Merge pull request #5230 from solgenomics/topic/open_pollinated
[sgn.git] / cgi-bin / about / tomato_project / index.pl
blob6a773b96791eb03a2cfdfc794a44bdb49008fdf4
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;
7 <center>
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 />
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>
31 <h3>PROJECT SUMMARY</h3>
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>
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>
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>
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>
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>
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>
142 </td>
143 </tr>
144 </table>
146 </center>
147 END_HEREDOC
148 $page->footer();