search

legumeinfo / datastore-issues

mostly for issues pertaining to the content of the legumeinfo datastore; may also relate to characteristics of its user interface or managing the mirroring process to the legfed instance
Other
1 stars 0 forks source link

Straighten out so-called Xana_x_Cornell49242.map/qtl.Gaitán-Solís_Duque_2002 #122

Closed sammyjava closed 2 years ago

sammyjava commented 2 years ago

First of all, I don't see how the citation for the map or QTL study has to do with a genetic map or QTL study - there is no genetic map reported, just a discussion of how the markers were developed. The map is actually purported to be a merge of Freyre-Skroch_1998 (plain B01-B11) plus Pérez-Vega, et al. 10.1007/s00122-010-1261-5 (B04.A, B04.B, etc.) although that paper does not report linkage groups, just nearest markers to QTLs.

We can just leave this alone, but maps without markers now fail my validation and are not loaded into BeanMine. In my opinion a genetic map without markers ain't a genetic map.

Close this if you don't care or cannot find the markers mapped to this combined map that were presumably used to divine the QTLs (in some other publication than Gaitán-Solís_Duque_2002, clearly, unless that was a private communication!).

sammyjava commented 2 years ago

I think this one needs some actual work, QTL study may wind up getting renamed for the correct paper.

sammyjava commented 2 years ago

OK, it finally jogged my memory that we'd actually been contacted about this red herring. I will build the proper Xana x Cornell49242 collections from the proper publications.

_I am starting to understand. Our difficulty interpreting the original email is that Galeano is a red herring. The problem is that the collection genetic/Xana_x_Cornell49242.gen.Gaitán-Solís_Duque_2002 references the publication "Gaitán-Solís, E., Duque, M. C., Edwards, K. J. & Tohme, J. Microsatellite Repeats in Common Bean (Phaseolus vulgaris ): Isolation, Characterization, and Cross-Species Amplification in Phaseolus ssp. Crop Sci. 42, 2128–2136 (2002)" … which doesn’t have anything to do with the Xana_x_Cornell49242 population or map. I’ll continue looking into it, but I think we’ll probably need to drop these: genetic/Xana_x_Cornell49242.gen.Gaitán-Solís_Duque_2002 maps/Xana_x_Cornell49242.map.Gaitán-Solís_Duque_2002 and add Xana_x_Cornell49242 collections associated with the publications that he references. I’ll try to have a closer look at it tomorrow while I am traveling, and will ask Scott (CC’d) to help with preparation of the new Ferreira collections (it does look like good work).__

sammyjava commented 2 years ago

Closing this ticket since it's really about building six new phavu QTL study collections. I'll remove these two.