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
Author    Correspondence author
Legume Genomics and Genetics, 2010, Vol. 1, No. 6   doi: 10.5376/lgg.2010.01.0006
Received: 15 Jun., 2010    Accepted: 06 Aug., 2010    Published: 12 Nov., 2010
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This article was first published in Molecular Plant Breeding (Regular Print Version), and here was authorized to redistribute under the terms of 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:

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
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