Integrating genome-wide association study with multi-tissue transcriptome analysis provides insights into the genetic architecture of teat traits in pigs

Chen, Wei; Cai, Xiaodian; Diao, Shuqi; Teng, Jinyan; Xu, Zhiting; Zhang, Wenjing; Zeng, Haonan; Zhong, Zhanming; Wu, Xibo; Gao, Yahui; Li, Jiaqi; Zhang, Zhe

doi:10.1016/j.jgg.2023.07.003

Cited by 1 publication

(1 citation statement)

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“…Over the past decade, Genome-Wide Association Studies (GWAS) have been applied to investigate the associations between genetic variations distributed across the genome of a species and traits of interest (Wei et al 2023;Yang et al 2021;Yengo et al 2022). For human diseases and traits, GWAS demonstrate that over 88% of the phenotype-associated variation lies outside protein-coding regions and is enriched in gene regulatory regions (Hindorff et al 2009).…”

Section: Discussionmentioning

confidence: 99%

Repressor elements provide insights into tissue development and phenotypes in the pig

Zhang,

Guo,

Liu

et al. 2024

Zoological Research

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Repressor elements play important roles in economic phenotypes of the pig, however, these elements remain poorly characterized. Here, we used H3K27me3, ATAC-seq and RNA-seq data derived from six tissues from three embryonic layers to identify 2 034 super repressor elements (SREs) and 22 223 typical repressor elements (TREs) in the pig genome. Among the identified repressor elements, many are shared by mesodermal and ectodermal tissues. SREs tightly regulate their target genes (within a specific genomic region, SREs act on a small number of target genes with strong effects) while the regulation by TREs is looser (TREs act on a wider range of target genes with weaker effects). Furthermore, in neuronal tissues, repressor element regulated genes start to be repressed during the stage of differentiation of stem cells to progenitor cells. Many regulatory elements were found to cooperate with each other (and have additive effects) to regulate the expression of KLF4. This study provides the first comprehensive pig repressor element map and should be a crucial reference for future studies on REs.

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