was more accumulated in astringent seeds. Additionally, lower accumulation of indole-3-acetic acid and more accumulation of salicylic acid (SA) were also identified in astringent seeds. Both SA and SoP were closely associated with the promotion of programmed cell death in astringent seeds. Collectively, our study revealed significant abnormal changes in phytohormones, lipids and various metabolites in astringent seeds, allowing us to propose a model for the development of astringent seeds in Chinese fir based on existing research and our findings. This work enriches our comprehension of astringent seeds and presents valuable bioindicators for the identification of astringent seeds.
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Affiliation(s)
- Ping Zheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (P.Z.); (M.S.); (X.C.); (J.L.); (G.C.)
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Mengqian Shen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (P.Z.); (M.S.); (X.C.); (J.L.); (G.C.)
| | - Ruoyu Liu
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Xinkai Cai
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (P.Z.); (M.S.); (X.C.); (J.L.); (G.C.)
| | - Jinting Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (P.Z.); (M.S.); (X.C.); (J.L.); (G.C.)
| | - Lulu Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (P.Z.); (M.S.); (X.C.); (J.L.); (G.C.)
| | - Yu Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Guangwei Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (P.Z.); (M.S.); (X.C.); (J.L.); (G.C.)
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (P.Z.); (M.S.); (X.C.); (J.L.); (G.C.)
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
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5
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Kränzlein M, Schmöckel SM, Geilfus CM, Schulze WX, Altenbuchinger M, Hrenn H, Roessner U, Zörb C. Lipid remodeling of contrasting maize ( Zea mays L.) hybrids under repeated drought. FRONTIERS IN PLANT SCIENCE 2023; 14:1050079. [PMID: 37235021 PMCID: PMC10206266 DOI: 10.3389/fpls.2023.1050079] [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: 09/21/2022] [Accepted: 04/17/2023] [Indexed: 05/28/2023]
Abstract
The role of recovery after drought has been proposed to play a more prominent role during the whole drought-adaption process than previously thought. Two maize hybrids with comparable growth but contrasting physiological responses were investigated using physiological, metabolic, and lipidomic tools to understand the plants' strategies of lipid remodeling in response to repeated drought stimuli. Profound differences in adaptation between hybrids were discovered during the recovery phase, which likely gave rise to different degrees of lipid adaptability to the subsequent drought event. These differences in adaptability are visible in galactolipid metabolism and fatty acid saturation patterns during recovery and may lead to a membrane dysregulation in the sensitive maize hybrid. Moreover, the more drought-tolerant hybrid displays more changes of metabolite and lipid abundance with a higher number of differences within individual lipids, despite a lower physiological response, while the responses in the sensitive hybrid are higher in magnitude but lower in significance on the level of individual lipids and metabolites. This study suggests that lipid remodeling during recovery plays a key role in the drought response of plants.
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Affiliation(s)
- Markus Kränzlein
- Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | | | | | - Waltraud X. Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Michael Altenbuchinger
- Department of Medical Bioinformatics, University Medical Center Göttingen, Göttingen, Germany
| | - Holger Hrenn
- Core Facility Hohenheim, University of Hohenheim, Stuttgart, Germany
| | - Ute Roessner
- Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Christian Zörb
- Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
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6
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Su H, Tan C, Liu Y, Chen X, Li X, Jones A, Zhu Y, Song Y. Physiology and Molecular Breeding in Sustaining Wheat Grain Setting and Quality under Spring Cold Stress. Int J Mol Sci 2022; 23:ijms232214099. [PMID: 36430598 PMCID: PMC9693015 DOI: 10.3390/ijms232214099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022] Open
Abstract
Spring cold stress (SCS) compromises the reproductive growth of wheat, being a major constraint in achieving high grain yield and quality in winter wheat. To sustain wheat productivity in SCS conditions, breeding cultivars conferring cold tolerance is key. In this review, we examine how grain setting and quality traits are affected by SCS, which may occur at the pre-anthesis stage. We have investigated the physiological and molecular mechanisms involved in floret and spikelet SCS tolerance. It includes the protective enzymes scavenging reactive oxygen species (ROS), hormonal adjustment, and carbohydrate metabolism. Lastly, we explored quantitative trait loci (QTLs) that regulate SCS for identifying candidate genes for breeding. The existing cultivars for SCS tolerance were primarily bred on agronomic and morphophysiological traits and lacked in molecular investigations. Therefore, breeding novel wheat cultivars based on QTLs and associated genes underlying the fundamental resistance mechanism is urgently needed to sustain grain setting and quality under SCS.
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Affiliation(s)
- Hui Su
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Cheng Tan
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yonghua Liu
- School of Horticulture, Hainan University, Haikou 570228, China
| | - Xiang Chen
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Xinrui Li
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Ashley Jones
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Yulei Zhu
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (Y.Z.); (Y.S.)
| | - Youhong Song
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence: (Y.Z.); (Y.S.)
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7
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Chakraborty A, Chaudhury R, Dutta S, Basak M, Dey S, Schäffner AR, Das M. Role of metabolites in flower development and discovery of compounds controlling flowering time. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 190:109-118. [PMID: 36113306 DOI: 10.1016/j.plaphy.2022.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 06/29/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
Flowering is one of the most important physiological processes of plants that ensures continuity of genetic flow from one generation to the next and also maintains food security. Therefore, impact of various climate-related abiotic stresses on flowering have been assessed to evaluate the long-term impact of global climate change. In contrast to the enormous volume of research that has been conducted at the genetic, transcriptional, post-transcriptional, and protein level, much less attention has been paid to understand the role of various metabolites in flower induction and floral organ development during normal growth or in stressed environmental condition. This review article aims at summarizing information on various primary (e.g., carbohydrates, lipids, fatty acid derivatives, protein and amino acids) and secondary metabolites (e.g., polyamines, phenolics, neuro-indoles, phenylpropanoid, flavonoids and terpenes) that have so far been identified either during flower induction or in individual floral organs implying their possible role in organ development. Specialized metabolites responsible for flower colour, scent and shape to support plant-pollinator interaction have been extensively reviewed by many research groups and hence are not considered in this article. Many of the metabolites discussed here may be used as metabolomarkers to identify tolerant crop genotypes. Several agrochemicals have been successfully used to release endodormancy in temperate trees. Along the same line, a strategy that combines metabolite profiling, screening of small-molecule libraries, and structural alteration of selected compounds has been proposed in order to identify novel lead compounds that can regulate flowering time when applied exogenously.
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Affiliation(s)
| | - Rim Chaudhury
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Smritikana Dutta
- Department of Life Sciences, Presidency University, Kolkata, India; Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Mridushree Basak
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Sonali Dey
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Anton R Schäffner
- Institute of Biochemical Plant Pathology, Department of Environmental Sciences, Helmholtz Zentrum München, München, Germany
| | - Malay Das
- Department of Life Sciences, Presidency University, Kolkata, India.
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8
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Cheong BE, Yu D, Martinez-Seidel F, Ho WWH, Rupasinghe TWT, Dolferus R, Roessner U. The Effect of Cold Stress on the Root-Specific Lipidome of Two Wheat Varieties with Contrasting Cold Tolerance. PLANTS 2022; 11:plants11101364. [PMID: 35631789 PMCID: PMC9147729 DOI: 10.3390/plants11101364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/01/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022]
Abstract
Complex glycerolipidome analysis of wheat upon low temperature stress has been reported for above-ground tissues only. There are no reports on the effects of cold stress on the root lipidome nor on tissue-specific responses of cold stress wheat roots. This study aims to investigate the changes of lipid profiles in the different developmental zones of the seedling roots of two wheat varieties with contrasting cold tolerance exposed to chilling and freezing temperatures. We analyzed 273 lipid species derived from 21 lipid classes using a targeted profiling approach based on MS/MS data acquired from schedule parallel reaction monitoring assays. For both the tolerant Young and sensitive Wyalkatchem species, cold stress increased the phosphatidylcholine and phosphatidylethanolamine compositions, but decreased the monohexosyl ceramide compositions in the root zones. We show that the difference between the two varieties with contrasting cold tolerance could be attributed to the change in the individual lipid species, rather than the fluctuation of the whole lipid classes. The outcomes gained from this study may advance our understanding of the mechanisms of wheat adaptation to cold and contribute to wheat breeding for the improvement of cold-tolerance.
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Affiliation(s)
- Bo Eng Cheong
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan Universiti, Kota Kinabalu 88400, Malaysia
- School of Bio Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (D.Y.); (F.M.-S.); (U.R.)
- Correspondence: ; Tel.: +60-88-320000 (ext. 8530)
| | - Dingyi Yu
- School of Bio Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (D.Y.); (F.M.-S.); (U.R.)
- Protein Chemistry and Metabolism Unit, St. Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Federico Martinez-Seidel
- School of Bio Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (D.Y.); (F.M.-S.); (U.R.)
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - William Wing Ho Ho
- Advanced Genomics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | | | - Rudy Dolferus
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT 2601, Australia;
| | - Ute Roessner
- School of Bio Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (D.Y.); (F.M.-S.); (U.R.)
- Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
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9
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Leske BA, Biddulph TB. Estimating Effects of Radiation Frost on Wheat Using a Field-Based Frost Control Treatment to Stop Freezing Damage. Genes (Basel) 2022; 13:genes13040578. [PMID: 35456385 PMCID: PMC9031182 DOI: 10.3390/genes13040578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Crop phenotyping experiments have long struggled to have a reliable control treatment that excludes frost and associated freezing damage to plants. Previous attempts used a barrier, such as a removable shelter or cloth to exclude frost. However, these methods were labour intensive and varied in their effectiveness. An automated diesel heater was used to protect field plots of wheat (Triticum aestivum L.) from frost damage. In 2018 and 2019 there were 22 and 33 radiation frost events from July to October at the field site. The heater maintained canopy air temperature above freezing (>0 °C) for the duration of the frost (~6−8 h). Heated plots had 2−3 °C warmer minimum canopy air temperatures. Cold and chilling damage was still present in heated plots and represented 20−30% floret sterility; freezing damage in non-heated plots accounted for an additional 10−30% floret sterility. Grain mapping revealed: grain set in the apical spikelets is most affected by frost damage; proximal florets (G1 and G2) contribute the most to grain yield, but distal (G3 and G4) are important contributors to grain yield when sterility in proximal florets occurs. These results demonstrate that a plot heater is a useful tool to study frost-induced freezing damage in cereal crops, by way of preventing freezing damage in heated field plots for direct comparison to naturally frosted plots. This approach could be used to develop improved damage functions for crop simulation models through a dose and timing-response experiment for natural frost incidence on cereal crops in field plots.
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Affiliation(s)
- Brenton A. Leske
- The Department of Primary Industries and Regional Development, 3 Baron Hay Court, South Perth, WA 6151, Australia;
- The School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Thomas Ben Biddulph
- The Department of Primary Industries and Regional Development, 3 Baron Hay Court, South Perth, WA 6151, Australia;
- Correspondence:
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10
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Kehelpannala C, Rupasinghe T, Hennessy T, Bradley D, Ebert B, Roessner U. The state of the art in plant lipidomics. Mol Omics 2021; 17:894-910. [PMID: 34699583 DOI: 10.1039/d1mo00196e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lipids are a group of compounds with diverse structures that perform several important functions in plants. To unravel and better understand their in vivo functions, plant biologists have been using various lipidomic technologies including liquid-chromatography (LC)-mass spectrometry (MS). However, there are still significant challenges in LC-MS based plant lipidomics, which need to be addressed. In this review, we provide an overview of the key developments in LC-MS based lipidomic approaches to detect and identify plant lipids with emphasis on areas that can be further improved. Given that the cellular lipidome is estimated to contain hundreds of thousands of lipids,1,2 many of the lipid structures remain to be discovered. Furthermore, the plant lipidome is considered to be significantly more complex compared to that of mammals. Recent technical developments in mass spectrometry have made the detection of novel lipids possible; hence, approaches that can be used for plant lipid discovery are also discussed.
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Affiliation(s)
- Cheka Kehelpannala
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | | | - Thomas Hennessy
- Agilent Technologies Australia Pty Ltd, 679 Springvale Road, Mulgrave, VIC 3170, Australia
| | - David Bradley
- Agilent Technologies Australia Pty Ltd, 679 Springvale Road, Mulgrave, VIC 3170, Australia
| | - Berit Ebert
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia.
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11
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Otterbach SL, Khoury H, Rupasinghe T, Mendis H, Kwan KH, Lui V, Natera SHA, Klaiber I, Allen NM, Jarvis DE, Tester M, Roessner U, Schmöckel SM. Characterization of epidermal bladder cells in Chenopodium quinoa. PLANT, CELL & ENVIRONMENT 2021; 44:3606-3622. [PMID: 34510479 DOI: 10.1111/pce.14181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/01/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Chenopodium quinoa (quinoa) is considered a superfood with its favourable nutrient composition and being gluten free. Quinoa has high tolerance to abiotic stresses, such as salinity, water deficit (drought) and cold. The tolerance mechanisms are yet to be elucidated. Quinoa has epidermal bladder cells (EBCs) that densely cover the shoot surface, particularly the younger parts of the plant. Here, we report on the EBC's primary and secondary metabolomes, as well as the lipidome in control conditions and in response to abiotic stresses. EBCs were isolated from plants after cold, heat, high-light, water deficit and salt treatments. We used untargeted gas chromatography-mass spectrometry (GC-MS) to analyse metabolites and untargeted and targeted liquid chromatography-MS (LC-MS) for lipids and secondary metabolite analyses. We identified 64 primary metabolites, including sugars, organic acids and amino acids, 19 secondary metabolites, including phenolic compounds, betanin and saponins and 240 lipids categorized in five groups including glycerolipids and phospholipids. We found only few changes in the metabolic composition of EBCs in response to abiotic stresses; these were metabolites related with heat, cold and high-light treatments but not salt stress. Na+ concentrations were low in EBCs with all treatments and approximately two orders of magnitude lower than K+ concentrations.
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Affiliation(s)
- Sophie L Otterbach
- Department Physiology of Yield Stability, Institute Crop Science, Faculty of Agriculture, University of Hohenheim, Stuttgart, Germany
| | - Holly Khoury
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Thusitha Rupasinghe
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Himasha Mendis
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Kim H Kwan
- Metabolomics Australia, The University of Melbourne, Parkville, Victoria, Australia
| | - Veronica Lui
- Metabolomics Australia, The University of Melbourne, Parkville, Victoria, Australia
| | - Siria H A Natera
- Metabolomics Australia, The University of Melbourne, Parkville, Victoria, Australia
| | - Iris Klaiber
- Core Facility Hohenheim (640). Mass Spectrometry Unit, University of Hohenheim, Stuttgart, Germany
| | - Nathaniel M Allen
- Department Physiology of Yield Stability, Institute Crop Science, Faculty of Agriculture, University of Hohenheim, Stuttgart, Germany
| | - David E Jarvis
- Department of Plant and Wildlife Sciences, College of Life Sciences, Brigham Young University, Provo, Utah, USA
| | - Mark Tester
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sandra M Schmöckel
- Department Physiology of Yield Stability, Institute Crop Science, Faculty of Agriculture, University of Hohenheim, Stuttgart, Germany
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12
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Metabolomics for Crop Breeding: General Considerations. Genes (Basel) 2021; 12:genes12101602. [PMID: 34680996 PMCID: PMC8535592 DOI: 10.3390/genes12101602] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
The development of new, more productive varieties of agricultural crops is becoming an increasingly difficult task. Modern approaches for the identification of beneficial alleles and their use in elite cultivars, such as quantitative trait loci (QTL) mapping and marker-assisted selection (MAS), are effective but insufficient for keeping pace with the improvement of wheat or other crops. Metabolomics is a powerful but underutilized approach that can assist crop breeding. In this review, basic methodological information is summarized, and the current strategies of applications of metabolomics related to crop breeding are explored using recent examples. We briefly describe classes of plant metabolites, cellular localization of metabolic pathways, and the strengths and weaknesses of the main metabolomics technique. Among the commercialized genetically modified crops, about 50 with altered metabolic enzyme activities have been identified in the International Service for the Acquisition of Agri-biotech Applications (ISAAA) database. These plants are reviewed as encouraging examples of the application of knowledge of biochemical pathways. Based on the recent examples of metabolomic studies, we discuss the performance of metabolic markers, the integration of metabolic and genomic data in metabolic QTLs (mQTLs) and metabolic genome-wide association studies (mGWAS). The elucidation of metabolic pathways and involved genes will help in crop breeding and the introgression of alleles of wild relatives in a more targeted manner.
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13
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Vilchez AC, Peppino Margutti M, Reyna M, Wilke N, Villasuso AL. Recovery from chilling modulates the acyl-editing of phosphatidic acid molecular species in barley roots (Hordeum vulgare L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:862-873. [PMID: 34536899 DOI: 10.1016/j.plaphy.2021.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
In plants, lipid metabolism and remodelling are key mechanisms for survival under temperature stress. The present study attempted to compare the lipid profile in barley roots both under chilling stress treatment and in the subsequent recovery to stress. Lipids were obtained through a single-extraction method with a polar solvent mixture, followed by mass spectrometry analysis. The results indicate that lipid metabolism was significantly affected by chilling. Most of the glycerolipids analysed returned to control values during short- and long-term recovery, whereas several representative phosphatidic acid (PA) molecular species were edited during long-term recovery. Most of the PA molecular species that increased in the long-term had the same acyl chains as the phosphatidylcholine (PC) species that decreased. C34:2 and C36:4 underwent the most remarkable changes. Given that the mechanisms underlying the acyl-editing of PC in barley roots remain elusive, we also evaluated the contribution of lysophosphatidylcholine acyltransferases (HvLPCAT) and phospholipase A (HvPLA). In line with the aforementioned results, the expression of the HvLPCAT and HvPLA genes was up-regulated during recovery from chilling. The differential acyl-editing of PA during recovery, which involves the remodelling of PC, might therefore be a regulatory mechanism of cold tolerance in barley.
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Affiliation(s)
- Ana Carolina Vilchez
- Universidad Nacional de Río Cuarto, FCEFQyN, Departamento de Biología Molecular, Río Cuarto, Córdoba, Argentina; CONICET, Universidad Nacional de Río Cuarto, Instituto de Biotecnología Ambiental y Salud, (INBIAS), Río Cuarto, Córdoba, Argentina
| | - Micaela Peppino Margutti
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina; CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Mercedes Reyna
- Universidad Nacional de Río Cuarto, FCEFQyN, Departamento de Biología Molecular, Río Cuarto, Córdoba, Argentina; CONICET, Universidad Nacional de Río Cuarto, Instituto de Biotecnología Ambiental y Salud, (INBIAS), Río Cuarto, Córdoba, Argentina
| | - Natalia Wilke
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina; CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Ana Laura Villasuso
- Universidad Nacional de Río Cuarto, FCEFQyN, Departamento de Biología Molecular, Río Cuarto, Córdoba, Argentina; CONICET, Universidad Nacional de Río Cuarto, Instituto de Biotecnología Ambiental y Salud, (INBIAS), Río Cuarto, Córdoba, Argentina.
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14
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Sun S, Lin M, Qi X, Chen J, Gu H, Zhong Y, Sun L, Muhammad A, Bai D, Hu C, Fang J. Full-length transcriptome profiling reveals insight into the cold response of two kiwifruit genotypes (A. arguta) with contrasting freezing tolerances. BMC PLANT BIOLOGY 2021; 21:365. [PMID: 34380415 PMCID: PMC8356467 DOI: 10.1186/s12870-021-03152-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/02/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Kiwifruit (Actinidia Lindl.) is considered an important fruit species worldwide. Due to its temperate origin, this species is highly vulnerable to freezing injury while under low-temperature stress. To obtain further knowledge of the mechanism underlying freezing tolerance, we carried out a hybrid transcriptome analysis of two A. arguta (Actinidi arguta) genotypes, KL and RB, whose freezing tolerance is high and low, respectively. Both genotypes were subjected to - 25 °C for 0 h, 1 h, and 4 h. RESULTS SMRT (single-molecule real-time) RNA-seq data were assembled using the de novo method, producing 24,306 unigenes with an N50 value of 1834 bp. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs showed that they were involved in the 'starch and sucrose metabolism', the 'mitogen-activated protein kinase (MAPK) signaling pathway', the 'phosphatidylinositol signaling system', the 'inositol phosphate metabolism', and the 'plant hormone signal transduction'. In particular, for 'starch and sucrose metabolism', we identified 3 key genes involved in cellulose degradation, trehalose synthesis, and starch degradation processes. Moreover, the activities of beta-GC (beta-glucosidase), TPS (trehalose-6-phosphate synthase), and BAM (beta-amylase), encoded by the abovementioned 3 key genes, were enhanced by cold stress. Three transcription factors (TFs) belonging to the AP2/ERF, bHLH (basic helix-loop-helix), and MYB families were involved in the low-temperature response. Furthermore, weighted gene coexpression network analysis (WGCNA) indicated that beta-GC, TPS5, and BAM3.1 were the key genes involved in the cold response and were highly coexpressed together with the CBF3, MYC2, and MYB44 genes. CONCLUSIONS Cold stress led various changes in kiwifruit, the 'phosphatidylinositol signaling system', 'inositol phosphate metabolism', 'MAPK signaling pathway', 'plant hormone signal transduction', and 'starch and sucrose metabolism' processes were significantly affected by low temperature. Moreover, starch and sucrose metabolism may be the key pathway for tolerant kiwifruit to resist low temperature damages. These results increase our understanding of the complex mechanisms involved in the freezing tolerance of kiwifruit under cold stress and reveal a series of candidate genes for use in breeding new cultivars with enhanced freezing tolerance.
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Affiliation(s)
- Shihang Sun
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Miaomiao Lin
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xiujuan Qi
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Jinyong Chen
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Hong Gu
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yunpeng Zhong
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Leiming Sun
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Abid Muhammad
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Danfeng Bai
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Chungen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jinbao Fang
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
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15
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Kehelpannala C, Rupasinghe T, Pasha A, Esteban E, Hennessy T, Bradley D, Ebert B, Provart NJ, Roessner U. An Arabidopsis lipid map reveals differences between tissues and dynamic changes throughout development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:287-302. [PMID: 33866624 PMCID: PMC8361726 DOI: 10.1111/tpj.15278] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 05/24/2023]
Abstract
Mass spectrometry is the predominant analytical tool used in the field of plant lipidomics. However, there are many challenges associated with the mass spectrometric detection and identification of lipids because of the highly complex nature of plant lipids. Studies into lipid biosynthetic pathways, gene functions in lipid metabolism, lipid changes during plant growth and development, and the holistic examination of the role of plant lipids in environmental stress responses are often hindered. Here, we leveraged a robust pipeline that we previously established to extract and analyze lipid profiles of different tissues and developmental stages from the model plant Arabidopsis thaliana. We analyzed seven tissues at several different developmental stages and identified more than 200 lipids from each tissue analyzed. The data were used to create a web-accessible in silico lipid map that has been integrated into an electronic Fluorescent Pictograph (eFP) browser. This in silico library of Arabidopsis lipids allows the visualization and exploration of the distribution and changes of lipid levels across selected developmental stages. Furthermore, it provides information on the characteristic fragments of lipids and adducts observed in the mass spectrometer and their retention times, which can be used for lipid identification. The Arabidopsis tissue lipid map can be accessed at http://bar.utoronto.ca/efp_arabidopsis_lipid/cgi-bin/efpWeb.cgi.
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Affiliation(s)
- Cheka Kehelpannala
- School of BioSciencesThe University of MelbourneMelbourneVIC3010Australia
| | | | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - Thomas Hennessy
- Agilent Technologies Australia Pty Ltd679 Springvale RoadMulgraveVIC3170Australia
| | - David Bradley
- Agilent Technologies Australia Pty Ltd679 Springvale RoadMulgraveVIC3170Australia
| | - Berit Ebert
- School of BioSciencesThe University of MelbourneMelbourneVIC3010Australia
| | - Nicholas J. Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - Ute Roessner
- School of BioSciencesThe University of MelbourneMelbourneVIC3010Australia
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Martinez-Seidel F, Suwanchaikasem P, Nie S, Leeming MG, Pereira Firmino AA, Williamson NA, Kopka J, Roessner U, Boughton BA. Membrane-Enriched Proteomics Link Ribosome Accumulation and Proteome Reprogramming With Cold Acclimation in Barley Root Meristems. FRONTIERS IN PLANT SCIENCE 2021; 12:656683. [PMID: 33995454 PMCID: PMC8121087 DOI: 10.3389/fpls.2021.656683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Due to their sessile nature, plants rely on root systems to mediate many biotic and abiotic cues. To overcome these challenges, the root proteome is shaped to specific responses. Proteome-wide reprogramming events are magnified in meristems due to their active protein production. Using meristems as a test system, here, we study the major rewiring that plants undergo during cold acclimation. We performed tandem mass tag-based bottom-up quantitative proteomics of two consecutive segments of barley seminal root apexes subjected to suboptimal temperatures. After comparing changes in total and ribosomal protein (RP) fraction-enriched contents with shifts in individual protein abundances, we report ribosome accumulation accompanied by an intricate translational reprogramming in the distal apex zone. Reprogramming ranges from increases in ribosome biogenesis to protein folding factors and suggests roles for cold-specific RP paralogs. Ribosome biogenesis is the largest cellular investment; thus, the vast accumulation of ribosomes and specific translation-related proteins during cold acclimation could imply a divergent ribosomal population that would lead to a proteome shift across the root. Consequently, beyond the translational reprogramming, we report a proteome rewiring. First, triggered protein accumulation includes spliceosome activity in the root tip and a ubiquitous upregulation of glutathione production and S-glutathionylation (S-GSH) assemblage machineries in both root zones. Second, triggered protein depletion includes intrinsically enriched proteins in the tip-adjacent zone, which comprise the plant immune system. In summary, ribosome and translation-related protein accumulation happens concomitantly to a proteome reprogramming in barley root meristems during cold acclimation. The cold-accumulated proteome is functionally implicated in feedbacking transcript to protein translation at both ends and could guide cold acclimation.
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Affiliation(s)
- Federico Martinez-Seidel
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Shuai Nie
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC, Australia
| | - Michael G. Leeming
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC, Australia
- School of Chemistry, The University of Melbourne, Parkville, VIC, Australia
| | | | - Nicholas A. Williamson
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Joachim Kopka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Berin A. Boughton
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Australian National Phenome Centre, Murdoch University, Murdoch, WA, Australia
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Raza A, Tabassum J, Kudapa H, Varshney RK. Can omics deliver temperature resilient ready-to-grow crops? Crit Rev Biotechnol 2021; 41:1209-1232. [PMID: 33827346 DOI: 10.1080/07388551.2021.1898332] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plants are extensively well-thought-out as the main source for nourishing natural life on earth. In the natural environment, plants have to face several stresses, mainly heat stress (HS), chilling stress (CS) and freezing stress (FS) due to adverse climate fluctuations. These stresses are considered as a major threat for sustainable agriculture by hindering plant growth and development, causing damage, ultimately leading to yield losses worldwide and counteracting to achieve the goal of "zero hunger" proposed by the Food and Agricultural Organization (FAO) of the United Nations. Notably, this is primarily because of the numerous inequities happening at the cellular, molecular and/or physiological levels, especially during plant developmental stages under temperature stress. Plants counter to temperature stress via a complex phenomenon including variations at different developmental stages that comprise modifications in physiological and biochemical processes, gene expression and differences in the levels of metabolites and proteins. During the last decade, omics approaches have revolutionized how plant biologists explore stress-responsive mechanisms and pathways, driven by current scientific developments. However, investigations are still required to explore numerous features of temperature stress responses in plants to create a complete idea in the arena of stress signaling. Therefore, this review highlights the recent advances in the utilization of omics approaches to understand stress adaptation and tolerance mechanisms. Additionally, how to overcome persisting knowledge gaps. Shortly, the combination of integrated omics, genome editing, and speed breeding can revolutionize modern agricultural production to feed millions worldwide in order to accomplish the goal of "zero hunger."
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Affiliation(s)
- Ali Raza
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Javaria Tabassum
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science (CAAS), Hangzhou, China
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.,The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia
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18
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Lipid Compositions and Geographical Discrimination of 94 Geographically Authentic Wheat Samples Based on UPLC-MS with Non-Targeted Lipidomic Approach. Foods 2020; 10:foods10010010. [PMID: 33374499 PMCID: PMC7822159 DOI: 10.3390/foods10010010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/19/2022] Open
Abstract
Wheat is the staple food for the world’s major populations. However, chemical characters of geographically authentic wheat samples, especially for the lipids, have not been deeply studied. The present research aimed to investigate lipid compositions of Chinese wheat samples and clarify the major markers that contribute to the geographical differences. A total of 94 wheat samples from eight main wheat-producing provinces in China were evaluated to differentiate their lipid compositions. Based on the data collected from ultra-high-performance-liquid-chromatography tandem time-of-flight mass spectrometry (UPLC-Q/TOF MS), an optimized non-targeted lipidomic method was utilized for analyses. As the results, 62 lipid compounds, including fatty acids, phospholipids, galactolipids, triglycerides, diglycerides, alkylresorcinol, and ceramide were tentatively identified. Partial least squares discriminant analysis (PLS-DA) demonstrated a more satisfying performance in distinguishing wheat samples from different origins compared with principal component analysis (PCA). Further, the abundances of triglycerides and glycerophospholipids with more unsaturated fatty acids were found greater in wheat samples from northern origins of China, while more glycolipids and unsaturated fatty acids arose in southern original wheat samples. These findings describe the lipid profiles of wheat samples in China and could contribute to the quality and safety control for the wheat flour products.
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19
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Kehelpannala C, Rupasinghe TWT, Hennessy T, Bradley D, Ebert B, Roessner U. A comprehensive comparison of four methods for extracting lipids from Arabidopsis tissues. PLANT METHODS 2020; 16:155. [PMID: 33292337 PMCID: PMC7713330 DOI: 10.1186/s13007-020-00697-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/24/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND The plant lipidome is highly complex, and the composition of lipids in different tissues as well as their specific functions in plant development, growth and stress responses have yet to be fully elucidated. To do this, efficient lipid extraction protocols which deliver target compounds in solution at concentrations adequate for subsequent detection, quantitation and analysis through spectroscopic methods are required. To date, numerous methods are used to extract lipids from plant tissues. However, a comprehensive analysis of the efficiency and reproducibility of these methods to extract multiple lipid classes from diverse tissues of a plant has not been undertaken. RESULTS In this study, we report the comparison of four different lipid extraction procedures in order to determine the most effective lipid extraction protocol to extract lipids from different tissues of the model plant Arabidopsis thaliana. CONCLUSION While particular methods were best suited to extract different lipid classes from diverse Arabidopsis tissues, overall a single-step extraction method with a 24 h extraction period, which uses a mixture of chloroform, isopropanol, methanol and water, was the most efficient, reproducible and the least labor-intensive to extract a broad range of lipids for untargeted lipidomic analysis of Arabidopsis tissues. This method extracted a broad range of lipids from leaves, stems, siliques, roots, seeds, seedlings and flowers of Arabidopsis. In addition, appropriate methods for targeted lipid analysis of specific lipids from particular Arabidopsis tissues were also identified.
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Affiliation(s)
- Cheka Kehelpannala
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Thusitha W T Rupasinghe
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Sciex, 2 Gilda Ct, Mulgrave, VIC, 3170, Australia
| | - Thomas Hennessy
- Agilent Technologies Australia Pty Ltd, 679 Springvale Road, Mulgrave, VIC, 3170, Australia
| | - David Bradley
- Agilent Technologies Australia Pty Ltd, 679 Springvale Road, Mulgrave, VIC, 3170, Australia
| | - Berit Ebert
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
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20
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Phenology and related traits for wheat adaptation. Heredity (Edinb) 2020; 125:417-430. [PMID: 32457509 PMCID: PMC7784700 DOI: 10.1038/s41437-020-0320-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
Wheat is a major food crop, with around 765 million tonnes produced globally. The largest wheat producers include the European Union, China, India, Russia, United States, Canada, Pakistan, Australia, Ukraine and Argentina. Cultivation of wheat across such diverse global environments with variation in climate, biotic and abiotic stresses, requires cultivars adapted to a range of growing conditions. One intrinsic way that wheat achieves adaptation is through variation in phenology (seasonal timing of the lifecycle) and related traits (e.g., those affecting plant architecture). It is important to understand the genes that underlie this variation, and how they interact with each other, other traits and the growing environment. This review summarises the current understanding of phenology and developmental traits that adapt wheat to different environments. Examples are provided to illustrate how different combinations of alleles can facilitate breeding of wheat varieties with optimal crop performance for different growing regions or farming systems.
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Cheong BE, Onyemaobi O, Wing Ho Ho W, Biddulph TB, Rupasinghe TWT, Roessner U, Dolferus R. Phenotyping the Chilling and Freezing Responses of Young Microspore Stage Wheat Spikes Using Targeted Metabolome and Lipidome Profiling. Cells 2020; 9:cells9051309. [PMID: 32466096 PMCID: PMC7291281 DOI: 10.3390/cells9051309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/16/2020] [Accepted: 05/20/2020] [Indexed: 12/22/2022] Open
Abstract
Chilling and frost conditions impose major yield restraints to wheat crops in Australia and other temperate climate regions. Unpredictability and variability of field frost events are major impediments for cold tolerance breeding. Metabolome and lipidome profiling were used to compare the cold response in spikes of cold-tolerant Young and sensitive variety Wyalkatchem at the young microspore (YM) stage of pollen development. We aimed to identify metabolite markers that can reliably distinguish cold-tolerant and sensitive wheat varieties for future cold-tolerance phenotyping applications. We scored changes in spike metabolites and lipids for both varieties during cold acclimation after initial and prolonged exposure to combined chilling and freezing cycles (1 and 4 days, respectively) using controlled environment conditions. The two contrasting wheat varieties showed qualitative and quantitative differences in primary metabolites involved in osmoprotection, but differences in lipid accumulation most distinctively separated the cold response of the two wheat lines. These results resemble what we previously observed in flag leaves of the same two wheat varieties. The fact that this response occurs in tissue types with very different functions indicates that chilling and freezing tolerance in these wheat lines is associated with re-modelling of membrane lipid composition to maintain membrane fluidity.
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Affiliation(s)
- Bo Eng Cheong
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Olive Onyemaobi
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT 2601, Australia;
| | - William Wing Ho Ho
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Thomas Ben Biddulph
- Department of Primary Industries and Regional Development, 3 Baron Hay Court, South Perth, WA 6151, Australia;
| | - Thusitha W. T. Rupasinghe
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Rudy Dolferus
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT 2601, Australia;
- Correspondence: ; Tel.: +61-2-6246 5010
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