PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs

Abstract

To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http:////pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.

Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations

“…The emergence of various biological function databases will also provide a new foundation for a more precise interpretation of gene functions between species [ 27 , 28 , 29 , 30 ]. In our study, we discovered a significant signal of admixture from Vietnam pigs to Diannan small-ear pigs.…”

“…By utilizing WGS analysis and establishing multi-omics databases, researchers can gain valuable insights into the biological significance of genetic information, particularly considering that many genes exhibit high homology across different species. This approach allows for the exploration of shared genetic features and functional elements across organisms, enabling comparative genomics studies [ 27 , 28 , 29 , 30 ]. For instance, the Pig Genotype-Tissue Expression (PigGTEx) project, which is a part of the Farm animal Genotype-Tissue Expression (FarmGTEx) project, utilized WGS analysis to investigate gene expression and gene regulatory effects in pigs.…”

“…Recent findings from the PigGTEx project have revealed that the tissue specificity of gene expression and gene regulatory effects are often conserved between pigs and humans. The public resources provided by PigGTEx offer a valuable platform for studying the evolution, genetic introgression, gene flow, complex traits, and molecular regulation between Yunnan pigs and pig populations in neighboring countries or regions within Southeast Asia [ 27 , 30 ]. They enable us to investigate the genetic and molecular mechanisms underlying important traits and the impact of genetic exchange and introgression events on pig populations in Yunnan and Southeast Asia as a whole [ 27 , 30 ].…”

Genome-Wide Association Study Meta-Analysis Elucidates Genetic Structure and Identifies Candidate Genes of Teat Number Traits in Pigs

“…For the significant SNPs associated with teat number traits, we discovered that some of them exhibited significant relationships with other traits. For instance, the SNP 7_102441757 demonstrated a strong association with loin muscle depth, and the genetic correlation between teat number and loin muscle depth was determined to be 0.99 from PigBiobank [ 32 ]. Additionally, teat number and backfat thickness displayed noteworthy loci, such as 7_97614602, with a genetic correlation of −0.3068.…”

Mapping and functional characterization of structural variation in 1060 pig genomes

“…As described previously [ 33 ], this was performed by examining their linkage disequilibrium with other functional variants produced by the Pig Genotype-Tissue Expression (PigGTEx) project. As part of the FarmGTEx project, the PigGTEx generated a comprehensive catalog of expression quantitative trait loci (eQTLs) and splicing quantitative trait loci (sQTLs) in 34 pig tissues, as well as conducted sequence-based genome-wide association studies (GWAS) and gene-based transcriptome-wide association studies (TWAS) for many complex traits in pigs [ 34 , 35 ]. Therefore, this SV catalog represents a valuable resource for studying diversity and evolutionary history in pigs and how domestication, trait-based breeding, and adaptive evolution have functionally shaped the pig genome.…”