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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, p. 2319-2328Article 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, p. 2319-2328
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, id: diva2:944773
Available from: 2016-06-30 Created: 2016-06-30 Last updated: 2018-02-26Bibliographically approved
In thesis
1. Understanding the genetic basis of complex traits
Open this publication in new window or tab >>Understanding the genetic basis of complex traits
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Recent advances in genetics and genomics have provided numerous opportunities to study the genetic basis of complex traits. Nevertheless, dissecting the genetic basis of complex traits is still challenged by the complex genetic architecture, in which many genes are involved, and many have small contributions to phenotypic variation, interactions with other genes or environmental factors. The aim of this thesis is to evaluate the genetic basis of the complex traits by exploring available genomic resources and analytical approaches. Four studies included in this thesis explore: the genetic basis of global transcriptome variation in natural population (Study I); the genetic basis of 8-week body weight in artificial selected chicken lines (Study II); the genetic basis of flowering time variation for Arabidopsis thaliana sampled from a wide range of ecological conditions (Study III and Study IV). Findings from this thesis show that the genetic architecture of complex traits involves many polymorphisms with variable effect sizes. Some of those polymorphisms are multi-allelic and have interactions with each other and environmental factors at the same time. The presence of many alleles with minor contributions to phenotypic variation in natural and artificially selected population demonstrates that response to natural and artificial selection has been achieved by polygenic adaptation. Furthermore, population-specific large-effect loci with long-range LD to QTL in functionally related pathways indicate that emergence and fixation of loci with large effects and co-evolution of loci in the related pathway is contributing to the local adaptation of Arabidopsis thaliana. Overall, this thesis shows the complexity of complex trait genetics and provides a few insights into study designs and analysis approaches for understanding the genetic basis of complex traits.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2018. p. 49
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1438
Keyword
genetic architecture, complex traits, epistasis, multi-allelic, genotype by environment interaction, polygenic adaptation
National Category
Medical and Health Sciences
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-343174 (URN)978-91-513-0260-7 (ISBN)
Public defence
2018-04-27, C8:301, BMC, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2018-04-04 Created: 2018-02-26 Last updated: 2018-04-24

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