Welcome to the FarmGTEx Project

A public resource for regulatory variants discovery and molecular phenotype prediction in farm animal species

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Overview

2018-

The Farm animal Genotype-Tissue Expression (FarmGTEx) project, an ongoing international collaborative endeavor, aims to provide a comprehensive public resource of tissue-specific genetic regulatory variants discovery and molecular phenotype prediction in farm animal species, which will have an enormous impact on fundamental biology discovery, livestock genetics and breeding, biotechnology, adaption, evolution, cross-species mapping, and human biomedicine.   

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Pilot

2018-2023 

In the pilot phase of FarmGTEx, by pulling together publicly available data from various sources via an uniform pipeline, we are adding value to the individual datasets, and creating a highly valuable resource of genetic regulatory variants across a wide range of tissues in major farm species for the whole community.

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Main

2022-2033

In the main phase of FarmGTEx, we aim to investigate the regulatory variants in over 50 tissue/cell types from over 1000 individuals for each farm animal species to achieve a truly comprehensive view of the regulatory landscape and its influence on complex traits of economic value. We will also fully develop the context-dependent FarmGTEx, e.g., genetic background, diet, sex, development, response and other environmental factors.

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Enhanced

2022-

In the enhanced phase of FarmGTEx, we aim to collect additional molecular data such as single-cell RNA-seq and other omics data types (e.g., epigenome, proteome, metabolome and microbiome) to further fill the gap between genome and phenome. All the knowledge obtained from FarmGTEx will be applied to interpret molecular mechanisms underlying complex traits of economic value, understand adaptive evolution and domestication, optimize genetic improvement programmes (including gene editing), and allow comparative genomics studies at different biological layers. 

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The ongoing species in the FarmGTEx

GoatGTEx

DuckGTEx

XxxGTEx

XxxGTEx

Upcoming Events


The FarmGTEx workshop of PAG30 is planned for Tuesday, January 17, 2023: 6:20 PM - 8:30 PM, Town and Country B, Town & Country Resort, 500 Hotel Cir N, San Diego, CA 92108. To complement FAANG-FarmGTEx TF, this event will focus on discussing the challenges in computational analysis of big and complex GTEx data, which will include five-six talks on RatGTEx, computational biology, statistical genetics and bioinformatics in model organisms and humans.

The white paper of FarmGTEx

We are drafting the white paper of the FarmGTEx, aiming to summarize the knowledge and lessons from the pilot phase, to identify the gaps, and to give perspectives for the coming phases of FarmGTEx. The white paper will be sent out to the community for review, comment and input as soon as possible.

The results from the pilot phase of PigGTEx was released 7th Nov. 2022. This resource includes gene expression from 9,530 RNA-seq samples, and five molecular QTLs (e.g., eQTLs and sQTLs) from 34 tissues in pigs. The data and the codes are public available.

The phase 1 of CattleGTEx

The new phase (phase 1) of CattleGTEx is starting now. The expected deadline of this phase will be on 1th Nov. 2024. If you are interested in collaborations, please contact us via cattlegtex@farmgtex.org or lingzhao.fang@qgg.au.dk

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