Maps Online

A number of the aforementioned maps are available on the internet at SGN (Mueller etal. 2005a), National Center for Biotechnology Information (NCBI) (Wheeler et al. 2004), and http://www.tomatomap.net (Van Deynze et al. 2006) (Tables 5-7).

The process of preparing genetic maps for display in the NCBI MapViewer includes populating the MapViewer database with ancillary information associated with the locus. This information includes the probe name, any GenBank accession(s) known, the UniSTS accession(s) for primers and the Entrez Gene id. This information is used to effect traversal of the databases within NCBI. Text searches of the data associated with loci can be performed. In addition to the search capability offered at the top of the homepage for MapViewer, http://www.ncbi.nlm.nih.gov/mapview, (encompassed by the large rectangle in upper right quadrant of Fig. 3) there are two indirect entry points - the link to PlantCentral http://www.ncbi.nlm.nih.gov/ genomes/PLANTS/PlantList.html (encompassed by the rectangle in upper left quadrant of Fig. 3) or the link at the top of the plant list on the MapViewer home page (encompassed by the small rectangle in upper right quadrant of Fig. 3).

Proceeding via the indirect entry points (depicted by following the dashed lines) generates the query page - shown in the lower left quadrant of Fig. 3. Within the querypage the query text ("TG128" in this example) is entered in the space outlined by a rectangle. Clicking the button encompassed by an ellipse generates the page in the lower right quadrant. Using the search capability on MapViewer is accomplished by adjusting the organisms at the arrow within the large rectangle, and entering the sought text in the box followed by clicking the "Go" button. The result is the lower right quadrant. Regardless of how one arrives at the lower right quadrant, clicking the "Display" button outlined by a rectangle generates Fig. 4.

The GenBank accession(s) associated with a locus are available for BLAST search. There are two indirect entry points - the link in PlantCentral http://www. ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html or the link at the top of the plant list on the MapViewer home page. Both of these are also included within the outlined areas in the top two quadrants of Fig. 3. As of this writing the nucleotide sequence for TG128

Table 7. "Other" maps listed by type, cultivar if known, number of plants, lines, or genome coverage. The number of components in the resource are indicated, and correspondence to genetic maps from populations in Table 6, if known

Map type

S. lycopersicum Cultivar

Lines or (coverage :■:)

Items

Correspondence to genetic maps

Linkage group

Online

Reference

Cytogenetic

1. Irradiated Red Cherry

naa

74 deficiencies

35 Morph, Resist

all

Khush and Rick 1968a, 1968b

Cytological

2. "Cherry"

1

9,058 Recombination Nodules

na

all

Sherman and Stack 1995

Cytogenetic

3. "Cherry"

1

3 multicopy genes

rDNA, TGR1, THG2

all

Zhong et al. 1996

Cytogenetic

4. Moneymaker

1

2 YACs

CT277 (pop 8)

2

Fuchs et al. 1996

Cytogenetic

5. "Cherry"

1

3 clones

TG46, TG400, TG523 (pop 8)

11

Peterson et al. 1999

Cytogenetic

6. VFNT Cherry

1

11 BACs

CAPS, RFLP (pop 10)

2, 4, 7, 8, 9, 10, 11 all

SGN

Wang et al. 2006

Cytogenetic

7. na

na

63 BACs

COS, overgo (pop 10)

SGN

"Tomato FISH map" SGN, 2007

Physical

8. Heinz 1706

(15::)

129,024 clones

BAC-end sequence, RFLP

all

SGN

Budiman et al. 2000

T-DNA insert

9. Moneymaker

529

140 inserts

PCR/CAPS (pop 9)

all

Gidoni et al. 2003

a not available a not available

Fig. 3. Navigating to Genetic Maps at NCBI. This illustrates the link-mediated flow through NCBI web pages to perform text searches of plant genetic map information. Following the "search" link in either rectangle-outlined areas in the top two quadrants generates the lower left quadrant. The query text (in this example "TG128") is entered in the space outlined by a rectangle in the lower left quadrant. The lower right quadrant is generated by both black arrows. Clicking the "Display" button in the lower right quadrant generates Fig. 4

Fig. 3. Navigating to Genetic Maps at NCBI. This illustrates the link-mediated flow through NCBI web pages to perform text searches of plant genetic map information. Following the "search" link in either rectangle-outlined areas in the top two quadrants generates the lower left quadrant. The query text (in this example "TG128") is entered in the space outlined by a rectangle in the lower left quadrant. The lower right quadrant is generated by both black arrows. Clicking the "Display" button in the lower right quadrant generates Fig. 4

NCBI

4CBI Map Viewer

S QL DE - MAP VIEW_ QA:M>pUiew Cas« ara, MVMeta seni ke=mapiriewnitt&_qa(qa J, EhtKn=Map'ViewB'±re3_Q A

PubMed

Bit

rez BLAST

□Ml M Tai orio my Structure 1

1 Search.

r

Find | Find in This View 1

BLAST The Plant Cfeiunns

Map Viewer Home Map Vi&irtier Help

Data As Table View

Maps & Options

Compress Map . Region Shown;

You are here:

You are here:

S.peruuianun Chr 7 Lper_94

Plant Genomes Comparative Map View

Query TG128 |"cleail

Master Map: Lper_94 (S.peruvianum, chr 7)

5uimriary of Maps

BLAST The Plant Cfeiunns

Maps & Options

C"

ID ID

Region Displayed: IIJIII 7hJIII cM ü. I urnç.prr. i rn i Hpr-*l XI s+lycaper£icaideE X] S. I qr.np^rr. i r iim XI s^lycnpersicuH+JX) S+peruuianuH X)

Chr 7 cheteiat_£eea

-TS252

Chr 7 Chetelat_28B2

Region Displayed: IIJIII 7hJIII cM ü. I urnç.prr. i rn i Hpr-*l XI s+lycaper£icaideE X] S. I qr.np^rr. i r iim XI s^lycnpersicuH+JX) S+peruuianuH X)

Chr 7 Chetelat_28B2

Chr 7 Lper_94

Sunuttiuy ofMaps:

Map 1 Chetelat_20D0 (^.lycopeisicoides, chr T^Table View Region Displayed 0JDD-90 J] cM Total Gene/Maiker On Chromosome: 8

Fig. 4. NCBI comparative maps of (from left to right) S. lycopersicum :■ S. lycopersicoides (Chetelat and Meglic 2000) (Table 6, pop 5), S. lycopersicoides :■ S. sitiens (Pertuze et al. 2002), S. lycopersicum :■ S. pennellii (Tanksley et al. 1992) (Table 6, pop 8), S. lycopersicum :■ S. pennellii (Bernatzky and Tanksley 1986) (Table 6, pop 8), S. peruvianum :■ S. peruvianum (Van Ooijen et al. 1994) (Table 6, pop 20)

Fig. 5. SGN comparative maps of (from left to right) S. lycopersicum x S. pennellii (Eshed and Zamir 1995) (Table 6, pop 9), S. lycopersicum (Budiman et al. 2000) (Table 7, map 8), S. lycopersicum x S. pennellii (Tanksley et al. 1992) (Table 6, pop 8), S. lycopersicum x S. pennellii (Fulton et al. 2002b) (Table 6, pop 10)

Fig. 5. SGN comparative maps of (from left to right) S. lycopersicum x S. pennellii (Eshed and Zamir 1995) (Table 6, pop 9), S. lycopersicum (Budiman et al. 2000) (Table 7, map 8), S. lycopersicum x S. pennellii (Tanksley et al. 1992) (Table 6, pop 8), S. lycopersicum x S. pennellii (Fulton et al. 2002b) (Table 6, pop 10)

has not been submitted to NCBI. If it were, the same display would be accessible using BLAST.

Figure 4 shows all of the maps that are currently available through the NCBI MapViewer ge-nomic display resource that have the TG128 probe associated with a locus. A line connects the TG128 probe-associated loci.

SGN features a number of tomato and other Solanaceous crop genetic maps and associated data. Figure 5 shows the same region on chromosome 7 as displayed in Fig. 4, with marker TG128 highlighted. From left to right the maps shown are: an IL map; arepresentationofBAC coverage fromaphysicalmap; a genetic linkage map, the same linkage map zoomed in, and a second genetic linkage map.

Access to the maps of SGN is provided on the SGN homepage (http://sgn.cornell.edu) through the maps menu. The menu lists a number of frequently used maps; all available maps can be viewed by clicking on the "show all maps" menu position. Each map has a top-level overview page that shows all linkage groups and their relative sizes, an abstract with background information, and statistics about the map including marker counts and types of markers. On the map overview markers can be located using a text search box. Clicking on one of the linkage groups in the overview displays an enlarged view of the linkage group in the comparative browser as the reference chromosome. In this mode, clicking on the reference chromosome will zoom into the region clicked, and selecting a comparison linkage group will display the comparison between the two linkage groups. For the reference chromosome, additional data tracks can be displayed, if available, such as associated physical map information and available ILs. Markers and maps can be clicked to access related data.

In addition to the map data, SGN stores detailed information about molecular markers. This includes sequences for RFLP markers and primers, sequence source (GenBank accession or SGN EST or unigene sequence id) and PCR reaction conditions for CAPS, SSR and other PCR based markers. SGN also houses the master database for the COS (Fulton et al. 2002b) and COSII markers (see Sect. 1.4.2,1.6.3). Currently, there are over 2,800 COSII markers available that have been developed to work on a maximum number of Asterid species (Wu et al. 2006). For the COSII, the database stores the alignment of the sequences that were used to develop the markers, the experimental PCR conditions for each accession that the markers were applied to, and sequence reads from the PCR products. The data for the different accessions is submitted by users who have used the primers in the species and accessions that are documented.

Using the SGN marker search, markers can be searched with a large number of search criteria, such as constraining the search to a species, chromosome, chromosome interval, marker type, LOD scores, association to a physical map, and more. The markers are also grouped into types such as COSII and COS.

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