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A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus)

A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus)
A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus)
Genomic scans for selection are a useful tool for identifying genes underlying phenotypic transitions. In this article, we describe the results of a genome scan designed to identify candidates for genes targeted by selection during the evolution of cultivated sunflower. This work involved screening 492 loci derived from ESTs on a large panel of wild, primitive (i.e., landrace), and improved sunflower (Helianthus annuus) lines. This sampling strategy allowed us to identify candidates for selectively important genes and investigate the likely timing of selection. Thirty-six genes showed evidence of selection during either domestication or improvement based on multiple criteria, and a sequence-based test of selection on a subset of these loci confirmed this result. In view of what is known about the structure of linkage disequilibrium across the sunflower genome, these genes are themselves likely to have been targeted by selection, rather than being merely linked to the actual targets. While the selection candidates showed a broad range of putative functions, they were enriched for genes involved in amino acid synthesis and protein catabolism. Given that a similar pattern has been detected in maize (Zea mays), this finding suggests that selection on amino acid composition may be a general feature of the evolution of crop plants. In terms of genomic locations, the selection candidates were significantly clustered near quantitative trait loci (QTL) that contribute to phenotypic differences between wild and cultivated sunflower, and specific instances of QTL colocalization provide some clues asto the roles that these genes may have played during sunflower evolution.
1040-4651
2931-2945
Chapman, M.A.
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Pashley, C.H.
161c935c-6165-4cb6-8f91-3b8c77cc1fe0
Wenzler, J.
0d24ed47-3790-44ee-8d88-4383f8027fc4
Hvala, J.
45316bbd-c9bb-4481-9e10-023a0687303b
Tang, S.
58c85272-6b59-4dac-ae81-8d6c7589f6cd
Knapp, S.J.
401b196b-cffb-445f-a5df-78666479edf5
Burke, J.M.
5110d8b4-546a-4e5d-9fa0-9ae93a818c09
Chapman, M.A.
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Pashley, C.H.
161c935c-6165-4cb6-8f91-3b8c77cc1fe0
Wenzler, J.
0d24ed47-3790-44ee-8d88-4383f8027fc4
Hvala, J.
45316bbd-c9bb-4481-9e10-023a0687303b
Tang, S.
58c85272-6b59-4dac-ae81-8d6c7589f6cd
Knapp, S.J.
401b196b-cffb-445f-a5df-78666479edf5
Burke, J.M.
5110d8b4-546a-4e5d-9fa0-9ae93a818c09

Chapman, M.A., Pashley, C.H., Wenzler, J., Hvala, J., Tang, S., Knapp, S.J. and Burke, J.M. (2008) A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus). The Plant Cell, 20 (11), 2931-2945. (doi:10.1105/tpc.108.059808). (PMID:19017747)

Record type: Article

Abstract

Genomic scans for selection are a useful tool for identifying genes underlying phenotypic transitions. In this article, we describe the results of a genome scan designed to identify candidates for genes targeted by selection during the evolution of cultivated sunflower. This work involved screening 492 loci derived from ESTs on a large panel of wild, primitive (i.e., landrace), and improved sunflower (Helianthus annuus) lines. This sampling strategy allowed us to identify candidates for selectively important genes and investigate the likely timing of selection. Thirty-six genes showed evidence of selection during either domestication or improvement based on multiple criteria, and a sequence-based test of selection on a subset of these loci confirmed this result. In view of what is known about the structure of linkage disequilibrium across the sunflower genome, these genes are themselves likely to have been targeted by selection, rather than being merely linked to the actual targets. While the selection candidates showed a broad range of putative functions, they were enriched for genes involved in amino acid synthesis and protein catabolism. Given that a similar pattern has been detected in maize (Zea mays), this finding suggests that selection on amino acid composition may be a general feature of the evolution of crop plants. In terms of genomic locations, the selection candidates were significantly clustered near quantitative trait loci (QTL) that contribute to phenotypic differences between wild and cultivated sunflower, and specific instances of QTL colocalization provide some clues asto the roles that these genes may have played during sunflower evolution.

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Published date: November 2008
Organisations: Faculty of Natural and Environmental Sciences, Centre for Biological Sciences

Identifiers

Local EPrints ID: 350275
URI: https://eprints.soton.ac.uk/id/eprint/350275
ISSN: 1040-4651
PURE UUID: df21c700-8d09-4fcb-b55d-dfa6cbba3e8c
ORCID for M.A. Chapman: ORCID iD orcid.org/0000-0002-7151-723X

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Date deposited: 25 Mar 2013 10:08
Last modified: 05 Nov 2019 01:37

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