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Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato
12/09/2020 UNION ACTIVITIES 66

Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato

 
Horticulture Research 2020 Jun 1;7:90.  doi: 10.1038/s41438-020-0314-4. eCollection 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.
 
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Figure 2: Regulatory network for the flavonoid biosynthesis pathway.
a Combined Manhattan plot of SNPs associated with the expression of 39 genes involved in flavonoid biosynthesis. Green dots indicate that these loci were also significantly associated with the accumulation of anthocyanins in the storage roots of sweet potato. The red horizontal dashed line represents the genome-wide suggestive threshold (−log10(P) = 5.39, α = 1). b IbMYB1-2 positively regulates 17 downstream genes in the flavonoid biosynthesis pathway. The yellow node indicates the candidate regulator, and blue nodes indicate regulated genes.
 
 
 
 
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