Microsatellite markers derived from Calophyllum inophyllum (Clusiaceae) expressed sequence tags

• Premise of the study: Robust markers are required (inter alia) for assessing origins of Calophyllum inophyllum populations on the Bonin Islands, Japan. Therefore, informative expressed sequence tag (EST)–based microsatellite or simple sequence repeat (SSRs) markers in the species were sought. • Me...

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Published inAmerican journal of botany Vol. 99; no. 1; pp. e28 - e32
Main Authors Setsuko, Suzuki, Uchiyama, Kentaro, Sugai, Kyoko, Hanaoka, So, Yoshimaru, Hiroshi
Format Journal Article
LanguageEnglish
Published United States Botanical Society of America 01.01.2012
Botanical Society of America, Inc
Subjects
Alleles
Base Sequence
Bonin (Ogasawara) Islands
Botany
Calophyllum - classification
Calophyllum - genetics
Calophyllum inophyllum
Clusiaceae
DNA Primers - genetics
DNA, Plant - genetics
Expressed Sequence Tags
Gene Library
Genes
Genetic Loci
Genetic Markers
Genetics, Population
Heterozygote
High-Throughput Nucleotide Sequencing
Japan
Microsatellite Repeats - genetics
Molecular Sequence Data
Phylogeography
Plant populations
Polymorphism
Polymorphism, Genetic
Population genetics
pyrosequencing
Seedlings - classification
Seedlings - genetics
Sequence Analysis, DNA
simple sequence repeat markers
Japan
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Summary:• Premise of the study: Robust markers are required (inter alia) for assessing origins of Calophyllum inophyllum populations on the Bonin Islands, Japan. Therefore, informative expressed sequence tag (EST)–based microsatellite or simple sequence repeat (SSRs) markers in the species were sought. • Methods and Results: Using 135378 ESTs derived from de novo pyrosequencing, primers for 475 EST‐SSRs were developed, 48 of which were tested for PCR amplification. Thirty‐six of the 48 primers showed clear amplification, with 23 displaying polymorphism in sampled populations. Expected heterozygosity in the samples from the Bonin Islands and Ryukyu Islands populations ranged from 0.041 to 0.697 and from 0.041 to 0.773, respectively. • Conclusions: As EST‐SSRs are potentially tightly linked with functional genes, and reportedly more transferable to related species than anonymous genomic SSRs, the developed primers have utility for future studies of the origins, genetic structure, and conservation of C. inophyllum and related species.
Bibliography:http://www.amjbot.org/site/misc/ifora.xhtml#2OpenAccessPolicy
Freely available online through the AJB Open Access option
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The authors are grateful to T. Nagamitsu, S. Ueno, Y. Kawamata, A. Hisamatsu, and other members of the Department of Forest Genetics of the Forestry and Forest Products Research Institute (FFPRI) for their support. They also thank T. Yasui (Ogasawara Wildlife Research Society) and K. Kato (Forest Tree Breeding Center of FFPRI) for providing plant materials. This research was funded by the Ministry of the Environment Government of Japan.
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ISSN:0002-9122
1537-2197
DOI:10.3732/ajb.1100299