701
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Komatsu S, Yanagawa Y. Cell wall proteomics of crops. FRONTIERS IN PLANT SCIENCE 2013; 4:17. [PMID: 23403621 PMCID: PMC3566523 DOI: 10.3389/fpls.2013.00017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/23/2013] [Indexed: 05/23/2023]
Abstract
Cell wall proteins play key roles in cell structure and metabolism, cell enlargement, signal transduction, responses to environmental stress, and many other physiological events. Agricultural crops are often used for investigating stress tolerance because cultivars with differing degrees of tolerance are available. Abiotic and biotic stress factors markedly influence the geographical distribution and yields of many crop species. Crop cell wall proteomics is of particular importance for improving crop productivity, particularly under unfavorable environmental conditions. To better understand the mechanisms underlying stress response in crops, cell wall proteomic analyses are being increasingly utilized. In this review, the methods of purification and purity assays of cell wall protein fractions from crops are described, and the results of protein identification using gel-based and gel-free proteomic techniques are presented. Furthermore, protein composition of the cell walls of rice, wheat, maize, and soybean are compared, and the role of cell wall proteins in crops under flooding and drought stress is discussed. This review will be useful for clarifying the role of the cell wall of crops in response to environmental stresses.
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Affiliation(s)
- Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Yuki Yanagawa
- Plant Science Center, RIKEN Yokohama InstituteYokohama, Japan
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702
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Bellieny-Rabelo D, Oliveira AEA, Venancio TM. Impact of whole-genome and tandem duplications in the expansion and functional diversification of the F-box family in legumes (Fabaceae). PLoS One 2013; 8:e55127. [PMID: 23390519 PMCID: PMC3563651 DOI: 10.1371/journal.pone.0055127] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 12/18/2012] [Indexed: 12/16/2022] Open
Abstract
F-box proteins constitute a large gene family that regulates processes from hormone signaling to stress response. F-box proteins are the substrate recognition modules of SCF E3 ubiquitin ligases. Here we report very distinct trends in family size, duplication, synteny and transcription of F-box genes in two nitrogen-fixing legumes, Glycine max (soybean) and Medicago truncatula (alfafa). While the soybean FBX genes emerged mainly through segmental duplications (including whole-genome duplications), M. truncatula genome is dominated by locally-duplicated (tandem) F-box genes. Many of these young FBX genes evolved complex transcriptional patterns, including preferential transcription in different tissues, suggesting that they have probably been recruited to important biochemical pathways (e.g. nodulation and seed development).
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Affiliation(s)
- Daniel Bellieny-Rabelo
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Antônia Elenir Amâncio Oliveira
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Thiago Motta Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
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703
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Venkateshwaran M, Volkening JD, Sussman MR, Ané JM. Symbiosis and the social network of higher plants. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:118-27. [PMID: 23246268 DOI: 10.1016/j.pbi.2012.11.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/19/2012] [Accepted: 11/20/2012] [Indexed: 05/22/2023]
Abstract
In the Internet era, communicating with friends and colleagues via social networks constitutes a significant proportion of our daily activities. Similarly animals and plants also interact with many organisms, some of which are pathogens and do no good for the plant, while others are beneficial symbionts. Almost all plants indulge in developing social networks with microbes, in particular with arbuscular mycorrhizal fungi, and emerging evidence indicates that most employ an ancient and widespread central 'social media' pathway made of signaling molecules within what is called the SYM pathway. Some plants, like legumes, are particularly active recruiters of friends, as they have established very sophisticated and beneficial interactions with nitrogen-fixing bacteria, also via the SYM pathway. Interestingly, many members of the Brassicaceae, including the model plant Arabidopsis thaliana, seem to have removed themselves from this ancestral social network and lost the ability to engage in mutually favorable interactions with arbuscular mycorrhizal fungi. Despite these generalizations, recent studies exploring the root microbiota of A. thaliana have found that in natural conditions, A. thaliana roots are colonized by many different bacterial species and therefore may be using different and probably more recent 'social media' for these interactions. In general, recent advances in the understanding of such molecular machinery required for plant-symbiont associations are being obtained using high throughput genomic profiling strategies including transcriptomics, proteomics and metabolomics. The crucial mechanistic understanding that such data reveal may provide the infrastructure for future efforts to genetically manipulate crop social networks for our own food and fiber needs.
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704
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Lagunes Espinoza LDC, Julier B. QTL detection for forage quality and stem histology in four connected mapping populations of the model legume Medicago truncatula. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:497-509. [PMID: 23099818 DOI: 10.1007/s00122-012-1996-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 10/06/2012] [Indexed: 05/14/2023]
Abstract
Forage quality combines traits related to protein content and energy value. High-quality forages contribute to increase farm autonomy by reducing the use of energy or protein-rich supplements. Genetic analyses in forage legume species are complex because of their tetraploidy and allogamy. Indeed, no genetic studies of quality have been published at the molecular level on these species. Nonetheless, mapping populations of the model species M. truncatula can be used to detect QTL for forage quality. Here, we studied a crossing design involving four connected populations of M. truncatula. Each population was composed of ca. 200 recombinant inbred lines (RIL). We sought population-specific QTL and QTL explaining the whole design variation. We grew parents and RIL in a greenhouse for 2 or 3 seasons and analysed plants for chemical composition of vegetative organs (protein content, digestibility, leaf-to-stem ratio) and stem histology (stem cross-section area, tissue proportions). Over the four populations and all the traits, QTL were found on all chromosomes. Among these QTL, only four genomic regions, on chromosomes 1, 3, 7 and 8, contributed to explaining the variations in the whole crossing design. Surprisingly, we found that quality QTL were located in the same genomic regions as morphological QTL. We thus confirmed the quantitative inheritance of quality traits and tight relationships between quality and morphology. Our findings could be explained by a co-location of genes involved in quality and morphology. This study will help to detect candidate genes involved in quantitative variation for quality in forage legume species.
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Affiliation(s)
- Luz Del Carmen Lagunes Espinoza
- INRA, UR 4, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères, Le Chêne, RD 150, BP 80006, 86600 Lusignan, France
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705
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Volpe V, Dell'Aglio E, Giovannetti M, Ruberti C, Costa A, Genre A, Guether M, Bonfante P. An AM-induced, MYB-family gene of Lotus japonicus (LjMAMI) affects root growth in an AM-independent manner. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:442-55. [PMID: 23051146 DOI: 10.1111/tpj.12045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 10/01/2012] [Accepted: 10/04/2012] [Indexed: 05/06/2023]
Abstract
The interaction between legumes and arbuscular mycorrhizal (AM) fungi is vital to the development of sustainable plant production systems. Here, we focus on a putative MYB-like (LjMAMI) transcription factor (TF) previously reported to be highly upregulated in Lotus japonicus mycorrhizal roots. Phylogenetic analyses revealed that the protein is related to a group of TFs involved in phosphate (Pi) starvation responses, the expression of which is independent of the Pi level, such as PHR1. GUS transformed plants and quantitative reverse transcription PCR revealed strong gene induction in arbusculated cells, as well as the presence of LjMAMI transcripts in lateral root primordia and root meristems, even in the absence of the fungus, and independently of Pi concentration. In agreement with its putative identification as a TF, an eGFP-LjMAMI chimera was localized to the nuclei of plant protoplasts, whereas in transgenic Lotus roots expressing the eGFP-LjMAMI fusion protein under the control of the native promoter, the protein was located in the nuclei of the arbusculated cells. Further expression analyses revealed a correlation between LjMAMI and LjPT4, a marker gene for mycorrhizal function. To elucidate the role of the LjMAMI gene in the mycorrhizal process, RNAi and overexpressing root lines were generated. All the lines retained their symbiotic capacity; however, RNAi root lines and composite plants showed an important reduction in root elongation and branching in the absence of the symbiont. The results support the involvement of the AM-responsive LjMAMI in non-symbiotic functions: i.e. root growth.
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Affiliation(s)
- Veronica Volpe
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, I-10125, Torino, Italy
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706
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Banasiak J, Biala W, Staszków A, Swarcewicz B, Kepczynska E, Figlerowicz M, Jasinski M. A Medicago truncatula ABC transporter belonging to subfamily G modulates the level of isoflavonoids. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1005-15. [PMID: 23314816 DOI: 10.1093/jxb/ers380] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Full-sized ATP-binding cassette (ABC) transporters of the G subfamily (ABCG) are considered to be essential components of the plant immune system. These proteins have been proposed to be implicated in the active transmembrane transport of various secondary metabolites. Despite the importance of ABCG-based transport for plant-microbe interactions, these proteins are still poorly recognized in legumes. The experiments described here demonstrated that the level of Medicago truncatula ABCG10 (MtABCG10) mRNA was elevated following application of fungal oligosaccharides to plant roots. Spatial expression pattern analysis with a reporter gene revealed that the MtABCG10 promoter was active in various organs, mostly within their vascular tissues. The corresponding protein was located in the plasma membrane. Silencing of MtABCG10 in hairy roots resulted in lower accumulation of the phenylpropanoid pathway-derived medicarpin and its precursors. PCR-based experiments indicated that infection with Fusarium oxysporum, a root-infecting pathogen, progressed faster in MtABCG10-silenced composite plants (consisting of wild-type shoots on transgenic roots) than in the corresponding controls. Based on the presented data, it is proposed that in Medicago, full-sized ABCG transporters might modulate isoflavonoid levels during the defence response associated with de novo synthesis of phytoalexins.
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Affiliation(s)
- Joanna Banasiak
- Institute of Bioorganic Chemistry PAS, Noskowskiego 12/14, Poznań, Poland
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707
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Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 2013; 31:240-6. [DOI: 10.1038/nbt.2491] [Citation(s) in RCA: 832] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/21/2012] [Indexed: 12/19/2022]
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708
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Varshney RK, Mohan SM, Gaur PM, Gangarao NVPR, Pandey MK, Bohra A, Sawargaonkar SL, Chitikineni A, Kimurto PK, Janila P, Saxena KB, Fikre A, Sharma M, Rathore A, Pratap A, Tripathi S, Datta S, Chaturvedi SK, Mallikarjuna N, Anuradha G, Babbar A, Choudhary AK, Mhase MB, Bharadwaj C, Mannur DM, Harer PN, Guo B, Liang X, Nadarajan N, Gowda CLL. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv 2013; 31:1120-34. [PMID: 23313999 DOI: 10.1016/j.biotechadv.2013.01.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 12/16/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, DF 06600, Mexico; The University of Western Australia, Crawley 6009, Australia; Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou 510640, China.
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709
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Yeoh CC, Balcerowicz M, Zhang L, Jaudal M, Brocard L, Ratet P, Putterill J. Fine mapping links the FTa1 flowering time regulator to the dominant spring1 locus in Medicago. PLoS One 2013; 8:e53467. [PMID: 23308229 PMCID: PMC3538541 DOI: 10.1371/journal.pone.0053467] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 11/29/2012] [Indexed: 12/27/2022] Open
Abstract
To extend our understanding of flowering time control in eudicots, we screened for mutants in the model legume Medicago truncatula (Medicago). We identified an early flowering mutant, spring1, in a T-DNA mutant screen, but spring1 was not tagged and was deemed a somaclonal mutant. We backcrossed the mutant to wild type R108. The F1 plants and the majority of F2 plants were early flowering like spring1, strongly indicating that spring1 conferred monogenic, dominant early flowering. We hypothesized that the spring1 phenotype resulted from over expression of an activator of flowering. Previously, a major QTL for flowering time in different Medicago accessions was located to an interval on chromosome 7 with six candidate flowering-time activators, including a CONSTANS gene, MtCO, and three FLOWERING LOCUS T (FT) genes. Hence we embarked upon linkage mapping using 29 markers from the MtCO/FT region on chromosome 7 on two populations developed by crossing spring1 with Jester. Spring1 mapped to an interval of ∼0.5 Mb on chromosome 7 that excluded MtCO, but contained 78 genes, including the three FT genes. Of these FT genes, only FTa1 was up-regulated in spring1 plants. We then investigated global gene expression in spring1 and R108 by microarray analysis. Overall, they had highly similar gene expression and apart from FTa1, no genes in the mapping interval were differentially expressed. Two MADS transcription factor genes, FRUITFULLb (FULb) and SUPPRESSOR OF OVER EXPRESSION OF CONSTANS1a (SOC1a), that were up-regulated in spring1, were also up-regulated in transgenic Medicago over-expressing FTa1. This suggested that their differential expression in spring1 resulted from the increased abundance of FTa1. A 6255 bp genomic FTa1 fragment, including the complete 5' region, was sequenced, but no changes were observed indicating that the spring1 mutation is not a DNA sequence difference in the FTa1 promoter or introns.
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Affiliation(s)
- Chin Chin Yeoh
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Martin Balcerowicz
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lulu Zhang
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mauren Jaudal
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lysiane Brocard
- Institut des Sciences du Végétal, CNRS, Gif sur Yvette, France
| | - Pascal Ratet
- Institut des Sciences du Végétal, CNRS, Gif sur Yvette, France
| | - Joanna Putterill
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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710
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Nelson DR, Goldstone JV, Stegeman JJ. The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120474. [PMID: 23297357 DOI: 10.1098/rstb.2012.0474] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The neighbourhoods of cytochrome P450 (CYP) genes in deuterostome genomes, as well as those of the cnidarians Nematostella vectensis and Acropora digitifera and the placozoan Trichoplax adhaerens were examined to find clues concerning the evolution of CYP genes in animals. CYP genes created by the 2R whole genome duplications in chordates have been identified. Both microsynteny and macrosynteny were used to identify genes that coexisted near CYP genes in the animal ancestor. We show that all 11 CYP clans began in a common gene environment. The evidence implies the existence of a single locus, which we term the 'cytochrome P450 genesis locus', where one progenitor CYP gene duplicated to create a tandem set of genes that were precursors of the 11 animal CYP clans: CYP Clans 2, 3, 4, 7, 19, 20, 26, 46, 51, 74 and mitochondrial. These early CYP genes existed side by side before the origin of cnidarians, possibly with a few additional genes interspersed. The Hox gene cluster, WNT genes, an NK gene cluster and at least one ARF gene were close neighbours to this original CYP locus. According to this evolutionary scenario, the CYP74 clan originated from animals and not from land plants nor from a common ancestor of plants and animals. The CYP7 and CYP19 families that are chordate-specific belong to CYP clans that seem to have originated in the CYP genesis locus as well, even though this requires many gene losses to explain their current distribution. The approach to uncovering the CYP genesis locus overcomes confounding effects because of gene conversion, sequence divergence, gene birth and death, and opens the way to understanding the biodiversity of CYP genes, families and subfamilies, which in animals has been obscured by more than 600 Myr of evolution.
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Affiliation(s)
- David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue Suite G01, Memphis, TN 38163, USA.
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711
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Verdier J, Dessaint F, Schneider C, Abirached-Darmency M. A combined histology and transcriptome analysis unravels novel questions on Medicago truncatula seed coat. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:459-70. [PMID: 23125357 PMCID: PMC3542040 DOI: 10.1093/jxb/ers304] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The seed coat is involved in the determination of seed quality traits such as seed size, seed composition, seed permeability, and hormonal regulation. Understanding seed coat structure is therefore a prerequisite to deciphering the genetic mechanisms that govern seed coat functions. By combining histological and transcriptomic data analyses, cellular and molecular events occurring during Medicago truncatula seed coat development were dissected in order to relate structure to function and pinpoint target genes potentially involved in seed coat traits controlling final seed quality traits. The analyses revealed the complexity of the seed coat transcriptome, which contains >30 000 genes. In parallel, a set of genes showing a preferential expression in seed coat that may be involved in more specific functions was identified. The study describes how seed coat anatomy and morphological changes affect final seed quality such as seed size, seed composition, seed permeability, and hormonal regulation. Putative regulator genes of different processes have been identified as potential candidates for further functional genomic studies to improve agronomical seed traits. The study also raises new questions concerning the implication of seed coat endopolyploidy in cell expansion and the participation of the seed coat in de novo abscisic acid biosynthesis at early seed filling.
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Affiliation(s)
- Jerome Verdier
- UMR 1347 Agroécologie AgroSup/INRA/uB F-21065 Dijon, France
| | - Fabrice Dessaint
- The Samuel Roberts Noble Foundation, Plant Biology Division, Ardmore OK 73401, USA
| | | | - Mona Abirached-Darmency
- UMR 1347 Agroécologie AgroSup/INRA/uB F-21065 Dijon, France
- To whom correspondence should be addressed. E-mail:
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712
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Sieh D, Watanabe M, Devers EA, Brueckner F, Hoefgen R, Krajinski F. The arbuscular mycorrhizal symbiosis influences sulfur starvation responses of Medicago truncatula. THE NEW PHYTOLOGIST 2013; 197:606-616. [PMID: 23190168 DOI: 10.1111/nph.12034] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/02/2012] [Indexed: 05/24/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction that occurs between the large majority of vascular plants and fungi of the phylum Glomeromycota. In addition to other nutrients, sulfur compounds are symbiotically transferred from AM fungus to host plants; however, the physiological importance of mycorrhizal-mediated sulfur for plant metabolism has not yet been determined. We applied different sulfur and phosphate fertilization treatments to Medicago truncatula and investigated whether mycorrhizal colonization influences leaf metabolite composition and the expression of sulfur starvation-related genes. The expression pattern of sulfur starvation-related genes indicated reduced sulfur starvation responses in mycorrhizal plants grown at 1 mM phosphate nutrition. Leaf metabolite concentrations clearly showed that phosphate stress has a greater impact than sulfur stress on plant metabolism, with no demand for sulfur at strong phosphate starvation. However, when phosphate nutrition is high enough, mycorrhizal colonization reduces sulfur stress responses, probably as a result of symbiotic sulfur uptake. Mycorrhizal colonization is able to reduce sulfur starvation responses in M. truncatula when the plant's phosphate status is high enough that sulfur starvation is of physiological importance. This clearly shows the impact of mycorrhizal sulfur transfer on plant metabolism.
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Affiliation(s)
- Daniela Sieh
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Emanuel A Devers
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Franziska Brueckner
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Franziska Krajinski
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
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713
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Ben C, Toueni M, Montanari S, Tardin MC, Fervel M, Negahi A, Saint-Pierre L, Mathieu G, Gras MC, Noël D, Prospéri JM, Pilet-Nayel ML, Baranger A, Huguet T, Julier B, Rickauer M, Gentzbittel L. Natural diversity in the model legume Medicago truncatula allows identifying distinct genetic mechanisms conferring partial resistance to Verticillium wilt. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:317-32. [PMID: 23213135 PMCID: PMC3528038 DOI: 10.1093/jxb/ers337] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Verticillium wilt is a major threat to alfalfa (Medicago sativa) and many other crops. The model legume Medicago truncatula was used as a host for studying resistance and susceptibility to Verticillium albo-atrum. In addition to presenting well-established genetic resources, this wild plant species enables to investigate biodiversity of the response to the pathogen and putative crosstalk between disease and symbiosis. Symptom scoring after root inoculation and modelling of disease curves allowed assessing susceptibility levels in recombinant lines of three crosses between susceptible and resistant lines, in a core collection of 32 lines, and in mutants affected in symbiosis with rhizobia. A GFP-expressing V. albo-atrum strain was used to study colonization of susceptible plants. Symptoms and colonization pattern in infected M. truncatula plants were typical of Verticillium wilt. Three distinct major quantitative trait loci were identified using a multicross, multisite design, suggesting that simple genetic mechanisms appear to control Verticillium wilt resistance in M. truncatula lines A17 and DZA45.5. The disease functional parameters varied largely in lines of the core collection. This biodiversity with regard to disease response encourages the development of association genetics and ecological approaches. Several mutants of the resistant line, impaired in different steps of rhizobial symbiosis, were affected in their response to V. albo-atrum, which suggests that mechanisms involved in the establishment of symbiosis or disease might have some common regulatory control points.
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Affiliation(s)
- Cécile Ben
- Université de Toulouse; INP, UPS; Laboratoire d’Écologie Fonctionnelle et Environnement (EcoLab); ENSAT, 18 chemin de Borderouge, 31326 Castanet Tolosan, France
- CNRS; EcoLab; 31326 Castanet Tolosan, France
| | - Maoulida Toueni
- Université de Toulouse; INP, UPS; Laboratoire d’Écologie Fonctionnelle et Environnement (EcoLab); ENSAT, 18 chemin de Borderouge, 31326 Castanet Tolosan, France
- CNRS; EcoLab; 31326 Castanet Tolosan, France
| | - Sara Montanari
- Université de Toulouse; INP, UPS; Laboratoire d’Écologie Fonctionnelle et Environnement (EcoLab); ENSAT, 18 chemin de Borderouge, 31326 Castanet Tolosan, France
| | | | - Magalie Fervel
- Barenbrug Tourneur Recherches, Negadis, 82600 Mas Grenier, France
| | - Azam Negahi
- Université de Toulouse; INP, UPS; Laboratoire d’Écologie Fonctionnelle et Environnement (EcoLab); ENSAT, 18 chemin de Borderouge, 31326 Castanet Tolosan, France
- CNRS; EcoLab; 31326 Castanet Tolosan, France
| | | | - Guillaume Mathieu
- Université de Toulouse; INP, UPS; Laboratoire d’Écologie Fonctionnelle et Environnement (EcoLab); ENSAT, 18 chemin de Borderouge, 31326 Castanet Tolosan, France
| | | | - Dominique Noël
- Barenbrug Tourneur Recherches, Negadis, 82600 Mas Grenier, France
| | | | - Marie-Laure Pilet-Nayel
- INRA, Agrocampus Ouest, Université de Rennes1, UMR118, Amélioration des Plantes et Biotechnologies Végétales, 35653 Le Rheu Cedex, Rennes, France
| | - Alain Baranger
- INRA, Agrocampus Ouest, Université de Rennes1, UMR118, Amélioration des Plantes et Biotechnologies Végétales, 35653 Le Rheu Cedex, Rennes, France
| | - Thierry Huguet
- Université de Toulouse; INP, UPS; Laboratoire d’Écologie Fonctionnelle et Environnement (EcoLab); ENSAT, 18 chemin de Borderouge, 31326 Castanet Tolosan, France
- CNRS; EcoLab; 31326 Castanet Tolosan, France
| | - Bernadette Julier
- INRA, UR 4, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères, Le Chêne, RD 150, BP 80006, 86600, Lusignan, France
| | - Martina Rickauer
- Université de Toulouse; INP, UPS; Laboratoire d’Écologie Fonctionnelle et Environnement (EcoLab); ENSAT, 18 chemin de Borderouge, 31326 Castanet Tolosan, France
- CNRS; EcoLab; 31326 Castanet Tolosan, France
| | - Laurent Gentzbittel
- Université de Toulouse; INP, UPS; Laboratoire d’Écologie Fonctionnelle et Environnement (EcoLab); ENSAT, 18 chemin de Borderouge, 31326 Castanet Tolosan, France
- CNRS; EcoLab; 31326 Castanet Tolosan, France
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714
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Kim DH, Parupalli S, Azam S, Lee SH, Varshney RK. Comparative sequence analysis of nitrogen fixation-related genes in six legumes. FRONTIERS IN PLANT SCIENCE 2013; 4:300. [PMID: 23986765 PMCID: PMC3749373 DOI: 10.3389/fpls.2013.00300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 07/20/2013] [Indexed: 05/20/2023]
Abstract
Legumes play an important role as food and forage crops in international agriculture especially in developing countries. Legumes have a unique biological process called nitrogen fixation (NF) by which they convert atmospheric nitrogen to ammonia. Although legume genomes have undergone polyploidization, duplication and divergence, NF-related genes, because of their essential functional role for legumes, might have remained conserved. To understand the relationship of divergence and evolutionary processes in legumes, this study analyzes orthologs and paralogs for selected 20 NF-related genes by using comparative genomic approaches in six legumes i.e., Medicago truncatula (Mt), Cicer arietinum, Lotus japonicus, Cajanus cajan (Cc), Phaseolus vulgaris (Pv), and Glycine max (Gm). Subsequently, sequence distances, numbers of synonymous substitutions per synonymous site (Ks) and non-synonymous substitutions per non-synonymous site (Ka) between orthologs and paralogs were calculated and compared across legumes. These analyses suggest the closest relationship between Gm and Cc and the highest distance between Mt and Pv in six legumes. Ks proportional plots clearly showed ancient genome duplication in all legumes, whole genome duplication event in Gm and also speciation pattern in different legumes. This study also reports some interesting observations e.g., no peak at Ks 0.4 in Gm-Gm, location of two independent genes next to each other in Mt and low Ks values for outparalogs for three genes as compared to other 12 genes. In summary, this study underlines the importance of NF-related genes and provides important insights in genome organization and evolutionary aspects of six legume species analyzed.
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Affiliation(s)
- Dong Hyun Kim
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Swathi Parupalli
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Sarwar Azam
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Suk-Ha Lee
- Department of Plant Science, Seoul National UniversitySeoul, South Korea
- Research Institute for Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
- CGIAR Generation Challenge Programme, c/o CIMMYTMexico DF, Mexico
- *Correspondence: Rajeev K. Varshney, Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), #300 Building, Hyderabad, AP 502 324, India e-mail:
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715
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Bustos-Sanmamed P, Bazin J, Hartmann C, Crespi M, Lelandais-Brière C. Small RNA pathways and diversity in model legumes: lessons from genomics. FRONTIERS IN PLANT SCIENCE 2013; 4:236. [PMID: 23847640 PMCID: PMC3707012 DOI: 10.3389/fpls.2013.00236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/15/2013] [Indexed: 05/20/2023]
Abstract
Small non-coding RNAs (smRNA) participate in the regulation of development, cell differentiation, adaptation to environmental constraints and defense responses in plants. They negatively regulate gene expression by degrading specific mRNA targets, repressing their translation or modifying chromatin conformation through homologous interaction with target loci. MicroRNAs (miRNA) and short-interfering RNAs (siRNA) are generated from long double stranded RNA (dsRNA) that are cleaved into 20-24-nucleotide dsRNAs by RNase III proteins called DICERs (DCL). One strand of the duplex is then loaded onto effective complexes containing different ARGONAUTE (AGO) proteins. In this review, we explored smRNA diversity in model legumes and compiled available data from miRBAse, the miRNA database, and from 22 reports of smRNA deep sequencing or miRNA identification genome-wide in three legumes: Medicago truncatula, soybean (Glycine max) and Lotus japonicus. In addition to conserved miRNAs present in other plant species, 229, 179, and 35 novel miRNA families were identified respectively in these 3 legumes, among which several seems legume-specific. New potential functions of several miRNAs in the legume-specific nodulation process are discussed. Furthermore, a new category of siRNA, the phased siRNAs, which seems to mainly regulate disease-resistance genes, was recently discovered in legumes. Despite that the genome sequence of model legumes are not yet fully completed, further analysis was performed by database mining of gene families and protein characteristics of DCLs and AGOs in these genomes. Although most components of the smRNA pathways are conserved, identifiable homologs of key smRNA players from non-legumes, like AGO10 or DCL4, could not yet be detected in M. truncatula available genomic and expressed sequence (EST) databases. In contrast to Arabidopsis, an important gene diversification was observed in the three legume models (for DCL2, AGO4, AGO2, and AGO10) or specifically in soybean for DCL1 and DCL4. Functional significance of these variant isoforms may reflect peculiarities of smRNA biogenesis and functions in legumes.
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Affiliation(s)
- Pilar Bustos-Sanmamed
- Centre National de la Recherche Scientifique, Institut des Sciences du VégétalGif-sur-Yvette Cedex, France
| | - Jérémie Bazin
- Centre National de la Recherche Scientifique, Institut des Sciences du VégétalGif-sur-Yvette Cedex, France
- Université Paris Diderot, U.F.R. Sciences du VivantParis Cedex 13, France
| | - Caroline Hartmann
- Centre National de la Recherche Scientifique, Institut des Sciences du VégétalGif-sur-Yvette Cedex, France
- Université Paris Diderot, U.F.R. Sciences du VivantParis Cedex 13, France
| | - Martin Crespi
- Centre National de la Recherche Scientifique, Institut des Sciences du VégétalGif-sur-Yvette Cedex, France
- *Correspondence: Martin Crespi, Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, Bât 23. Avenue de la Terrasse, 91198 Gif sur Yvette, France e-mail:
| | - Christine Lelandais-Brière
- Centre National de la Recherche Scientifique, Institut des Sciences du VégétalGif-sur-Yvette Cedex, France
- Université Paris Diderot, U.F.R. Sciences du VivantParis Cedex 13, France
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716
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Michelmore RW, Christopoulou M, Caldwell KS. Impacts of resistance gene genetics, function, and evolution on a durable future. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:291-319. [PMID: 23682913 DOI: 10.1146/annurev-phyto-082712-102334] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Studies on resistance gene function and evolution lie at the confluence of structural and molecular biology, genetics, and plant breeding. However, knowledge from these disparate fields has yet to be extensively integrated. This review draws on ideas and information from these different fields to elucidate the influences driving the evolution of different types of resistance genes in plants and the concurrent evolution of virulence in pathogens. It provides an overview of the factors shaping the evolution of recognition, signaling, and response genes in the context of emerging functional information along with a consideration of the new opportunities for durable resistance enabled by high-throughput DNA sequencing technologies.
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717
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Abstract
Symbiotic nitrogen fixation by rhizobia in legume root nodules injects approximately 40 million tonnes of nitrogen into agricultural systems each year. In exchange for reduced nitrogen from the bacteria, the plant provides rhizobia with reduced carbon and all the essential nutrients required for bacterial metabolism. Symbiotic nitrogen fixation requires exquisite integration of plant and bacterial metabolism. Central to this integration are transporters of both the plant and the rhizobia, which transfer elements and compounds across various plant membranes and the two bacterial membranes. Here we review current knowledge of legume and rhizobial transport and metabolism as they relate to symbiotic nitrogen fixation. Although all legume-rhizobia symbioses have many metabolic features in common, there are also interesting differences between them, which show that evolution has solved metabolic problems in different ways to achieve effective symbiosis in different systems.
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Affiliation(s)
- Michael Udvardi
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA.
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718
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Boscari A, del Giudice J, Ferrarini A, Venturini L, Zaffini AL, Delledonne M, Puppo A. Expression dynamics of the Medicago truncatula transcriptome during the symbiotic interaction with Sinorhizobium meliloti: which role for nitric oxide? PLANT PHYSIOLOGY 2013; 161:425-39. [PMID: 23136381 PMCID: PMC3532272 DOI: 10.1104/pp.112.208538] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Medicago truncatula is one of the most studied model plants. Nevertheless, the genome of this legume remains incompletely determined. We used RNA-Seq to characterize the transcriptome during the early organogenesis of the nodule and during its functioning. We detected 37,333 expressed transcription units; to our knowledge, 1,670 had never been described before and were functionally annotated. We identified 7,595 new transcribed regions, mostly corresponding to 5' and 3' untranslated region extensions and new exons associated with 5,264 previously annotated genes. We also inferred 23,165 putative transcript isoforms from 6,587 genes and measured the abundance of transcripts for each isoform, which suggests an important role for alternative splicing in the generation of proteome diversity in M. truncatula. Finally, we carried out a differential expression analysis, which provided a comprehensive view of transcriptional reprogramming during nodulation. In particular, depletion of nitric oxide in roots inoculated with Sinorhizobium meliloti greatly increased our understanding of the role of this reactive species in the optimal establishment of the symbiotic interaction, revealing differential patterns of expression for 2,030 genes and pointing to the inhibition of the expression of defense genes.
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719
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Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol 2012; 31:135-41. [DOI: 10.1038/nbt.2478] [Citation(s) in RCA: 369] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 12/06/2012] [Indexed: 11/09/2022]
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720
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Del C Orozco-Mosqueda M, Santoyo G, Farías-Rodríguez R, Macías-Rodríguez L, Valencia-Cantero E. Identification and expression analysis of multiple FRO gene copies in Medicago truncatula. GENETICS AND MOLECULAR RESEARCH 2012; 11:4402-10. [PMID: 23096909 DOI: 10.4238/2012.october.9.7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Iron (Fe) is an essential element for plant growth. Commonly, this element is found in an oxidized form in soil, which is poorly available for plants. Therefore, plants have evolved ferric-chelate reductase enzymes (FRO) to reduce iron into a more soluble ferrous form. Fe scarcity in plants induce the FRO enzyme activity. Although the legume Medicago truncatula has been employed as a model for FRO activity studies, only one copy of the M. truncatula MtFRO1 gene has been characterized so far. In this study, we identified multiple gene copies of the MtFRO gene in the genome of M. truncatula by an in silico search, using BLAST analysis in the database of the M. truncatula Genome Sequencing Project and the National Center for Biotechnology Information, and also determined whether they are functional. We identified five genes apart from MtFRO1, which had been already characterized. All of the MtFRO genes exhibited high identity with homologous FRO genes from Lycopersicon esculentum, Citrus junos and Arabidopsis thaliana. The gene copies also presented characteristic conserved FAD and NADPH motifs, transmembrane regions and oxidoreductase signature motifs. We also detected expression in five of the putative MtFRO sequences by semiquantitative RT-PCR analysis, performed with mRNA from root and shoot tissues. Iron scarcity might be a condition for an elevated expression of the MtFRO genes observed in different M. truncatula tissues.
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Affiliation(s)
- Ma Del C Orozco-Mosqueda
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
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722
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Cerri MR, Frances L, Laloum T, Auriac MC, Niebel A, Oldroyd GE, Barker DG, Fournier J, de Carvalho-Niebel F. Medicago truncatula ERN transcription factors: regulatory interplay with NSP1/NSP2 GRAS factors and expression dynamics throughout rhizobial infection. PLANT PHYSIOLOGY 2012; 160:2155-72. [PMID: 23077241 PMCID: PMC3510138 DOI: 10.1104/pp.112.203190] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Rhizobial nodulation factors (NFs) activate a specific signaling pathway in Medicago truncatula root hairs that involves the complex interplay of Nodulation Signaling Pathway1 (NSP1)/NSP2 GRAS and Ethylene Response Factor Required for Nodulation1 (ERN1) transcription factors (TFs) to achieve full ENOD11 transcription. ERN1 acts as a direct transcriptional regulator of ENOD11 through the activation of the NF-responsive "NF box." Here, we show that NSP1, when combined with NSP2, can act as a strong positive regulator of ERN1 and ENOD11 transcription. Although ERN1 and NSP1/NSP2 both activate ENOD11, two separate promoter regions are involved that regulate expression during consecutive symbiotic stages. Our findings indicate that ERN1 is required to activate NF-elicited ENOD11 expression exclusively during early preinfection, while NSP1/NSP2 mediates ENOD11 expression during subsequent rhizobial infection. The relative contributions of ERN1 and the closely related ERN2 to the rhizobial symbiosis were then evaluated by comparing their regulation and in vivo dynamics. ERN1 and ERN2 exhibit expression profiles compatible with roles during NF signaling and subsequent infection. However, differences in expression levels and spatiotemporal profiles suggest specialized functions for these two TFs, ERN1 being involved in stages preceding and accompanying infection thread progression while ERN2 is only involved in certain stages of infection. By cross complementation, we show that ERN2, when expressed under the control of the ERN1 promoter, can restore both NF-elicited ENOD11 expression and nodule formation in an ern1 mutant background. This indicates that ERN1 and ERN2 possess similar biological activities and that functional diversification of these closely related TFs relies primarily on changes in tissue-specific expression patterns.
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723
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Nussbaumer T, Martis MM, Roessner SK, Pfeifer M, Bader KC, Sharma S, Gundlach H, Spannagl M. MIPS PlantsDB: a database framework for comparative plant genome research. Nucleic Acids Res 2012. [PMID: 23203886 PMCID: PMC3531202 DOI: 10.1093/nar/gks1153] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB–plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834–D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.
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Affiliation(s)
- Thomas Nussbaumer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany
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724
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Nakatsuka T, Yamada E, Saito M, Hikage T, Ushiku Y, Nishihara M. Construction of the first genetic linkage map of Japanese gentian (Gentianaceae). BMC Genomics 2012. [PMID: 23186361 PMCID: PMC3561071 DOI: 10.1186/1471-2164-13-672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Background Japanese gentians (Gentiana triflora and Gentiana scabra) are amongst the most popular floricultural plants in Japan. However, genomic resources for Japanese gentians have not yet been developed, mainly because of the heterozygous genome structure conserved by outcrossing, the long juvenile period, and limited knowledge about the inheritance of important traits. In this study, we developed a genetic linkage map to improve breeding programs of Japanese gentians. Results Enriched simple sequence repeat (SSR) libraries from a G. triflora double haploid line yielded almost 20,000 clones using 454 pyrosequencing technology, 6.7% of which could be used to design SSR markers. To increase the number of molecular markers, we identified three putative long terminal repeat (LTR) sequences using the recently developed inter-primer binding site (iPBS) method. We also developed retrotransposon microsatellite amplified polymorphism (REMAP) markers combining retrotransposon and inter-simple sequence repeat (ISSR) markers. In addition to SSR and REMAP markers, modified amplified fragment length polymorphism (AFLP) and random amplification polymorphic DNA (RAPD) markers were developed. Using 93 BC1 progeny from G. scabra backcrossed with a G. triflora double haploid line, 19 linkage groups were constructed with a total of 263 markers (97 SSR, 97 AFLP, 39 RAPD, and 30 REMAP markers). One phenotypic trait (stem color) and 10 functional markers related to genes controlling flower color, flowering time and cold tolerance were assigned to the linkage map, confirming its utility. Conclusions This is the first reported genetic linkage map for Japanese gentians and for any species belonging to the family Gentianaceae. As demonstrated by mapping of functional markers and the stem color trait, our results will help to explain the genetic basis of agronomic important traits, and will be useful for marker-assisted selection in gentian breeding programs. Our map will also be an important resource for further genetic analyses such as mapping of quantitative trait loci and map-based cloning of genes in this species.
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Affiliation(s)
- Takashi Nakatsuka
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate 024-0003, Japan
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725
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Kim B, Yu HJ, Park SG, Shin JY, Oh M, Kim N, Mun JH. Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing. BMC PLANT BIOLOGY 2012; 12:218. [PMID: 23163954 PMCID: PMC3554443 DOI: 10.1186/1471-2229-12-218] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 11/14/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are one of the functional non-coding small RNAs involved in the epigenetic control of the plant genome. Although plants contain both evolutionary conserved miRNAs and species-specific miRNAs within their genomes, computational methods often only identify evolutionary conserved miRNAs. The recent sequencing of the Brassica rapa genome enables us to identify miRNAs and their putative target genes. In this study, we sought to provide a more comprehensive prediction of B. rapa miRNAs based on high throughput small RNA deep sequencing. RESULTS We sequenced small RNAs from five types of tissue: seedlings, roots, petioles, leaves, and flowers. By analyzing 2.75 million unique reads that mapped to the B. rapa genome, we identified 216 novel and 196 conserved miRNAs that were predicted to target approximately 20% of the genome's protein coding genes. Quantitative analysis of miRNAs from the five types of tissue revealed that novel miRNAs were expressed in diverse tissues but their expression levels were lower than those of the conserved miRNAs. Comparative analysis of the miRNAs between the B. rapa and Arabidopsis thaliana genomes demonstrated that redundant copies of conserved miRNAs in the B. rapa genome may have been deleted after whole genome triplication. Novel miRNA members seemed to have spontaneously arisen from the B. rapa and A. thaliana genomes, suggesting the species-specific expansion of miRNAs. We have made this data publicly available in a miRNA database of B. rapa called BraMRs. The database allows the user to retrieve miRNA sequences, their expression profiles, and a description of their target genes from the five tissue types investigated here. CONCLUSIONS This is the first report to identify novel miRNAs from Brassica crops using genome-wide high throughput techniques. The combination of computational methods and small RNA deep sequencing provides robust predictions of miRNAs in the genome. The finding of numerous novel miRNAs, many with few target genes and low expression levels, suggests the rapid evolution of miRNA genes. The development of a miRNA database, BraMRs, enables us to integrate miRNA identification, target prediction, and functional annotation of target genes. BraMRs will represent a valuable public resource with which to study the epigenetic control of B. rapa and other closely related Brassica species. The database is available at the following link: http://bramrs.rna.kr [1].
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Affiliation(s)
- Bumjin Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea
| | - Hee-Ju Yu
- Department of Life Sciences, The Catholic University of Korea, 43 Jibong-ro Wonmi-gu, Bucheon, 420-743, Korea
| | - Sin-Gi Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea
| | - Ja Young Shin
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea
| | - Mijin Oh
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea
| | - Namshin Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro Yuseong-gu, Daejeon, 305-806, Korea
| | - Jeong-Hwan Mun
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea
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726
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Partial complementation of Sinorhizobium meliloti bacA mutant phenotypes by the Mycobacterium tuberculosis BacA protein. J Bacteriol 2012; 195:389-98. [PMID: 23161027 DOI: 10.1128/jb.01445-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Sinorhizobium meliloti BacA ABC transporter protein plays an important role in its nodulating symbiosis with the legume alfalfa (Medicago sativa). The Mycobacterium tuberculosis BacA homolog was found to be important for the maintenance of chronic murine infections, yet its in vivo function is unknown. In the legume plant as well as in the mammalian host, bacteria encounter host antimicrobial peptides (AMPs). We found that the M. tuberculosis BacA protein was able to partially complement the symbiotic defect of an S. meliloti BacA-deficient mutant on alfalfa plants and to protect this mutant in vitro from the antimicrobial activity of a synthetic legume peptide, NCR247, and a recombinant human β-defensin 2 (HBD2). This finding was also confirmed using an M. tuberculosis insertion mutant. Furthermore, M. tuberculosis BacA-mediated protection of the legume symbiont S. meliloti against legume defensins as well as HBD2 is dependent on its attached ATPase domain. In addition, we show that M. tuberculosis BacA mediates peptide uptake of the truncated bovine AMP, Bac7(1-16). This process required a functional ATPase domain. We therefore suggest that M. tuberculosis BacA is important for the transport of peptides across the cytoplasmic membrane and is part of a complete ABC transporter. Hence, BacA-mediated protection against host AMPs might be important for the maintenance of latent infections.
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727
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Lauressergues D, Delaux PM, Formey D, Lelandais-Brière C, Fort S, Cottaz S, Bécard G, Niebel A, Roux C, Combier JP. The microRNA miR171h modulates arbuscular mycorrhizal colonization of Medicago truncatula by targeting NSP2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:512-22. [PMID: 22775306 DOI: 10.1111/j.1365-313x.2012.05099.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Most land plants live symbiotically with arbuscular mycorrhizal fungi. Establishment of this symbiosis requires signals produced by both partners: strigolactones in root exudates stimulate pre-symbiotic growth of the fungus, which releases lipochito-oligosaccharides (Myc-LCOs) that prepare the plant for symbiosis. Here, we have investigated the events downstream of this early signaling in the roots. We report that expression of miR171h, a microRNA that targets NSP2, is up-regulated in the elongation zone of the root during colonization by Rhizophagus irregularis (formerly Glomus intraradices) and in response to Myc-LCOs. Fungal colonization was much reduced by over-expressing miR171h in roots, mimicking the phenotype of nsp2 mutants. Conversely, in plants expressing an NSP2 mRNA resistant to miR171h cleavage, fungal colonization was much increased and extended into the elongation zone of the roots. Finally, phylogenetic analyses revealed that miR171h regulation of NSP2 is probably conserved among mycotrophic plants. Our findings suggest a regulatory mechanism, triggered by Myc-LCOs, that prevents over-colonization of roots by arbuscular mycorrhizal fungi by a mechanism involving miRNA-mediated negative regulation of NSP2.
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Affiliation(s)
- Dominique Lauressergues
- Université de Toulouse, UMR 5546, Laboratoire de Recherche en Sciences Végétales, 31326 Castanet-Tolosan Cedex, France
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Mapping the genetic basis of symbiotic variation in legume-rhizobium interactions in Medicago truncatula. G3-GENES GENOMES GENETICS 2012; 2:1291-303. [PMID: 23173081 PMCID: PMC3484660 DOI: 10.1534/g3.112.003269] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 08/19/2012] [Indexed: 01/30/2023]
Abstract
Mutualisms are known to be genetically variable, where the genotypes differ in the fitness benefits they gain from the interaction. To date, little is known about the loci that underlie such genetic variation in fitness or whether the loci influencing fitness are partner specific, and depend on the genotype of the interaction partner. In the legume-rhizobium mutualism, one set of potential candidate genes that may influence the fitness benefits of the symbiosis are the plant genes involved in the initiation of the signaling pathway between the two partners. Here we performed quantitative trait loci (QTL) mapping in Medicago truncatula in two different rhizobium strain treatments to locate regions of the genome influencing plant traits, assess whether such regions are dependent on the genotype of the rhizobial mutualist (QTL × rhizobium strain), and evaluate the contribution of sequence variation at known symbiosis signaling genes. Two of the symbiotic signaling genes, NFP and DMI3, colocalized with two QTL affecting average fruit weight and leaf number, suggesting that natural variation in nodulation genes may potentially influence plant fitness. In both rhizobium strain treatments, there were QTL that influenced multiple traits, indicative of either tight linkage between loci or pleiotropy, including one QTL with opposing effects on growth and reproduction. There was no evidence for QTL × rhizobium strain or genotype × genotype interactions, suggesting either that such interactions are due to small-effect loci or that more genotype-genotype combinations need to be tested in future mapping studies.
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729
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Gaid MM, Sircar D, Müller A, Beuerle T, Liu B, Ernst L, Hänsch R, Beerhues L. Cinnamate:CoA ligase initiates the biosynthesis of a benzoate-derived xanthone phytoalexin in Hypericum calycinum cell cultures. PLANT PHYSIOLOGY 2012; 160:1267-80. [PMID: 22992510 PMCID: PMC3490583 DOI: 10.1104/pp.112.204180] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/17/2012] [Indexed: 05/23/2023]
Abstract
Although a number of plant natural products are derived from benzoic acid, the biosynthesis of this structurally simple precursor is poorly understood. Hypericum calycinum cell cultures accumulate a benzoic acid-derived xanthone phytoalexin, hyperxanthone E, in response to elicitor treatment. Using a subtracted complementary DNA (cDNA) library and sequence information about conserved coenzyme A (CoA) ligase motifs, a cDNA encoding cinnamate:CoA ligase (CNL) was isolated. This enzyme channels metabolic flux from the general phenylpropanoid pathway into benzenoid metabolism. HcCNL preferred cinnamic acid as a substrate but failed to activate benzoic acid. Enzyme activity was strictly dependent on the presence of Mg²⁺ and K⁺ at optimum concentrations of 2.5 and 100 mM, respectively. Coordinated increases in the Phe ammonia-lyase and HcCNL transcript levels preceded the accumulation of hyperxanthone E in cell cultures of H. calycinum after the addition of the elicitor. HcCNL contained a carboxyl-terminal type 1 peroxisomal targeting signal made up by the tripeptide Ser-Arg-Leu, which directed an amino-terminal reporter fusion to the peroxisomes. Masking the targeting signal by carboxyl-terminal reporter fusion led to cytoplasmic localization. A phylogenetic tree consisted of two evolutionarily distinct clusters. One cluster was formed by CoA ligases related to benzenoid metabolism, including HcCNL. The other cluster comprised 4-coumarate:CoA ligases from spermatophytes, ferns, and mosses, indicating divergence of the two clades prior to the divergence of the higher plant lineages.
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730
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D'Erfurth I, Le Signor C, Aubert G, Sanchez M, Vernoud V, Darchy B, Lherminier J, Bourion V, Bouteiller N, Bendahmane A, Buitink J, Prosperi JM, Thompson R, Burstin J, Gallardo K. A role for an endosperm-localized subtilase in the control of seed size in legumes. THE NEW PHYTOLOGIST 2012; 196:738-751. [PMID: 22985172 DOI: 10.1111/j.1469-8137.2012.04296.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 07/25/2012] [Indexed: 05/08/2023]
Abstract
Here, we report a subtilase gene (SBT1.1) specifically expressed in the endosperm of Medicago truncatula and Pisum sativum seeds during development, which is located at a chromosomal position coinciding with a seed weight quantitative trait locus (QTL). Association studies between SBT1.1 polymorphisms and seed weights in ecotype collections provided further evidence for linkage disequilibrium between the SBT1.1 locus and a seed weight locus. To investigate the possible contribution of SBT1.1 to the control of seed weight, a search for TILLING (Targeting Induced Local Lesions in Genomes) mutants was performed. An inspection of seed phenotype revealed a decreased weight and area of the sbt1.1 mutant seeds, thus inferring a role of SBT1.1 in the control of seed size in the forage and grain legume species. Microscopic analyses of the embryo, representing the major part of the seed, revealed a reduced number of cells in the MtP330S mutant, but no significant variation in cell size. SBT1.1 is therefore most likely to be involved in the control of cotyledon cell number, rather than cell expansion, during seed development. This raises the hypothesis of a role of SBT1.1 in the regulation of seed size by providing molecules that can act as signals to control cell division within the embryo.
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Affiliation(s)
- I D'Erfurth
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - C Le Signor
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - G Aubert
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - M Sanchez
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - V Vernoud
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - B Darchy
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - J Lherminier
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - V Bourion
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - N Bouteiller
- INRA/CNRS (Centre National de la Recherche Scientifique), Unité de Recherche en Génomique Végétale, CP5708, 91057, Evry, France
| | - A Bendahmane
- INRA/CNRS (Centre National de la Recherche Scientifique), Unité de Recherche en Génomique Végétale, CP5708, 91057, Evry, France
| | - J Buitink
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, 49045, Angers, France
| | - J M Prosperi
- INRA, UMR1334 Amélioration Génétique et Adaptation des Plantes, 34060, Montpellier, France
| | - R Thompson
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - J Burstin
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - K Gallardo
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
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731
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Doidy J, van Tuinen D, Lamotte O, Corneillat M, Alcaraz G, Wipf D. The Medicago truncatula sucrose transporter family: characterization and implication of key members in carbon partitioning towards arbuscular mycorrhizal fungi. MOLECULAR PLANT 2012; 5:1346-58. [PMID: 22930732 DOI: 10.1093/mp/sss079] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We identified de novo sucrose transporter (SUT) genes involved in long-distance transport of sucrose from photosynthetic source leaves towards sink organs in the model leguminous species Medicago truncatula. The identification and functional analysis of sugar transporters provide key information on mechanisms that underlie carbon partitioning in plant-microorganism interactions. In that way, full-length sequences of the M. truncatula SUT (MtSUT) family were retrieved and biochemical characterization of MtSUT members was performed by heterologous expression in yeast. The MtSUT family now comprises six genes which distribute among Dicotyledonous clades. MtSUT1-1 and MtSUT4-1 are key members in regard to their expression profiles in source leaves and sink roots and were characterized as functional H(+)/sucrose transporters. Physiological and molecular responses to phosphorus supply and inoculation by the arbuscular mycorrhizal fungus (AMF) Glomus intraradices was studied by gene expression and sugar quantification analyses. Sucrose represents the main sugar transport form in M. truncatula and the expression profiles of MtSUT1-1, MtSUT2, and MtSUT4-1 highlight a fine-tuning regulation for beneficial sugar fluxes towards the fungal symbiont. Taken together, these results suggest distinct functions for proteins from the SUT1, SUT2, and SUT4 clades in plant and in biotrophic interactions.
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Affiliation(s)
- Joan Doidy
- UMR INRA 1347, Agrosup, Université de Bourgogne, Agroécologie, Pôle Interactions Plantes Microorganismes ERL CNRS 6300, BP 86510, 21065 Dijon Cedex, France
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732
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Li X, Acharya A, Farmer AD, Crow JA, Bharti AK, Kramer RS, Wei Y, Han Y, Gou J, May GD, Monteros MJ, Brummer EC. Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing. BMC Genomics 2012; 13:568. [PMID: 23107476 PMCID: PMC3533575 DOI: 10.1186/1471-2164-13-568] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 10/18/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Alfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. Marker assisted breeding strategies can enhance alfalfa improvement efforts, particularly if many genome-wide markers are available. Transcriptome sequencing enables efficient high-throughput discovery of single nucleotide polymorphism (SNP) markers for a complex polyploid species. RESULT The transcriptomes of 27 alfalfa genotypes, including elite breeding genotypes, parents of mapping populations, and unimproved wild genotypes, were sequenced using an Illumina Genome Analyzer IIx. De novo assembly of quality-filtered 72-bp reads generated 25,183 contigs with a total length of 26.8 Mbp and an average length of 1,065 bp, with an average read depth of 55.9-fold for each genotype. Overall, 21,954 (87.2%) of the 25,183 contigs represented 14,878 unique protein accessions. Gene ontology (GO) analysis suggested that a broad diversity of genes was represented in the resulting sequences. The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels. High resolution melting (HRM) analysis was used to validate 91% of 192 putative SNPs identified by sequencing. Both allelic variants at about 95% of SNP sites identified among five wild, unimproved genotypes are still present in cultivated alfalfa, and all four US breeding programs also contain a high proportion of these SNPs. Thus, little evidence exists among this dataset for loss of significant DNA sequence diversity from either domestication or breeding of alfalfa. Structure analysis indicated that individuals from the subspecies falcata, the diploid subspecies caerulea, and the tetraploid subspecies sativa (cultivated tetraploid alfalfa) were clearly separated. CONCLUSION We used transcriptome sequencing to discover large numbers of SNPs segregating in elite breeding populations of alfalfa. Little loss of SNP diversity was evident between unimproved and elite alfalfa germplasm. The EST and SNP markers generated from this study are publicly available at the Legume Information System ( http://medsa.comparative-legumes.org/) and can contribute to future alfalfa research and breeding applications.
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Affiliation(s)
- Xuehui Li
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Ananta Acharya
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - John A Crow
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Arvind K Bharti
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Robin S Kramer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Yanling Wei
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Yuanhong Han
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Jiqing Gou
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Gregory D May
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Maria J Monteros
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - E Charles Brummer
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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733
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Haag AF, Arnold MFF, Myka KK, Kerscher B, Dall'Angelo S, Zanda M, Mergaert P, Ferguson GP. Molecular insights into bacteroid development duringRhizobium-legume symbiosis. FEMS Microbiol Rev 2012. [DOI: 10.1111/1574-6976.2012.12003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Andreas F. Haag
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Markus F. F. Arnold
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Kamila K. Myka
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Bernhard Kerscher
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Sergio Dall'Angelo
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | | | - Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique; Gif-sur-Yvette Cedex; France
| | - Gail P. Ferguson
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
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734
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Shi LX, Theg SM. The chloroplast protein import system: from algae to trees. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:314-31. [PMID: 23063942 DOI: 10.1016/j.bbamcr.2012.10.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/07/2012] [Accepted: 10/01/2012] [Indexed: 01/15/2023]
Abstract
Chloroplasts are essential organelles in the cells of plants and algae. The functions of these specialized plastids are largely dependent on the ~3000 proteins residing in the organelle. Although chloroplasts are capable of a limited amount of semiautonomous protein synthesis - their genomes encode ~100 proteins - they must import more than 95% of their proteins after synthesis in the cytosol. Imported proteins generally possess an N-terminal extension termed a transit peptide. The importing translocons are made up of two complexes in the outer and inner envelope membranes, the so-called Toc and Tic machineries, respectively. The Toc complex contains two precursor receptors, Toc159 and Toc34, a protein channel, Toc75, and a peripheral component, Toc64/OEP64. The Tic complex consists of as many as eight components, namely Tic22, Tic110, Tic40, Tic20, Tic21 Tic62, Tic55 and Tic32. This general Toc/Tic import pathway, worked out largely in pea chloroplasts, appears to operate in chloroplasts in all green plants, albeit with significant modifications. Sub-complexes of the Toc and Tic machineries are proposed to exist to satisfy different substrate-, tissue-, cell- and developmental requirements. In this review, we summarize our understanding of the functions of Toc and Tic components, comparing these components of the import machinery in green algae through trees. We emphasize recent findings that point to growing complexities of chloroplast protein import process, and use the evolutionary relationships between proteins of different species in an attempt to define the essential core translocon components and those more likely to be responsible for regulation. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Lan-Xin Shi
- Department of Plant Biology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA.
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735
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Bagchi R, Salehin M, Adeyemo OS, Salazar C, Shulaev V, Sherrier DJ, Dickstein R. Functional assessment of the Medicago truncatula NIP/LATD protein demonstrates that it is a high-affinity nitrate transporter. PLANT PHYSIOLOGY 2012; 160:906-16. [PMID: 22858636 PMCID: PMC3461564 DOI: 10.1104/pp.112.196444] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 08/01/2012] [Indexed: 05/18/2023]
Abstract
The Medicago truncatula NIP/LATD (for Numerous Infections and Polyphenolics/Lateral root-organ Defective) gene encodes a protein found in a clade of nitrate transporters within the large NRT1(PTR) family that also encodes transporters of dipeptides and tripeptides, dicarboxylates, auxin, and abscisic acid. Of the NRT1(PTR) members known to transport nitrate, most are low-affinity transporters. Here, we show that M. truncatula nip/latd mutants are more defective in their lateral root responses to nitrate provided at low (250 μm) concentrations than at higher (5 mm) concentrations; however, nitrate uptake experiments showed no discernible differences in uptake in the mutants. Heterologous expression experiments showed that MtNIP/LATD encodes a nitrate transporter: expression in Xenopus laevis oocytes conferred upon the oocytes the ability to take up nitrate from the medium with high affinity, and expression of MtNIP/LATD in an Arabidopsis chl1(nrt1.1) mutant rescued the chlorate susceptibility phenotype. X. laevis oocytes expressing mutant Mtnip-1 and Mtlatd were unable to take up nitrate from the medium, but oocytes expressing the less severe Mtnip-3 allele were proficient in nitrate transport. M. truncatula nip/latd mutants have pleiotropic defects in nodulation and root architecture. Expression of the Arabidopsis NRT1.1 gene in mutant Mtnip-1 roots partially rescued Mtnip-1 for root architecture defects but not for nodulation defects. This suggests that the spectrum of activities inherent in AtNRT1.1 is different from that possessed by MtNIP/LATD, but it could also reflect stability differences of each protein in M. truncatula. Collectively, the data show that MtNIP/LATD is a high-affinity nitrate transporter and suggest that it could have another function.
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Affiliation(s)
| | | | - O. Sarah Adeyemo
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 (R.B., M.S., O.S.A., C.S., V.S., R.D.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (D.J.S.)
| | - Carolina Salazar
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 (R.B., M.S., O.S.A., C.S., V.S., R.D.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (D.J.S.)
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 (R.B., M.S., O.S.A., C.S., V.S., R.D.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (D.J.S.)
| | - D. Janine Sherrier
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 (R.B., M.S., O.S.A., C.S., V.S., R.D.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (D.J.S.)
| | - Rebecca Dickstein
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 (R.B., M.S., O.S.A., C.S., V.S., R.D.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (D.J.S.)
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736
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Ho-Huu J, Ronfort J, De Mita S, Bataillon T, Hochu I, Weber A, Chantret N. Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.). BMC Evol Biol 2012; 12:195. [PMID: 23025552 PMCID: PMC3517903 DOI: 10.1186/1471-2148-12-195] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 09/20/2012] [Indexed: 01/01/2023] Open
Abstract
Background Gene duplications are a molecular mechanism potentially mediating generation of functional novelty. However, the probabilities of maintenance and functional divergence of duplicated genes are shaped by selective pressures acting on gene copies immediately after the duplication event. The ratio of non-synonymous to synonymous substitution rates in protein-coding sequences provides a means to investigate selective pressures based on genic sequences. Three molecular signatures can reveal early stages of functional divergence between gene copies: change in the level of purifying selection between paralogous genes, occurrence of positive selection, and transient relaxed purifying selection following gene duplication. We studied three pairs of genes that are known to be involved in an interaction with symbiotic bacteria and were recently duplicated in the history of the Medicago genus (Fabaceae). We sequenced two pairs of polygalacturonase genes (Pg11-Pg3 and Pg11a-Pg11c) and one pair of auxine transporter-like genes (Lax2-Lax4) in 17 species belonging to the Medicago genus, and sought for molecular signatures of differentiation between copies. Results Selective histories revealed by these three signatures of molecular differentiation were found to be markedly different between each pair of paralogs. We found sites under positive selection in the Pg11 paralogs while Pg3 has mainly evolved under purifying selection. The most recent paralogs examined Pg11a and Pg11c, are both undergoing positive selection and might be acquiring new functions. Lax2 and Lax4 paralogs are both under strong purifying selection, but still underwent a temporary relaxation of purifying selection immediately after duplication. Conclusions This study illustrates the variety of selective pressures undergone by duplicated genes and the effect of age of the duplication. We found that relaxation of selective constraints immediately after duplication might promote adaptive divergence.
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Affiliation(s)
- Joan Ho-Huu
- INRA - Institut National de la Recherche Agronomique, UMR AGAP, Montpellier, 34060, France
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737
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Cam Y, Pierre O, Boncompagni E, Hérouart D, Meilhoc E, Bruand C. Nitric oxide (NO): a key player in the senescence of Medicago truncatula root nodules. THE NEW PHYTOLOGIST 2012; 196:548-560. [PMID: 22937888 DOI: 10.1111/j.1469-8137.2012.04282.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/15/2012] [Indexed: 05/23/2023]
Abstract
Nitric oxide (NO) is a signalling and defence molecule involved in diverse plant developmental processes, as well as in the plant response to pathogens. NO has also been detected at different steps of the symbiosis between legumes and rhizobia. NO is required for an optimal establishment of the Medicago truncatula-Sinorhizobium meliloti symbiotic interaction, but little is known about the role of NO in mature nodules. Here, we investigate the role of NO in the late steps of symbiosis. Genetic and pharmacological approaches were conducted to modulate the NO level inside root nodules, and their effects on nitrogen fixation and root nodule senescence were monitored. An increase in endogenous NO levels led to a decrease in nitrogen fixation and early nodule senescence, characterized by cytological modifications of the nodule structure and the early expression of a specific senescence marker. By contrast, a decrease in NO levels led to a delay in nodule senescence. Together, our results strongly suggest that NO is a signal in developmental as well as stress-induced nodule senescence. In addition, this work demonstrates the pivotal role of the bacterial NO detoxification response in the prevention of early nodule senescence, and hence the maintenance of efficient symbiosis.
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Affiliation(s)
- Yvan Cam
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, 24 Chemin de Borde Rouge - Auzeville, CS 52627, F-31326, Castanet-Tolosan Cedex, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, 24 Chemin de Borde Rouge - Auzeville, CS 52627, F-31326, Castanet-Tolosan Cedex, France
| | - Olivier Pierre
- 'Institut Sophia Agrobiotech', UMR ISA, INRA 1355-CNRS 7254-Université de Nice-Sophia Antipolis (UNS), 400 route des Chappes BP 167, F-06903, Sophia-Antipolis Cedex, France
| | - Eric Boncompagni
- 'Institut Sophia Agrobiotech', UMR ISA, INRA 1355-CNRS 7254-Université de Nice-Sophia Antipolis (UNS), 400 route des Chappes BP 167, F-06903, Sophia-Antipolis Cedex, France
| | - Didier Hérouart
- 'Institut Sophia Agrobiotech', UMR ISA, INRA 1355-CNRS 7254-Université de Nice-Sophia Antipolis (UNS), 400 route des Chappes BP 167, F-06903, Sophia-Antipolis Cedex, France
| | - Eliane Meilhoc
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, 24 Chemin de Borde Rouge - Auzeville, CS 52627, F-31326, Castanet-Tolosan Cedex, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, 24 Chemin de Borde Rouge - Auzeville, CS 52627, F-31326, Castanet-Tolosan Cedex, France
| | - Claude Bruand
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, 24 Chemin de Borde Rouge - Auzeville, CS 52627, F-31326, Castanet-Tolosan Cedex, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, 24 Chemin de Borde Rouge - Auzeville, CS 52627, F-31326, Castanet-Tolosan Cedex, France
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738
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Loridon K, Burgarella C, Chantret N, Martins F, Gouzy J, Prospéri JM, Ronfort J. Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula. Mol Ecol Resour 2012; 13:84-95. [PMID: 23017123 DOI: 10.1111/1755-0998.12021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 01/09/2023]
Abstract
Extensive genomic resources are available in the model legume Medicago truncatula. Here, we present the discovery and design of the first array of single-nucleotide polymorphism (SNP) markers in M. truncatula through large-scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 M. truncatula accessions. Both anonymous fragments and fragments targeting candidate genes for flowering phenology and symbiosis were surveyed for nucleotide variation in almost 230 kb of unique genomic regions. A set of 384 SNP markers was designed for an Illumina's GoldenGate assay, genotyped on a collection of 192 inbred lines (CC192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNPs were of high quality and exhibited polymorphism in the CC192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNPs. Analysis of the allele frequency spectrum in the CC192 showed a reduced ascertainment bias, mostly limited to very rare alleles (frequency <0.01). The substantial polymorphism detected at the species and population levels, the high marker quality and the potential to survey large samples of individuals make this set of SNP markers a valuable tool to improve our understanding of the effect of demographic and selective factors that shape the natural genetic diversity within the selfing species Medicago truncatula.
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Affiliation(s)
- Karine Loridon
- INRA, UMR AGAP, 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
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739
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Deschamps S, Llaca V, May GD. Genotyping-by-Sequencing in Plants. BIOLOGY 2012; 1:460-83. [PMID: 24832503 PMCID: PMC4009820 DOI: 10.3390/biology1030460] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 08/07/2012] [Accepted: 09/13/2012] [Indexed: 12/12/2022]
Abstract
The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS). This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application.
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Affiliation(s)
- Stéphane Deschamps
- DuPont Agricultural Biotechnology, Experimental Station, PO Box 80353, 200 Powder Mill Road, Wilmington, DE 19880-0353, USA.
| | - Victor Llaca
- DuPont Agricultural Biotechnology, Experimental Station, PO Box 80353, 200 Powder Mill Road, Wilmington, DE 19880-0353, USA.
| | - Gregory D May
- DuPont Pioneer, 7300 NW 62nd Ave., P.O. Box 1004, Johnston, IA 50131-1004, USA.
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740
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Rose CM, Venkateshwaran M, Volkening JD, Grimsrud PA, Maeda J, Bailey DJ, Park K, Howes-Podoll M, den Os D, Yeun LH, Westphall MS, Sussman MR, Ané JM, Coon JJ. Rapid phosphoproteomic and transcriptomic changes in the rhizobia-legume symbiosis. Mol Cell Proteomics 2012; 11:724-44. [PMID: 22683509 PMCID: PMC3434772 DOI: 10.1074/mcp.m112.019208] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 06/07/2012] [Indexed: 11/06/2022] Open
Abstract
Symbiotic associations between legumes and rhizobia usually commence with the perception of bacterial lipochitooligosaccharides, known as Nod factors (NF), which triggers rapid cellular and molecular responses in host plants. We report here deep untargeted tandem mass spectrometry-based measurements of rapid NF-induced changes in the phosphorylation status of 13,506 phosphosites in 7739 proteins from the model legume Medicago truncatula. To place these phosphorylation changes within a biological context, quantitative phosphoproteomic and RNA measurements in wild-type plants were compared with those observed in mutants, one defective in NF perception (nfp) and one defective in downstream signal transduction events (dmi3). Our study quantified the early phosphorylation and transcription dynamics that are specifically associated with NF-signaling, confirmed a dmi3-mediated feedback loop in the pathway, and suggested "cryptic" NF-signaling pathways, some of them being also involved in the response to symbiotic arbuscular mycorrhizal fungi.
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Affiliation(s)
- Christopher M. Rose
- From the ‡Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
- ‖Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | | | - Jeremy D. Volkening
- ¶Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Paul A. Grimsrud
- ¶Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Junko Maeda
- §Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
| | - Derek J. Bailey
- From the ‡Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
- ‖Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - Kwanghyun Park
- ‖Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
- **Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin 53706
| | | | - Désirée den Os
- §Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
- §§Present address: Penn State Biology Department, University Park, Pennsylvania 16802
| | - Li Huey Yeun
- §Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
| | - Michael S. Westphall
- From the ‡Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
- ‖Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - Michael R. Sussman
- ¶Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
- ‖Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - Jean-Michel Ané
- §Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
| | - Joshua J. Coon
- From the ‡Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
- ‖Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
- ‡‡Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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741
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Charon C, Bruggeman Q, Thareau V, Henry Y. Gene duplication within the Green Lineage: the case of TEL genes. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5061-5077. [PMID: 22865910 DOI: 10.1093/jxb/ers181] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent years have witnessed a breathtaking increase in the availability of genome sequence data, providing evidence of the highly duplicate nature of eukaryotic genomes. Plants are exceptional among eukaryotic organisms in that duplicate loci compose a large fraction of their genomes, partly because of the frequent occurrence of polyploidy (or whole-genome duplication) events. Tandem gene duplication and transposition have also contributed to the large number of duplicated genes in plant genomes. Evolutionary analyses allowed the dynamics of duplicate gene evolution to be studied and several models were proposed. It seems that, over time, many duplicated genes were lost and some of those that were retained gained new functions and/or expression patterns (neofunctionalization) or subdivided their functions and/or expression patterns between them (subfunctionalization). Recent studies have provided examples of genes that originated by duplication with successive diversification within plants. In this review, we focused on the TEL (TERMINAL EAR1-like) genes to illustrate such mechanisms. Emerged from the mei2 gene family, these TEL genes are likely to be land plant-specific. Phylogenetic analyses revealed one or two TEL copies per diploid genome. TEL gene degeneration and loss in several Angiosperm species such as in poplar and maize seem to have occurred. In Arabidopsis thaliana, whose genome experienced at least three polyploidy events followed by massive gene loss and genomic reorganization, two TEL genes were retained and two new shorter TEL-like (MCT) genes emerged. Molecular and expression analyses suggest for these genes sub- and neofunctionalization events, but confirmation will come from their functional characterization.
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Affiliation(s)
- Céline Charon
- Institut de Biologie des Plantes-CNRS (UMR8618), Université Paris-Sud 11, Saclay Plant Sciences, F-91405 Orsay Cedex, France.
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742
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Ranjan A, Ichihashi Y, Sinha NR. The tomato genome: implications for plant breeding, genomics and evolution. Genome Biol 2012; 13:167. [PMID: 22943138 PMCID: PMC3491363 DOI: 10.1186/gb-2012-13-8-167] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The genome sequence of tomato (Solanum lycopersicum), one of the most important vegetable crops, has recently been decoded. We address implications of the tomato genome for plant breeding, genomics and evolutionary studies, and its potential to fuel future crop biology research.
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743
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Epstein B, Branca A, Mudge J, Bharti AK, Briskine R, Farmer AD, Sugawara M, Young ND, Sadowsky MJ, Tiffin P. Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae. PLoS Genet 2012; 8:e1002868. [PMID: 22876202 PMCID: PMC3410850 DOI: 10.1371/journal.pgen.1002868] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 06/13/2012] [Indexed: 11/18/2022] Open
Abstract
The symbiosis between rhizobial bacteria and legume plants has served as a model for investigating the genetics of nitrogen fixation and the evolution of facultative mutualism. We used deep sequence coverage (>100×) to characterize genomic diversity at the nucleotide level among 12 Sinorhizobium medicae and 32 S. meliloti strains. Although these species are closely related and share host plants, based on the ratio of shared polymorphisms to fixed differences we found that horizontal gene transfer (HGT) between these species was confined almost exclusively to plasmid genes. Three multi-genic regions that show the strongest evidence of HGT harbor genes directly involved in establishing or maintaining the mutualism with host plants. In both species, nucleotide diversity is 1.5–2.5 times greater on the plasmids than chromosomes. Interestingly, nucleotide diversity in S. meliloti but not S. medicae is highly structured along the chromosome – with mean diversity (θπ) on one half of the chromosome five times greater than mean diversity on the other half. Based on the ratio of plasmid to chromosome diversity, this appears to be due to severely reduced diversity on the chromosome half with less diversity, which is consistent with extensive hitchhiking along with a selective sweep. Frequency-spectrum based tests identified 82 genes with a signature of adaptive evolution in one species or another but none of the genes were identified in both species. Based upon available functional information, several genes identified as targets of selection are likely to alter the symbiosis with the host plant, making them attractive targets for further functional characterization. Facultative mutualisms are relationships between two species that can live independently, but derive benefits when living together with their mutualistic partners. The facultative mutualism between rhizobial bacteria and legume plants contributes approximately half of all biologically fixed nitrogen, an essential plant nutrient, and is an important source of nitrogen to both natural and agricultural ecosystems. We resequenced the genomes of 44 strains of two closely related species of the genus Sinorhizobium that form facultative mutualisms with the model legme Medicago truncatula. These data provide one of the most complete examinations of genomic diversity segregating within microbial species that are not causative agents of human illness. Our analyses reveal that horizontal gene transfer, a common source of new genes in microbial species, disproportionately affects genes with direct roles in the rhizobia-plant symbiosis. Analyses of nucleotide diversity segregating within each species suggests that strong selection, along with genetic hitchhiking has sharply reduced diversity along an entire chromosome half in S. meliloti. Despite the two species' ecological similarity, we did not find evidence for selection acting on the same genetic targets. In addition to providing insight into the evolutionary history of rhizobial, this study shows the feasibility and potential power of applying population genomic analyses to microbial species.
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Affiliation(s)
- Brendan Epstein
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Antoine Branca
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Arvind K. Bharti
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Roman Briskine
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Andrew D. Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Masayuki Sugawara
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nevin D. Young
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Michael J. Sadowsky
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, United States of America
- BioTechnology Institute, St. Paul, Minnesota, United States of America
- * E-mail: (MJS); (PT)
| | - Peter Tiffin
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail: (MJS); (PT)
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744
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Giacomelli L, Nanni V, Lenzi L, Zhuang J, Dalla Serra M, Banfield MJ, Town CD, Silverstein KAT, Baraldi E, Moser C. Identification and characterization of the defensin-like gene family of grapevine. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1118-31. [PMID: 22550957 DOI: 10.1094/mpmi-12-11-0323] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Defensins are a class of small and diverse cysteine-rich proteins found in plants, insects, and vertebrates, which share a common tertiary structure and usually exert broad-spectrum antimicrobial activities. We used a bioinformatic approach to scan the Vitis vinifera genome and identified 79 defensin-like sequences (DEFL) corresponding to 46 genes and allelic variants, plus 33 pseudogenes and gene fragments. Expansion and diversification of grapevine DEFL has occurred after the split from the last common ancestor with the genera Medicago and Arabidopsis. Grapevine DEFL localization on the 'Pinot Noir' genome revealed the presence of several clusters likely evolved through local duplications. By sequencing reverse-transcription polymerase chain reaction products, we could demonstrate the expression of grapevine DEFL with no previously reported record of expression. Many of these genes are predominantly or exclusively expressed in tissues linked to plant reproduction, consistent with findings in other plant species, and some of them accumulated at fruit ripening. The transcripts of five DEFL were also significantly upregulated in tissues infected with Botrytis cinerea, a necrotrophic mold, suggesting a role of these genes in defense against this pathogen. Finally, three novel defensins were discovered among the identified DEFL. They inhibit B. cinerea conidia germination when expressed as recombinant proteins.
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Affiliation(s)
- Lisa Giacomelli
- IASMA Research and Innovation Centre, San Michele all'Adige, Italy
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745
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Hiremath PJ, Kumar A, Penmetsa RV, Farmer A, Schlueter JA, Chamarthi SK, Whaley AM, Carrasquilla-Garcia N, Gaur PM, Upadhyaya HD, Kavi Kishor PB, Shah TM, Cook DR, Varshney RK. Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:716-32. [PMID: 22703242 PMCID: PMC3465799 DOI: 10.1111/j.1467-7652.2012.00710.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 04/05/2012] [Accepted: 04/25/2012] [Indexed: 05/20/2023]
Abstract
A set of 2486 single nucleotide polymorphisms (SNPs) were compiled in chickpea using four approaches, namely (i) Solexa/Illumina sequencing (1409), (ii) amplicon sequencing of tentative orthologous genes (TOGs) (604), (iii) mining of expressed sequence tags (ESTs) (286) and (iv) sequencing of candidate genes (187). Conversion of these SNPs to the cost-effective and flexible throughput Competitive Allele Specific PCR (KASPar) assays generated successful assays for 2005 SNPs. These marker assays have been designated as Chickpea KASPar Assay Markers (CKAMs). Screening of 70 genotypes including 58 diverse chickpea accessions and 12 BC(3) F(2) lines showed 1341 CKAMs as being polymorphic. Genetic analysis of these data clustered chickpea accessions based on geographical origin. Genotyping data generated for 671 CKAMs on the reference mapping population (Cicer arietinum ICC 4958 × Cicer reticulatum PI 489777) were compiled with 317 unpublished TOG-SNPs and 396 published markers for developing the genetic map. As a result, a second-generation genetic map comprising 1328 marker loci including novel 625 CKAMs, 314 TOG-SNPs and 389 published marker loci with an average inter-marker distance of 0.59 cM was constructed. Detailed analyses of 1064 mapped loci of this second-generation chickpea genetic map showed a higher degree of synteny with genome of Medicago truncatula, followed by Glycine max, Lotus japonicus and least with Vigna unguiculata. Development of these cost-effective CKAMs for SNP genotyping will be useful not only for genetics research and breeding applications in chickpea, but also for utilizing genome information from other sequenced or model legumes.
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Affiliation(s)
- Pavana J Hiremath
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
- Osmania UniversityHyderabad, India
| | - Ashish Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | | | - Andrew Farmer
- National Center for Genome Resources (NCGR)Santa Fe, NM, USA
| | | | - Siva K Chamarthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | | | | | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | | | - Trushar M Shah
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
- Generation Challenge Program (GCP)Mexico DF, Mexico
- *Correspondence (Tel +91 40 30713305; fax +91 40 30713074/3075; email )
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746
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Geurts R, Lillo A, Bisseling T. Exploiting an ancient signalling machinery to enjoy a nitrogen fixing symbiosis. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:438-43. [PMID: 22633856 DOI: 10.1016/j.pbi.2012.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/26/2012] [Indexed: 05/20/2023]
Abstract
For almost a century now it has been speculated that a transfer of the largely legume-specific symbiosis with nitrogen fixing rhizobium would be profitable in agriculture [1,2]. Up to now such a step has not been achieved, despite intensive research in this era. Novel insights in the underlying signalling networks leading to intracellular accommodation of rhizobium as well as mycorrhizal fungi of the Glomeromycota order show extensive commonalities between both interactions. As mycorrhizae symbiosis can be established basically with most higher plant species it raises questions why is it only in a few taxonomic lineages that the underlying signalling network could be hijacked by rhizobium. Unravelling this will lead to insights that are essential to achieve an old dream.
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Affiliation(s)
- Rene Geurts
- Wageningen University, Department of Plant Science, Laboratory of Molecular Biology, Droevendaalsesteeg 1, 6709BP Wageningen, The Netherlands
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747
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Doležel J, Vrána J, Safář J, Bartoš J, Kubaláková M, Simková H. Chromosomes in the flow to simplify genome analysis. Funct Integr Genomics 2012; 12:397-416. [PMID: 22895700 PMCID: PMC3431466 DOI: 10.1007/s10142-012-0293-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 07/30/2012] [Indexed: 11/25/2022]
Abstract
Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 10(2)-10(4) chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.
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Affiliation(s)
- Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, Czech Republic.
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748
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Czaja LF, Hogekamp C, Lamm P, Maillet F, Martinez EA, Samain E, Dénarié J, Küster H, Hohnjec N. Transcriptional responses toward diffusible signals from symbiotic microbes reveal MtNFP- and MtDMI3-dependent reprogramming of host gene expression by arbuscular mycorrhizal fungal lipochitooligosaccharides. PLANT PHYSIOLOGY 2012; 159:1671-85. [PMID: 22652128 PMCID: PMC3425205 DOI: 10.1104/pp.112.195990] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The formation of root nodules and arbuscular mycorrhizal (AM) roots is controlled by a common signaling pathway including the calcium/calmodulin-dependent kinase Doesn't Make Infection3 (DMI3). While nodule initiation by lipochitooligosaccharide (LCO) Nod factors is well characterized, diffusible AM fungal signals were only recently identified as sulfated and nonsulfated LCOs. Irrespective of different outcomes, the perception of symbiotic LCOs in Medicago truncatula is mediated by the LysM receptor kinase M. truncatula Nod factor perception (MtNFP). To shed light on transcriptional responses toward symbiotic LCOs and their dependence on MtNFP and Ca(2+) signaling, we performed genome-wide expression studies of wild-type, Nod-factor-perception mutant1, and dmi3 mutant roots challenged with Myc- and Nod-LCOs. We show that Myc-LCOs lead to transient, quick responses in the wild type, whereas Nod-LCOs require prolonged incubation for maximal expression activation. While Nod-LCOs are most efficient for an induction of persistent transcriptional changes, sulfated Myc-LCOs are less active, and nonsulfated Myc-LCOs display the lowest capacity to activate and sustain expression. Although all symbiotic LCOs up-regulated a common set of genes, discrete subsets were induced by individual LCOs, suggesting common and specific functions for these in presymbiotic signaling. Surprisingly, even sulfated fungal Myc-LCOs and Sinorhizobium meliloti Nod-LCOs, having very similar structures, each elicited discrete subsets of genes, while a mixture of both Myc-LCOs activated responses deviating from those induced by single treatments. Focusing on the precontact phase, we identified signaling-related and transcription factor genes specifically up-regulated by Myc-LCOs. Comparative gene expression studies in symbiotic mutants demonstrated that transcriptional reprogramming by AM fungal LCOs strictly depends on MtNFP and largely requires MtDMI3.
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749
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Heath KD, McGhee KE. Coevolutionary constraints? The environment alters tripartite interaction traits in a legume. PLoS One 2012; 7:e41567. [PMID: 22859998 PMCID: PMC3408487 DOI: 10.1371/journal.pone.0041567] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/24/2012] [Indexed: 11/19/2022] Open
Abstract
Third party species, which interact with one or both partners of a pairwise species interaction, can shift the ecological costs and the evolutionary trajectory of the focal interaction. Shared genes that mediate a host's interactions with multiple partners have the potential to generate evolutionary constraints, making multi-player interactions critical to our understanding of the evolution of key interaction traits. Using a field quantitative genetics approach, we studied phenotypic and genetic correlations among legume traits for rhizobium and herbivore interactions in two light environments. Shifts in plant biomass allocation mediated negative phenotypic correlations between symbiotic nodule number and herbivory in the field, whereas positive genetic covariances suggested shared genetic pathways between nodulation and herbivory response. Trait variance-covariance (G) matrices were not equal in sun and shade, but nevertheless responses to independent and correlated selection are expected to be similar in both environments. Interactions between plants and aboveground antagonists might alter the evolutionary potential of traits mediating belowground mutualisms (and vice versa). Thus our understanding of legume-rhizobium genetics and coevolution may be incomplete without a grasp of how these networks overlap with other plant interactions.
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Affiliation(s)
- Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
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750
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Zhang N, Venkateshwaran M, Boersma M, Harms A, Howes-Podoll M, den Os D, Ané JM, Sussman MR. Metabolomic profiling reveals suppression of oxylipin biosynthesis during the early stages of legume-rhizobia symbiosis. FEBS Lett 2012; 586:3150-8. [DOI: 10.1016/j.febslet.2012.06.046] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 06/27/2012] [Accepted: 06/28/2012] [Indexed: 11/28/2022]
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