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Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.)

Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.)
Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.)
Due to their highly polymorphic and codominant nature, simple-sequence repeat (SSR) markers are a common choice for assaying genetic diversity and genetic mapping. In this paper, we describe the generation of an expressed-sequence tag (EST) collection for the oilseed crop safflower and the subsequent development of EST–SSR markers for the genetic analysis of safflower and related species. We assembled 40,874 reads into 19,395 unigenes, of which 4,416 (22.8%) contained at least one SSR. Primer pairs were developed and tested for 384 of these loci, resulting in a collection of 104 polymorphic markers that amplify reliably across 27 accessions (3 species) of the genus Carthamus. These markers exhibited a high level of polymorphism, with an average of 6.0 ± 0.4 alleles per locus and an average gene diversity of 0.54 ± 0.03 across Carthamus species. In terms of cross-taxon transferability, 50% of these primer pairs produced an amplicon in at least one other species in the Asteraceae, and 28% produced an amplicon in at least one species outside the safflower subfamily (i.e., lettuce, sunflower, and/or Gerbera). These markers represent a valuable resource for the genetic analysis of safflower and related species, and also have the potential to facilitate comparative map-based analyses across a broader array of taxa within the Asteraceae.
0040-5752
85-91
Chapman, Mark A.
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Hvala, John
86d1185b-c60c-4820-a263-6a5b6971029f
Strever, Jason
837e5945-76e5-403c-a48e-54463b098e90
Matvienko, Marta
76de17bb-4601-40a9-84c1-0257c782e94b
Kozik, Alexander
a325511c-7030-4e9b-bb9d-3dc1cc75be15
Michelmore, Richard W.
5f7a43be-0c3b-4fb0-8d47-dc30f0c26d4b
Tang, Shunxue
71c2474e-92b9-4814-bcbf-e7b8dec812a5
Knapp, Steven J.
1f90f391-2672-4efd-a1cf-5e03327f54d4
Burke, John M.
f74dabe1-09b5-4473-9860-6eb876588d09
Chapman, Mark A.
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Hvala, John
86d1185b-c60c-4820-a263-6a5b6971029f
Strever, Jason
837e5945-76e5-403c-a48e-54463b098e90
Matvienko, Marta
76de17bb-4601-40a9-84c1-0257c782e94b
Kozik, Alexander
a325511c-7030-4e9b-bb9d-3dc1cc75be15
Michelmore, Richard W.
5f7a43be-0c3b-4fb0-8d47-dc30f0c26d4b
Tang, Shunxue
71c2474e-92b9-4814-bcbf-e7b8dec812a5
Knapp, Steven J.
1f90f391-2672-4efd-a1cf-5e03327f54d4
Burke, John M.
f74dabe1-09b5-4473-9860-6eb876588d09

Chapman, Mark A., Hvala, John, Strever, Jason, Matvienko, Marta, Kozik, Alexander, Michelmore, Richard W., Tang, Shunxue, Knapp, Steven J. and Burke, John M. (2009) Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.). Theoretical and Applied Genetics, 120 (1), 85-91. (doi:10.1007/s00122-009-1161-8).

Record type: Article

Abstract

Due to their highly polymorphic and codominant nature, simple-sequence repeat (SSR) markers are a common choice for assaying genetic diversity and genetic mapping. In this paper, we describe the generation of an expressed-sequence tag (EST) collection for the oilseed crop safflower and the subsequent development of EST–SSR markers for the genetic analysis of safflower and related species. We assembled 40,874 reads into 19,395 unigenes, of which 4,416 (22.8%) contained at least one SSR. Primer pairs were developed and tested for 384 of these loci, resulting in a collection of 104 polymorphic markers that amplify reliably across 27 accessions (3 species) of the genus Carthamus. These markers exhibited a high level of polymorphism, with an average of 6.0 ± 0.4 alleles per locus and an average gene diversity of 0.54 ± 0.03 across Carthamus species. In terms of cross-taxon transferability, 50% of these primer pairs produced an amplicon in at least one other species in the Asteraceae, and 28% produced an amplicon in at least one species outside the safflower subfamily (i.e., lettuce, sunflower, and/or Gerbera). These markers represent a valuable resource for the genetic analysis of safflower and related species, and also have the potential to facilitate comparative map-based analyses across a broader array of taxa within the Asteraceae.

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Published date: 1 December 2009
Organisations: Centre for Biological Sciences

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Local EPrints ID: 352747
URI: https://eprints.soton.ac.uk/id/eprint/352747
ISSN: 0040-5752
PURE UUID: 2e691889-4ca4-42b8-9aba-5c752e97ed00
ORCID for Mark A. Chapman: ORCID iD orcid.org/0000-0002-7151-723X

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Date deposited: 20 May 2013 13:28
Last modified: 06 Jun 2018 12:25

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Author: Mark A. Chapman ORCID iD
Author: John Hvala
Author: Jason Strever
Author: Marta Matvienko
Author: Alexander Kozik
Author: Richard W. Michelmore
Author: Shunxue Tang
Author: Steven J. Knapp
Author: John M. Burke

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