Molecular Biology and Genetics |
|
Plant Biotechnology |
| Electronic Journal of Biotechnology ISSN: 0717-3458 |
Vol.
13 No. 5, Issue of September 15, 2010 |
| © 2010 by Pontificia Universidad Católica
de Valparaíso -- Chile |
Received December 2, 2009
/ Accepted May 26, 2010 |
| DOI: 10.2225/vol13-issue5-fulltext-5 |
|
Identification of SSR
markers using soybean (Glycine max) ESTs from globular stage
embryos
Ai Qin Li#
High-Tech Research
Center
Shandong Academy of
Agricultural Sciences
Key Laboratory for
Genetic Improvement of Crop, Animal
and Poultry of Shandong
Province
Key Laboratory of Crop
Genetic Improvement and Biotechnology
Huanghuaihai, Ministry of
Agriculture
Ji’nan 250100, P.R. China
Chuan Zhi Zhao#
High-Tech Research Center
Shandong Academy of
Agricultural Sciences
Key Laboratory for
Genetic Improvement of Crop, Animal
and Poultry of Shandong
Province
Key Laboratory of Crop
Genetic Improvement and Biotechnology
Huanghuaihai, Ministry
of Agriculture
Ji’nan 250100, P.R. China
Xing Jun Wang*
High-Tech Research
Center
Shandong Academy of
Agricultural Sciences
Key Laboratory for
Genetic Improvement of Crop, Animal
and Poultry of Shandong
Province
Key Laboratory of Crop
Genetic Improvement and Biotechnology
Huanghuaihai, Ministry
of Agriculture
Ji’nan 250100, P.R. China
E-mail: xingjunw@hotmail.com
Zhan Ji Liu
High-Tech Research Center
Shandong Academy of
Agricultural Sciences
Key Laboratory for
Genetic Improvement of Crop, Animal
and Poultry of Shandong
Province
Key Laboratory of Crop
Genetic Improvement and Biotechnology
Huanghuaihai, Ministry
of Agriculture
Ji’nan 250100, P.R. China
Li Feng Zhang
Crop Research Institute
Shandong Academy of
Agricultural Sciences
Ji’nan 250100, P.R. China
Guo Qi Song
High-Tech Research Center
Shandong Academy of
Agricultural Sciences
Key Laboratory for
Genetic Improvement of Crop, Animal
and Poultry of Shandong
Province
Key Laboratory of Crop
Genetic Improvement and Biotechnology
Huanghuaihai, Ministry
of Agriculture
Ji’nan 250100, P.R. China
Juan Yin
High-Tech Research Center
Shandong Academy of
Agricultural Sciences
Key Laboratory for
Genetic Improvement of Crop, Animal
and Poultry of Shandong
Province
Key Laboratory of Crop
Genetic Improvement and Biotechnology
Huanghuaihai, Ministry
of Agriculture
Ji’nan 250100, P.R. China
Chang Sheng Li
High-Tech
Research Center
Shandong Academy of
Agricultural Sciences
Key Laboratory for
Genetic Improvement of Crop, Animal
and Poultry of Shandong
Province
Key Laboratory of Crop
Genetic Improvement and Biotechnology
Huanghuaihai, Ministry
of Agriculture
Ji’nan 250100, P.R. China
Han Xia
High-Tech Research Center
Shandong Academy of
Agricultural Sciences
Key Laboratory for
Genetic Improvement of Crop, Animal
and Poultry of Shandong
Province
Key Laboratory of Crop
Genetic Improvement and Biotechnology
Huanghuaihai, Ministry
of Agriculture
Ji’nan 250100, P.R. China
Yu Ping Bi
High-Tech Research
Center
Shandong Academy of
Agricultural Sciences
Key Laboratory for
Genetic Improvement of Crop, Animal
and Poultry of Shandong
Province
Key Laboratory of Crop
Genetic Improvement and Biotechnology
Huanghuaihai, Ministry
of Agriculture
Ji’nan 250100, P.R. China
*Corresponding author
#These authors
contributed equally to this paper
Financial support: This work was supported by Shandong Provincial Natural Sciences Foundation, China (Y2008D44), Shandong province “Taishan Scholar” foundation, Doctoral Foundation of Shandong Province (2006BS06008) and grants from Shandong Academy of Agricultural Sciences (2007YCX001, 2006YBS001).
Keywords: 454
sequencing, EST, Glycine max, polymorphism, SSR.
Abbreviations: |
EST: expressed sequence tags
PCR: polymerase chain reaction
SSR: simple sequence
repeat |
Microsatellites, or
simple sequence repeats (SSRs), in expressed sequence tags (ESTs) provide an
opportunity for low cost SSR development. We looked for EST-SSRs in 403,511 ESTs (generated
by 454 sequencing and representing 70,654 contigs and 52,082
singletons) from soybean globular stage embryos. Among 122,736 unique ESTs, 3,729
contained one or more SSRs. In total, 3,989 SSRs were identified including 304 mono, 1,374
di, 2,208 tri, 70 tetra, 13 penta and 20 hexanucleotide SSRs. Thirty three
EST-SSRs were selected for primer design and polymorphism analysis using twenty
soybean cultivars and one wild-type soybean. Successful amplification was
obtained using 21 of these primer pairs, 11 of which detected polymorphisms in
these soybean cultivars. These results demonstrated that 454 high
throughput sequencing is a powerful tool for molecular marker development. From the 3,989
identified SSRs we expect to obtain a large number of makers with polymorphism among
different soybean cultivars, which would be useful for analysis of genetic diversity
and maker assisted selection in the soybean breeding programs.
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