Annemarie's explanation on PlantLines

Copied by TG from #481

The problem with the Line_number in RIPR or PlantLine in BIP is that they are probably not actual "PlantLine Names" as I assume the definition for PlantLine is used in the BIP. The definition of PlantLine is ambiguous, which makes things very confusing. I feel I have tried to explain it somewhere else before, but maybe I just wanted to.

So here the story about "Lines": starting at the end of the story, the trait scores... Trait Scores are the ultimate information you want to collect from any plant types you have. Trait Scores are used to assess the diversity within the genetic material =the plants. This genetic material can come from different sources: 1) through evolution and then collection of plant material from all over the world by researchers (Diversity foundation A) 2) through crossing two plants which are found/suspected to have strongly differing trait(s) and hence genetic material in order to assess where the genetic origin for a specific trait may lay ("mapping population") 3) through "induced evolution" ( experts probably will roll their eyes at this expression..) by mutagenesis, where seeds from one plant are exposed to e.g. chemicals or radioactivity, which makes them mutagenise and the subsequent generation of that plant have slightly different genetic material than the original plant. 4) by using a diversity set that contains registered varieties to better assess their phenotypic (trait) diversity ( Diversity Foundation B).

To my understanding, this is where the term LINE comes in. I think it is mostly an experimental setup term but in the case of 2) and 3), it is considered a standalone term to identify each of the plants, as they all have different genetic material from each other and from the parent(s) and are hence totally new. it is important for (pre-) breeders and scientists to tell them apart. As, because of differing genetic material, the trait scores will be slightly different in some of those lines.. In these cases,lines are unique identifiers not just within the experiment but also for everyone outside the experiment. Some of these lines will only be used for locating a certain trait on the genome. Other lines may be used for breeding future lines as they may carry a good trait combination, which people want to combine with other lines that carry good trait combinations. other lines may already be so good that they can be turned into Cultivars, which means that their genetical material becomes fixed and becomes commercially available.

The reason why the RIPR data carries this term is more for internal experimental reasons ( and as Lenka sais because some analysis tools prefer numbers to letters). There, a line is associated with a cultivar and as cultivars are externally universally recognised identifiers for their corresponding genetic material, they are the important bits for external recognition in the dataset. This means, that the line name for a cultivar can differ from Project to Project(!!), as it is just used as internal identifier- and i think this is not useful for the BIP..

In my humble opinion, the separation of line and cultivar into two different tables in CropStore is probably only done because the intention of Crop Store was partly to facilitate what has been done in 2) and 3),- the creation of maps ( which is what all the QTLs and markers and linkage maps in BIP are about). The way I understand things is that the aim of the BIP has shifted a bit away from the CropStore aim. The BIP aims to simply store phenotypical data for now. Once this is properly sat up and things are standardised, it can be expanded and the phenotypical data integrated with other data types.

All in All, both line name and cultivar name are supposed to act as unique identifier for some genetic material in order to relate back to the traits that can be associated with this genetic material. In experimental setups where the cultivar name is used, like in RIPR, the line number in a separate column doesn't have the same informational value as in trait scoring trials with material derived from methods in 2) and 3). The RIPR project is more of a mix between 1) and 4).