Development and Characterization of EST-SSR Markers from NCBI and cDNA Library in Cultivated Peanut (Arachis hypogaea L.)
Shandong Peanut Research Institute, Qingdao, 266100
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
© 2010 BioPublisher Publishing Platform
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)
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.
EST-SSR; Peanut; Development; Characterization