foxtail millet maps

[Junjian Ni]

Hi Brian,

Thanks for your info. Here are several points from me:

1. For the 04 Doust map, I got the map and marker position data directly
from Dr. Andrew Doust while we curated his PNAS paper. We have not
collected Devos-98 map right now, seemingly.

2. As you pointed out, it seems that two maps (chromosomes, chro V and
VIII) have different orientations (top markers-> down, starting marker
becomes the ending marker on that chro) based on two papers (98-TAG,
04-PNAS). I guess probably as the time goes, the research community change
the rule/view for those maps. I look forward to hearing more from Drs.
Devos and Doust.

3. For that inversed chromosome issue (caused by publication, source,
etc), in Gramene, we generally don't change the map order/orientation from
the paper while doing data collection. We try to follow what the original
paper said/displayed/provided mostly. On the another hand, we provide a
map-flip function in CMap so that users can change map orientation while
necessary.

Thanks again for your info.

With best regards.

Ni


> Katrien,
>
> The foxtail millet maps are public.
> http://tinyurl.com/3coyeq shows the chromosome where the 98 RFLP map and
> the 04 Doust map seem to have the chromosome reversed.
> The 98 RFLP map data is from Figure 1 of the TAG 96:63-68 paper. The
> Doust 04 data was collected from Gramene in September 2005. I have
> checked the current Gramene data - it is the same as the material I
> collected.
>
> http://tinyurl.com/3ygru3 shows the same chromosome inversion at Gramene
> along with a data entry error by me - the very first locus on the
> chromosome is from chromosome IV. I have corrected the error in the data
> here and the correction will become public sometime soon. The current
> Gramene data is the same as that which I collected.
>
> The Gramene material exactly reflects figure 4 of PNAS 101:9045-9050.
>
> I have cc Gramene and Dr. Doust.
>
> --
> Brian Smith-White
> Staff Scientist
> National Center for Biotechnology Information
> National Library of Medicine
> National Institutes of Health
> 8600 Rockville Pike
> Bldg 45 Room 6AS.41D-51
> Bethesda, MD 20894
> Voice: 301.402.4047
>
>


Junjian Ni
Gramene Curator
G15, Bradfield Hall,
Cornell University,
Ithaca, NY 14853