Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana

Maximilian O. Press, Rajiv C. McCoy, Ashley N. Hall, Joshua M. Akey, Christine Queitsch

Research output: Contribution to journalArticle

4 Scopus citations

Abstract

Short tandem repeat (STR) mutations may comprise more than half of the mutations in eukaryotic coding DNA, yet STR variation is rarely examined as a contributor to complex traits. We assessed this contribution across a collection of 96 strains of Arabidopsis thaliana, genotyping 2046 STR loci each, using highly parallel STR sequencing with molecular inversion probes. We found that 95% of examined STRs are polymorphic, with a median of six alleles per STR across these strains. STR expansions (large copy number increases) are found in most strains, several of which have evident functional effects. These include three of six intronic STR expansions we found to be associated with intron retention. Coding STRs were depleted of variation relative to noncoding STRs, and we detected a total of 56 coding STRs (11%) showing low variation consistent with the action of purifying selection. In contrast, some STRs show hypervariable patterns consistent with diversifying selection. Finally, we detected 133 novel STR-phenotype associations under stringent criteria, most of which could not be detected with SNPs alone, and validated some with follow-up experiments. Our results support the conclusion that STRs constitute a large, unascertained reservoir of functionally relevant genomic variation.

Original languageEnglish (US)
Pages (from-to)1169-1178
Number of pages10
JournalGenome Research
Volume28
Issue number8
DOIs
StatePublished - Aug 2018

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Fingerprint Dive into the research topics of 'Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana'. Together they form a unique fingerprint.

  • Cite this