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Article|01 Jun 2020|OPEN
Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato
Lei Zhang1, Yicheng Yu1, Tianye Shi1, Meng Kou2, Jian Sun1, Tao Xu1, Qiang Li2, Shaoyuan Wu1, Qinghe Cao2,, Wenqian Hou1, & Zongyun Li1,
1Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116 Jiangsu Province, People’s Republic of China
2Xuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAAS, Xuzhou 221121 Jiangsu Province, People’s Republic of China

Horticulture Research 7,
Article number: 20090 (2020)
doi: 10.1038/hortres.2020.90
Views: 289

Received: 20 Nov 2019
Revised: 23 Mar 2020
Accepted: 30 Mar 2020
Published online: 01 Jun 2020

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 IbMYB1-2 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.