TitleMassive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana.
Publication TypeJournal Article
Year of Publication2018
AuthorsPress, MO, McCoy, RC, Hall, AN, Akey, JM, Queitsch, C
JournalGenome Res
Volume28
Issue8
Pagination1169-1178
Date Published2018 08
ISSN1549-5469
KeywordsAlleles, Arabidopsis, DNA Copy Number Variations, Genotype, Microsatellite Repeats, Mutation, Polymorphism, Single Nucleotide
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 , 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.

DOI10.1101/gr.231753.117
Alternate JournalGenome Res.
PubMed ID29970452
PubMed Central IDPMC6071631
Grant ListDP2 OD008371 / OD / NIH HHS / United States
R01 GM122088 / GM / NIGMS NIH HHS / United States
T32 GM007270 / GM / NIGMS NIH HHS / United States