The ChickenGTEx portal: a pan-tissue catalogue of regulatory variants shaping transcriptomic and phenotypic diversity

A systematic dissection of the functional impacts of non-coding variations across diverse tissues and cell types is essential for deciphering the molecular architecture underlying complex traits. Given the significance of chickens as both a key livestock species and a fundamental model organism, the development of an integrative genomics resource is imperative. Leveraging SNP-to-gene-to-trait linking strategies-including molecular quantitative trait loci (molQTL), regulatory elements, and context- or environment-dependent regulatory heterogeneity-we developed the ChickenGTEx portal (http://chicken.farmgtex.org), which provides a comprehensive catalogue of regulatory effects on transcriptomic and phenotypic diversity across tissues, cell types, and sexes. Key features of the resource include a genotype imputation panel of 2869 chickens from 123 breeds worldwide, five types of molecular phenotypes across 28 tissues, ∼2.2 million molQTL, 806 229 fine-mapped molQTL, 1956 context-dependent molQTL, 257 genome-wide profiles of 7 epigenetic marks (representing 15 chromatin states) from 23 tissues, 185 376 single-cell expression profiles across 191 cell clusters from 9 tissues, and 96 386 gene-trait associations covering 108 economically important traits. In summary, the ChickenGTEx portal will serve as an invaluable resource for advancing research in fundamental and evolutionary biology, chicken precision breeding, and eventually human biomedicine.