The University of Southampton
University of Southampton Institutional Repository

Identifying genomic regions targeted during eggplant domestication using transcriptome data

Identifying genomic regions targeted during eggplant domestication using transcriptome data
Identifying genomic regions targeted during eggplant domestication using transcriptome data

Identifying genes and traits that have diverged during domestication provides key information of importance for maintaining and even increasing yield and nutrients in existing crops. A "bottom-up"population genetics approach was used to identify signatures of selection across the eggplant genome, to better understand the process of domestication. RNA-seq data were obtained for 4 wild eggplants (Solanum insanum L.) and 16 domesticated eggplants (S. melongena L.) and mapped to the eggplant genome. Single-nucleotide polymorphism (SNPs) exhibiting signatures of selection in domesticates were identified as those exhibiting high FST between the 2 populations (evidence of significant divergence) and low πfor the domesticated population (indicative of a selective sweep). Some of these regions appear to overlap with previously identified quantitative trait loci for domestication traits. Genes in regions of linkage disequilibrium surrounding these SNPs were searched against the Arabidopsis thaliana and tomato genomes to find orthologs. Subsequent gene ontology (GO) enrichment analysis identified over-representation of GO terms related to photosynthesis and response to the environment. This work reveals genomic changes involved in eggplant domestication and improvement, and how this compares to observed changes in the tomato genome, revealing shared chromosomal regions involved in the domestication of both species.

Solanum melongena, domestication, eggplant, selection, transcriptomics
0022-1503
519-525
Page, Anna
17800ba3-c0b8-4ddf-b78c-94273b67189c
Chapman, Mark
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Page, Anna
17800ba3-c0b8-4ddf-b78c-94273b67189c
Chapman, Mark
8bac4a92-bfa7-4c3c-af29-9af852ef6383

Page, Anna and Chapman, Mark (2021) Identifying genomic regions targeted during eggplant domestication using transcriptome data. Journal of Heredity, 112 (6), 519-525, [esab035]. (doi:10.1093/jhered/esab035).

Record type: Article

Abstract

Identifying genes and traits that have diverged during domestication provides key information of importance for maintaining and even increasing yield and nutrients in existing crops. A "bottom-up"population genetics approach was used to identify signatures of selection across the eggplant genome, to better understand the process of domestication. RNA-seq data were obtained for 4 wild eggplants (Solanum insanum L.) and 16 domesticated eggplants (S. melongena L.) and mapped to the eggplant genome. Single-nucleotide polymorphism (SNPs) exhibiting signatures of selection in domesticates were identified as those exhibiting high FST between the 2 populations (evidence of significant divergence) and low πfor the domesticated population (indicative of a selective sweep). Some of these regions appear to overlap with previously identified quantitative trait loci for domestication traits. Genes in regions of linkage disequilibrium surrounding these SNPs were searched against the Arabidopsis thaliana and tomato genomes to find orthologs. Subsequent gene ontology (GO) enrichment analysis identified over-representation of GO terms related to photosynthesis and response to the environment. This work reveals genomic changes involved in eggplant domestication and improvement, and how this compares to observed changes in the tomato genome, revealing shared chromosomal regions involved in the domestication of both species.

Text
esab035 - Accepted Manuscript
Download (579kB)

More information

e-pub ahead of print date: 15 June 2021
Published date: 1 September 2021
Additional Information: Publisher Copyright: © 2021 The American Genetic Association. 2021. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Keywords: Solanum melongena, domestication, eggplant, selection, transcriptomics

Identifiers

Local EPrints ID: 449916
URI: http://eprints.soton.ac.uk/id/eprint/449916
ISSN: 0022-1503
PURE UUID: 2172ad79-f18c-4836-b17d-341ca016ff92
ORCID for Mark Chapman: ORCID iD orcid.org/0000-0002-7151-723X

Catalogue record

Date deposited: 25 Jun 2021 16:31
Last modified: 17 Mar 2024 06:39

Export record

Altmetrics

Contributors

Author: Anna Page
Author: Mark Chapman ORCID iD

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×