Lister and Dean RI map database and mapping service moves to NASC
Mary Anderson, Nottingham Arabidopsis Stock Centre, University of Nottingham, Department of Life Science, Nottingham, NG7 2RD
email: arabidopsis@nottingham.ac.uk
On the 19th July, Clare Lister (John Innes Centre, Norwich, UK) formally handed over the recombinant inbred (RI) map database for the Lister and Dean RI lines, which she has developed over the last four years, to the Nottingham Arabidopsis Stock Centre (NASC). NASC will now maintain the database, display regular updates to the RI map and continue to offer a mapping service to the community.
Anyone can send in their mapping data to NASC for mapping. The positions of all markers mapped by NASC will be made publically available through the NASC WWW server. The mapping data will be run once a week and the main map updated once a month.
The segregation data for the 67 loci described in Lister and Dean (1993) is available at NASC and through AtDB but the central database will not be distributed. The aim is to produce one large integrated map rather than many non-integrated ones.
Please note that NASC can supply information about the probes on request. However, NASC does not distribute any of the markers. DNA markers must be obtained from either the Arabidopsis Biological Resource Center (ABRC) or from the investigators themselves. Stocks of the RI lines are available from NASC and ABRC.
As promised at the 7th International Arabidopsis meeting at Norwich, Clare has made one last version of the map. This is available as a text file, as individual postscript files for printing, or as graphics from our FTP site. The latest map carries 592 markers.
How to submit data to NASC.
RI mapping is conducted using Mapmaker (Lander et al 1987) and so the data has to conform to the Mapmaker format. We have designed a special form for data submission to help you send in the data in the correct format. Although the form is only currently supported by Netscape version 3.0, we are working on a version complient with all forms-capable browsers. We recommend that you use this form for data submission and that you fill in the information for each line. It has been designed to allow us to automatically enter your data and so circumvents any potential problems with typing errors.
However, we can also receive data by email to arabidopsis@nottingham.ac.uk. Label your message RIDATA. If sending your information by email please adhere strictly to the following format, indicating the numbers of the RI lines used and including the data in (RI) numerical order.
Enter your scores for the RI lines data into a Text file (eg. MacExcel, or another text file) as follows:-
A = like Columbia parent
B = like Landsberg parent
H = heterozygote (if possible to score)
- = unscorable or no score
Marker names should start with a * followed by a letter (small or capital) ie. *w23 and should have a single space or tab between each entry. Names MUST BE LESS than EIGHT characters. Mapmaker, the programme we use for mapping, is not case sensitive and so reads "a" and "A" as the same thing. Please check the current names used for Loci, so as not to generate conflicts.Your file should look like this:
RI line Number 4 5 13 14 17 25 29Save as TEXT ONLY.
*A1 A A B - A B B
*b2 B B B A H - B
*C4 B A - A B B A
For information on how to map your own data using Mapmaker, please refer to the brief description carried in the NASC on-line catalogue.
Reference
Lister C. and Dean C. (1993). Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana. Plant Journal 4, 745-750