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Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing. Proc Natl Acad Sci U S A 2017; 114:1195-1200. [PMID: 28096391 DOI: 10.1073/pnas.1620119114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We have applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. A more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy.
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Wang X, Shi W, Rinehart T. Transcriptomes That Confer to Plant Defense against Powdery Mildew Disease in Lagerstroemia indica. Int J Genomics 2015; 2015:528395. [PMID: 26247009 PMCID: PMC4515301 DOI: 10.1155/2015/528395] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 05/06/2015] [Indexed: 11/26/2022] Open
Abstract
Transcriptome analysis was conducted in two popular Lagerstroemia cultivars: "Natchez" (NAT), a white flower and powdery mildew resistant interspecific hybrid and "Carolina Beauty" (CAB), a red flower and powdery mildew susceptible L. indica cultivar. RNA-seq reads were generated from Erysiphe australiana infected leaves and de novo assembled. A total of 37,035 unigenes from 224,443 assembled contigs in both genotypes were identified. Approximately 85% of these unigenes have known function. Of them, 475 KEGG genes were found significantly different between the two genotypes. Five of the top ten differentially expressed genes (DEGs) involved in the biosynthesis of secondary metabolites (plant defense) and four in flavonoid biosynthesis pathway (antioxidant activities or flower coloration). Furthermore, 5 of the 12 assembled unigenes in benzoxazinoid biosynthesis and 7 of 11 in flavonoid biosynthesis showed higher transcript abundance in NAT. The relative abundance of transcripts for 16 candidate DEGs (9 from CAB and 7 from NAT) detected by qRT-PCR showed general agreement with the abundances of the assembled transcripts in NAT. This study provided the first transcriptome analyses in L. indica. The differential transcript abundance between two genotypes indicates that it is possible to identify candidate genes that are associated with the plant defenses or flower coloration.
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Affiliation(s)
- Xinwang Wang
- USDA-ARS, Crop Germplasm Research, College Station, TX 77845, USA
- Texas A&M AgriLife Research and Extension Center, Dallas, TX 75252, USA
| | - Weibing Shi
- Department of Plant Pathology, Texas A&M University, College Station, TX 77843, USA
| | - Timothy Rinehart
- USDA-ARS, Thad Cochran Southern Horticultural Laboratory, Poplarville, MS 39470, USA
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Neale DB, Langley CH, Salzberg SL, Wegrzyn JL. Open access to tree genomes: the path to a better forest. Genome Biol 2013; 14:120. [PMID: 23796049 PMCID: PMC3706761 DOI: 10.1186/gb-2013-14-6-120] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
An open-access culture and a well-developed comparative-genomics infrastructure must be developed in forest trees to derive the full potential of genome sequencing in this diverse group of plants that are the dominant species in much of the earth's terrestrial ecosystems.
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Creux N, De Castro M, Ranik M, Spokevicius A, Bossinger G, Maritz-Olivier C, Myburg Z. In silico and functional characterization of the promoter of a Eucalyptussecondary cell wall associated cellulose synthase gene (EgCesA1). BMC Proc 2011. [PMCID: PMC3239950 DOI: 10.1186/1753-6561-5-s7-p107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Liu R, Wang B, Guo W, Wang L, Zhang T. Differential gene expression and associated QTL mapping for cotton yield based on a cDNA-AFLP transcriptome map in an immortalized F2. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:439-54. [PMID: 21512772 DOI: 10.1007/s00122-011-1597-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Accepted: 04/05/2011] [Indexed: 05/12/2023]
Abstract
cDNA-AFLP techniques have found new applications in recent years. Currently, the methodology is used to establish differential gene expression and construct linkage maps. In the present study, a transcriptome map based on cDNA-AFLP techniques was constructed using an immortalized F(2) (IF(2)) population of 171 lines. The lines were derived from intercrosses between 180 recombinant inbred lines (RILs) of the cotton hybrid Xiangzamian 2 (Gossypium. hirsutum L.). A total of 302 transcriptome-derived fragments (TDFs) were mapped onto 26 linkage groups that covered 2,477.06 cM in length with an average distance of 8.23 cM between two markers. Seventy-one QTL for yield and yield component traits were detected by CIM procedures based on four environments, with 13 QTL identified in at least two environments. Some TDFs co-located with yield QTL were subsequently sequenced and analyzed by online homology searches. Potential candidate genes for yield and yield component traits were found to encode proteins involved in DNA replication, transcription, translation, and biosynthesis regulation. Furthermore, genes regulating metabolic processes signal transduction, transport, and structural components of organelles were identified. Correlation analysis between expression patterns of TDFs and trait performance detected six TDFs positively correlated to both yield and yield heterosis: six TDFs positively correlated to yield, and seven TDFs to yield heterosis. These TDFs have potential for cloning the functional genes responsible for each corresponding trait and have future value in marker-assisted selection.
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Affiliation(s)
- Renzhong Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, China
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Abstract
Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment - enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, California 95616, USA.
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Wang L, Guo K, Li Y, Tu Y, Hu H, Wang B, Cui X, Peng L. Expression profiling and integrative analysis of the CESA/CSL superfamily in rice. BMC PLANT BIOLOGY 2010; 10:282. [PMID: 21167079 PMCID: PMC3022907 DOI: 10.1186/1471-2229-10-282] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Accepted: 12/20/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND The cellulose synthase and cellulose synthase-like gene superfamily (CESA/CSL) is proposed to encode enzymes for cellulose and non-cellulosic matrix polysaccharide synthesis in plants. Although the rice (Oryza sativa L.) genome has been sequenced for a few years, the global expression profiling patterns and functions of the OsCESA/CSL superfamily remain largely unknown. RESULTS A total of 45 identified members of OsCESA/CSL were classified into two clusters based on phylogeny and motif constitution. Duplication events contributed largely to the expansion of this superfamily, with Cluster I and II mainly attributed to tandem and segmental duplication, respectively. With microarray data of 33 tissue samples covering the entire life cycle of rice, fairly high OsCESA gene expression and rather variable OsCSL expression were observed. While some members from each CSL family (A1, C9, D2, E1, F6 and H1) were expressed in all tissues examined, many of OsCSL genes were expressed in specific tissues (stamen and radicles). The expression pattern of OsCESA/CSL and OsBC1L which extensively co-expressed with OsCESA/CSL can be divided into three major groups with ten subgroups, each showing a distinct co-expression in tissues representing typically distinct cell wall constitutions. In particular, OsCESA1, -3 & -8 and OsCESA4, -7 & -9 were strongly co-expressed in tissues typical of primary and secondary cell walls, suggesting that they form as a cellulose synthase complex; these results are similar to the findings in Arabidopsis. OsCESA5/OsCESA6 is likely partially redundant with OsCESA3 for OsCESA complex organization in the specific tissues (plumule and radicle). Moreover, the phylogenetic comparison in rice, Arabidopsis and other species can provide clues for the prediction of orthologous gene expression patterns. CONCLUSIONS The study characterized the CESA/CSL of rice using an integrated approach comprised of phylogeny, transcriptional profiling and co-expression analyses. These investigations revealed very useful clues on the major roles of CESA/CSL, their potentially functional complement and their associations for appropriate cell wall synthesis in higher plants.
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Affiliation(s)
- Lingqiang Wang
- National Key Laboratory of Crop Genetic Improvement, Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Kai Guo
- National Key Laboratory of Crop Genetic Improvement, Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
- College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Yu Li
- National Key Laboratory of Crop Genetic Improvement, Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Yuanyuan Tu
- National Key Laboratory of Crop Genetic Improvement, Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Huizhen Hu
- National Key Laboratory of Crop Genetic Improvement, Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Bingrui Wang
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Xiaocan Cui
- College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Liangcai Peng
- National Key Laboratory of Crop Genetic Improvement, Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
- College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
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Yordanov YS, Regan S, Busov V. Members of the LATERAL ORGAN BOUNDARIES DOMAIN transcription factor family are involved in the regulation of secondary growth in Populus. THE PLANT CELL 2010; 22:3662-77. [PMID: 21097711 PMCID: PMC3015109 DOI: 10.1105/tpc.110.078634] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/04/2010] [Accepted: 10/26/2010] [Indexed: 05/18/2023]
Abstract
Regulation of secondary (woody) growth is of substantial economic and environmental interest but is poorly understood. We identified and subsequently characterized an activation-tagged poplar (Populus tremula × Populus alba) mutant with enhanced woody growth and changes in bark texture caused primarily by increased secondary phloem production. Molecular characterization of the mutation through positioning of the tag and retransformation experiments shows that the phenotype is conditioned by activation of an uncharacterized gene that encodes a novel member of the LATERAL ORGAN BOUNDARIES DOMAIN (LBD) family of transcription factors. Homology analysis showed highest similarity to an uncharacterized LBD1 gene from Arabidopsis thaliana, and we consequently named it Populus tremula × Populus alba (Pta) LBD1. Dominant-negative suppression of Pta LBD1 via translational fusion with the repressor SRDX domain caused decreased diameter growth and suppressed and highly irregular phloem development. In wild-type plants, LBD1 was most highly expressed in the phloem and cambial zone. Two key Class I KNOTTED1-like homeobox genes that promote meristem identity in the cambium were downregulated, while an Altered Phloem Development gene that is known to promote phloem differentiation was upregulated in the mutant. A set of four LBD genes, including the LBD1 gene, was predominantly expressed in wood-forming tissues, suggesting a broader regulatory role of these transcription factors during secondary woody growth in poplar.
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Affiliation(s)
- Yordan S. Yordanov
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan 49931-1295
| | - Sharon Regan
- Department of Biology, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Victor Busov
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan 49931-1295
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Barros E, van Staden CA, Lezar S. A microarray-based method for the parallel analysis of genotypes and expression profiles of wood-forming tissues in Eucalyptus grandis. BMC Biotechnol 2009; 9:51. [PMID: 19473481 PMCID: PMC2698882 DOI: 10.1186/1472-6750-9-51] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 05/27/2009] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. The most serious problem affecting the quality and yield of solid wood products is the occurrence of end splitting in logs. Selection of E. grandis planting stock that exhibit preferred wood qualities is thus a priority of the South African forestry industry. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven different E. grandis trees. RESULTS A 1578-probe cDNA microarray was constructed by arraying 768 cDNA-AFLP clones and 810 cDNA library clones from seven individual E. grandis trees onto silanised slides. The results revealed that 32% of the spotted fragments showed distinct expression patterns (with a fold change of at least 1.4 or -1.4 and a p value of 0.01) could be grouped into clusters representing co-expressed genes. Evaluation of the binary distribution of cDNA-AFLP fragments on the array showed that the individual genotypes could be discriminated. CONCLUSION A simple, yet general method was developed for genotyping and expression profiling of wood-forming tissue of E. grandis trees differing in their splitting characteristics and in their lignin contents. Evaluation of gene expression profiles and the binary distribution of cDNA-AFLP fragments on the chip suggest that the prototype chip developed could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programmes.
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Affiliation(s)
- Eugenia Barros
- CSIR – Biosciences, Meiring Naude Road, Brummeria, Pretoria, 0001, South Africa
| | | | - Sabine Lezar
- CSIR – Biosciences, Meiring Naude Road, Brummeria, Pretoria, 0001, South Africa
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Minic Z, Jamet E, San-Clemente H, Pelletier S, Renou JP, Rihouey C, Okinyo DPO, Proux C, Lerouge P, Jouanin L. Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes. BMC PLANT BIOLOGY 2009; 9:6. [PMID: 19149885 PMCID: PMC2649120 DOI: 10.1186/1471-2229-9-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Accepted: 01/16/2009] [Indexed: 05/17/2023]
Abstract
BACKGROUND Different strategies (genetics, biochemistry, and proteomics) can be used to study proteins involved in cell biogenesis. The availability of the complete sequences of several plant genomes allowed the development of transcriptomic studies. Although the expression patterns of some Arabidopsis thaliana genes involved in cell wall biogenesis were identified at different physiological stages, detailed microarray analysis of plant cell wall genes has not been performed on any plant tissues. Using transcriptomic and bioinformatic tools, we studied the regulation of cell wall genes in Arabidopsis stems, i.e. genes encoding proteins involved in cell wall biogenesis and genes encoding secreted proteins. RESULTS Transcriptomic analyses of stems were performed at three different developmental stages, i.e., young stems, intermediate stage, and mature stems. Many genes involved in the synthesis of cell wall components such as polysaccharides and monolignols were identified. A total of 345 genes encoding predicted secreted proteins with moderate or high level of transcripts were analyzed in details. The encoded proteins were distributed into 8 classes, based on the presence of predicted functional domains. Proteins acting on carbohydrates and proteins of unknown function constituted the two most abundant classes. Other proteins were proteases, oxido-reductases, proteins with interacting domains, proteins involved in signalling, and structural proteins. Particularly high levels of expression were established for genes encoding pectin methylesterases, germin-like proteins, arabinogalactan proteins, fasciclin-like arabinogalactan proteins, and structural proteins. Finally, the results of this transcriptomic analyses were compared with those obtained through a cell wall proteomic analysis from the same material. Only a small proportion of genes identified by previous proteomic analyses were identified by transcriptomics. Conversely, only a few proteins encoded by genes having moderate or high level of transcripts were identified by proteomics. CONCLUSION Analysis of the genes predicted to encode cell wall proteins revealed that about 345 genes had moderate or high levels of transcripts. Among them, we identified many new genes possibly involved in cell wall biogenesis. The discrepancies observed between results of this transcriptomic study and a previous proteomic study on the same material revealed post-transcriptional mechanisms of regulation of expression of genes encoding cell wall proteins.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- Laboratoire de Biologie Cellulaire, Institut National de la Recherche Agronomique (INRA), Route de St-Cyr, 78026 Versailles Cedex, France
| | - Elisabeth Jamet
- Surfaces Cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS-UPS, Université de Toulouse, 24 Chemin de Borde Rouge, BP42617, 31326-Castanet-Tolosan, France
| | - Hélène San-Clemente
- Surfaces Cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS-UPS, Université de Toulouse, 24 Chemin de Borde Rouge, BP42617, 31326-Castanet-Tolosan, France
| | - Sandra Pelletier
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114, UEVE, 91057 Evry cedex, France
| | - Jean-Pierre Renou
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114, UEVE, 91057 Evry cedex, France
| | - Christophe Rihouey
- Faculté des Sciences, FRE CNRS 3090, IFRMP23, Université de Rouen, F-76821 Mont Saint Aignan Cedex, France
| | - Denis PO Okinyo
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
| | - Caroline Proux
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114, UEVE, 91057 Evry cedex, France
| | - Patrice Lerouge
- Faculté des Sciences, FRE CNRS 3090, IFRMP23, Université de Rouen, F-76821 Mont Saint Aignan Cedex, France
| | - Lise Jouanin
- Laboratoire de Biologie Cellulaire, Institut National de la Recherche Agronomique (INRA), Route de St-Cyr, 78026 Versailles Cedex, France
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Ritter E, Ruiz de Galarreta JI, van Eck HJ, Sánchez I. Construction of a potato transcriptome map based on the cDNA-AFLP technique. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:1003-1013. [PMID: 18317719 DOI: 10.1007/s00122-008-0731-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 02/09/2008] [Indexed: 05/26/2023]
Abstract
The cDNA-AFLP technique can be used to monitor differential gene expression, but also for linkage mapping. Extending previous works, we have now constructed an integrated linkage map of the potato transcriptome based on the said technique that has a length of around 800 cM and contains nearly 700 transcriptome derived fragments (TDFs). At the same time, most of these markers are anchored to the bins of a highly saturated reference map in potato, combining in this way the information provided by different marker types. Moreover, we detected and confirmed an elevated degree of allelic fragments with this marker type, which was present in nearly half of all primer combinations and involved around 20% of all fragments. These properties were particularly useful to establish anchor points for integrating the individual parental linkage maps. Comparative expression profiling in different plant materials revealed that only a few additional TDFs were obtained which were specific for mature leaves or tubers compared to the TDFs present in whole in vitro plants. Since TDF markers are derived from coding regions, they generally also represent sequences with a biological function. In four case studies, co-migrating TDFs in different Solanum wild species always represented potential alleles based on elevated homologies among them. Two resistance gene homologs were identified by analysing TDFs, which were co-located with known QTLs.
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Affiliation(s)
- E Ritter
- NEIKER, The Basque Institute of Agricultural Research and Development, PO Box 46, E01080 Vitoria, Spain
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[Phloem, transport between organs and long-distance signalling]. C R Biol 2008; 331:334-46. [PMID: 18472079 DOI: 10.1016/j.crvi.2008.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Revised: 03/03/2008] [Accepted: 03/05/2008] [Indexed: 01/17/2023]
Abstract
Phloem plays a major role in carbohydrate partitioning in the plant. It also controls the redistribution of various metabolites such as amino acids, vitamins, hormones, and ions. The molecular mechanisms responsible for phloem loading and unloading have been particularly well characterised, with the identification of sucrose and polyol transporters. The discovery of the role of phloem in the long-distance translocation of macromolecules, proteins, mRNA and small RNA has modified our understanding of the regulation of the coordination of some developmental and adaptation processes. This review details recent results concerning the transport and long-distance signalling that take place in the phloem.
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