Genome-wide Analysis of Expression Quantitative Trait Loci (eQTLs) Reveals the Regulatory Architecture of Gene Expression Variation in the Storage Roots of Sweet Potato

Overview

Journal Hortic Res

Publisher Oxford University Press

Date 2020 Jun 13

PMID 32528702

Citations 23

Authors

Lei Zhang

Yicheng Yu

Tianye Shi

Meng Kou

Jian Sun

Tao Xu

Qiang Li

Shaoyuan Wu

Qinghe Cao

Wenqian Hou

Zongyun Li

Affiliations

Soon will be listed here.

Abstract

Dissecting the genetic regulation of gene expression is critical for understanding phenotypic variation and species evolution. However, our understanding of the transcriptional variability in sweet potato remains limited. Here, we analyzed two publicly available datasets to explore the landscape of transcriptomic variations and its genetic basis in the storage roots of sweet potato. The comprehensive analysis identified a total of 724,438 high-confidence single nucleotide polymorphisms (SNPs) and 26,026 expressed genes. Expression quantitative trait locus (eQTL) analysis revealed 4408 eQTLs regulating the expression of 3646 genes, including 2261 local eQTLs and 2147 distant eQTLs. Two distant eQTL hotspots were found with target genes significantly enriched in specific functional classifications. By combining the information from regulatory network analyses, eQTLs and association mapping, we found that acts as a master regulator and is the major gene responsible for the activation of anthocyanin biosynthesis in the storage roots of sweet potato. Our study provides the first insight into the genetic architecture of genome-wide expression variation in sweet potato and can be used to investigate the potential effects of genetic variants on key agronomic traits in sweet potato.

Citing Articles

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