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Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae)

Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae)
Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae)
The development of universal markers that can be assayed across taxa, but which are polymorphic within taxa, can facilitate both comparative map-based studies and phylogenetic analyses. Here we describe the development of such markers for use in the Asteraceae, which includes the crops lettuce, sunflower, and safflower as well as dozens of locally important crop and weed species. Using alignments of a conserved orthologous set (COS) of ESTs from lettuce and sunflower and genomic sequences of Arabidopsis, we designed a suite of primer pairs that are conserved across species, but which are predicted to flank introns. We then tested 192 such primer pairs in 8 species from across the family. Of these, 163 produced an amplicon in at least 1 taxon, and 125 amplified in at least half of the taxa surveyed. Thirty-nine amplified in all 8 species. Comparisons amongst sequences within the lettuce and sunflower EST databases indicate that the vast majority of these loci will be polymorphic. As a direct test of the utility of these markers outside the lettuce and sunflower subfamilies, we sequenced a subset of ten loci from a panel of cultivated safflower individuals. All 10 loci proved to be single-locus, and nine of the 10 loci were polymorphic with an average of 12.8 SNPs per kb. Taken together, these loci will provide an initial backbone for comparative genetic analyses within the Asteraceae. Moreover, our results indicate that these loci are phylogenetically informative, and hence can be used to resolve evolutionary relationships between taxa within the family as well as within species.
0040-5752
747-755
Chapman, M.A.
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Chang, J.-C.
4d8f6f3a-98fd-49a1-a569-8d398babd625
Weisman, D.
cf3591ae-42a3-42aa-96f6-1a954aedaf8a
Kesseli, R.V.
65047443-dc82-4cee-9870-5a6b7c668f3a
Burke, J.M.
5110d8b4-546a-4e5d-9fa0-9ae93a818c09
Chapman, M.A.
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Chang, J.-C.
4d8f6f3a-98fd-49a1-a569-8d398babd625
Weisman, D.
cf3591ae-42a3-42aa-96f6-1a954aedaf8a
Kesseli, R.V.
65047443-dc82-4cee-9870-5a6b7c668f3a
Burke, J.M.
5110d8b4-546a-4e5d-9fa0-9ae93a818c09

Chapman, M.A., Chang, J.-C., Weisman, D., Kesseli, R.V. and Burke, J.M. (2007) Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae). Theoretical and Applied Genetics, 115 (6), 747-755. (doi:10.1007/s00122-007-0605-2).

Record type: Article

Abstract

The development of universal markers that can be assayed across taxa, but which are polymorphic within taxa, can facilitate both comparative map-based studies and phylogenetic analyses. Here we describe the development of such markers for use in the Asteraceae, which includes the crops lettuce, sunflower, and safflower as well as dozens of locally important crop and weed species. Using alignments of a conserved orthologous set (COS) of ESTs from lettuce and sunflower and genomic sequences of Arabidopsis, we designed a suite of primer pairs that are conserved across species, but which are predicted to flank introns. We then tested 192 such primer pairs in 8 species from across the family. Of these, 163 produced an amplicon in at least 1 taxon, and 125 amplified in at least half of the taxa surveyed. Thirty-nine amplified in all 8 species. Comparisons amongst sequences within the lettuce and sunflower EST databases indicate that the vast majority of these loci will be polymorphic. As a direct test of the utility of these markers outside the lettuce and sunflower subfamilies, we sequenced a subset of ten loci from a panel of cultivated safflower individuals. All 10 loci proved to be single-locus, and nine of the 10 loci were polymorphic with an average of 12.8 SNPs per kb. Taken together, these loci will provide an initial backbone for comparative genetic analyses within the Asteraceae. Moreover, our results indicate that these loci are phylogenetically informative, and hence can be used to resolve evolutionary relationships between taxa within the family as well as within species.

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Published date: October 2007
Organisations: Centre for Biological Sciences

Identifiers

Local EPrints ID: 352744
URI: https://eprints.soton.ac.uk/id/eprint/352744
ISSN: 0040-5752
PURE UUID: 0463ed02-ffea-40ba-bf73-c590401f2ef3
ORCID for M.A. Chapman: ORCID iD orcid.org/0000-0002-7151-723X

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Date deposited: 04 Jun 2013 14:27
Last modified: 20 Jul 2019 00:39

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Contributors

Author: M.A. Chapman ORCID iD
Author: J.-C. Chang
Author: D. Weisman
Author: R.V. Kesseli
Author: J.M. Burke

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