Progress 10/01/07 to 09/30/08
Outputs
OUTPUTS: Plant domestication represents an accelerated form of evolution, resulting in exaggerated changes in the tissues/organs of greatest interest to humans (e.g. seeds, roots, tubers). One of the most extreme cases has been the evolution of tomato fruit. Cultivated tomatoes produce fruit as much as 1000 times larger than their wild progenitors. Quantitative trait mapping studies have shown that a relatively small number of genes were involved in this dramatic transition; these genes control two processes: 1) cell cycle and 2) organ number determination. The key gene in the first process has been isolated and corresponds to fw2.2, a negative regulator of cell division. However, until now, nothing was known about the molecular basis of the second process. We have now shown that the second major step toward in the evolution of extreme fruit size was due to regulatory change of a YABBY-like transcription factor (fasciated) that controls carpel number during flower/fruit development. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
This research may help reconstruct events involved in the domestication of tomato and other fruit bearing crop species. Understanding the molecular and developmental basis of natural variation (especially quantitative traits) will aid both in breeding and in potential biotechnology approaches for crop improvement. Results from this project will also shed light on the nature and molecular basis of quantitative trait variation. Finally, we have cloned and identified the cause of two major evolutionary/domestication events in tomato - development of multiple carpels toward extreme fruit size and stigma exsertion (which controls mating system). This work thus has implications for breeding/genetic engineering for fruit size/yield and alternation of mating systems - potentially of use in developing hybrid crops.
Publications
- Cong B, Barerro L, Tanksley (2008) Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nature Genetics 40:800-804.
- Grandillo S, Tanksley S, Zamir D (2008) Exploitation of Natural Biodiversity Through Genomics. In: Genome Assisted Crop Improvement, R Varshney, R Tuberosa (eds). pp 122-149.
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Progress 01/01/07 to 12/31/07
Outputs
Fruit size/shape and stigma exsertion are traits that underwent major modification during the evolution and domestication of tomato. All are quantitatively inherited and have been difficult to approach with the tools of molecular biology. The long term goals of this project was to identify, isolate and understand the molecular bases of the key loci underlying fruit size/shape and stigma exsertion variation in tomato. Specific findings are listed below: A change in the position of the pollen-bearing anthers relative to the stigmatic surface of the pistil is commonly associated with the evolution of autogamy. Most wild tomato species are allogamous and bear flowers with highly exserted stigmas . We cloned Style2.1, the major quantitative trait locus (QTL) responsible for a key floral attribute (style length) associated with the evolution of self-pollination in cultivated tomatoes. The gene encodes a putative transcription factor that regulates cell elongation in
developing styles. The transition from cross-pollination to self-pollination was accompanied, not by a change in the STYLE2.1 protein, but rather by a mutation in the Style2.1 promoter that results in a down regulation of Style2.1 expression during flower development. Fruit size is a quantitative trait, and QTL mapping studies have shown a relatively small number of genes were involved in this dramatic transition and can be traced to changes in two processes: 1) cell cycle control 2) organ pattern control. We have cloned the first QTL in the second process. We show was due to regulatory change of a Yabby-like transcription factor (fasciated) that controls carpel number during flower/fruit development.
Impacts
This research may help reconstruct events involved in the domestication of tomato and other fruit bearing crop species. Understanding the molecular and developmental basis of natural variation (especially quantitative traits) will aid both in breeding and in potential biotechnology approaches for crop improvement. Results from this project will also shed light on the nature and molecular basis of quantitative trait variation. Finally, we have cloned and identified the cause of two major evolutionary/domestication events in tomato - development of multiple carpels toward extreme fruit size and stigma exsertion (which controls mating system). This work thus has implications for breeding/genetic engineering for fruit size/yield and alternation of mating systems - potentially of use in developing hybrid crops.
Publications
- Tanksley S., Fulton T. 2007. Dissecting quantitative trait variation - examples from the tomato. Euphytica 145: 365-370
- Chen K, Cong B, Wing R, Vrebalov J, Tanksley S. 2007. Regulatory Mutation in a Cell Elongation Transcription Factor Responsible for the Evolution of Autogamy in Cultivated Tomatoes. Science 318, 643
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Progress 01/01/06 to 12/31/06
Outputs
Fruit size and shape are two major factors determining yield, quality and consumer acceptability in many crops. Both are quantitatively inherited and have been difficult to approach with the tools of molecular biology. The long term goals of this project was to identify, isolate and understand the molecular bases of the key loci underlying size and shape variation of tomato fruit. Specific findings are listed below: FW2.2: Fw2.2 is a major QTL controlling fruit size in tomato. Results from this project indicate that that fw2.2 alleles modulate fruit size through changes in gene regulation (timing and level of expression) rather than changes in the FW2.2 protein itself. Results also indicate that the effect of fw2.2 on fruit mass is mediated by repressing cell division in placental and pericarp tissues, respectively. FW2.2 does not share sequence homology to any protein of known function. Results from two-hybrid screens and binding assays provide strong evidence that
FW2.2 physically interacts at or near the cell membrane with the regulatory (beta) subunit of a CKII kinase. CKII kinases are well-studied in both yeast and animals where they form part of cell cycle related signaling pathway. These results provide a possible glimpse into how ancient and conserved regulatory processes can be co-opted in the evolution of novel organs such as fruit. FASCIATED: Mutation(s) at the fasciated locus was key steps in the production of extreme fruit size during the domestication of tomato. A developmental indicate that the fasciated gene directly affects floral meristem size and is expressed prior to even the earliest stages of flower organogenesis. As a result, mature fruit of fasciated mutants have more carpels (locules), a greater fruit diameter and increased fruit mass. The discovery that fasciated affects the size of the floral meristem led to a search for candidate genes from Arabidopsis known to be involved in floral meristem development. Surprisingly,
none mapped to the fasciated locus. However, orthologs of WUS, WIG, and STM map to the locule number locus on chromosome 2, with WUS showing this highest association with locule number. To isolate the fascinated gene, a BAC contig, spanning the fascinated gene, was sequenced and high resolution mapping used to narrow the interval to a few candidate genes. This top candidate gene has now been put into transformation for complementation testing. Preliminary results suggest that this gene is the fascinated gene - a result that will be verified by T1 progeny testing and RNA analysis.
Impacts
Results from this project shed light on the nature and molecular basis of quantitative trait variation and contribute to a critical, but largely unexplored aspect of plant development: how ovaries are transformed from small reproductive organs into the large, conspicuous fruit that display the array of shapes and sizes that we associate with modern agriculture. In addition, this research may help reconstruct events involved in the domestication of tomato and other fruit bearing crop species. Understanding the molecular and developmental basis of natural variation (especially quantitative traits) will aid both in breeding and in potential biotechnology approaches for crop improvement. This is especially true, since most of the key traits (e.g. yield, stress resistance, etc) are quantitatively inherited. Little is currently know about the molecular and developmental bases of natural/quantitative variation. The results accomplished during this project makes a substantial
contribution to this emerging and important area of study.
Publications
- Barrero L.S., B. Cong, F. Wu, and S.D. Tanksley. 2006. Developmental characterization of the fasciated locus and mapping of Arabidopsis candidate genes involved in the control of floral meristem size and carpel number in tomato. Genome 49:991-1006
- Cong B. and Tanksley S.D. 2006. FW2.2 and cell cycle control in developing tomato fruit: a possible example of gene co-option in the evolution of a novel organ. Plant Mole Biol 62:867-880
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Progress 01/01/05 to 12/31/05
Outputs
The identification and validation of orthologous genes across diverse taxa is a key enabler of studies in comparative genome mapping, molecular systematics and gene evolution/diversification. However, with few exceptions, an insufficient number of bona fide orthologous gene sets have been identified for most taxa. Using the euasterid clade of flowering plants (which comprises nearly one-quarter of all flowering plants) , we report herein the development and application of a set of algorithms to identify 2869 single copy, conserved orthologs (COSII) common to most, if not all, euasterid species as well as the model species Arabidopsis. Moreover, alignment of orthologs across multiple euasterid species enabled the design of Universal PCR Primers which can be used to amplify the corresponding orthologous sequences from a broad range of taxa. Functional annotation revealed that the orthologs thus identified encode a higher-than-expected frequency of proteins transported
and utilized in organelles, and a paucity of proteins associated with cell walls, proteins kinases, transcription factors, and signal transduction. The utility of this large set of orthologs is demonstrated for both phylogenetic studies (across distantly as well as closely related taxa) and in the generation of comparative maps across taxa such as divergent as tomato and coffee.
Impacts
We have demonstrated an approach for utilizing partial sequence datasets (in this case EST-derived unigenes sets) to identify and validate large numbers of high quality orthologous genes across related taxa - including taxa that span multiple plant families. This approach has been used to identify 2869 such orthologs (termed COSII genes) in species belong to the euasterid I clade of higher plants, which includes such important crop species as tomato, potato, eggplant, pepper, Petunia, tobacco, sweet potato, olives, mints, sesame and coffee. Further, we demonstrate that alignment of orthologous sequences can be used to design Universal Primers which can be used to amplify the same ortholog from many related plant species, including those for which no sequence data are currently available. Finally, we demonstrate the utility of COSII markers and Universal Primers in phylogenetic studies (both among closely related taxa and more distant taxa spanning multiple plant
families) and in comparative (synteny) mapping for species that span across plant families (e.g. tomato versus coffee). These COSII genes should thus go along ways toward uniting the genomics and biology of this large and important clade of flowering plants. The algorithms used to identify and validate this large set of orthologs may also prove useful for similar applications in other taxonomic clades where partial sequence datasets are available.
Publications
- No publications reported this period
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Progress 01/01/04 to 12/31/04
Outputs
COSII Markers for Comparative Mapping and Molecular Breeding. We have taken advantage of new or enlarged sequence databases for species in the family Solanaceae and Rubiaceae, along with a new set of algorithms, to derive a new set of more robust COS (Conserved Ortholog Set) genes whose orthology is supported by both sequence similarity and phylogenetics. Each of the approximately 1500 COSII ortholog sets has a clear, single copy gene match in the Arabidopsis genome, providing a direct connection with this important model plant and opening the possibility of identifying additional ortholog members in other dicot species. These new COS genes have been selected in such a way that 'Universal Primers' could be designed which amplify both exonic and intronic regions in most, if not all, solanaceous species and related taxa in the Asterid I clade of dicot plant species, making them useful to a wider segment of the plant science community. Development of a set of PCR-based
anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments. Tomato and potato EST sequences contained in the Solanaceae Genomics Network (SGN) database were screened for simple sequence repeat (SSR) motifs. A total of 609 SSRs were identified and assayed on S. lycopersicum LA925 (formerly L. esculentum) and S. pennellii LA716 (formerly L. pennellii). SSRs that did not amplify, gave multiple band products, or did not exhibit a polymorphism that could be readily detected on standard agarose gels in either of these species were eliminated. A set of 76 SSRs meeting these criteria was then placed on the S. lycopersicum (LA925) x S. pennellii (LA716) high density map. To provide complete coverage of the genome at intervals not greater than 34 cM, a set of 76 selected cleaved amplified polymorphism (CAP) markers was also developed and mapped onto the same population. These 152 PCR-based anchor markers are uniformly distributed and
encompass 95 percent of the genome with an average spacing of 10.0 cM. Moreover, the markers are embedded within a high-density map containing 1,500 markers (map can be found at http://www.sgn.cornell.edu). These PCR-based markers were further used to characterize S. pennellii introgression lines (Eshed and Zamir 1995) and should prove helpful in utilizing these stocks for high resolution mapping experiments. The majority of these anchor markers also exhibit polymorphism between S. lycopersicum and two wild species commonly used as parents for mapping experiments, S. pimpinellifolium (formerly L. pimpinellifolium) and S. habrochaites (formerly L. hirsutum), indicating that they will be useful for mapping in other interspecific populations.
Impacts
The COSII genes have the following properties, multiple, independent tests support their classification as true orthologs, occurring as single genes in Arabidopsis and other plant databases tested, making them more useful in searching other plant genomes for additional orthologs. Universal COSII Primers have been designed and tested and can be used to PCR-amplify corresponding orthologs from other related Asterid I plant species, including those for which no sequence data is available. These new COSII markers and universal primers should expedite molecular breeding research in all Solanaceae (tomato, potato, pepper, eggplant, petunia) and Rubiaceae (coffee) species leading to unification of synteny maps for these and other species in the Asterid clade of higher plants. The PCR-based map of tomato described above is comprised of a set of PCR-anchor markers, based on SSRs and CAPs, covering the entire tomato genome at regular intervals and can be readily analyzed on
standard agarose gels. This resource will be valuable for those wishing to map genes quickly, easily and cheaply. The map is anchored in a high-density map containing more than 1,500 markers, identification of markers for fine mapping is also facilitated. We've surveyed 109 EST derived SSRs for polymorphism in cultivated tomato and other species in the genus Solanum. The results indicate many of the loci will be useful for mapping in wild species-derived populations, suggesting the markers may also be appropriate for germplasm fingerprinting/identification, studies of species relationships, taxonomy and breeding.
Publications
- van der Knaap, E., Sanyal, A. Jackson, S.A. S.D. Tanksley. 2004. High-Resolution FineMapping and FISH analysis of sun a Locus Controlling Tomato Fruit Shape, Reveals a Region of the Tomato Genome Prone to DNA Rearrangements. Genetics In press
- Chen, Kai-Yi, Tanksley, S. D. 2004. High Resolution Mapping and Functional Analysis of se2.1: a Major Stigma Exsertion QTL Associated with the Evolution from Allogamy to Autogamy in the Genus Lycopersicon. Genetics In press
- Barrero L.S., and S. D. Tanksley. 2004. Evaluating the Genetic Basis of Multiple-locule Fruit ina Broad Cross Section of Tomato Cultivars. Theor Appl Genet 109: 669-679
- Frary, Amy, Fritz, Lisa A., and S. D. Tanksley. 2004. A Comparative Study of the Genetic Bases of Natural Variation in Morphology of Tomato Leaves, Sepals, and Petals. Theor Appl Genet 109: 523-533
- Frary, A., T. M. Fulton, D. Zamir, S. D. Tanksley. 2004. Advanced Backcross QTL Analysis of a Lycopersicon Esculentum x L. Pennellii Cross and Identification of Possible Orthologs in the Solanaceae. Theor Appl Genet 108, no. 3: 485
- Tanksley, S. D. Supplement 2004. The Genetic, Developmental and Molecular Bases of Fruit Size and Shape Variation in Tomato. Plant Cell Special Issue 16: S181-S189
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Progress 01/01/02 to 12/31/02
Outputs
We have identified more than 150 QTLs , most coming from wild tomato species. These QTLs control a variety of traits including yield and fruit quality. A number of these QTLs have been transferred into elite processing varieties and shown to improve the performance. These new experimental hybrids are now being evaluated. We have also cloned two QTLs (fw2.2 and ovate) controlling fruit size and shape.
Impacts
(N/A)
Publications
- No publications reported this period
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