1
|
Arvas YE, Marakli S, Kaya Y, Kalendar R. The power of retrotransposons in high-throughput genotyping and sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1174339. [PMID: 37180380 PMCID: PMC10167742 DOI: 10.3389/fpls.2023.1174339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023]
Abstract
The use of molecular markers has become an essential part of molecular genetics through their application in numerous fields, which includes identification of genes associated with targeted traits, operation of backcrossing programs, modern plant breeding, genetic characterization, and marker-assisted selection. Transposable elements are a core component of all eukaryotic genomes, making them suitable as molecular markers. Most of the large plant genomes consist primarily of transposable elements; variations in their abundance contribute to most of the variation in genome size. Retrotransposons are widely present throughout plant genomes, and replicative transposition enables them to insert into the genome without removing the original elements. Various applications of molecular markers have been developed that exploit the fact that these genetic elements are present everywhere and their ability to stably integrate into dispersed chromosomal localities that are polymorphic within a species. The ongoing development of molecular marker technologies is directly related to the deployment of high-throughput genotype sequencing platforms, and this research is of considerable significance. In this review, the practical application to molecular markers, which is a use of technology of interspersed repeats in the plant genome were examined using genomic sources from the past to the present. Prospects and possibilities are also presented.
Collapse
Affiliation(s)
- Yunus Emre Arvas
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, Trabzon, Türkiye
| | - Sevgi Marakli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Türkiye
| | - Yılmaz Kaya
- Agricultural Biotechnology Department, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Ruslan Kalendar
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| |
Collapse
|
2
|
Raizada A, Souframanien J. Transcriptome sequencing, de novo assembly, characterisation of wild accession of blackgram (Vigna mungo var. silvestris) as a rich resource for development of molecular markers and validation of SNPs by high resolution melting (HRM) analysis. BMC PLANT BIOLOGY 2019; 19:358. [PMID: 31419947 PMCID: PMC6697964 DOI: 10.1186/s12870-019-1954-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/31/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Blackgram [Vigna mungo (L.) Hepper], is an important legume crop of Asia with limited genomic resources. We report a comprehensive set of genic simple sequence repeat (SSR) and single nucleotide polymorphism (SNPs) markers using Illumina MiSeq sequencing of transcriptome and its application in genetic variation analysis and mapping. RESULTS Transcriptome sequencing of immature seeds of wild blackgram, V. mungo var. silvestris by Illumina MiSeq technology generated 1.9 × 107 reads, which were assembled into 40,178 transcripts (TCS) with an average length of 446 bp covering 2.97 GB of the genome. A total of 38,753 CDS (Coding sequences) were predicted from 40,178 TCS and 28,984 CDS were annotated through BLASTX and mapped to GO and KEGG database resulting in 140 unique pathways. The tri-nucleotides were most abundant (39.9%) followed by di-nucleotide (30.2%). About 60.3 and 37.6% of SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Among SNPs, the most abundant substitution type were transitions (Ts) (61%) followed by transversions (Tv) type (39%), with a Ts/Tv ratio of 1.58. A total of 2306 DEGs were identified by RNA Seq between wild and cultivar and validation was done by quantitative reverse transcription polymerase chain reaction. In this study, we genotyped SNPs with a validation rate of 78.87% by High Resolution Melting (HRM) Assay. CONCLUSION In the present study, 1621genic-SSR and 1844 SNP markers were developed from immature seed transcriptome sequence of blackgram and 31 genic-SSR markers were used to study genetic variations among different blackgram accessions. Above developed markers contribute towards enriching available genomic resources for blackgram and aid in breeding programmes.
Collapse
Affiliation(s)
- Avi Raizada
- Nuclear Agriculture and Biotechnology Division, BARC, Trombay, Mumbai, Trombay, 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Anushakti Nagar, 400094, India
| | - J Souframanien
- Nuclear Agriculture and Biotechnology Division, BARC, Trombay, Mumbai, Trombay, 400085, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Anushakti Nagar, 400094, India.
| |
Collapse
|
3
|
Mamontova T, Lukasheva E, Mavropolo-Stolyarenko G, Proksch C, Bilova T, Kim A, Babakov V, Grishina T, Hoehenwarter W, Medvedev S, Smolikova G, Frolov A. Proteome Map of Pea ( Pisum sativum L.) Embryos Containing Different Amounts of Residual Chlorophylls. Int J Mol Sci 2018; 19:E4066. [PMID: 30558315 PMCID: PMC6320946 DOI: 10.3390/ijms19124066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 02/06/2023] Open
Abstract
Due to low culturing costs and high seed protein contents, legumes represent the main global source of food protein. Pea (Pisum sativum L.) is one of the major legume crops, impacting both animal feed and human nutrition. Therefore, the quality of pea seeds needs to be ensured in the context of sustainable crop production and nutritional efficiency. Apparently, changes in seed protein patterns might directly affect both of these aspects. Thus, here, we address the pea seed proteome in detail and provide, to the best of our knowledge, the most comprehensive annotation of the functions and intracellular localization of pea seed proteins. To address possible intercultivar differences, we compared seed proteomes of yellow- and green-seeded pea cultivars in a comprehensive case study. The analysis revealed totally 1938 and 1989 nonredundant proteins, respectively. Only 35 and 44 proteins, respectively, could be additionally identified after protamine sulfate precipitation (PSP), potentially indicating the high efficiency of our experimental workflow. Totally 981 protein groups were assigned to 34 functional classes, which were to a large extent differentially represented in yellow and green seeds. Closer analysis of these differences by processing of the data in KEGG and String databases revealed their possible relation to a higher metabolic status and reduced longevity of green seeds.
Collapse
Affiliation(s)
- Tatiana Mamontova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany.
- Department of Biochemistry, St. Petersburg State University, St. Petersburg 199178, Russia.
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University, St. Petersburg 199178, Russia.
| | | | - Carsten Proksch
- Proteome Analytics, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Tatiana Bilova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany.
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - Ahyoung Kim
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany.
| | - Vladimir Babakov
- Research Institute of Hygiene, Occupational Pathology, and Human Ecology, Federal Medicobiological Agency, 188663 Kapitolovo, Russia.
| | - Tatiana Grishina
- Department of Biochemistry, St. Petersburg State University, St. Petersburg 199178, Russia.
| | - Wolfgang Hoehenwarter
- Proteome Analytics, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany.
- Department of Biochemistry, St. Petersburg State University, St. Petersburg 199178, Russia.
| |
Collapse
|
4
|
Wang WQ, Wang Y, Zhang Q, Møller IM, Song SQ. Changes in the mitochondrial proteome of developing maize seed embryos. PHYSIOLOGIA PLANTARUM 2018; 163:552-572. [PMID: 29575040 DOI: 10.1111/ppl.12725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 05/19/2023]
Abstract
Mitochondria are required for seed development, but little information is available about their function and role during this process. We isolated the mitochondria from developing maize (Zea mays L. cv. Nongda 108) embryos and investigated the mitochondrial membrane integrity and respiration as well as the mitochondrial proteome using two proteomic methods, the two-dimensional gel electrophoresis (2-DE) and sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH). Mitochondrial membrane integrity and respiration were maintained at a high level up to 21 days after pollination (DAP) and decreased thereafter, while total mitochondrial number, cytochrome c oxidase activity and respiration per embryo exhibited a bell-shaped change with peaks at 35-45 DAP. A total of 286 mitochondrial proteins changed in abundance during embryo development. During early stages of seed development (up to 21 DAP), proteins involved in energy production, basic metabolism, protein import and folding as well as removal of reactive oxygen species dominated, while during mid or late stages (35-70 DAP), some stress- and detoxification-related proteins increased in abundance. Our study, for the first time, depicted a relatively comprehensive map of energy production by mitochondria during embryo development. The results revealed that mitochondria were very active during the early stages of maize embryo development, while at the late stages of development, the mitochondria became more quiescent, but well-protected, presumably to ensure that the embryo passes through maturation, drying and long-term storage. These results advance our understanding of seed development at the organelle level.
Collapse
Affiliation(s)
- Wei-Qing Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Yue Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Qi Zhang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Ian M Møller
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
- Department of Molecular Biology and Genetics, Aarhus University, DK-4200 Slagelse, Denmark
| | - Song-Quan Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| |
Collapse
|
5
|
Song Y, He L, Wang XD, Smith N, Wheeler S, Garg ML, Rose RJ. Regulation of Carbon Partitioning in the Seed of the Model Legume Medicago truncatula and Medicago orbicularis: A Comparative Approach. FRONTIERS IN PLANT SCIENCE 2017; 8:2070. [PMID: 29312368 PMCID: PMC5733034 DOI: 10.3389/fpls.2017.02070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/20/2017] [Indexed: 05/20/2023]
Abstract
The proportion of starch, protein and oil in legume seeds is species dependent. The model legume, Medicago truncatula, has predominantly oil and protein stores. To investigate the regulation of seed oil production we compared M. truncatula with M. orbicularis, which has less oil and protein. The types of protein and fatty acids are similar between the two species. Electron microscopy indicated that the size and distribution of the oil bodies in M. orbicularis, is consistent with reduced oil production. M. orbicularis has more extruded endosperm mucilage compared to M. truncatula. The cotyledons have a greater cell wall content, visualized as thicker cell walls. The reduced oil content in M. orbicularis is associated with increased expression of the MtGLABRA2-like (MtGL2) transcription factor, linked to an inverse relationship between mucilage and oil content in Arabidopsis. The expression of the pectin biosynthesis GALACTURONOSYLTRANSFERASE (GAUT) genes, is also increased in M. orbicularis. These increases in extruded mucilage and cell wall storage components in M. orbicularis are accompanied by reduced expression of transcriptional regulators of oil biosynthesis, MtLEAFY COTYLEDON1-LIKE (MtL1L), MtABSCISIC ACID-INSENSITIVE3 (MtABI3), and MtWRINKLED-like (MtWRI), in M. orbicularis. The reduced oil in M. orbicularis, is consistent with increased synthesis of cell wall polysaccharides and decreased expression of master transcription factors regulating oil biosynthesis and embryo maturation. Comparative investigations between these two Medicago species is a useful system to investigate the regulation of oil content and carbon partitioning in legumes.
Collapse
Affiliation(s)
- Youhong Song
- School of Agronomy, Anhui Agricultural University, Hefei, China
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Liang He
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xin-Ding Wang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Nathan Smith
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Simon Wheeler
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Manohar L. Garg
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Ray J. Rose
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| |
Collapse
|
6
|
Song Y, Wang XD, Rose RJ. Oil body biogenesis and biotechnology in legume seeds. PLANT CELL REPORTS 2017; 36:1519-1532. [PMID: 28866824 PMCID: PMC5602053 DOI: 10.1007/s00299-017-2201-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/23/2017] [Indexed: 05/08/2023]
Abstract
The seeds of many legume species including soybean, Pongamia pinnata and the model legume Medicago truncatula store considerable oil, apart from protein, in their cotyledons. However, as a group, legume storage strategies are quite variable and provide opportunities for better understanding of carbon partitioning into different storage products. Legumes with their ability to fix nitrogen can also increase the sustainability of agricultural systems. This review integrates the cell biology, biochemistry and molecular biology of oil body biogenesis before considering biotechnology strategies to enhance oil body biosynthesis. Cellular aspects of packaging triacylglycerol (TAG) into oil bodies are emphasized. Enhancing seed oil content has successfully focused on the up-regulation of the TAG biosynthesis pathways using overexpression of enzymes such as diacylglycerol acyltransferase1 and transcription factors such as WRINKLE1 and LEAFY COTYLEDON1. While these strategies are central, decreasing carbon flow into other storage products and maximizing the packaging of oil bodies into the cytoplasm are other strategies that need further examination. Overall there is much potential for integrating carbon partitioning, up-regulation of fatty acid and TAG synthesis and oil body packaging, for enhancing oil levels. In addition to the potential for integrated strategies to improving oil yields, the capacity to modify fatty acid composition and use of oil bodies as platforms for the production of recombinant proteins in seed of transgenic legumes provide other opportunities for legume biotechnology.
Collapse
Affiliation(s)
- Youhong Song
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Xin-Ding Wang
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Ray J Rose
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia.
| |
Collapse
|
7
|
Le Signor C, Aimé D, Bordat A, Belghazi M, Labas V, Gouzy J, Young ND, Prosperi JM, Leprince O, Thompson RD, Buitink J, Burstin J, Gallardo K. Genome-wide association studies with proteomics data reveal genes important for synthesis, transport and packaging of globulins in legume seeds. THE NEW PHYTOLOGIST 2017; 214:1597-1613. [PMID: 28322451 DOI: 10.1111/nph.14500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/27/2017] [Indexed: 05/25/2023]
Abstract
Improving nutritional seed quality is an important challenge in grain legume breeding. However, the genes controlling the differential accumulation of globulins, which are major contributors to seed nutritional value in legumes, remain largely unknown. We combined a search for protein quantity loci with genome-wide association studies on the abundance of 7S and 11S globulins in seeds of the model legume species Medicago truncatula. Identified genomic regions and genes carrying polymorphisms linked to globulin variations were then cross-compared with pea (Pisum sativum), leading to the identification of candidate genes for the regulation of globulin abundance in this crop. Key candidates identified include genes involved in transcription, chromatin remodeling, post-translational modifications, transport and targeting of proteins to storage vacuoles. Inference of a gene coexpression network of 12 candidate transcription factors and globulin genes revealed the transcription factor ABA-insensitive 5 (ABI5) as a highly connected hub. Characterization of loss-of-function abi5 mutants in pea uncovered a role for ABI5 in controlling the relative abundance of vicilin, a sulfur-poor 7S globulin, in pea seeds. This demonstrates the feasibility of using genome-wide association studies in M. truncatula to reveal genes that can be modulated to improve seed nutritional value.
Collapse
Affiliation(s)
- Christine Le Signor
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Delphine Aimé
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Amandine Bordat
- Unité Mixte de Recherche (UMR) 1332 Biologie du Fruit et Pathologie, INRA, 33882, Villenave d'Ornon, France
| | - Maya Belghazi
- UMR 7286 - CRN2M, Centre d'Analyses Protéomiques de Marseille, CNRS, Aix-Marseille Université, Marseille, France
| | - Valérie Labas
- INRA, UMR85 Physiologie de la Reproduction et des Comportements-Centre National de la Recherche Scientifique (CNRS) UMR 7247-Université François Rabelais-Institut Français du Cheval et de l'Equitation, Laboratoire de Spectrométrie de Masse, Plate-forme d'Analyse Intégrative des Biomolécules, 37380, Nouzilly, France
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, INRA, Université de Toulouse, Castanet-Tolosan, France
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St Paul, MN, 55108, USA
| | - Jean-Marie Prosperi
- Genetic Improvement and Adaptation of Mediterranean and Tropical Plants (AGAP), INRA, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier Supagro, 34060, Montpellier, France
| | - Olivier Leprince
- Institut de recherche en horticulture et semences (IRHS), INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Richard D Thompson
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Julia Buitink
- Institut de recherche en horticulture et semences (IRHS), INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| |
Collapse
|
8
|
Gupta M, Bhaskar PB, Sriram S, Wang PH. Integration of omics approaches to understand oil/protein content during seed development in oilseed crops. PLANT CELL REPORTS 2017; 36:637-652. [PMID: 27796489 DOI: 10.1007/s00299-016-2064-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/11/2016] [Indexed: 05/23/2023]
Abstract
Oilseed crops, especially soybean (Glycine max) and canola/rapeseed (Brassica napus), produce seeds that are rich in both proteins and oils and that are major sources of energy and nutrition worldwide. Most of the nutritional content in the seed is accumulated in the embryo during the seed filling stages of seed development. Understanding the metabolic pathways that are active during seed filling and how they are regulated are essential prerequisites to crop improvement. In this review, we summarize various omics studies of soybean and canola/rapeseed during seed filling, with emphasis on oil and protein traits, to gain a systems-level understanding of seed development. Currently, most (80-85%) of the soybean and rapeseed reference genomes have been sequenced (950 and 850 megabases, respectively). Parallel to these efforts, extensive omics datasets from different seed filling stages have become available. Transcriptome and proteome studies have detected preponderance of starch metabolism and glycolysis enzymes to be the possible cause of higher oil in B. napus compared to other crops. Small RNAome studies performed during the seed filling stages have revealed miRNA-mediated regulation of transcription factors, with the suggestion that this interaction could be responsible for transitioning the seeds from embryogenesis to maturation. In addition, progress made in dissecting the regulation of de novo fatty acid synthesis and protein storage pathways is described. Advances in high-throughput omics and comprehensive tissue-specific analyses make this an exciting time to attempt knowledge-driven investigation of complex regulatory pathways.
Collapse
Affiliation(s)
- Manju Gupta
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Pudota B Bhaskar
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | | | - Po-Hao Wang
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| |
Collapse
|
9
|
Kurdyukov S, Song Y, Tiew TWY, Wang XD, Nolan KE, Rose RJ. Protocols for Obtaining Zygotic and Somatic Embryos for Studying the Regulation of Early Embryo Development in the Model Legume Medicago truncatula. J Vis Exp 2015:e52635. [PMID: 26131626 DOI: 10.3791/52635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Early embryogenesis starting from a single cell zygote goes through rapid cell division and morphogenesis, and is morphologically characterized by pre-globular, globular, heart, torpedo and cotyledon stages. This progressive development is under the tight regulation of a complex molecular network. Harvesting sufficient early embryos at a similar stage of development is essential for investigating the cellular and molecular regulation of early embryogenesis. This is not straightforward since early embryogenesis undergoes rapid morphogenesis in a short while e.g. 8 days for Medicago truncatula to reach the early cotyledon stage. Here, we address the issue by two approaches. The first one establishes a linkage between embryo development and pod morphology in helping indicate the stage of the zygotic embryo. This is particularly based on the number of pod spirals and development of the spines. An alternative way to complement the in vivo studies is via culturing leaf explants to produce somatic embryos. The medium includes an unusual hormone combination - an auxin (1-naphthaleneacetic acid), a cytokinin (6-benzylaminopurine), abscisic acid and gibberellic acid. The different stages can be discerned growing out of the callus without dissection.
Collapse
Affiliation(s)
- Sergey Kurdyukov
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Youhong Song
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Terence W-Y Tiew
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Xin-Ding Wang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Kim E Nolan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Ray J Rose
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia;
| |
Collapse
|
10
|
Sekhon RS, Hirsch CN, Childs KL, Breitzman MW, Kell P, Duvick S, Spalding EP, Buell CR, de Leon N, Kaeppler SM. Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination. PLANT PHYSIOLOGY 2014; 165:658-669. [PMID: 24710068 PMCID: PMC4044855 DOI: 10.1104/pp.114.235424] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Seed size is a component of grain yield and an important trait in crop domestication. To understand the mechanisms governing seed size in maize (Zea mays), we examined transcriptional and developmental changes during seed development in populations divergently selected for large and small seed size from Krug, a yellow dent maize cultivar. After 30 cycles of selection, seeds of the large seed population (KLS30) have a 4.7-fold greater weight and a 2.6-fold larger size compared with the small seed population (KSS30). Patterns of seed weight accumulation from the time of pollination through 30 d of grain filling showed an earlier onset, slower rate, and earlier termination of grain filling in KSS30 relative to KLS30. This was further supported by transcriptome patterns in seeds from the populations and derived inbreds. Although the onset of key genes was earlier in small seeds, similar maximum transcription levels were observed in large seeds at later stages, suggesting that functionally weaker alleles, rather than transcript abundance, may be the basis of the slow rate of seed filling in KSS30. Gene coexpression networks identified several known genes controlling cellularization and proliferation as well as novel genes that will be useful candidates for biotechnological approaches aimed at altering seed size in maize and other cereals.
Collapse
Affiliation(s)
- Rajandeep S Sekhon
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Candice N Hirsch
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Kevin L Childs
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Matthew W Breitzman
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Paul Kell
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Susan Duvick
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Edgar P Spalding
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - C Robin Buell
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Natalia de Leon
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Shawn M Kaeppler
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| |
Collapse
|
11
|
Kurdyukov S, Song Y, Sheahan MB, Rose RJ. Transcriptional regulation of early embryo development in the model legume Medicago truncatula. PLANT CELL REPORTS 2014; 33:349-62. [PMID: 24258241 PMCID: PMC3909251 DOI: 10.1007/s00299-013-1535-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/23/2013] [Accepted: 11/02/2013] [Indexed: 05/18/2023]
Abstract
Cultivated legumes account for more than a quarter of primary crop production worldwide. The protein- and oil-rich seed of cultivated legumes provides around one-third of the protein in the average human diet, with soybeans (Glycine max (L.) Merr) being the single largest source of vegetable oil. Despite their critical importance to human and animal nutrition, we lack an understanding of how early seed development in legumes is orchestrated at the transcriptional level. We developed a method to isolate ovules from the model legume, Medicago truncatula Gaertn, at specific stages of embryogenesis, on the basis of flower and pod morphology. Using these isolated ovules we profiled the expression of candidate homeobox, AP2 domain and B3 domain-containing transcription factors. These genes were identified by available information and sequence homology, and five distinctive patterns of transcription were found that correlated with specific stages of early seed growth and development. Co-expression of some genes could be related to common regulatory sequences in the promoter or 3'-UTR regions. These expression patterns were also related to the expression of B3-domain transcription factors important in seed filling (MtFUS3-like and MtABI3-like). Localisation of gene expression by promoter-GUS fusions or in situ hybridisation aided understanding of the role of the transcription factors. This study provides a framework to enhance the understanding of the integrated transcriptional regulation of legume embryo growth and development and seed filling.
Collapse
Affiliation(s)
- Sergey Kurdyukov
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308 Australia
- Present Address: Kolling Institute of Medical Research, Kolling Building, Royal North Shore Hospital, St Leonards, NSW 2065 Australia
| | - Youhong Song
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308 Australia
| | - Michael B. Sheahan
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308 Australia
| | - Ray J. Rose
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308 Australia
| |
Collapse
|
12
|
Smýkal P, Vernoud V, Blair MW, Soukup A, Thompson RD. The role of the testa during development and in establishment of dormancy of the legume seed. FRONTIERS IN PLANT SCIENCE 2014; 5:351. [PMID: 25101104 PMCID: PMC4102250 DOI: 10.3389/fpls.2014.00351] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/30/2014] [Indexed: 05/19/2023]
Abstract
Timing of seed germination is one of the key steps in plant life cycles. It determines the beginning of plant growth in natural or agricultural ecosystems. In the wild, many seeds exhibit dormancy and will only germinate after exposure to certain environmental conditions. In contrast, crop seeds germinate as soon as they are imbibed usually at planting time. These domestication-triggered changes represent adaptations to cultivation and human harvesting. Germination is one of the common sets of traits recorded in different crops and termed the "domestication syndrome." Moreover, legume seed imbibition has a crucial role in cooking properties. Different seed dormancy classes exist among plant species. Physical dormancy (often called hardseededness), as found in legumes, involves the development of a water-impermeable seed coat, caused by the presence of phenolics- and suberin-impregnated layers of palisade cells. The dormancy release mechanism primarily involves seed responses to temperature changes in the habitat, resulting in testa permeability to water. The underlying genetic controls in legumes have not been identified yet. However, positive correlation was shown between phenolics content (e.g., pigmentation), the requirement for oxidation and the activity of catechol oxidase in relation to pea seed dormancy, while epicatechin levels showed a significant positive correlation with soybean hardseededness. myeloblastosis family of transcription factors, WD40 proteins and enzymes of the anthocyanin biosynthesis pathway were involved in seed testa color in soybean, pea and Medicago, but were not tested directly in relation to seed dormancy. These phenolic compounds play important roles in defense against pathogens, as well as affecting the nutritional quality of products, and because of their health benefits, they are of industrial and medicinal interest. In this review, we discuss the role of the testa in mediating legume seed germination, with a focus on structural and chemical aspects.
Collapse
Affiliation(s)
- Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacký University in OlomoucOlomouc, Czech Republic
- *Correspondence: Petr Smýkal, Department of Botany, Faculty of Sciences, Palacký University in Olomouc, Šlechtitelů 11, 783 71 Olomouc, Czech Republic e-mail:
| | | | - Matthew W. Blair
- Department of Agricultural and Environmental Sciences, Tennessee State UniversityNashville, TN, USA
| | - Aleš Soukup
- Department of Experimental Plant Biology, Charles UniversityPrague, Czech Republic
| | | |
Collapse
|
13
|
Xue W, Batushansky A, Toubiana D, Botnick I, Szymanski J, Khozin-Goldberg I, Nikoloski Z, Lewinsohn E, Fait A. The investment in scent: time-resolved metabolic processes in developing volatile-producing Nigella sativa L. seeds. PLoS One 2013; 8:e73061. [PMID: 24019893 PMCID: PMC3760832 DOI: 10.1371/journal.pone.0073061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 07/17/2013] [Indexed: 12/19/2022] Open
Abstract
The interplay of processes in central and specialized metabolisms during seed development of Nigella sativa L. was studied by using a high-throughput metabolomics technology and network-based analysis. Two major metabolic shifts were identified during seed development: the first was characterized by the accumulation of storage lipids (estimated as total fatty acids) and N-compounds, and the second by the biosynthesis of volatile organic compounds (VOCs) and a 30% average decrease in total fatty acids. Network-based analysis identified coordinated metabolic processes during development and demonstrated the presence of five network communities. Enrichment analysis indicated that different compound classes, such as sugars, amino acids, and fatty acids, are largely separated and over-represented in certain communities. One community displayed several terpenoids and the central metabolites, shikimate derived amino acids, raffinose, xylitol and glycerol-3-phosphate. The latter are related to precursors of the mevalonate-independent pathway for VOC production in the plastid; also plastidial fatty acid 18∶3n-3 abundant in "green" seeds grouped with several major terpenes. The findings highlight the interplay between the components of central metabolism and the VOCs. The developmental regulation of Nigella seed metabolism during seed maturation suggests a substantial re-allocation of carbon from the breakdown of fatty acids and from N-compounds, probably towards the biosynthesis of VOCs.
Collapse
Affiliation(s)
- Wentao Xue
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Albert Batushansky
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - David Toubiana
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Ilan Botnick
- Newe Ya’ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Jedrzej Szymanski
- Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Inna Khozin-Goldberg
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Zoran Nikoloski
- Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Efraim Lewinsohn
- Newe Ya’ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Aaron Fait
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| |
Collapse
|
14
|
Li X, Islam S, Yang H, Ma W, Yan G. Identification of chromosome regions controlling seed storage proteins of narrow-leafed lupin (Lupinus angustifolius). JOURNAL OF PLANT RESEARCH 2013; 126:395-401. [PMID: 23090157 DOI: 10.1007/s10265-012-0530-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 09/23/2012] [Indexed: 06/01/2023]
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) is a valuable legume crop for animal feed and human health food because of its high proteins content. However, the genetics of seed storage proteins is unclear, limiting further improvement of protein quantity and quality. In this study, matrix-assisted laser desorption/ionization time of flight mass spectrometry was used for the first time to analyze lupin seed storage proteins and the spectra generated was treated as markers to investigate the chromosome locations controlling seed storage proteins in the narrow-leafed lupin. In a recombinant inbred line population of 89 individuals, 48 polymorphic protein peaks were identified and seven of which were successfully mapped onto four existing linkage groups: two on NLL-04, three on NLL-05, one on NLL-07 and one on NLL-14, with LOD values ranging from 2.6 to 7.7 confirming a significant linkage. Most protein-based markers showed distorted segregation and were failed to be integrated into the reference map. Among them, 31 were grouped into six clusters and the other ten were totally unlinked. This study provides a significant clue to study the comparative genomics/proteomics among legumes as well as for protein marker-assisted breeding. The distribution pattern of genes controlling seed storage protein revealed in this study probably exists universally among legumes or even all plants and animals. Whether genes controlling seed storage protein share the same gene expression pattern controlling other enzymes and what is the mechanism behind it are the questions which remain to be answered in the future.
Collapse
Affiliation(s)
- Xin Li
- Institute of Agriculture, The University of Western Australia, Crawley, Perth, WA, Australia
| | | | | | | | | |
Collapse
|
15
|
Sreenivasulu N, Wobus U. Seed-development programs: a systems biology-based comparison between dicots and monocots. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:189-217. [PMID: 23451786 DOI: 10.1146/annurev-arplant-050312-120215] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Seeds develop differently in dicots and monocots, especially with respect to the major storage organs. High-resolution transcriptome data have provided the first insights into the molecular networks and pathway interactions that function during the development of individual seed compartments. Here, we review mainly recent data obtained by systems biology-based approaches, which have allowed researchers to construct and model complex metabolic networks and fluxes and identify key limiting steps in seed development. Comparative coexpression network analyses define evolutionarily conservative (FUS3/ABI3/LEC1) and divergent (LEC2) networks in dicots and monocots. Finally, we discuss the determination of seed size--an important yield-related characteristic--as mediated by a number of processes (maternal and epigenetic factors, fine-tuned regulation of cell death in distinct seed compartments, and endosperm growth) and underlying genes defined through mutant analyses. Altogether, systems approaches can make important contributions toward a more complete and holistic knowledge of seed biology and thus support strategies for knowledge-based molecular breeding.
Collapse
Affiliation(s)
- Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany.
| | | |
Collapse
|
16
|
Wang WQ, Møller IM, Song SQ. Proteomic analysis of embryonic axis of Pisum sativum seeds during germination and identification of proteins associated with loss of desiccation tolerance. J Proteomics 2012; 77:68-86. [PMID: 22796356 DOI: 10.1016/j.jprot.2012.07.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 06/20/2012] [Accepted: 07/02/2012] [Indexed: 12/26/2022]
Abstract
Seed germination is an important stage in life cycle of higher plants. The germination processes and its associated loss of desiccation tolerance, however, are still poorly understood. In present study, pea seeds were used to study changes in embryonic axis proteome during germination by 2-DE and mass spectrometry. We identified a total of 139 protein spots showing a significant (>2-fold) change during germination. The results show that seed germination is not only the activation of a series of metabolic processes, but also involves reorganization of cellular structure and activation of protective systems. To uncouple the physiological processes of germination and its associated loss of desiccation tolerance, we used the fact that pea seeds have different desiccation tolerance when imbibed in water, CaCl(2) and methylviologen at the same germination stage. We compared the proteome amongst these seeds to identify the candidate proteins associated with the loss of desiccation tolerance and found a total of seven proteins - tubulin alpha-1 chain, seed biotin-containing protein SBP65, P54 protein, vicilin, vicilin-like antimicrobial peptides 2-3, convicilin and TCP-1/cpn60 chaperonin family protein. The metabolic function of these proteins indicates that seed desiccation tolerance is related to pathogen defense, protein conformation conservation and cell structure stabilization.
Collapse
Affiliation(s)
- Wei-Qing Wang
- Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
| | | | | |
Collapse
|
17
|
Repetto O, Rogniaux H, Larré C, Thompson R, Gallardo K. The seed nuclear proteome. FRONTIERS IN PLANT SCIENCE 2012; 3:289. [PMID: 23267364 PMCID: PMC3526781 DOI: 10.3389/fpls.2012.00289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Indexed: 05/13/2023]
Abstract
Understanding the regulatory networks coordinating seed development will help to manipulate seed traits, such as protein content and seed weight, in order to increase yield and seed nutritional value of important food crops, such as legumes. Because of the cardinal role of the nucleus in gene expression, sub-proteome analyses of nuclei from developing seeds were conducted, taking advantage of the sequences available for model species. In this review, we discuss the strategies used to separate and identify the nuclear proteins at a stage when the seed is preparing for reserve accumulation. We present how these data provide an insight into the complexity and distinctive features of the seed nuclear proteome. We discuss the presence of chromatin-modifying enzymes and proteins that have roles in RNA-directed DNA methylation and which may be involved in modifying genome architecture in preparation for seed filling. Specific features of the seed nuclei at the transition between the stage of cell divisions and that of cell expansion and reserve deposition are described here which may help to manipulate seed quality traits, such as seed weight.
Collapse
Affiliation(s)
- Ombretta Repetto
- UMR1347 Agroécologie, Institut National de la Recherche AgronomiqueDijon, France
| | - Hélène Rogniaux
- UR1268 Biopolymers, Interactions, Assemblies, Institut National de la Recherche AgronomiqueNantes, France
| | - Colette Larré
- UR1268 Biopolymers, Interactions, Assemblies, Institut National de la Recherche AgronomiqueNantes, France
| | - Richard Thompson
- UMR1347 Agroécologie, Institut National de la Recherche AgronomiqueDijon, France
| | - Karine Gallardo
- UMR1347 Agroécologie, Institut National de la Recherche AgronomiqueDijon, France
- *Correspondence: Karine Gallardo, UMR1347 Agroécologie, Institut National de la Recherche Agronomique, 17 rue de Sully, BP 86510, Dijon, France. e-mail:
| |
Collapse
|
18
|
Wang XD, Song Y, Sheahan MB, Garg ML, Rose RJ. From embryo sac to oil and protein bodies: embryo development in the model legume Medicago truncatula. THE NEW PHYTOLOGIST 2012; 193:327-38. [PMID: 21988647 DOI: 10.1111/j.1469-8137.2011.03925.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
• The cell and developmental biology of zygotic embryogenesis in the model legume Medicago truncatula has received little attention. We studied M. truncatula embryogenesis from embryo sac until cotyledon maturation, including oil and protein body biogenesis. • We characterized embryo development using light and electron microscopy, measurement of protein and lipid fatty acid accumulation and by profiling the expression of key seed storage genes. • Embryo sac development in M. truncatula is of the Polygonum type. A distinctive multicellular hypophysis and suspensor develops before the globular stage and by the early cotyledon stage, the procambium connects the developing apical meristems. In the storage parenchyma of cotyledons, ovoid oil bodies surround protein bodies and the plasma membrane. Four major lipid fatty acids accumulate as cotyledons develop, paralleling the expression of OLEOSIN and the storage protein genes, VICILIN and LEGUMIN. • Zygotic embryogenesis in M. truncatula features the development of a distinctive multicellular hypophysis and an endopolyploid suspensor with basal transfer cell. A clear procambial connection between the apical meristems is evident and there is a characteristic arrangement of oil bodies in the cotyledons and radicle. Our data help link embryogenesis to the genetic regulation of oil and protein body biogenesis in legume seed.
Collapse
Affiliation(s)
- Xin-Ding Wang
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Newcastle, Australia
| | | | | | | | | |
Collapse
|
19
|
Agrawal GK, Rakwal R. Rice proteomics: A move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology. Proteomics 2011; 11:1630-49. [DOI: 10.1002/pmic.201000696] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 01/05/2011] [Accepted: 01/24/2011] [Indexed: 12/13/2022]
|
20
|
Foley RC, Gao LL, Spriggs A, Soo LYC, Goggin DE, Smith PMC, Atkins CA, Singh KB. Identification and characterisation of seed storage protein transcripts from Lupinus angustifolius. BMC PLANT BIOLOGY 2011; 11:59. [PMID: 21457583 PMCID: PMC3078879 DOI: 10.1186/1471-2229-11-59] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 04/04/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND In legumes, seed storage proteins are important for the developing seedling and are an important source of protein for humans and animals. Lupinus angustifolius (L.), also known as narrow-leaf lupin (NLL) is a grain legume crop that is gaining recognition as a potential human health food as the grain is high in protein and dietary fibre, gluten-free and low in fat and starch. RESULTS Genes encoding the seed storage proteins of NLL were characterised by sequencing cDNA clones derived from developing seeds. Four families of seed storage proteins were identified and comprised three unique α, seven β, two γ and four δ conglutins. This study added eleven new expressed storage protein genes for the species. A comparison of the deduced amino acid sequences of NLL conglutins with those available for the storage proteins of Lupinus albus (L.), Pisum sativum (L.), Medicago truncatula (L.), Arachis hypogaea (L.) and Glycine max (L.) permitted the analysis of a phylogenetic relationships between proteins and demonstrated, in general, that the strongest conservation occurred within species. In the case of 7S globulin (β conglutins) and 2S sulphur-rich albumin (δ conglutins), the analysis suggests that gene duplication occurred after legume speciation. This contrasted with 11S globulin (α conglutin) and basic 7S (γ conglutin) sequences where some of these sequences appear to have diverged prior to speciation. The most abundant NLL conglutin family was β (56%), followed by α (24%), δ (15%) and γ (6%) and the transcript levels of these genes increased 103 to 106 fold during seed development. We used the 16 NLL conglutin sequences identified here to determine that for individuals specifically allergic to lupin, all seven members of the β conglutin family were potential allergens. CONCLUSION This study has characterised 16 seed storage protein genes in NLL including 11 newly-identified members. It has helped lay the foundation for efforts to use molecular breeding approaches to improve lupins, for example by reducing allergens or increasing the expression of specific seed storage protein(s) with desirable nutritional properties.
Collapse
Affiliation(s)
- Rhonda C Foley
- The WAIMR Centre for Food and Genomic Medicine, Perth, Western Australia, Australia
- CSIRO, Plant Industry, Private Bag 5, Wembley, Western Australia, Australia
| | - Ling-Ling Gao
- The WAIMR Centre for Food and Genomic Medicine, Perth, Western Australia, Australia
- CSIRO, Plant Industry, Private Bag 5, Wembley, Western Australia, Australia
| | - Andrew Spriggs
- CSIRO, Plant Industry, Black Mountain, Canberra, Australia
| | - Lena YC Soo
- School of Biological Science, University of Sydney, Sydney, Australia
| | - Danica E Goggin
- School of Plant Biology, University of Western Australia, Crawley, Western Australia, Australia
| | - Penelope MC Smith
- School of Biological Science, University of Sydney, Sydney, Australia
| | - Craig A Atkins
- The WAIMR Centre for Food and Genomic Medicine, Perth, Western Australia, Australia
- School of Plant Biology, University of Western Australia, Crawley, Western Australia, Australia
| | - Karam B Singh
- The WAIMR Centre for Food and Genomic Medicine, Perth, Western Australia, Australia
- CSIRO, Plant Industry, Private Bag 5, Wembley, Western Australia, Australia
- The UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
| |
Collapse
|
21
|
Seed proteomics. J Proteomics 2011; 74:389-400. [DOI: 10.1016/j.jprot.2010.12.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/08/2010] [Accepted: 12/10/2010] [Indexed: 12/29/2022]
|
22
|
Kaufmann K, Smaczniak C, de Vries S, Angenent GC, Karlova R. Proteomics insights into plant signaling and development. Proteomics 2011; 11:744-55. [DOI: 10.1002/pmic.201000418] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/29/2010] [Accepted: 11/02/2010] [Indexed: 12/11/2022]
|
23
|
Miernyk JA, Preťová A, Olmedilla A, Klubicová K, Obert B, Hajduch M. Using proteomics to study sexual reproduction in angiosperms. ACTA ACUST UNITED AC 2010; 24:9-22. [PMID: 20830489 DOI: 10.1007/s00497-010-0149-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 08/21/2010] [Indexed: 12/18/2022]
Abstract
While a relative latecomer to the postgenomics era of functional biology, the application of mass spectrometry-based proteomic analysis has increased exponentially over the past 10 years. Some of this increase is the result of transition of chemists, physicists, and mathematicians to the study of biology, and some is due to improved methods, increased instrument sensitivity, and better techniques of bioinformatics-based data analysis. Proteomic Biological processes are typically studied in isolation, and seldom are efforts made to coordinate results obtained using structural, biochemical, and molecular-genetic strategies. Mass spectrometry-based proteomic analysis can serve as a platform to bridge these disparate results and to additionally incorporate both temporal and anatomical considerations. Recently, proteomic analyses have transcended their initial purely descriptive applications and are being employed extensively in studies of posttranslational protein modifications, protein interactions, and control of metabolic networks. Herein, we provide a brief introduction to sample preparation, comparison of gel-based versus gel-free methods, and explanation of data analysis emphasizing plant reproductive applications. We critically review the results from the relatively small number of extant proteomics-based analyses of angiosperm reproduction, from flowers to seedlings, and speculate on the utility of this strategy for future developments and directions.
Collapse
Affiliation(s)
- Ján A Miernyk
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovak Republic
| | | | | | | | | | | |
Collapse
|