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Transcribed microsatellite allele lengths are often correlated with gene expression in natural sunflower populations
Author(s) -
Ranathunge Chathurani,
Wheeler Gregory L.,
Chimahusky Melody E.,
Perkins Andy D.,
Pramod Sreepriya,
Welch Mark E.
Publication year - 2020
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.15440
Subject(s) - biology , microsatellite , genetics , allele , gene , population , helianthus annuus , phenotype , untranslated region , sunflower , rna , demography , sociology , agronomy
Abstract Microsatellites are common in genomes of most eukaryotic species. Due to their high mutability, an adaptive role for microsatellites has been considered. However, little is known concerning the contribution of microsatellites towards phenotypic variation. We used populations of the common sunflower ( Helianthus annuus ) at two latitudes to quantify the effect of microsatellite allele length on phenotype at the level of gene expression. We conducted a common garden experiment with seed collected from sunflower populations in Kansas and Oklahoma followed by an RNA‐Seq experiment on 95 individuals. The effect of microsatellite allele length on gene expression was assessed across 3,325 microsatellites that could be consistently scored. Our study revealed 479 microsatellites at which allele length significantly correlates with gene expression (eSTRs). When irregular allele sizes not conforming to the motif length were removed, the number of eSTRs rose to 2,379. The percentage of variation in gene expression explained by eSTRs ranged from 1%–86% when controlling for population and allele‐by‐population interaction effects at the 479 eSTRs. Of these eSTRs, 70.4% are in untranslated regions (UTRs). A gene ontology (GO) analysis revealed that eSTRs are significantly enriched for GO terms associated with cis ‐ and trans ‐regulatory processes. Our findings suggest that a substantial number of transcribed microsatellites can influence gene expression.