QTL-Browser - Grapedia

Grapevine-QTL Browser: A dream coming true

Collections of results from different QTL (Quantitative Trait Loci) studies have been implemented both in model plants and in crops, mainly cereals, to facilitate the access to information and enhance the impact of existing data on plant improvement activities. To date, cataloguing, summarizing, and making FAIR the plethora of increasing QTL information are the next challenge for the grapevine (Vitis spp.) community. To ensure we do not lose valuable data, the multitude of identified QTLs – along with the related raw data like genotypes, phenotypes, and environmental information from published experiments – must be stored in dedicated public databases for effective utilization.

Within the GRAPEDIA initiative, this wealth of QTL information is planned to be anchored firstly to the grapevine reference PN40024.v4 genome and secondly to the published and upcoming diverse genomes. The generated “Vitis-QTL browser” would (i) enhance our understanding of the genetic regulation of different phenotypes, (ii) reveal consistent QTLs across studies (consensus genomic intervals), which are particularly valuable for marker-assisted breeding deployment, (iii) assist the QTL cloning process and facilitate the integration of candidate genes and superior alleles into biological and biotechnological applications.

Silvia Vezzulli, Laura Costantini
Fondazione Edmund Mach, Italy

(Abstract from Grapedia Annual Meeting, 11-13 September 2023, Valencia, Spain)

OUR INTENTION

To create a team of motivated experts who can contribute, in different ways and steps, to this ambitious goal.

For this reason, we organized the First Grapevine QTL hackathon on the 19th October 2023 at the University of Verona, Italy. All participants were European, including a member from Israel.

In Verona, we presented the initiative, shared the approach, defined the milestones (including a first publication), and started working on QTL data extraction from scientific papers.

We also defined the Working Groups, with relative leaders, for QTL-related data curation (see attached file). We are sure you will be able to match yourself with at least one of these Working Groups.

If you wish for further info, you are welcome to join the Google Group mailing list grapevine-qtl@fmach.it or contact grapedia(at)grapedia.org stating your wish to be part of the Grapevine QTL effort.

A Grapevine-QTL frontend application has recently been developed for data uploading.

UPDATE – JANUARY 2025:

Thanks to everyone’s efforts we are pleased to report that we have reached the historic milestone of 2,150 annotated QTLs (37% of the total)! We have well surpassed the goal of 1,843 QTLs expected by the end of November 2024, which is simply fantastic!

The meeting held in mid Dec 2024 with all Team Referees was very fruitful.

We will integrate our list with QTL Papers published up to 31st December 2024.

We have agreed on mid-March deadline for the QTL curators to complete the entire annotation work; this will give the Team Referees more time for post-curation.

As planned, by that time we will have collected all the missing information to be able to update in particular the Vitis Ontology, but also the list of SSR and SNP markers with associated info.

Further details will be communicated to the Team Referees soon.

Thanking You All!

From the enthusiastic FEM Team: Silvia, Laura, Paola & Marco

UPDATE – JULY 2025:

Thanks to the many efforts we are pleased to inform you that we have reached another historic milestone of 6,097 annotated QTLs! These coverall (100%) the 155 papers on bi-parental populations published up until February 2025.

This is awesome!

Building on our existing work, we are curating 45 additional papers on QTLs (or QTNs), derived from GWAS.

The post-curation of the Phenological class has been completed (490 QTLs) as well as VO-related terms have been updated/integrated by the dedicated colleagues who remain in collaboration with us.

At FEM the ultra post-curation started (marker name/info check etc) to properly feed the ChromoMap input files. Currently, the SSR database (name, primers/sequences etc.) is being updated by the dedicated Team. Regarding SNPs, it will be basic to retrieve the genome version in presence of their offset info.

Finally, the curation of 459 CG info – with Integrape validation level 2-6 and published into 50 papers – has been reached by the dedicated Team. The progress is at 50% (approx. 100 papers in total).

Next steps:

i) short-term @FEM team: visualize the ultra-post curated Phenological QTLome through ChromoMap and integrate the underlying above-mentioned CGs (by position) towards the finalization of the First Paper.

ii) mid-term @Task leader team: finalize the post-curation of the assigned Trait class; prior to this task, we will arrange a meeting to support and give the Task leader best practices, also based on direct experience. The VO update will follow.

iii) regarding “bi-parental QTLs”: we should consider that the post-curation of all Trait class QTLs should be completed in a reasonable time during the early fall, not to make the already annotated data too old.

iv) regarding “GWAS QTLs”: we look forward to receiving a general curation plan by engaged colleagues.

v) regarding our “dream coming true”: we really wish to have QTL Browser infrastructure and navigability by 2026

Our Second Paper, the endeavor, will be a scientific bomb!

Thanking You All for the trust, engagement and membership.