Expression quantitative trait locus studies in the era of single-cell omics

Jie Luo; Xinyi Wu; Yuan Cheng; Guang Chen; Jian Wang; Xijiao Song

doi:10.3389/fgene.2023.1182579

Expression quantitative trait locus studies in the era of single-cell omics

Front Genet. 2023 May 22:14:1182579. doi: 10.3389/fgene.2023.1182579. eCollection 2023.

Authors

Jie Luo¹, Xinyi Wu², Yuan Cheng², Guang Chen¹, Jian Wang¹, Xijiao Song¹

Affiliations

¹ State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
² Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.

Abstract

Genome-wide association studies have revealed that the regulation of gene expression bridges genetic variants and complex phenotypes. Profiling of the bulk transcriptome coupled with linkage analysis (expression quantitative trait locus (eQTL) mapping) has advanced our understanding of the relationship between genetic variants and gene regulation in the context of complex phenotypes. However, bulk transcriptomics has inherited limitations as the regulation of gene expression tends to be cell-type-specific. The advent of single-cell RNA-seq technology now enables the identification of the cell-type-specific regulation of gene expression through a single-cell eQTL (sc-eQTL). In this review, we first provide an overview of sc-eQTL studies, including data processing and the mapping procedure of the sc-eQTL. We then discuss the benefits and limitations of sc-eQTL analyses. Finally, we present an overview of the current and future applications of sc-eQTL discoveries.

Keywords: bulk RNA-seq; cell-type-specific; genetic variants; sc-eQTL; scRNA-seq.

Publication types

Review

Grants and funding

This study was supported by the Key Research and Development Program of Zhejiang (2021C02052) and the Natural Science Foundation of Zhejiang Province (LY20C150004).