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Abstract Detail


Ranathunge, Chathurani [1], Wheeler, Gregory [2], Perkins, Andy [3], Welch, Mark [4].

Microsatellites as tuning knobs of adaptation: A study on the enrichment of microsatellites in differentially expressed genes across latitudinal populations of common sunflower (Helianthus annuus L.).

Natural populations of widely distributed common sunflower (Helianthus annuus L.) are highly adapted to their local environments. In this study, seeds from six natural populations of common sunflower from two latitudes in Kansas and Oklahoma were grown in a common garden to test a potential gene regulatory role for transcribed microsatellites. The common garden experiment demonstrated that phenotypic variance among populations is largely explained by underlying genetic variation. An RNA-Seq experiment was conducted on 95 individuals and differential gene expression was inferred using DESeq and edgeR programs. Differentially expressed (DE) genes commonly identified by both programs and non-differentially expressed (NDE) genes were both mined for the presence of transcribed microsatellites using the SciRoKo program to assess microsatellite enrichment in both gene groups. A custom perl script was used to identify the abundance of different microsatellite motif types in the DE and NDE gene groups. A gene ontology (GO) analysis was conducted on the microsatellite containing DE genes. RNA-Seq produced an average of 42.8 million reads per individual. DESeq and edgeR identified 1521 and 1955 significantly differentially expressed genes respectively. Both programs identified 825 common genes as significantly differentially expressed among the two latitudes. SciRoKo results revealed the presence of 25% and 23% microsatellite containing genes in DE and NDE gene groups respectively. The DE genes showed a significant enrichment for mononucleotide repeats while they were significantly depauperate in trinucleotides. The GO analysis revealed the presence of microsatellites in genes related to developmental processes and stress response in plants. The distinct patterns of microsatellite evolution observed within DE genes among populations grown in a common garden are consistent with a proposed causal role for these microsatellites in locally adapted populations of common sunflower. The study provided empirical evidence to test the role of transcribed microsatellites as cis-regulatory elements in gene expression regulation.

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1 - Mississippi State University, Biological Sciences, 219 Harned Hall, 295 Lee Blvd, Mississippi State, Starkville, MS, 39762, USA
2 - Ohio State University, Evolution, Ecology and Organismal Biology, 318 W 12th Ave, Columbus, OH, 43210, USA
3 - Mississippi State University, Computer Science and Engineering, 302 Butler Hall 665 George Perry Street, Mississippi State, Starkville, MS, 39762, United States
4 - Mississippi State University, Biological Sciences, 219 Harned Hall, 295 Lee Blvd, Mississippi State, Starkville, MS, 39762, United States

gene expression
differential expression

Presentation Type: Oral Paper
Session: 11, Genetics
Location: 105/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 3:00 PM
Number: 11007
Abstract ID:559
Candidate for Awards:Margaret Menzel Award

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