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Fatiukha A, Deblieck M, Klymiuk V, Merchuk-Ovnat L, Peleg Z, Ordon F, Fahima T, Korol A, Saranga Y, Krugman T. Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat. Int J Mol Sci 2021; 22:ijms22041723. [PMID: 33572141 PMCID: PMC7915520 DOI: 10.3390/ijms22041723] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/12/2023] Open
Abstract
Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Mathieu Deblieck
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Lianne Merchuk-Ovnat
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Zvi Peleg
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Frank Ordon
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Yehoshua Saranga
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Correspondence: ; Tel.: +972-04-8240783
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Deblieck M, Fatiukha A, Grundman N, Merchuk-Ovnat L, Saranga Y, Krugman T, Pillen K, Serfling A, Makalowski W, Ordon F, Perovic D. GenoTypeMapper: graphical genotyping on genetic and sequence-based maps. Plant Methods 2020; 16:123. [PMID: 32944061 PMCID: PMC7488165 DOI: 10.1186/s13007-020-00665-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable. RESULTS We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time. CONCLUSIONS In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.
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Affiliation(s)
- Mathieu Deblieck
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Andrii Fatiukha
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Abba Khoushy Ave 199, 3498838 Haifa, Israel
| | - Norbert Grundman
- Faculty of Medicine, Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Niels-Stensen Strasse 14, 48149 Münster, Germany
| | - Lianne Merchuk-Ovnat
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel
| | - Yehoshua Saranga
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel
| | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Abba Khoushy Ave 199, 3498838 Haifa, Israel
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Department of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Wojciech Makalowski
- Faculty of Medicine, Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Niels-Stensen Strasse 14, 48149 Münster, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
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Merchuk-Ovnat L, Ovnat Z, Amir-Segev O, Kutsher Y, Saranga Y, Reuveni M. CoverageTool: A semi-automated graphic software: applications for plant phenotyping. Plant Methods 2019; 15:90. [PMID: 31404403 PMCID: PMC6683572 DOI: 10.1186/s13007-019-0472-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/26/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Characterization and quantification of visual plant traits is often limited to the use of tools and software that were developed to address a specific context, making them unsuitable for other applications. CoverageTool is flexible multi-purpose software capable of area calculation in cm2, as well as coverage area in percentages, suitable for a wide range of applications. RESULTS Here we present a novel, semi-automated and robust tool for detailed characterization of visual plant traits. We demonstrate and discuss the application of this tool to quantify a broad spectrum of plant phenotypes/traits such as: tissue culture parameters, ground surface covered by annual plant canopy, root and leaf projected surface area, and leaf senescence area ratio. The CoverageTool software provides easy to use functions to analyze images. While use of CoverageTool involves subjective operator color selections, applying them uniformly to full sets of samples makes it possible to provide quantitative comparison between test subjects. CONCLUSION The tool is simple and straightforward, yet suitable for the quantification of biological and environmental effects on a wide variety of visual plant traits. This tool has been very useful in quantifying different plant phenotypes in several recently published studies, and may be useful for many applications.
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Affiliation(s)
- Lianne Merchuk-Ovnat
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, P. O. Box 6, 5025001 Bet Dagan, Israel
| | | | - Orit Amir-Segev
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, P. O. Box 6, 5025001 Bet Dagan, Israel
| | - Yaarit Kutsher
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, P. O. Box 6, 5025001 Bet Dagan, Israel
| | - Yehoshua Saranga
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Moshe Reuveni
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, P. O. Box 6, 5025001 Bet Dagan, Israel
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Merchuk-Ovnat L, Silberman R, Laiba E, Maurer A, Pillen K, Faigenboim A, Fridman E. Genome scan identifies flowering-independent effects of barley HsDry2.2 locus on yield traits under water deficit. J Exp Bot 2018; 69:1765-1779. [PMID: 29365127 PMCID: PMC5888960 DOI: 10.1093/jxb/ery016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/09/2018] [Indexed: 05/02/2023]
Abstract
Increasing crop productivity under conditions of climate change requires the identification, selection, and utilization of novel alleles for breeding. In this study, we analysed the genotype and field phenotype of the barley HEB-25 multi-parent mapping population under well-watered and water-limited environments for two years. A genome-wide association study (GWAS) for genotype × environment interactions was performed for 10 traits including flowering time (heading time, HEA) and plant grain yield (PGY). Comparison of the GWAS for traits per se (i.e. regardless of the environment) with a study for quantitative trait loci (QTLs) × environment interactions (Q×E), indicates the prevalence of Q×E mostly for reproductive traits. One Q×E locus on chromosome 2, Hordeum spontaneum Dry2.2 (HsDry2.2), showed a positive and conditional effect on PGY and grain number (GN). The wild allele significantly reduced HEA; however, this earliness was not conditioned by water deficit. Furthermore, BC2F1 lines segregating for the HsDry2.2 locus showed that the wild allele conferred an advantage over the cultivated allele in PGY, GN, and harvest index, as well as modified shoot morphology, a longer grain-filling period, and reduced senescence (only under drought). This suggests the presence of an adaptation mechanism against water deficit rather than an escape mechanism. The study highlights the value of evaluating wild relatives in search of novel alleles and provides clues to resilience mechanisms underlying crop adaptations to abiotic stress.
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Affiliation(s)
- Lianne Merchuk-Ovnat
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Roi Silberman
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
- The Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot Israel
| | - Efrat Laiba
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Adi Faigenboim
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Eyal Fridman
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
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Merchuk-Ovnat L, Fahima T, Ephrath JE, Krugman T, Saranga Y. Ancestral QTL Alleles from Wild Emmer Wheat Enhance Root Development under Drought in Modern Wheat. Front Plant Sci 2017; 8:703. [PMID: 28536586 PMCID: PMC5422550 DOI: 10.3389/fpls.2017.00703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/18/2017] [Indexed: 05/17/2023]
Abstract
A near-isogenic line (NIL-7A-B-2), introgressed with a quantitative trait locus (QTL) on chromosome 7AS from wild emmer wheat (Triticum turgidum ssp. dicoccoides) into the background of bread wheat (T. aestivum L.) cv. BarNir, was recently developed and studied in our lab. NIL-7A-B-2 exhibited better productivity and photosynthetic capacity than its recurrent parent across a range of environments. Here we tested the hypothesis that root-system modifications play a major role in NIL-7A-B-2's agronomical superiority. Root-system architecture (dry matter and projected surface area) and shoot parameters of NIL-7A-B-2 and 'BarNir' were evaluated at 40, 62, and 82 days after planting (DAP) in a sand-tube experiment, and root tip number was assessed in a 'cigar-roll' seedling experiment, both under well-watered and water-limited (WL) treatments. At 82 DAP, under WL treatment, NIL-7A-B-2 presented greater investment in deep roots (depth 40-100 cm) than 'BarNir,' with the most pronounced effect recorded in the 60-80 cm soil depth (60 and 40% increase for root dry matter and surface area, respectively). NIL-7A-B-2 had significantly higher root-tip numbers (∼48%) per plant than 'BarNir' under both treatments. These results suggest that the introgression of 7AS QTL from wild emmer wheat induced a deeper root system under progressive water stress, which may enhance abiotic stress resistance and productivity of domesticated wheat.
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Affiliation(s)
- Lianne Merchuk-Ovnat
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of JerusalemRehovot, Israel
| | - Tzion Fahima
- Institute of Evolution, University of HaifaHaifa, Israel
| | - Jhonathan E. Ephrath
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevBeersheba, Israel
| | - Tamar Krugman
- Institute of Evolution, University of HaifaHaifa, Israel
| | - Yehoshua Saranga
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of JerusalemRehovot, Israel
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Merchuk-Ovnat L, Fahima T, Krugman T, Saranga Y. Ancestral QTL alleles from wild emmer wheat improve grain yield, biomass and photosynthesis across enviroinments in modern wheat. Plant Sci 2016; 251:23-34. [PMID: 27593460 DOI: 10.1016/j.plantsci.2016.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/04/2016] [Accepted: 05/05/2016] [Indexed: 05/18/2023]
Abstract
Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving drought resistance in domesticated wheat. Nevertheless, wild germplasm has not been widely used in wheat breeding for abiotic stress resilience. In the current study, a near isogenic line NIL-7A-B-2, introgressed with a drought-related QTL from wild emmer wheat on chromosome 7A, and its recurrent parent, bread wheat cv. BarNir, were investigated under four environments across 2 years-water-limited and well-watered conditions in a rain-protected screen-house (Year 1) and two commercial open field plots under ample precipitation (Year 2). NIL-7A-B-2 exhibited an advantage over BarNir in grain yield and biomass production under most environments. Further physiological analyses suggested that enhanced photosynthetic capacity and photochemistry combined with higher flag leaf area are among the factors underlying the improved productivity of NIL-7A-B-2. These were coupled with improved sink capacity in NIL-7A-B-2, manifested by greater yield components than its parental line. This study provides further support for our previous findings that introgression of wild emmer QTL alleles, using marker assisted selection, can enhance grain yield and biomass production across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of yield and drought resistance.
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Affiliation(s)
- Lianne Merchuk-Ovnat
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Yehoshua Saranga
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel.
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Merchuk-Ovnat L, Barak V, Fahima T, Ordon F, Lidzbarsky GA, Krugman T, Saranga Y. Ancestral QTL Alleles from Wild Emmer Wheat Improve Drought Resistance and Productivity in Modern Wheat Cultivars. Front Plant Sci 2016; 7:452. [PMID: 27148287 PMCID: PMC4832586 DOI: 10.3389/fpls.2016.00452] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/22/2016] [Indexed: 05/21/2023]
Abstract
Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs) from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum) and bread (T. aestivum) wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4) were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690-710 mm) and water-limited (290-320 mm) conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS), and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS). In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass-specifically under drought (7AS QTL in cv. Bar Nir background), under both treatments (2BS QTL), and a greater stability across treatments (1BL QTL). The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance.
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Affiliation(s)
- Lianne Merchuk-Ovnat
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Vered Barak
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Tzion Fahima
- Institute of Evolution and Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Institute for Resistance Research and Stress ToleranceQuedlinburg, Germany
| | - Gabriel A. Lidzbarsky
- Institute of Evolution and Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Tamar Krugman
- Institute of Evolution and Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Yehoshua Saranga
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
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