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Malle S, Eskandari M, Morrison M, Belzile F. Genome-wide association identifies several QTLs controlling cysteine and methionine content in soybean seed including some promising candidate genes. Sci Rep 2020; 10:21812. [PMID: 33311570 PMCID: PMC7733516 DOI: 10.1038/s41598-020-78907-w] [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: 12/11/2019] [Accepted: 11/26/2020] [Indexed: 11/24/2022] Open
Abstract
Soybean is an important source of protein, oil and carbohydrates, as well as other beneficial nutrients. A major function of proteins in nutrition is to supply adequate amounts of amino acids. Although they are essential for human nutrition, the sulfur-containing amino acids cysteine (Cys) and methionine (Met) are often limited and the genetic control of their content in soybean seeds is poorly characterized. This study aimed to characterize the phenotypic variation and identify quantitative trait loci (QTL) associated with Cys and Met content in a core set of 137 soybean lines, representative of the genetic diversity among Canadian short-season soybean, spanning maturity groups 000-II (MG000-II). Significant phenotypic differences were found among these lines for Cys, Met and Cys + Met content. Using both a mixed linear model and six multi-locus methods with a catalogue of 2.18 M SNPs, we report a total of nine QTLs and seventeen QTNs of which seven comprise promising candidate genes. This work allowed us to reproducibly detect multiple novel loci associated with sulfur-containing amino acid content. The markers and genes identified in this study may be useful for soybean genetic improvement aiming to increase Cys and Met content.
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Affiliation(s)
- Sidiki Malle
- Département de Phytologie, Faculty of Agricultural and Food Sciences and Institute for Integrative and Systems Biology (IBIS), Laval University, Quebec City, QC, Canada
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Ridgetown, ON, Canada
| | - Malcolm Morrison
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - François Belzile
- Département de Phytologie, Faculty of Agricultural and Food Sciences and Institute for Integrative and Systems Biology (IBIS), Laval University, Quebec City, QC, Canada.
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Luthria DL, Maria John KM, Marupaka R, Natarajan S. Recent update on methodologies for extraction and analysis of soybean seed proteins. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:5572-5580. [PMID: 29971799 DOI: 10.1002/jsfa.9235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/26/2018] [Accepted: 06/29/2018] [Indexed: 06/08/2023]
Abstract
Soybean is one of the best sources of plant protein. Development of improved soybean cultivars through classical breeding and new biotech approaches is important to meet the growing global demand for soybeans. There is a critical need to investigate changes in protein content and profiles to ensure the safety and nutritional quality of new soybean varieties and their food products. A proteomics study begins with an optimal combination of extraction, separation and detection approaches. This review attempts to provide a summary of current updates in the methodologies used for extraction, separation and detection of protein from soybean, the basic foundations for good proteomic research. This information can be effectively used to investigate modifications in protein content and profiles in new varieties of soybeans and other crops. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Devanand L Luthria
- Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD, USA
| | | | - Ramesh Marupaka
- Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD, USA
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Layek SS, Mohanty TK, Kumaresan A, Parks JE. Cryopreservation of bull semen: Evolution from egg yolk based to soybean based extenders. Anim Reprod Sci 2016; 172:1-9. [PMID: 27509873 DOI: 10.1016/j.anireprosci.2016.04.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/19/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
Abstract
Since the inception of bovine semen cryopreservation, egg yolk and milk based extenders have been used to protect sperm from the detrimental effects of cooling and freezing. In recent years, demand for alternatives to conventional commercial extenders has arisen as the risk of introducing exotic diseases through transporting egg yolk based products has been recognized. Egg yolk can also interfere with sperm evaluation and the presence of particulate material in the extender may reduce fertility. Soybeans contain lecithin, a phospholipid fraction that can substitute for high molecular weight lipoprotein and phospholipids from egg yolk and prevent or ameliorate damage to the sperm plasma membrane that occurs during extension, cooling, and cryopreservation. Soy lecithin based extenders have been evaluated for processing and freezing bovine semen, although extender from soybean milk has not been studied as extensively. Commercially available soy lecithin based extenders are used increasingly but remain under scrutiny and are not universally accepted. With these observations in mind, this review is intended to examine effects of conventional cryopreservation procedures, methods of assessment, and potential for developing soybean extract as an acceptable alternative to traditional egg yolk and milk based extenders for bull sperm cryopreservation.
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Affiliation(s)
- S S Layek
- Livestock Research Centre, National Dairy Research Institute, Karnal, 132 001 Haryana, India
| | - T K Mohanty
- Livestock Research Centre, National Dairy Research Institute, Karnal, 132 001 Haryana, India
| | - A Kumaresan
- Livestock Research Centre, National Dairy Research Institute, Karnal, 132 001 Haryana, India
| | - J E Parks
- Department of Animal Science, Cornell University, Ithaca, NY 14850, USA.
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Ma Y, Kan G, Zhang X, Wang Y, Zhang W, Du H, Yu D. Quantitative Trait Loci (QTL) Mapping for Glycinin and β-Conglycinin Contents in Soybean (Glycine max L. Merr.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3473-83. [PMID: 27070305 DOI: 10.1021/acs.jafc.6b00167] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Compared to β-conglycinin, glycinin contains 3-4 times the methionine and cysteine (sulfur-containing amino acids), accounting for approximately 40 and 30%, respectively, of the total storage protein in soybean. Increasing the soybean storage protein content while improving the ratio of glycinin to β-conglycinin is of great significance for soybean breeding and soy food products. The objective of this study is to analyze the genetic mechanism regulating the glycinin and β-conglycinin contents of soybean by using a recombinant inbred line (RIL) population derived from a cross between Kefeng No. 1 and Nannong 1138-2. Two hundred and twenty-one markers were used to map quantitative trait loci (QTLs) for glycinin (11S) and β-conglycinin (7S) contents, the ratio of glycinin to β-conglycinin (RGC), and the sum of glycinin and β-conglycinin (SGC). A total of 35 QTLs, 3 pairs of epistatic QTLs, and 5 major regions encompassing multiple QTLs were detected. Genes encoding the subunits of β-conglycinin were localized to marker intervals sat_418-satt650 and sat_196-sat_303, which are linked to RGC and SGC; marker sat_318, associated with 11S, 7S, and SGC, was located near Glyma10g04280 (Gy4), which encodes a subunit of glycinin. These results, which take epistatic interactions into account, will improve our understanding of the genetic basis of 11S and 7S contents and will lay a foundation for marker-assisted selection (MAS) breeding of soybean and improving the quality of soybean products.
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Affiliation(s)
- Yujie Ma
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Xinnan Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Yongli Wang
- Biofuels Institute, School of the Environment, Jiangsu University , Zhenjiang 212013, China
| | - Wei Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Hongyang Du
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
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Silva RDC, Carmo LST, Luis ZG, Silva LP, Scherwinski-Pereira JE, Mehta A. Proteomic identification of differentially expressed proteins during the acquisition of somatic embryogenesis in oil palm (Elaeis guineensis Jacq.). J Proteomics 2014; 104:112-27. [PMID: 24675181 DOI: 10.1016/j.jprot.2014.03.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/24/2014] [Accepted: 03/12/2014] [Indexed: 01/03/2023]
Abstract
UNLABELLED In the present study we have identified and characterized the proteins expressed during different developmental stages of Elaeis guineensis calli obtained from zygotic embryos. We were interested in the possible proteomic changes that would occur during the acquisition of somatic embryogenesis and therefore samples were collected from zygotic embryos (E1), swollen explants 14days (E2) in induction medium, primary callus (E3), and pro-embryogenic callus (E4). The samples were grinded in liquid nitrogen, followed by total protein extraction using phenol and extraction buffer. Proteins were analyzed by two-dimensional electrophoresis (2-DE) and the differentially expressed protein spots were analyzed by MALDI-TOF mass spectrometry (MS and MS/MS). Interestingly, we have identified proteins, which can be used as potential candidates for future studies aiming at the development of biomarkers for embryogenesis acquisition and for the different stages leading to pro-embryogenic callus formation such as type IIIa membrane protein cp-wap13, fructokinase and PR proteins. The results obtained shed some light on the biochemical events involved in the process of somatic embryogenesis of E. guineensis obtained from zygotic embryos. The use of stage-specific protein markers can help monitor cell differentiation and contribute to improve the protocols for successfully cloning the species. BIOLOGICAL SIGNIFICANCE Understanding the fate and dynamics of cells and tissues during callus formation is essential to understand totipotency and the mechanisms involved during acquisition of somatic embryogenesis (SE). In this study we have investigated the early stages of somatic embryogenesis induction in oil palm and have identified potential markers as well as proteins potentially involved in embryogenic competence acquisition. The use of these proteins can help improve tissue culture protocols in order to increase regeneration rates. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Rafael de Carvalho Silva
- PPGBIOTEC, Departamento de Biologia, Universidade Federal do Amazonas, CEP 69077-000, Manaus, AM, Brazil
| | | | - Zanderluce Gomes Luis
- PPGBOT, Departamento de Botanica, Instituto de Biologia, Universidade de Brasilia, CEP 70910-900, Brasília, DF, Brazil
| | - Luciano Paulino Silva
- Embrapa Recursos Genéticos e Biotecnologia, Av. W5 Norte Final, CEP 70770-917, Brasília, DF, Brazil
| | - Jonny Everson Scherwinski-Pereira
- Embrapa Recursos Genéticos e Biotecnologia, Av. W5 Norte Final, CEP 70770-917, Brasília, DF, Brazil; PPGBOT, Departamento de Botanica, Instituto de Biologia, Universidade de Brasilia, CEP 70910-900, Brasília, DF, Brazil.
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Av. W5 Norte Final, CEP 70770-917, Brasília, DF, Brazil.
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Magni C, Ballabio C, Restani P, Fuggetta D, Alessandri C, Mari A, Bernardini R, Iacono ID, Arlorio M, Duranti M. Molecular insight into IgE-mediated reactions to sesame (Sesamum indicum L.) seed proteins. Ann Allergy Asthma Immunol 2011; 105:458-64. [PMID: 21130384 DOI: 10.1016/j.anai.2010.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 09/26/2010] [Accepted: 10/03/2010] [Indexed: 11/15/2022]
Abstract
BACKGROUND Food allergy is becoming a major public health concern in recent times. Several sesame seed allergenic proteins have been identified. However, sensitization toward these proteins does not follow a common and unique pattern of clinical reactivity, as shown by the differential geographic recognition of single proteins. OBJECTIVE To evaluate the sensitization profiles of 18 Italian individuals who experienced clinical symptoms after sesame seed consumption, including 4 anaphylactic reactions. METHODS Using an in vitro approach, we adopted a 2-dimensional electrophoretic technique combined with immunoblotting analyses by using sera from 18 Italian sesame-allergic patients. RESULTS We showed the prevalent and almost exclusive reactivity of the sesame 11S globulin. We shed light on the active role of the basic subunit of this globulin family. The limited accessibility of this polypeptide chain, unless the interchain disulphide bonds are cleaved, may be one of the reasons for its structural/functional stability and, thus, great potential for induction of IgE reactivity. CONCLUSIONS These results confirmed previous findings on the reactivity of the basic subunit of 11S globulin in various legume species. Moreover, this experimental approach proved to be useful for the noninvasive screening of specific reactivities in sensitized patients.
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Affiliation(s)
- Chiara Magni
- Department of AgriFood Molecular Sciences, Università degli Studi di Milano, Milan, Italy
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Zilić SM, Barać MB, Pesić MB, Mladenović Drinić SD, Ignjatović-Micić DD, Srebrić MB. Characterization of proteins from kernel of different soybean varieties. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2011; 91:60-7. [PMID: 20812371 DOI: 10.1002/jsfa.4148] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 07/21/2010] [Accepted: 08/02/2010] [Indexed: 05/29/2023]
Abstract
BACKGROUND Total soybean proteins, storage proteins, glycinin (11S) and β-conglycinin (7S) fractions and their respective subunits in seven soybean varieties were analyzed. In this work we also present the correlation between concentration and activity of bioactive proteins, lipoxygenase and proteinase inhibitors. RESULTS Glycinin and β-conglycinin comprise about 750 g kg(-1) of the bean storage protein and as such account for both quantity and quality of the kernel protein. The 11S concentration of the varieties studied ranged from 503.4 to 602.9 g kg(-1) and those of 7S varied from 178.2 to 230.6 g kg(-1) of total extractable proteins. The ratio of 11S/7S proteins varied from 2.43 to 3.29 among the varieties. A very strong positive correlation was found between the concentration of Kunitz trypsin inhibitor and activity of total trypsin inhibitor (r = 0.96). However, lipoxygenase concentration did not show a strong correlation with lipoxygenase activity. CONCLUSION It appears that among the seven ZP soybean genotypes there are genotypes with different amounts of subunits that should be bred in the future for a desired level of protein components.
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Affiliation(s)
- Sladana M Zilić
- Maize Research Institute, Zemun Polje, Department of Technology, Belgrade-Zemun, Serbia.
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Bässler OY, Weiss J, Wienkoop S, Lehmann K, Scheler C, Dölle S, Schwarz D, Franken P, George E, Worm M, Weckwerth W. Evidence for novel tomato seed allergens: IgE-reactive legumin and vicilin proteins identified by multidimensional protein fractionation-mass spectrometry and in silico epitope modeling. J Proteome Res 2009; 8:1111-22. [PMID: 19203290 DOI: 10.1021/pr800186d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Tomato fruit and seed allergens were detected by IgE-immunoblotting using sera from 18 adult tomato-sensitized patients selected based on a positive history skin prick test (SPT) and specific Immunglobulin (Ig) E-levels. Isolated tomato seed total protein showed high SPT activity comparable or even higher than tomato fruit protein. For the molecular characterization of tomato seed allergens, a multidimensional protein fractionation strategy and LC-MS/MS was used. Two legumin- and vicilin-proteins were purified and showed strong IgE-reactivity in immunoblots. Individual patient sera exhibited varying IgE-sensitivity against the purified proteins. In silico structural modeling indicates high homology between epitopes of known walnut allergens and the detected IgE-crossreactive tomato proteins.
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Affiliation(s)
- Olivia Y Bässler
- Max Planck Institute of Molecular Plant Physiology, D-14467 Potsdam, Germany, Universitat Potsdam GoFORSYS, D-14467 Potsdam, Germany
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Zarkadas CG, Gagnon C, Gleddie S, Khanizadeh S, Cober ER, Guillemette RJ. Assessment of the protein quality of fourteen soybean [Glycine max (L.) Merr.] cultivars using amino acid analysis and two-dimensional electrophoresis. Food Res Int 2007. [DOI: 10.1016/j.foodres.2006.08.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Plants store amino acids for longer periods in the form of specific storage proteins. These are deposited in seeds, in root and shoot tubers, in the wood and bark parenchyma of trees and in other vegetative organs. Storage proteins are protected against uncontrolled premature degradation by several mechanisms. The major one is to deposit the storage proteins into specialized membrane-bounded storage organelles, called protein bodies (PB). In the endosperm cells of maize and rice prolamins are sequestered into PBs which are derived from the endoplasmic reticulum (ER). Globulins, the typical storage proteins of dicotyledonous plants, and prolamins of some cereals are transported from the ER through the Golgi apparatus and then into protein storage vacuoles (PSV) which later become transformed into PBs. Sorting and targeting of storage proteins begins during their biosynthesis on membrane-bound polysomes where an N-terminal signal peptide mediates their segregation into the lumen of the ER. After cleavage of the signal peptide, the polypeptides are glycosylated and folded with the aid of chaperones. While still in the ER, disulfide bridges are formed which stabilize the structure and several polypeptides are joined to form an oligomer which has the proper conformation to be either deposited in ER-derived PB or to be further transferred to the PSV. At the trans-Golgi cisternae transport vesicles are sequestered which carry the storage proteins to the PSV. Several storage proteins are also processed after arriving in the PSVs in order to generate a conformation that is capable of final deposition. Some storage protein precursors have short N- or C-terminal targeting sequences which are detached after arrival in the PSV. Others have been shown to have internal sequence regions which could act as targeting information. In some cases positive targeting information is known to mediate sorting into the PSV whereas in other cases aggregation and membrane association seem to be major sorting mechanisms.
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Affiliation(s)
- K Müntz
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
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