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Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Div Computat Genet, Dept Clin Sci, SE-75651 Uppsala, Sweden. (Carlborg)
Univ Edinburgh, Usher Inst Populat Hlth Sci & Informat, Edinburgh EH16 4UX, Midlothian, Scotland; Univ Edinburgh, MRC Inst Genet & Mol Med, MRC Human Genet Unit, Edinburgh EH16 4UX, Midlothian, Scotland; Karolinska Inst, Dept Med Epidemiol & Biostat, SE-17177 Stockholm, Sweden.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Div Computat Genet, Dept Clin Sci, SE-75651 Uppsala, Sweden. (Carlborg)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Div Computat Genet, Dept Clin Sci, SE-75651 Uppsala, Sweden. (Carlborg)ORCID iD: 0000-0002-2722-5264
2016 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 8, 2319-2328 p.Article in journal (Refereed) Published
Abstract [en]

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 reanalysed 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 leaf 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, 2,669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. 646 cis-eQTLs regulated genes that lacked detectable transcripts in some accessions, 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 on 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.

Place, publisher, year, edition, pages
2016. Vol. 6, no 8, 2319-2328 p.
Keyword [en]
eQTL mapping; RNA sequencing; gene expression; Arabidopsis thaliana; structural variation
National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-298144DOI: 10.1534/g3.116.030874ISI: 000381282300008PubMedID: 27226169OAI: oai:DiVA.org:uu-298144DiVA: diva2:944773
Available from: 2016-06-30 Created: 2016-06-30 Last updated: 2017-11-28Bibliographically approved

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Zan, YanjunForsberg, SimonCarlborg, Orjan
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