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G3 (Bethesda). 2016 Aug 9;6(8):2319-28. doi: 10.1534/g3.116.030874.

Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions.

Author information

1
Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Sweden Department of Clinical Sciences, Division of Computational Genetics, Swedish University of Agricultural Sciences, SE-756 51 Uppsala, Sweden.
2
Department of Clinical Sciences, Division of Computational Genetics, Swedish University of Agricultural Sciences, SE-756 51 Uppsala, Sweden Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, United Kingdom Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77 Stockholm, Sweden MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, EH16 4UX United Kingdom.
3
Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Sweden Department of Clinical Sciences, Division of Computational Genetics, Swedish University of Agricultural Sciences, SE-756 51 Uppsala, Sweden orjan.carlborg@imbim.uu.se.

Abstract

An increased knowledge of the genetic regulation of expression in Arabidopsis thaliana is likely to provide important insights about the basis of the plant's extensive phenotypic variation. Here, we reanalyzed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of natural A. thaliana accessions. Transcripts from more than half of all genes were detected in the leaves of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions, but no transcripts at all in others, and this pattern was correlated with the genome-wide genotype. In total, 2669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. A total of 646 cis-eQTL-regulated genes that lacked detectable transcripts in some accessions was found, and for 159 of these we identified one, or several, common structural variants in the populations that were shown to be likely contributors to the lack of detectable RNA transcripts for these genes. This study thus provides new insights into the overall genetic regulation of global gene expression diversity in the leaf of natural A. thaliana accessions. Further, it also shows that strong cis-acting polymorphisms, many of which are likely to be structural variations, make important contributions to the transcriptional variation in the worldwide A. thaliana population.

KEYWORDS:

Arabidopsis thaliana; RNA sequencing; eQTL mapping; gene expression; structural variation

PMID:
27226169
PMCID:
PMC4978887
DOI:
10.1534/g3.116.030874
[Indexed for MEDLINE]
Free PMC Article

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