With a priori Knowledge of Map Position

Once a PCR-based molecular linkage map is constructed, the need arises to develop markers in regions lacking sufficient coverage. Once these regions are identified, information from high-density molecular maps can be leveraged to develop markers that are targeted to specific regions of interest. The SGN database offers information about various tomato linkage maps covering the entire genome with more than 2,400 markers including RFLP, SSR and COS (Table 5). The sequences of RFLP markers can be retrieved, primers designed, alleles amplified, and sequencing performed to identify the nature of available polymorphism. In particular, RFLP markers with the TG prefix correspond to single or low copy genomic fragments which are particularly suitable for marker development of closely related species (e.g., Bai et al. 2004a; Frary et al. 2005). Primer information is available for the SSR and COS markers hosted at SGN, thus these markers can be tested directly for polymorphisms between the parents of a mapping population. Furthermore, BAC-clones from a S. lycopersicum cv. Heinz1706 genomic library are anchored to the genetic map and BAC-end or entire BAC-sequences are available at SGN. This sequence information allows users to design PCR primers and sequence the amplified products derived from parents of interest in order to develop markers targeted to specific regions. An added feature of the BAC-end sequence resources is that these segments are often derived from intergenic regions offering higher chances for polymorphism detection. Although the approach of marker development for targeted regions of the genome works well for interspecific crosses, this approach is only marginally

-TG58 - LeOH36

~|CT100301 I

-|CT1Q126i]

~ SSR2S6 "cos103

" TG608 "|cosi44|

' TG337

~ TG537

TG176 SSR327

| CT1036711

Chr3

"H- TG479

-SSR110 - SSR383

- TG424

- TG328

|CT10255I|

-|CT10082ll

- TG241 -SSR223

TG419 TG60

|LeOH73|

I I Intron markers ------BAC and BAC end marker

- in silico markers (SSR and SNP)

TG180 TG68

TG565 ' TG111

Fig. 2. PCR-based molecular linkage map of S. pimpinellifolium LA1589 :■: S. lycopersicum cv. Rio Grande F2 population (Gonzalo and van der Knaap, unpublished). The map was constructed using Mapmaker v3.0 and the Kosambi mapping function. The markers are located on the right whereas map distances in cM are indicated on the left of the linkage groups. Marker information (primer sequences and polymorphisms) are available at SGN and www.tomatomap.net (Table 5). Markers obtained by in silico analysis are underlined with a solid line. Markers developed from BAC-ends or the entire BACs are underlined with a dash line. Markers obtained by mining intron sequences are boxed. Unlabeled markers are PCR-converted RFLP markers

Table 5. Web sites used for marker development in tomato (S. lycopersicum)

Purpose

Features

Reference

http://www.sgn.cornell.edu

http://www.kazusa.or.jp/jsol/ microtom/index.html

http://www.tomatomap.net

http://www.ncbi.nlm.nih.gov http://www.tigr.org

Solanaceae resource

Tomato resource

Tomato information source

Molecular biology information

Analysis of genome sequences

http://www.dpw.wau.nl/pv/CAPStomato/ Tomato marker information

http://www.potatogenome.net/ Potato genome sequence portal

http://www.arabidopsis.org Arabidopsis resource

http://cgpdb.ucdavis.edu/sitemap.html Composite database,

COS marker discovery http://frodo.wi.mit.edu Primer design

http://helix.wustl.edu/dcaps/dcaps

Primer design (dCAPS, CAPS)

Physical and genetic maps; genome and marker sequence information; bioinformatic tools

Tomato full-length cDNA; gene expression; polymorphic markers Molecular map; sequence information; polymorphism within cultivated germplasm; genetic maps

Sequence information; publications; bioinformatics tools

Genome, SSR and EST databases; bioinformatic tools

Tomato CAPS markers

Potato genome sequence

Annotated genome sequence; gene expression; seed stocks; biochemical pathways; bioinformatics tools COS markers for tomato; bioinformatics tools Primer3 program dCAPS Finder2.0

Mueller et al. 2005a

Tsugane et al. 2005

Van Deynze, van der Knaap and Francis, unpublished

Wheeler et al. 2006

Bai et al. 2004a

Rhee et al. 2003

Rozen and Skaletsky 2000

Neffet al. 199S

effective within the cultivated germplasm pool due to the low rate of polymorphism (Yang and Francis, unpublished).

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