Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes

Choudhury, Rimjhim Roy; Rogivue, Aude; Gugerli, Felix; Parisod, Christian Gérard (2019). Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes. Molecular Ecology, 28(6), pp. 1550-1562. Wiley-Blackwell 10.1111/mec.15014

[img] Text
Choudhury_et_al-2019-Molecular_Ecology.pdf - Accepted Version
Restricted to registered users only until 12 January 2020.
Available under License Publisher holds Copyright.

Download (1MB) | Request a copy

Abstract Recombination and selection drive the extent of linkage disequilibrium (LD) among loci and therefore affect the reshuffling of adaptive genetic variation. However, it is poorly known to what extent the enrichment of transposable elements (TEs) in recombinationally-inert regions reflects their inefficient removal by purifying selection and whether the presence of polymorphic TEs can modify the local recombination rate. In this study, we investigate how TEs and recombination interact at fine scale along chromosomes and possibly support linked selection in natural populations. Whole-genome sequencing data of 304 individuals from nearby alpine populations of Arabis alpina were used to show that the density of polymorphic TEs is specifically correlated with local LD along chromosomes. Consistent with TEs modifying recombination, the characterization of 28 such LD blocks of up to 5.5Mb in length revealed strong evidence of selective sweeps at a few loci through either site frequency spectrum or haplotype structure. A majority of these blocks were enriched in genes related to ecologically relevant functions such as responses to cold, salt stress or photoperiodism. In particular, the S-locus (i.e. supergene responsible for strict outcrossing) was identified in a LD block with high levels of polymorphic TEs and evidence of selection. Another such LD block was enriched in cold-responding genes and presented evidence of adaptive loci related to photoperiodism and flowering being increasingly linked by polymorphic TEs. These results are consistent with the hypothesis that TEs modify recombination landscapes and thus interact with selection in driving blocks of linked adaptive loci in natural populations. This article is protected by copyright. All rights reserved.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS)
08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS) > Ecological Genomics

UniBE Contributor:

Choudhury, Rimjhim Roy and Parisod, Christian Gérard

Subjects:

500 Science > 580 Plants (Botany)

ISSN:

0962-1083

Publisher:

Wiley-Blackwell

Language:

English

Submitter:

Peter Alfred von Ballmoos-Haas

Date Deposited:

05 Feb 2019 15:39

Last Modified:

22 Apr 2019 01:31

Publisher DOI:

10.1111/mec.15014

PubMed ID:

30633406

Uncontrolled Keywords:

Arabis alpina, linkage disequilibrium, linked selection, recombination, retrotransposons, whole-genome sequencing

BORIS DOI:

10.7892/boris.123718

URI:

https://boris.unibe.ch/id/eprint/123718

Actions (login required)

Edit item Edit item
Provide Feedback