cgi-bin/about/tomato_project/index.pl

   1 use strict;
   2 use CXGN::Page;
   3 my $page=CXGN::Page->new('index.html','html2pl converter');
   4 $page->header('NSF_SPONSORED TOMATO GENOMICS PROJECT');
   5 print<<END_HEREDOC;
   6
   7 <center>
   8
   9
  10 <table summary="" width="720" align="center">
  11 <tr>
  12 <td>
  13 <center>
  14 <h2>Welcome to the NSF-Funded Tomato Genomics Project</h2>
  15 <a href=
  16 "https://www.fastlane.nsf.gov/servlet/showaward?award=0116076">NSF
  17 #0116076</a></center><br />
  18
  19 <p>Welcome to the information pages for the Tomato Genomics Project
  20 (#0116076). This project is funded by the <a href=
  21 "http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5338">National Science
  22 Foundation Plant Genome Research Program</a>.
  23 The purpose of these pages is to provide information on the goals
  24 of the project, the P.I's involved in the project and public
  25 resources developed as part of this project. If you have
  26 suggestions/comments about this site or the Tomato Genomics Project
  27 please e-mail <a href=
  28 "mailto:sdt4\@cornell.edu">Steve Tanklsley</a>. For more details,
  29 click on any of the topics below.</p>
  30
  31 <h3>PROJECT SUMMARY</h3>
  32
  33 <p>This project is the continuation and expansion of our previous tomato genome project <a href=
  34 "nsf_9872617/index.pl">(NSF#9872617)</a> with an emphasis on physical, evolutionary and
  35 functional genomics of the Solanaceae. In the first part of the
  36 project a physical map, comprised of a set of overlapping BAC
  37 clones, is being constructed for the tomato genome and anchored
  38 against the genetic maps of tomato, other solanaceous species, and
  39 the arabidopsis genome. This will be accomplished by using a set of
  40 1000 conserved ortholog (COS) markers shared between the
  41 arabidopsis and solanaceous genomes. The anchored BAC physical map
  42 will: 1) facilitate positional cloning; 2) elucidate the
  43 organization/distribution of genes with respect to centromeres,
  44 heterchromatin, euchromatin and meiotic recombination; 3) provide a
  45 new method for precise mapping; 4) provide the foundation and clone
  46 resource for eventual tomato genome sequencing; and 5) shed light
  47 on the nature of genome evolution in higher plants and help
  48 establish a syntenic network though which genomic information can
  49 be shared and compared among plants. To further investigate genome
  50 organization and to determine the level of microsynteny among the
  51 Solanaceae, a set of orthologous BAC clones from solanaceous
  52 species will be sequenced and compared with each other and to
  53 corresponding portions of the arabidopsis genome.</p>
  54
  55 <p>In the second part of the project, we apply two virus-induced
  56 gene-silencing (VIGS) approaches as a means of associating gene
  57 sequence with function. We continue to focus on defense responses
  58 and fruit development - processes for which tomato is an excellent
  59 model. In the first approach, we are developing a normalized,
  60 elicitor-induced cDNA library of Nicotiana benthamiana in a potato
  61 virus X (PVX) vector and use it for VIGS of orthologs to a set of
  62 differentially-expressed tomato genes and also a set of 5,000
  63 random genes. The plants so derived are screened for a variety of
  64 defense responses including alterations in ethylene-regulated
  65 phenotypes. In the second approach, we will use PVX constructs to
  66 develop stable tomato transformants. These lines will contain
  67 promising defense and ethylene response genes from the transient
  68 VIGS analysis as well as genes specifically implicated in fruit
  69 development/ripening. Results from these studies will provide new
  70 information on the feasibility of large scale gene silencing for
  71 tomato functional genomics and will result in the targeted
  72 development of a comprehensive set of heritable gene repression
  73 lines focused on two biological processes for which tomato is an
  74 optimal model.</p>
  75
  76 <p>Finally, we are developing and distributing new resources for
  77 genetic/genomic research in solanaceous species, including: 1) a
  78 tomato non-redundant unigene set; 2) tomato cDNA microarrays; 3)
  79 DNA, plantlets, and associated data sets from an F2 synteny mapping
  80 population and seeds from a permanent RI mapping population; 4) 200
  81 stable gene silenced tomato lines, 5) VIGs libraries (for transient
  82 silencing); 6) set of tiled tomato BAC clones; and 7) new
  83 solanaceous BAC libraries. To facilitate distribution of genomic
  84 information for tomato in particular and for solanaceous species in
  85 a comparative genomic context, we continue development of the
  86 Solanaceae Genome Network database - a genomics database that ties
  87 together information on sequence and genetic/physical maps among
  88 solanaceous species and anchors this information against the
  89 arabidopsis genome sequence. We will also develop a tomato gene
  90 expression profiling database to curate and deliver cDNA microarray
  91 data to the research public.</p>
  92
  93 <p>Implementation of this comprehensive tomato genomics project
  94 will result in development of additional functional and structural
  95 genomics tools built upon those developed in our previous proposal
  96 and with extended applicability from tomato to the broader
  97 Solanaceae. Functional genomics applications and the resulting
  98 public databases will allow us and others to expand knowledge in
  99 the areas of defense response, fruit development and genome
 100 evolution.</p>
 101
 102 <h3>PRINCIPAL INVESTIGATORS</h3>
 103 <table summary="">
 104 <tr>
 105 <td width="100"><u>Project P.I.s</u></td>
 106 <td width="150"><u>Contact</u></td>
 107 <td><u>Organization</u></td>
 108 </tr>
 109 <tr>
 110 <td>S. Tanksley</td>
 111 <td><a href="mailto:sdt4\@cornell.edu">sdt4\@cornell.edu</a></td>
 112 <td>Cornell University</td>
 113 </tr>
 114 <tr>
 115 <td>J. Giovannoni</td>
 116 <td><a href="mailto:jjg33\@cornell.edu">jjg33\@cornell.edu</a></td>
 117 <td>Texas A&amp;M</td>
 118 </tr>
 119 <tr>
 120 <td>G. Martin</td>
 121 <td><a href="mailto:gbm7\@cornell.edu">gbm7\@cornell.edu</a></td>
 122 <td>Boyce Thompson Institute for Plant Research (BTI)</td>
 123 </tr>
 124 <tr>
 125 <td>R. Wing</td>
 126 <td><a href=
 127 "mailto:rwing\@ag.arizona.edu">rwing\@ag.arizona.edu</a></td>
 128 <td>Arizona Genome Initiative</td>
 129 </tr>
 130 </table>
 131
 132 <div style="text-align:left; float:left">
 133 <h3>MEMBERS OF ADVISORY GROUP</h3>
 134 Harry Klee, U. Florida, chair<br />
 135 Sue Rhee, Carnegie Institution of Washington<br />
 136 Dani Zamir, Hebrew U., Israel<br />
 137 Danesh Kumar, Yale U.<br /></div>
 138 <div style="text-align:center; float: right;"><img src=
 139 "/documents/help/about/tomato_project/nsf-logo3.gif" width="91" height="100" border="0" alt="" /></div>
 140 <div style="clear: both"></div>
 141
 142 </td>
 143 </tr>
 144 </table>
 145
 146 </center>
 147 END_HEREDOC
 148 $page->footer();