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Legume Genomics and Genetics (online), 2010, Vol. 1, No.6, 30-33
http://lgg.sophiapublisher.com
Research Report Open Access
Development and Characterization of EST-SSR Markers from NCBI and cDNA
Library in Cultivated Peanut (
Arachis hypogaea L.
)
Jinyan Wang , Lijuan Pan , Qingli Yang , Shanlin Yu
Shandong Peanut Research Institute, Qingdao 266100
corresponding author email: rice407@163.com;
Authors
Legume Genomics and Genetics 2010, Vol.1 No.6 DOI:10.5376/lgg.2010.01.0006
Received: 15 Jul., 2010
Accepted: 6 Aug., 2010
Published: 10 Oct., 2010
This article was first published in the Molecular Plant Breeding (Regular Print Version), and here was authorized to redistribute under the terms of the Creative
Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article as:
Wang et al., 2009, Development and Characterization of EST-SSR Markers from NCBI and cDNA Library in Cultivated Peanut (
Arachis hypogaea
L.),
Molecular Plant Breeding, 7(4): 806-810 (DOI: 10.3969/mpb.007.000806)
Abstract
86 132 ESTs downloaded from GenBank in NCBI and 12 501 ESTs from cDNA library constructed by high-oil
linoleic acid accession E12 were analysed. After the preprocession, there were 18 051 singletons and 9 972 contigs in the GenBank
of NCBI and cDNA library. Totally 3 104 SSR locis had been screened by MISA software, accounting for 11.08% for these
non-redundant ESTs. All SSR locis are divided into di-nucleotide, thi-nucleotide, tetra-nucleotide, penta-nucleotide, hexa-nucleotide
and multi-nucleotide etc., and thi-nucleotide motif is the most motifs and the frequency was 43.0% and 56.8% in NCBI and cDNA
libraray, respectively. The number of di- and penta-nucleotide motifs were second and third in all motifs. And the hexa-nucleotide
was the least motif both in NCBI and cDNA library. In all repeat motifs nucleotide, AG/TC was the most motifs and accounted for
8.65% and 13.42% in NCBI and cDNA library respectively. Among the tri-nucleotide repeats, CTT/GAA was the most frequent
motif, accounting for 6.7% and 13.42%, respectively. The repeat unit number of SSR locis is between 4 and 51.
Keywords
EST-SSR; Peanut; Development; Characterization
Background
Peanut, or groundnut (
Arachis hypogaea
L., 2n=4×=
40), as a source of oil and protein, is the second-most
important grain legume crop after soybean in most
tropical and subtropical areas of the world (Dwivedi et
al., 2003). The seed is comprised of around 50% oil,
of which approximately 80% consist of oleic acid
(36%~67%) and linoleic acids (15%~43%) (Moore and
nauft, 1989). Additionally, the largest use is for oil,
with the meal being used as a high-protein dietary supp-
lement for human and animal consumption. In China
and other countries, the peanut seed oil is used mainly
in the cooking. Meanwhile, peanut may be used for
fodder, and the shells used for fuel or livestock feed
(Savage and Keenan, 1994).
Cultivated peanut exhibits a considerable amount of
variability for various morphological, physiological,
and agronomic traits. However, the genetic diversity
observed is much lower in DNA level by RAPD
(random amplified polymorphic DNA), AFLP (amp-
lified fragment length polymorphisms), RFLP (restrict-
tion fragment length polymorphisms) (Kochert et al.,
1996; Hilu et al., 1995; Herselman, 2003). The low level
of variation in cultivated peanut has been attributed to
the barriers to gene flow from related diploid species
to domesticated peanut as a consequence of the poly-
ploidization event (Young et al., 1996). And the rea-
son that few elite breeding lines and litter exotic germ-
plasm are used in the breeding programs is other cause
of the narrow genetic base.
Simple sequence repeat (SSR) markers are micro-
satellite loci that can be amplified by polymerase chain
reaction PCR) using primers designed for unique flan-
king sequences. Polymorphism is based on variation
in the number of repeats in different genotypes owing
to polymerase slippage and point mutations (Kruglyak
et al., 1998). SSR markers are (i) highly informative,
(ii) locus-specific and frequently show co-dominant
inheritance, (iii) adaptable to high-throughput geno-
typing, and (iv) simple to maintain and distribute. In
recent years, significant efforts have been made to de-
velop the SSR markers in groundnut and more than
800 SSR markers have been gained (Hopkins et al.,
1999; He et al., 2003; Ferguson et al., 2004; Cuc et al.,
2008). SSR markers include genomic SSR markers
and EST-derived SSR markers. Genomic SSR mar-
kers have some disadvantages. Firstly, genomic SSR
markers are derived from genomic BAC library, most
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