Genomics Inform.  2016 Dec;14(4):211-215. 10.5808/GI.2016.14.4.211.

Investigation of Splicing Quantitative Trait Loci in Arabidopsis thaliana

Affiliations
  • 1Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea. sskimb@ssu.ac.kr

Abstract

The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs across 141 strains of Arabidopsis thaliana with publicly available next generation sequencing datasets. As a result, we found 1,694 candidate sQTLs in Arabidopsis thaliana at a false discovery rate of 0.01. Furthermore, among the candidate sQTLs, we found 25 sQTLs that overlapped with the list of previously examined trait-associated single nucleotide polymorphisms (SNPs). In summary, this sQTL analysis provides new insight into genetic elements affecting alternative splicing patterns in Arabidopsis thaliana and the mechanism of previously reported trait-associated SNPs.

Keyword

QTL mapping; RNA-seq; sQTLs
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