201
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Lifschitz E, Ayre BG, Eshed Y. Florigen and anti-florigen - a systemic mechanism for coordinating growth and termination in flowering plants. FRONTIERS IN PLANT SCIENCE 2014; 5:465. [PMID: 25278944 PMCID: PMC4165217 DOI: 10.3389/fpls.2014.00465] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/27/2014] [Indexed: 05/18/2023]
Abstract
Genetic studies in Arabidopsis established FLOWERING LOCUS T (FT) as a key flower-promoting gene in photoperiodic systems. Grafting experiments established unequivocal one-to-one relations between SINGLE FLOWER TRUSS (SFT), a tomato homolog of FT, and the hypothetical florigen, in all flowering plants. Additional studies of SFT and SELF PRUNING (SP, homolog of TFL1), two antagonistic genes regulating the architecture of the sympodial shoot system, have suggested that transition to flowering in the day-neutral and perennial tomato is synonymous with "termination." Dosage manipulation of its endogenous and mobile, graft-transmissible levels demonstrated that florigen regulates termination and transition to flowering in an SP-dependent manner and, by the same token, that high florigen levels induce growth arrest and termination in meristems across the tomato shoot system. It was thus proposed that growth balances, and consequently the patterning of the shoot systems in all plants, are mediated by endogenous, meristem-specific dynamic SFT/SP ratios and that shifts to termination by changing SFT/SP ratios are triggered by the imported florigen, the mobile form of SFT. Florigen is a universal plant growth hormone inherently checked by a complementary antagonistic systemic system. Thus, an examination of the endogenous functions of FT-like genes, or of the systemic roles of the mobile florigen in any plant species, that fails to pay careful attention to the balancing antagonistic systems, or to consider its functions in day-neutral or perennial plants, would be incomplete.
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Affiliation(s)
- Eliezer Lifschitz
- Department of Biology, Technion – Israel Institute of TechnologyHaifa, Israel
| | - Brian G. Ayre
- Department of Biological Sciences, University of North Texas, DentonTX, USA
| | - Yuval Eshed
- Department of Plant Sciences, Weizmann Institute of ScienceRehovot, Israel
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202
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Hackett CA, Bradshaw JE, Bryan GJ. QTL mapping in autotetraploids using SNP dosage information. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1885-904. [PMID: 24981609 PMCID: PMC4145212 DOI: 10.1007/s00122-014-2347-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 06/07/2014] [Indexed: 05/23/2023]
Abstract
Dense linkage maps derived by analysing SNP dosage in autotetraploids provide detailed information about the location of, and genetic model at, quantitative trait loci. Recent developments in sequencing and genotyping technologies enable researchers to generate high-density single nucleotide polymorphism (SNP) genotype data for mapping studies. For polyploid species, the SNP genotypes are informative about allele dosage, and Hackett et al. (PLoS ONE 8:e63939, 2013) presented theory about how dosage information can be used in linkage map construction and quantitative trait locus (QTL) mapping for an F1 population in an autotetraploid species. Here, QTL mapping using dosage information is explored for simulated phenotypic traits of moderate heritability and possibly non-additive effects. Different mapping strategies are compared, looking at additive and more complicated models, and model fitting as a single step or by iteratively re-weighted modelling. We recommend fitting an additive model without iterative re-weighting, and then exploring non-additive models for the genotype means estimated at the most likely position. We apply this strategy to re-analyse traits of high heritability from a potato population of 190 F1 individuals: flower colour, maturity, height and resistance to late blight (Phytophthora infestans (Mont.) de Bary) and potato cyst nematode (Globodera pallida), using a map of 3839 SNPs. The approximate confidence intervals for QTL locations have been improved by the detailed linkage map, and more information about the genetic model at each QTL has been revealed. For several of the reported QTLs, candidate SNPs can be identified, and used to propose candidate trait genes. We conclude that the high marker density is informative about the genetic model at loci of large effects, but that larger populations are needed to detect smaller QTLs.
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203
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Spoel SH, van Ooijen G. Circadian redox signaling in plant immunity and abiotic stress. Antioxid Redox Signal 2014; 20:3024-39. [PMID: 23941583 PMCID: PMC4038994 DOI: 10.1089/ars.2013.5530] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/13/2013] [Indexed: 11/12/2022]
Abstract
SIGNIFICANCE Plant crops are critically important to provide quality food and bio-energy to sustain a growing human population. Circadian clocks have been shown to deliver an adaptive advantage to plants, vastly increasing biomass production by efficient anticipation to the solar cycle. Plant stress, on the other hand, whether biotic or abiotic, prevents crops from reaching maximum productivity. RECENT ADVANCES Stress is associated with fluctuations in cellular redox and increased phytohormone signaling. Recently, direct links between circadian timekeeping, redox fluctuations, and hormone signaling have been identified. A direct implication is that circadian control of cellular redox homeostasis influences how plants negate stress to ensure growth and reproduction. CRITICAL ISSUES Complex cellular biochemistry leads from perception of stress via hormone signals and formation of reactive oxygen intermediates to a physiological response. Circadian clocks and metabolic pathways intertwine to form a confusing biochemical labyrinth. Here, we aim to find order in this complex matter by reviewing current advances in our understanding of the interface between these networks. FUTURE DIRECTIONS Although the link is now clearly defined, at present a key question remains as to what extent the circadian clock modulates redox, and vice versa. Furthermore, the mechanistic basis by which the circadian clock gates redox- and hormone-mediated stress responses remains largely elusive.
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Affiliation(s)
- Steven H. Spoel
- Institute for Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Gerben van Ooijen
- Institute for Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- SythSys, University of Edinburgh, Edinburgh, United Kingdom
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204
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Morris WL, Hancock RD, Ducreux LJM, Morris JA, Usman M, Verrall SR, Sharma SK, Bryan G, McNicol JW, Hedley PE, Taylor MA. Day length dependent restructuring of the leaf transcriptome and metabolome in potato genotypes with contrasting tuberization phenotypes. PLANT, CELL & ENVIRONMENT 2014; 37:1351-63. [PMID: 24236539 DOI: 10.1111/pce.12238] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 11/04/2013] [Accepted: 11/05/2013] [Indexed: 05/24/2023]
Abstract
Recent advances have defined some of the components of photoperiodic signalling that lead to tuberization in potato including orthologues of FLOWERING LOCUS T (StSP6A) and CYCLING DOF FACTOR (StCDF1). The aim of the current study is to investigate the molecular basis of permissive tuber initiation under long days in Solanum tuberosum Neo-Tuberosum by comparative analysis with an obligate short-day S. tuberosum ssp. Andigena accession. We show that the Neo-Tuberosum accession, but not the Andigena, contains alleles that encode StCDF1 proteins modified in the C-terminal region, likely to evade long day inhibition of StSP6A expression. We also identify an allele of StSP6A from the Neo-Tuberosum accession, absent in the Andigena, which is expressed under long days. Other leaf transcripts and metabolites that show different abundances in tuberizing and non-tuberizing samples were identified adding detail to tuberization-associated processes. Overall, the data presented in this study highlight the subtle interplay between components of the clock-CONSTANS-StSP6A axis which collectively may interact to fine-tune the timing of tuberization.
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Affiliation(s)
- Wayne L Morris
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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205
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Ham BK, Lucas WJ. The angiosperm phloem sieve tube system: a role in mediating traits important to modern agriculture. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1799-1816. [PMID: 24368503 DOI: 10.1093/jxb/ert417] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The plant vascular system serves a vital function by distributing water, nutrients and hormones essential for growth and development to the various organs of the plant. In this review, attention is focused on the role played by the phloem as the conduit for delivery of both photosynthate and information macromolecules, especially from the context of its mediation in traits that are important to modern agriculture. Resource allocation of sugars and amino acids, by the phloem, to specific sink tissues is of importance to crop yield and global food security. Current findings are discussed in the context of a hierarchical control network that operates to integrate resource allocation to competing sinks. The role of plasmodesmata that connect companion cells to neighbouring sieve elements and phloem parenchyma cells is evaluated in terms of their function as valves, connecting the sieve tube pressure manifold system to the various plant tissues. Recent studies have also revealed that plasmodesmata and the phloem sieve tube system function cooperatively to mediate the long-distance delivery of proteins and a diverse array of RNA species. Delivery of these information macromolecules is discussed in terms of their roles in control over the vegetative-to-floral transition, tuberization in potato, stress-related signalling involving miRNAs, and genetic reprogramming through the delivery of 24-nucleotide small RNAs that function in transcriptional gene silencing in recipient sink organs. Finally, we discuss important future research areas that could contribute to developing agricultural crops with engineered performance characteristics for enhance yield potential.
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Affiliation(s)
- Byung-Kook Ham
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
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206
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Zhou J, Fang H, Shan J, Gao X, Chen L, Xie C, Xie T, Liu J. A major QTL located on chromosome V associates with in vitro tuberization in a tetraploid potato population. Mol Genet Genomics 2014; 289:575-87. [PMID: 24619101 DOI: 10.1007/s00438-014-0832-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/19/2014] [Indexed: 11/24/2022]
Abstract
The cultivated potato (Solanum tuberosum L.) is an autotetraploid species. The complexity of tetrasomic inheritance and the lack of pure lines increase the difficulty of genetic analysis of the inherited characteristics. Tuberization is the determinant step for economic yield of potato. To understand the complex genetic basis of tuberization of the cultivated potato, we developed linkage maps for a tetraploid population (F1) of 237 genotypes and mapped QTLs for the percent of in vitro tuberized plantlets (% IVT). The paternal map for E108 (well tuberized) covered 948 cM and included 12 linkage groups, all of which contained all four homologous chromosomes. The maternal map for E20 (nontuberized) covered 1,286 cM and included 14 linkage groups, 12 of which contained all four homologous chromosomes. All 12 chromosomes of potato were tagged using the SSR markers. A major QTL (MT05) with additive effect was detected on chromosome V of E108 which explained 16.23 % of the variation for % IVT, and two minor QTLs (mt05 and mt09) displaying simplex dominant effects were located on chromosome V and chromosome IX of E20 which explained 5.33 and 4.59 % of the variation for % IVT, respectively. Based on the additive model of MT05, the segregation ratio of the gametic genotypes (Q-: qq = 5:1) matched the ratio of the tuberized genotypes to the nontuberized genotypes in the population suggesting that the segregation of in vitro tuberization in this population is controlled by a major-effect gene or genes. The mapping results of three important candidate genes indicated that the QTL causal genes detected in our study are new. In this study, we developed the almost complete linkage maps of a tetraploid population, identified a major QTL on chromosome V affecting in vitro tuberization, suggested a major-effect gene with minor modifiers model controlling this trait and found that the QTLs identified here correspond to new tuberization genes. Our work provides new and useful information about the genetic basis for tuberization of this autotetraploid crop.
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Affiliation(s)
- Jun Zhou
- National Center for Vegetable Improvement (Central China), Wuhan, China
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207
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Corrales AR, Nebauer SG, Carrillo L, Fernández-Nohales P, Marqués J, Renau-Morata B, Granell A, Pollmann S, Vicente-Carbajosa J, Molina RV, Medina J. Characterization of tomato Cycling Dof Factors reveals conserved and new functions in the control of flowering time and abiotic stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:995-1012. [PMID: 24399177 DOI: 10.1093/jxb/ert451] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA binding with One Finger (DOF) transcription factors are involved in multiple aspects of plant growth and development but their precise roles in abiotic stress tolerance are largely unknown. Here we report a group of five tomato DOF genes, homologous to Arabidopsis Cycling DOF Factors (CDFs), that function as transcriptional regulators involved in responses to drought and salt stress and flowering-time control in a gene-specific manner. SlCDF1-5 are nuclear proteins that display specific binding with different affinities to canonical DNA target sequences and present diverse transcriptional activation capacities in vivo. SlCDF1-5 genes exhibited distinct diurnal expression patterns and were differentially induced in response to osmotic, salt, heat, and low-temperature stresses. Arabidopsis plants overexpressing SlCDF1 or SlCDF3 showed increased drought and salt tolerance. In addition, the expression of various stress-responsive genes, such as COR15, RD29A, and RD10, were differentially activated in the overexpressing lines. Interestingly, overexpression in Arabidopsis of SlCDF3 but not SlCDF1 promotes late flowering through modulation of the expression of flowering control genes such as CO and FT. Overall, our data connect SlCDFs to undescribed functions related to abiotic stress tolerance and flowering time through the regulation of specific target genes and an increase in particular metabolites.
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Affiliation(s)
- Alba-Rocío Corrales
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus Montegancedo, Autopista M40 (km 38), 28223 Madrid, Spain
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208
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D'hoop BB, Keizer PLC, Paulo MJ, Visser RGF, van Eeuwijk FA, van Eck HJ. Identification of agronomically important QTL in tetraploid potato cultivars using a marker-trait association analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:731-48. [PMID: 24408376 DOI: 10.1007/s00122-013-2254-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 12/13/2013] [Indexed: 05/23/2023]
Abstract
Nineteen tuber quality traits in potato were phenotyped in 205 cultivars and 299 breeder clones. Association analysis using 3364 AFLP loci and 653 SSR-alleles identified QTL for these traits. Two association mapping panels were analysed for marker-trait associations to identify quantitative trait loci (QTL). The first panel comprised 205 historical and contemporary tetraploid potato cultivars that were phenotyped in field trials at two locations with two replicates (the academic panel). The second panel consisted of 299 potato cultivars and included recent breeds obtained from five Dutch potato breeding companies and reference cultivars (the industrial panel). Phenotypic data for the second panel were collected during subsequent clonal selection generations at the individual breeding companies. QTL were identified for 19 agro-morphological and quality traits. Two association mapping models were used: a baseline model without, and a more advanced model with correction for population structure and genetic relatedness. Correction for population structure and genetic relatedness was performed with a kinship matrix estimated from marker information. The detected QTL partly not only confirmed previous studies, e.g. for tuber shape and frying colour, but also new QTL were found like for after baking darkening and enzymatic browning. Pleiotropic effects could be discerned for several QTL.
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Affiliation(s)
- Björn B D'hoop
- Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
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209
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Hancock RD, Morris WL, Ducreux LJM, Morris JA, Usman M, Verrall SR, Fuller J, Simpson CG, Zhang R, Hedley PE, Taylor MA. Physiological, biochemical and molecular responses of the potato (Solanum tuberosum L.) plant to moderately elevated temperature. PLANT, CELL & ENVIRONMENT 2014; 37:439-50. [PMID: 23889235 DOI: 10.1111/pce.12168] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/25/2013] [Indexed: 05/18/2023]
Abstract
Although significant work has been undertaken regarding the response of model and crop plants to heat shock during the acclimatory phase, few studies have examined the steady-state response to the mild heat stress encountered in temperate agriculture. In the present work, we therefore exposed tuberizing potato plants to mildly elevated temperatures (30/20 °C, day/night) for up to 5 weeks and compared tuber yield, physiological and biochemical responses, and leaf and tuber metabolomes and transcriptomes with plants grown under optimal conditions (22/16 °C). Growth at elevated temperature reduced tuber yield despite an increase in net foliar photosynthesis. This was associated with major shifts in leaf and tuber metabolite profiles, a significant decrease in leaf glutathione redox state and decreased starch synthesis in tubers. Furthermore, growth at elevated temperature had a profound impact on leaf and tuber transcript expression with large numbers of transcripts displaying a rhythmic oscillation at the higher growth temperature. RT-PCR revealed perturbation in the expression of circadian clock transcripts including StSP6A, previously identified as a tuberization signal. Our data indicate that potato plants grown at moderately elevated temperatures do not exhibit classic symptoms of abiotic stress but that tuber development responds via a diversity of biochemical and molecular signals.
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Affiliation(s)
- Robert D Hancock
- Cellular and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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210
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Abelenda JA, Navarro C, Prat S. Flowering and tuberization: a tale of two nightshades. TRENDS IN PLANT SCIENCE 2014; 19:115-22. [PMID: 24139978 DOI: 10.1016/j.tplants.2013.09.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/13/2013] [Accepted: 09/18/2013] [Indexed: 05/27/2023]
Abstract
The concept of florigen, postulated in the early 1930s, has taken form after the identification of the FLOWERING LOCUS T (FT) protein as the flowering-inducing signal. Besides their role in flowering, FT genes were subsequently reported to play additional functions in other biological processes. This is particularly relevant in the nightshades, where the FT genes appear to have undergone considerable expansion at the functional level and gained a new role in the control of storage organ formation in potato (Solanum tuberosum). Neofunctionalization of FT homologs in the nightshades identifies these proteins as a new class of primary signaling components that modulate development and organogenesis in these agronomic relevant species.
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Affiliation(s)
- José A Abelenda
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CSIC) Campus de Cantoblanco, c/Darwin 3, 28049 Madrid, Spain
| | - Cristina Navarro
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CSIC) Campus de Cantoblanco, c/Darwin 3, 28049 Madrid, Spain
| | - Salomé Prat
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CSIC) Campus de Cantoblanco, c/Darwin 3, 28049 Madrid, Spain.
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211
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Golembeski GS, Kinmonth-Schultz HA, Song YH, Imaizumi T. Photoperiodic flowering regulation in Arabidopsis thaliana.. ADVANCES IN BOTANICAL RESEARCH 2014; 72:1-28. [PMID: 25684830 PMCID: PMC4326075 DOI: 10.1016/b978-0-12-417162-6.00001-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Photoperiod, or the duration of light in a given day, is a critical cue that flowering plants utilize to effectively assess seasonal information and coordinate their reproductive development in synchrony with the external environment. The use of the model plant, Arabidopsis thaliana, has greatly improved our understanding of the molecular mechanisms that determine how plants process and utilize photoperiodic information to coordinate a flowering response. This mechanism is typified by the transcriptional activation of FLOWERING LOCUS T (FT) gene by the transcription factor CONSTANS (CO) under inductive long-day conditions in Arabidopsis. FT protein then moves from the leaves to the shoot apex, where floral meristem development can be initiated. As a point of integration from a variety of environmental factors in the context of a larger system of regulatory pathways that affect flowering, the importance of photoreceptors and the circadian clock in CO regulation throughout the day has been a key feature of the photoperiodic flowering pathway. In addition to these established mechanisms, the recent discovery of a photosynthate derivative trehalose-6-phosphate as an activator of FT in leaves has interesting implications for the involvement of photosynthesis in the photoperiodic flowering response that were suggested from previous physiological experiments in flowering induction.
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Affiliation(s)
| | | | - Young Hun Song
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA 98195, USA
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212
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Sonnewald S, Sonnewald U. Regulation of potato tuber sprouting. PLANTA 2014; 239:27-38. [PMID: 24100410 DOI: 10.1007/s00425-013-1968-z] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/25/2013] [Indexed: 05/07/2023]
Abstract
Following tuber induction, potato tubers undergo a period of dormancy during which visible bud growth is inhibited. The length of the dormancy period is under environmental, physiological and hormonal control. Sucrose availability is one prerequisite for bud break. In the absence of sucrose, no bud break occurs. Thus, sucrose is likely to serve as nutrient and signal molecule at the same time. The mode of sucrose sensing is only vaguely understood, but most likely involves trehalose-6-phosphate and SnRK1 signalling networks. This conclusion is supported by the observation that ectopically manipulation of trehalose-6-phosphate levels influences the length of the dormancy period. Once physiological competence is achieved, sprouting is controlled by the level of phytohormones. Two phytohormones, ABA and ethylene, are supposed to suppress tuber sprouting; however, the exact role of ethylene remains to be elucidated. Cytokinins and gibberellins are required for bud break and sprout growth, respectively. The fifth classical phytohormone, auxin, seems to play a role in vascular development. During the dormancy period, buds are symplastically isolated, which changes during bud break. In parallel to the establishment of symplastic connectivity, vascular tissue develops below the growing bud most likely to support the outgrowing sprout with assimilates mobilised in parenchyma cells. Sprouting leads to major quality losses of stored potato tubers. Therefore, control of tuber sprouting is a major objective in potato breeding. Although comparative transcriptome analysis revealed a large number of genes differentially expressed in growing versus dormant buds, no master-regulator of potato tuber sprouting has been identified so far.
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Affiliation(s)
- Sophia Sonnewald
- Lehrstuhl für Biochemie, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstrasse 5, 91058, Erlangen, Germany,
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213
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The spectrum of mutations controlling complex traits and the genetics of fitness in plants. Curr Opin Genet Dev 2013; 23:665-71. [DOI: 10.1016/j.gde.2013.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 10/07/2013] [Accepted: 10/24/2013] [Indexed: 11/18/2022]
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214
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Draffehn AM, Li L, Krezdorn N, Ding J, Lübeck J, Strahwald J, Muktar MS, Walkemeier B, Rotter B, Gebhardt C. Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity. FRONTIERS IN PLANT SCIENCE 2013; 4:423. [PMID: 24294214 PMCID: PMC3827546 DOI: 10.3389/fpls.2013.00423] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/05/2013] [Indexed: 05/23/2023]
Abstract
Resistance to pathogens is essential for survival of wild and cultivated plants. Pathogen susceptibility causes major losses of crop yield and quality. Durable field resistance combined with high yield and other superior agronomic characters are therefore, important objectives in every crop breeding program. Precision and efficacy of resistance breeding can be enhanced by molecular diagnostic tools, which result from knowledge of the molecular basis of resistance and susceptibility. Breeding uses resistance conferred by single R genes and polygenic quantitative resistance. The latter is partial but considered more durable. Molecular mechanisms of plant pathogen interactions are elucidated mainly in experimental systems involving single R genes, whereas most genes important for quantitative resistance in crops like potato are unknown. Quantitative resistance of potato to Phytophthora infestans causing late blight is often compromised by late plant maturity, a negative agronomic character. Our objective was to identify candidate genes for quantitative resistance to late blight not compromised by late plant maturity. We used diagnostic DNA-markers to select plants with different field levels of maturity corrected resistance (MCR) to late blight and compared their leaf transcriptomes before and after infection with P. infestans using SuperSAGE (serial analysis of gene expression) technology and next generation sequencing. We identified 2034 transcripts up or down regulated upon infection, including a homolog of the kiwi fruit allergen kiwellin. 806 transcripts showed differential expression between groups of genotypes with contrasting MCR levels. The observed expression patterns suggest that MCR is in part controlled by differential transcript levels in uninfected plants. Functional annotation suggests that, besides biotic and abiotic stress responses, general cellular processes such as photosynthesis, protein biosynthesis, and degradation play a role in MCR.
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Affiliation(s)
- Astrid M. Draffehn
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Li Li
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Jia Ding
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Jens Lübeck
- Saka-Pflanzenzucht GmbH & Co. KGWindeby, Germany
| | | | - Meki S. Muktar
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Birgit Walkemeier
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Christiane Gebhardt
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
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215
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Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3-GENES GENOMES GENETICS 2013; 3:2031-47. [PMID: 24062527 PMCID: PMC3815063 DOI: 10.1534/g3.113.007153] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker−based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal “pseudomolecules”.
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Barrell PJ, Meiyalaghan S, Jacobs JME, Conner AJ. Applications of biotechnology and genomics in potato improvement. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:907-20. [PMID: 23924159 DOI: 10.1111/pbi.12099] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/12/2013] [Accepted: 06/16/2013] [Indexed: 05/12/2023]
Abstract
Potato is the third most important global food crop and the most widely grown noncereal crop. As a species highly amenable to cell culture, it has a long history of biotechnology applications for crop improvement. This review begins with a historical perspective on potato improvement using biotechnology encompassing pathogen elimination, wide hybridization, ploidy manipulation and applications of cell culture. We describe the past developments and new approaches for gene transfer to potato. Transformation is highly effective for adding single genes to existing elite potato clones with no, or minimal, disturbances to their genetic background and represents the only effective way to produce isogenic lines of specific genotypes/cultivars. This is virtually impossible via traditional breeding as, due to the high heterozygosity in the tetraploid potato genome, the genetic integrity of potato clones is lost upon sexual reproduction as a result of allele segregation. These genetic attributes have also provided challenges for the development of genetic maps and applications of molecular markers and genomics in potato breeding. Various molecular approaches used to characterize loci, (candidate) genes and alleles in potato, and associating phenotype with genotype are also described. The recent determination of the potato genome sequence has presented new opportunities for genomewide assays to provide tools for gene discovery and enabling the development of robustly unique marker haplotypes spanning QTL regions. The latter will be useful in introgression breeding and whole-genome approaches such as genomic selection to improve the efficiency of selecting elite clones and enhancing genetic gain over time.
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Affiliation(s)
- Philippa J Barrell
- The New Zealand Institute for Plant & Food Research Limited, Christchurch, New Zealand
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217
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Bolger ME, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer KFX. Plant genome sequencing - applications for crop improvement. Curr Opin Biotechnol 2013; 26:31-7. [PMID: 24679255 DOI: 10.1016/j.copbio.2013.08.019] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/24/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
It is over 10 years since the genome sequence of the first crop was published. Since then, the number of crop genomes sequenced each year has increased steadily. The amazing pace at which genome sequences are becoming available is largely due to the improvement in sequencing technologies both in terms of cost and speed. Modern sequencing technologies allow the sequencing of multiple cultivars of smaller crop genomes at a reasonable cost. Though many of the published genomes are considered incomplete, they nevertheless have proved a valuable tool to understand important crop traits such as fruit ripening, grain traits and flowering time adaptation.
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Affiliation(s)
- Marie E Bolger
- RWTH Aachen University, IBMG Institute for Botany and Molecular Genetics, Aachen, Germany
| | - Bernd Weisshaar
- CeBiTec, Department of Biology, Bielefeld University, Bielefeld, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland (OT) Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland (OT) Gatersleben, Germany
| | - Björn Usadel
- RWTH Aachen University, IBMG Institute for Botany and Molecular Genetics, Aachen, Germany; IBG-2: Plant Sciences, Institute for Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany.
| | - Klaus F X Mayer
- MIPS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
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218
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Noguero M, Atif RM, Ochatt S, Thompson RD. The role of the DNA-binding One Zinc Finger (DOF) transcription factor family in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 209:32-45. [PMID: 23759101 DOI: 10.1016/j.plantsci.2013.03.016] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 03/19/2013] [Accepted: 03/22/2013] [Indexed: 05/18/2023]
Abstract
The DOF (DNA-binding One Zinc Finger) family of transcription factors is involved in many fundamental processes in higher plants, including responses to light and phytohormones as well as roles in seed maturation and germination. DOF transcription factor genes are restricted in their distribution to plants, where they are in many copies in both gymnosperms and angiosperms and also present in lower plants such as the moss Physcomitrella patens and in the alga Chlamydomonas reinhardtii which possesses a single DOF gene. DOF transcription factors bind to their promoter targets at the consensus sequence AAAG. This binding depends upon the presence of the highly conserved DOF domain in the protein. Depending on the target gene, DOF factor binding may activate or repress transcription. DOF factors are expressed in most if not all tissues of higher plants, but frequently appear to be functionally redundant. Recent next-generation sequencing data provide a more comprehensive survey of the distribution of DOF sequence classes among plant species and within tissue types, and clues as to the evolution of functions assumed by this transcription factor family. DOFs do not appear to be implicated in the initial differentiation of the plant body plan into organs via the resolution of meristematic zones, in contrast to MADS-box and homeobox transcription factors, which are found in other non-plant eukaryotes, and this may reflect a more recent evolutionary origin.
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219
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220
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Uitdewilligen JGAML, Wolters AMA, D’hoop BB, Borm TJA, Visser RGF, van Eck HJ. A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One 2013; 8:e62355. [PMID: 23667470 PMCID: PMC3648547 DOI: 10.1371/journal.pone.0062355] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 03/20/2013] [Indexed: 11/23/2022] Open
Abstract
Assessment of genomic DNA sequence variation and genotype calling in autotetraploids implies the ability to distinguish among five possible alternative allele copy number states. This study demonstrates the accuracy of genotyping-by-sequencing (GBS) of a large collection of autotetraploid potato cultivars using next-generation sequencing. It is still costly to reach sufficient read depths on a genome wide scale, across the cultivated gene pool. Therefore, we enriched cultivar-specific DNA sequencing libraries using an in-solution hybridisation method (SureSelect). This complexity reduction allowed to confine our study to 807 target genes distributed across the genomes of 83 tetraploid cultivars and one reference (DM 1–3 511). Indexed sequencing libraries were paired-end sequenced in 7 pools of 12 samples using Illumina HiSeq2000. After filtering and processing the raw sequence data, 12.4 Gigabases of high-quality sequence data was obtained, which mapped to 2.1 Mb of the potato reference genome, with a median average read depth of 63× per cultivar. We detected 129,156 sequence variants and genotyped the allele copy number of each variant for every cultivar. In this cultivar panel a variant density of 1 SNP/24 bp in exons and 1 SNP/15 bp in introns was obtained. The average minor allele frequency (MAF) of a variant was 0.14. Potato germplasm displayed a large number of relatively rare variants and/or haplotypes, with 61% of the variants having a MAF below 0.05. A very high average nucleotide diversity (π = 0.0107) was observed. Nucleotide diversity varied among potato chromosomes. Several genes under selection were identified. Genotyping-by-sequencing results, with allele copy number estimates, were validated with a KASP genotyping assay. This validation showed that read depths of ∼60–80× can be used as a lower boundary for reliable assessment of allele copy number of sequence variants in autotetraploids. Genotypic data were associated with traits, and alleles strongly influencing maturity and flesh colour were identified.
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Affiliation(s)
- Jan G. A. M. L. Uitdewilligen
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
| | - Anne-Marie A. Wolters
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
| | - Bjorn B. D’hoop
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
| | - Theo J. A. Borm
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
| | - Richard G. F. Visser
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
| | - Herman J. van Eck
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
- * E-mail:
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221
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Suárez-López P. A critical appraisal of phloem-mobile signals involved in tuber induction. FRONTIERS IN PLANT SCIENCE 2013; 4:253. [PMID: 23882274 PMCID: PMC3712254 DOI: 10.3389/fpls.2013.00253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 07/23/2013] [Indexed: 05/04/2023]
Abstract
The identification of FLOWERING LOCUS T (FT) and several FT homologs as phloem-mobile proteins that regulate flowering has sparked the search for additional homologs involved in the long-distance regulation of other developmental processes. Given that flowering and tuber induction share regulatory pathways, the quest for long-distance tuberization signals has been further stimulated. Several tuberization regulators have been proposed as mobile molecules, including the FT family protein StSP6A, the plant growth regulators gibberellins and the microRNA miR172. Although some of these hypotheses are attractive and plausible, evidence that these molecules are transmissible in potato has yet to be obtained. Two mRNAs encoding transcription factors, StBEL5 and POTATO HOMEOBOX 1 (POTH1), are mobile and correlate with tuber induction. However, evidence that StBEL5 or POTH1 are required for tuberization is not available yet. Therefore, there are several good candidates for long-distance molecules in the tuberization process. Further research should test their role as systemic tuberization signals.
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Affiliation(s)
- Paula Suárez-López
- *Correspondence: Paula Suárez-López, Molecular Genetics Department, Centre for Research in Agricultural Genomics, CSIC - IRTA - UAB - UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain e-mail:
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222
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Olsen KM, Wendel JF. Crop plants as models for understanding plant adaptation and diversification. FRONTIERS IN PLANT SCIENCE 2013; 4:290. [PMID: 23914199 PMCID: PMC3729982 DOI: 10.3389/fpls.2013.00290] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/13/2013] [Indexed: 05/19/2023]
Abstract
Since the time of Darwin, biologists have understood the promise of crop plants and their wild relatives for providing insight into the mechanisms of phenotypic evolution. The intense selection imposed by our ancestors during plant domestication and subsequent crop improvement has generated remarkable transformations of plant phenotypes. Unlike evolution in natural settings, descendent and antecedent conditions for crop plants are often both extant, providing opportunities for direct comparisons through crossing and other experimental approaches. Moreover, since domestication has repeatedly generated a suite of "domestication syndrome" traits that are shared among crops, opportunities exist for gaining insight into the genetic and developmental mechanisms that underlie parallel adaptive evolution. Advances in our understanding of the genetic architecture of domestication-related traits have emerged from combining powerful molecular technologies with advanced experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies may be combined with high-throughput evaluations of the various "omics" involved in trait transformation, revealing a diversity of underlying causative mutations affecting phenotypes and their downstream propagation through biological networks. We summarize the state of our knowledge of the mutational spectrum that generates phenotypic novelty in domesticated plant species, and our current understanding of how domestication can reshape gene expression networks and emergent phenotypes. An exploration of traits that have been subject to similar selective pressures across crops (e.g., flowering time) suggests that a diversity of targeted genes and causative mutational changes can underlie parallel adaptation in the context of crop evolution.
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Affiliation(s)
- Kenneth M. Olsen
- Biology Department, Washington UniversitySt. Louis, MO, USA
- *Correspondence: Kenneth M. Olsen, Biology Department, Washington University, Campus Box 1137, St. Louis, MO 63130-4899, USA e-mail:
| | - Jonathan F. Wendel
- Ecology, Evolution, and Organismal Biology Department, Iowa State UniversityAmes, IA, USA
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