Yes. Please refer to the QTL Tutorial, Help page and FAQ at http://www.gramene.org/tutorials/qtl.html.

Users can search all of the QTL related with a particular trait for a specific species. Users also can view which trait is associated with a QTL of interest and find where it is located on a map, while constructing comparisons with other grass species. You can determine which markers delimit a particular QTL using the maps provided. You can determine which other genes are located within the same region as drought tolerant genes, for example. Users can also view the germplasm that were used as parents to generate a mapping population to map a particular QTL. For most rice QTL, you can also see a Gramene infered genome region and found related features such as gene models and SNPs within the region.

Gramene attempts to curate all QTL from public resources. Currently, Gramene has finished curating most of the QTL for rice (from the years 1994 to June of 2006). Gramene has also integrated QTL from MaizeGDB and GrainGenes, and started to curate published QTL from maize, barley, oat, wheat, sorghum, pearl millet, foxtail millet, and wild rice as well.

Although Gramene attempts to curate all QTL in grasses from public resources, there are some published QTL not in the database. Gramene has not covered most QTL in grasses other than rice due to limited resources and curators. Even for rice, for the articles on which the marker and QTL position have not been explicitly displayed, and contacting the authors results in no further informatation, the curators can decide not to curate them so that Gramene can assure the QTL in our database are in good quality.

Gramene does not currently present QTL information from non-published sources, such as personal communication.

A trait category (see http://www.gramene.org/db/qtl/qtl_display) is a category which has been used in Gramene to group traits based on their agronomic implications. With trait categories in place, researchers can browse traits and the QTL associated with them even when the exact trait name in Gramene is not known. Although the relationship between trait and trait category can become complicated, Gramene provides a rather simple structure so that a trait only belongs to one trait category.

The QTL trait categories have been defined in the QTL Help Document at http://www.gramene.org/qtl/help.html

Gramene curators assign trait symbols based on the trait name. Trait symbols generally are composed of several characters selected from the trait name. Those trait symbols have been used to represent QTL on the original QTL maps. For Gramene inferred QTL display, the combinations of QTL accession and trait symbol have been utilized to display a QTL.

The QTL detail page provides a link to the Trait Ontology (TO) accession, and that summary page provides the definition.

Mostly, no. Gramene displays QTL on the individual maps that have been generated from the original QTL mapping studies. With Gramene's comparative mapping interface (in Maps <http://www.gramene.org/cmap/>), researchers can compare QTL maps to other genetic maps. In the case that there are several versions of a map generated with the same genetic population, Gramene generally will use the most updated map to display the QTL. One point we would like to emphasize, for the majority of rice QTL, Gramene currently provide inferred genome regions, thus the rice genome or Gramene annotated TIGR sequence map could be considered as the rice consensus map for rice QTL.

You can get this information by selecting the "i" (information) button at the top of a QTL map. On the resulting Map Set Info page information including name, species, map type, a description of development of that mapping population, related germplasms and reference(s) is provided.

No. Currently Gramene doesn't provide all information associated with a particular QTL, such as statistical parameters, environments under which the QTL were studied. Those will be curated in the future if resources are available.

All 83 QTL have been curated from the paper of Wang et al. (1994). We curated those following our standard curation procedure. According to our rule, QTL detected by different traits (in some cases, they could be parameters used for trait evaluation) or different environments are treated as different unique single QTL. While two single QTL have interaction, they will be also treated as two single QTLs, but the relationship of them will be explained by free text comments. So, for that paper: AQEN001-010: corresponding to all QTL in Table 1, and the QTL detected by lesion number in Fig 2. AQEN011-017: QTL detected with diseased leaf area in Fig 2. AQEN018-019: QTL detected with lesion size in Fig 2. AQEN020-59: QTL pairs with interaction effects in Table 2. AQEN060-082: QTL detected with diseased leaf area at other two sites in Table 3 (Cavinti, Sitiung).

Currently, we have provided two types of associated markers for a particular QTL, Co-localized markers and neighboring markers. However, we didn't catch every detail info such as best score and allele info. This more comprehensive info might occur when we have raw data and redo the analysis. To get those associated markers for the QTLs, you can check the QTL detailed page. We are also considering to provide a batch downloading mechanism, and that could be available in the summer of 2007.

Yes, it's possible now. From the QTL detail page, you can see two types of associated markers for a particular QTL. Co-localized markers are the markers co-localized or overlapped with a QTL region on the original QTL map, and neighboring markers are those not overlapped but closely adjacent to a QTL region. We hope the info helpful for users to perform QTL fine mapping, map-based positional cloning, and marker-assisted selection (MAS) in plant breeding.