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Eggplant domestication: pervasive gene flow, feralization, and transcriptomic divergence

Eggplant domestication: pervasive gene flow, feralization, and transcriptomic divergence
Eggplant domestication: pervasive gene flow, feralization, and transcriptomic divergence
In the context of food security, examining the genomics of domestication will help identify genes underlying adaptive and economically important phenotypes, for example, larger fruit, improved taste, and loss of agronomically inferior phenotypes. Examination of genome-scale single nucleotide polymorphisms demonstrates the relationships between wild ancestors of eggplant (Solanum melongena L.), confirming that Solanum insanum L. is the wild progenitor. This species is split roughly into an Eastern (Malaysian, Thai, and Vietnamese) and Western (Indian, Madagascan, and Sri Lankan) group, with domesticates derived from the former. Additional “wild” accessions from India appear to be feral escapes, derived multiple times from domesticated varieties through admixture. Accessions with small egg-shaped fruit are generally found intermixed with East Asian Solanum insanum confirming they are primitive relative to the large-fruited domesticates. Comparative transcriptomics was used to track the loci under selection. Sequence analysis revealed a genetic bottleneck reducing variation by almost 50% in the primitive accessions relative to the wild species and a further 10% in the landraces. We also show evidence for selection on genes with a role in response to wounding and apoptosis. Genes showing a significant difference in expression between wild and primitive or between primitive and landrace genepools were mostly (>75%) downregulated in the derived populations and enriched for gene ontologies related to defense, flowering, signaling, and response to biotic and abiotic stimuli. This work reveals genomic changes involved in crop domestication and improvement, and the population genetics work explains why defining the eggplant domestication trajectory has been so challenging
1359-1372
Page, Anna
17800ba3-c0b8-4ddf-b78c-94273b67189c
Gibson, Jane
855033a6-38f3-4853-8f60-d7d4561226ae
Meyer, Rachel S.
c8e7c6d1-1d06-44f4-810f-34108eeb8d01
Chapman, Mark
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Page, Anna
17800ba3-c0b8-4ddf-b78c-94273b67189c
Gibson, Jane
855033a6-38f3-4853-8f60-d7d4561226ae
Meyer, Rachel S.
c8e7c6d1-1d06-44f4-810f-34108eeb8d01
Chapman, Mark
8bac4a92-bfa7-4c3c-af29-9af852ef6383

Page, Anna, Gibson, Jane, Meyer, Rachel S. and Chapman, Mark (2019) Eggplant domestication: pervasive gene flow, feralization, and transcriptomic divergence. Molecular Biology and Evolution, 36 (7), 1359-1372. (doi:10.1093/molbev/msz062).

Record type: Article

Abstract

In the context of food security, examining the genomics of domestication will help identify genes underlying adaptive and economically important phenotypes, for example, larger fruit, improved taste, and loss of agronomically inferior phenotypes. Examination of genome-scale single nucleotide polymorphisms demonstrates the relationships between wild ancestors of eggplant (Solanum melongena L.), confirming that Solanum insanum L. is the wild progenitor. This species is split roughly into an Eastern (Malaysian, Thai, and Vietnamese) and Western (Indian, Madagascan, and Sri Lankan) group, with domesticates derived from the former. Additional “wild” accessions from India appear to be feral escapes, derived multiple times from domesticated varieties through admixture. Accessions with small egg-shaped fruit are generally found intermixed with East Asian Solanum insanum confirming they are primitive relative to the large-fruited domesticates. Comparative transcriptomics was used to track the loci under selection. Sequence analysis revealed a genetic bottleneck reducing variation by almost 50% in the primitive accessions relative to the wild species and a further 10% in the landraces. We also show evidence for selection on genes with a role in response to wounding and apoptosis. Genes showing a significant difference in expression between wild and primitive or between primitive and landrace genepools were mostly (>75%) downregulated in the derived populations and enriched for gene ontologies related to defense, flowering, signaling, and response to biotic and abiotic stimuli. This work reveals genomic changes involved in crop domestication and improvement, and the population genetics work explains why defining the eggplant domestication trajectory has been so challenging

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Chapman MS FINAL+figs - Accepted Manuscript
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Accepted/In Press date: 20 February 2019
e-pub ahead of print date: 30 April 2019
Published date: July 2019

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Local EPrints ID: 431568
URI: http://eprints.soton.ac.uk/id/eprint/431568
PURE UUID: be82d912-0157-46e4-9288-fe4a54f56cf8
ORCID for Jane Gibson: ORCID iD orcid.org/0000-0002-0973-8285
ORCID for Mark Chapman: ORCID iD orcid.org/0000-0002-7151-723X

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Date deposited: 07 Jun 2019 16:30
Last modified: 18 Feb 2021 17:21

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Author: Anna Page
Author: Jane Gibson ORCID iD
Author: Rachel S. Meyer
Author: Mark Chapman ORCID iD

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